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b/docs/assets/images/userguides/bell/run-examples-apps-windows-menu.png differ diff --git a/docs/index.md b/docs/index.md index 8d0c58cd..afae29c9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -115,7 +115,7 @@ Follow these steps to get up and running on RCAC clusters. **128 cores/node | 256 GB RAM | 100 Gbps HDR Infiniband** - [:octicons-arrow-right-24: Bell User Guide](https://www.rcac.purdue.edu/knowledge/bell) + [:octicons-arrow-right-24: Bell User Guide](userguides/bell/index.md) - :material-server:{ .lg .middle } __Negishi__ diff --git a/docs/snippets/examples/apps/ansysfluent.md b/docs/snippets/examples/apps/ansysfluent.md new file mode 100644 index 00000000..65680ec7 --- /dev/null +++ b/docs/snippets/examples/apps/ansysfluent.md @@ -0,0 +1,43 @@ +# Ansys Fluent + +[Ansys](https://www.ansys.com) is a CAE/multiphysics engineering simulation software that utilizes finite element analysis for numerically solving a wide variety of mechanical problems. The software contains a list of packages and can simulate many structural properties such as strength, toughness, elasticity, thermal expansion, fluid dynamics as well as acoustic and electromagnetic attributes. + +## Ansys Licensing + +The Ansys licensing on our community clusters is maintained by Purdue ECN group. There are two types of licenses: teaching and research. For more information, please refer to [ECN Ansys licensing page](https://engineering.purdue.edu/ECN/Support/KB/Docs/ANSYSFLUENTLicensing). If you are interested in purchasing your own research license, please send email to **software@ecn.purdue.edu**. + +## Ansys Workflow + +Ansys software consists of several sub-packages such as Workbench and Fluent. Most simulations are performed using the Ansys Workbench console, a GUI interface to manage and edit the simulation workflow. It requires X11 forwarding for remote display so a SSH client software with X11 support or a remote desktop portal is required. Please see [Logging In](../../../accounts.md#logging-in-to-bell) section for more details. To ensure preferred performance, [ThinLinc](../../../accounts.md#thinlinc) remote desktop connection is highly recommended. + +Typically users break down larger structures into small components in geometry with each of them modeled and tested individually. A user may start by defining the dimensions of an object, adding weight, pressure, temperature, and other physical properties. + +Ansys Fluent is a computational fluid dynamics (CFD) simulation software known for its advanced physics modeling capabilities and accuracy. Fluent offers unparalleled analysis capabilities and provides all the tools needed to design and optimize new equipment and to troubleshoot existing installations. + +In the following sections, we provide step-by-step instructions to lead you through the process of using Fluent. We will create a classical elbow pipe model and simulate the fluid dynamics when water flows through the pipe. The project files have been generated and can be downloaded via [fluent\_tutorial.zip](https://www.rcac.purdue.edu/knowledge/run/examples/apps/ansys/fluent_tutorial.zip). + +## Loading Ansys Module + +Different versions of Ansys are installed on the clusters and can be listed with `module spider` or `module avail` command in the terminal. + +``` +$ module avail ansys/ +---------------------- Core Applications ----------------------------- + ansys/2019R3 ansys/2020R1 ansys/2021R2 ansys/2022R1 (D) +``` + +Before launching Ansys Workbench, a specific version of Ansys module needs to be loaded. For example, you can `module load ansys/2021R2` to use the latest Ansys 2021R2. If no version is specified, the default module -> (D) (`ansys/2022R1` in this case) will be loaded. You can also check the loaded modules with `module list` command. + +## Launching Ansys Workbench + +Open a terminal on Bell, enter `rcac-runwb2` to launch Ansys Workbench. + +!!! Note + You can also use `runwb2` to launch Ansys Workbench. The main difference between `runwb2`and `rcac-runwb2` is that the latter sets the project folder to be in your scratch space. Ansys has an known bug that it might crash when the project folder is set to `$HOME` on our systems. + +## In This Section + +- [Case Calculating with Fluent](ansysfluent/case_calculating_with_fluent.md) +- [Fluent Text User Interface and Journal File](ansysfluent/fluent_text_user_interface_and_journal_file.md) +- [Preparing Case Files for Fluent](ansysfluent/preparing_case_files_for_fluent.md) +- [Submitting Fluent jobs to SLURM](ansysfluent/submit_fluent_jobs_to_slurm.md) diff --git a/docs/snippets/examples/apps/ansysfluent/case_calculating_with_fluent.md b/docs/snippets/examples/apps/ansysfluent/case_calculating_with_fluent.md new file mode 100644 index 00000000..fd788e9f --- /dev/null +++ b/docs/snippets/examples/apps/ansysfluent/case_calculating_with_fluent.md @@ -0,0 +1,57 @@ +# Case Calculating with Fluent + +## Calculation with Fluent + +Now all the files are ready for the Fluent calculations. Both “Geometry” and “Mesh” cells should have green checks. We can set up the CFD simulation parameters in the Ansys Fluent by double-clicking the “Setup” cell. + +Ansys Fluent Launcher can be started by selecting “editing” on the “Setup” cell with many startup options (e.g. Precision, Parallel, Display). Note that “Dimension” is fixed to “3D” because we are using a 3D model in this project. + +

+ Ansys Fluent Launcher options +

+ +

Ansys Fluent Launcher options.

+ +After the Fluent is opened, an Ansys Fluent settings file `FFF.set` is written under the folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`. + +Then we are going to set up all the necessary parameters for Fluent computation. Here are the key steps for the setup: + +1. Setting up the domain: + * Change the units for length to be consistent with the Mesh; + * Check the mesh statistics and quality; +2. Setting up physics: + * Solver: “Energy”, “Viscous Model”, “Near-Wall Treatment”; + * Materials; + * Zones; + * Boundaries: Inlet, Outlet, Internal, Symmetry, Wall; +3. Solving: + * Solution Methods; + * Reports; + * Initialization; + * Iterations and output frequency. + +Then the calculation will be carried out and the results will be written out into `FFF-1.cas.gz` under folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`. + +This file contains all the settings and simulation results which can be loaded for post analysis and re-computation (more details will be introduced in the following sections). If only configurations and settings within the Fluent are needed, we can open independent Fluent or submit Fluent jobs with bash commands by loading the existing case in order to facilitate the computation process. + +Parameters used in demo case (use default if not assigned): + +1. Domain Setup: Length Units=”mm”; +2. Solver: Energy=”on”; Viscous Model=”k-epsilon”; Near-Wall Treatment=”Enhanced Wall Treatment”; +3. Materials: water (Density=1000[kg/m^3]; Specific Heat=4216[J/kg-k]; Thermal Conductivity=0.677[w/m-k]; Viscosity=8e-4[kg/m-s]); +4. Zones=”fluid (water)”; +5. Inlet=”velocity-inlet-large” (Velocity Magnitude=0.4m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=100mm; Thermal Temperature=293.15k) &”velocity-inlet-small” (Velocity Magnitude=1.2m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=25mm; Thermal Temperature=313.15k); Internal=”interior-fluid”; Symmetry=”symmetry”; Wall=”wall-fluid”; +6. Solution Methods: Gradient=”Green-Gauss Node Based”; +7. Report: plot residual and “Facet Maximum” for “pressure-outlet” +8. Hybrid Initialization; +9. 300 iterations. + +## Results analysis + +The best methods to view and analyze the simulation should be the Ansys Fluent (directly after computation) or the Ansys CFD-Post (entering “Results” in Ansys Workbench). Both methods are straightforward so we will not cover this part in this tutorial. Here is a final simulation result showing the temperature of the symmetry after 300 iterations for reference: + +

+ Simulated temperature +

+ +

Simulated temperature profile of the symmetry.

diff --git a/docs/snippets/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md b/docs/snippets/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md new file mode 100644 index 00000000..d88645e2 --- /dev/null +++ b/docs/snippets/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md @@ -0,0 +1,100 @@ +# Fluent Text User Interface and Journal File + +## Fluent Text User Interface (TUI) + +If you pay attention to the “Console” window in the Fluent window when setting up and carrying out the calculation, corresponding commands can be found and executed one after another. Almost all the setting processes can be accomplished by the command lines, which is called Fluent Text User Interface (TUI). Here are the main commands in Fluent TUI: + +``` + + + adjoint/ parallel/ solve/ + define/ plot/ surface/ + display/ preferences/ turbo-workflow/ + exit print-license-usage views/ + file/ report/ + mesh/ server/ + +``` + +For example, instead of opening a case by clicking buttons in Ansys Fluent, we can type `/file read-case case_file_name.cas.gz` to open the saved case. + +## Fluent Journal Files + +A Fluent journal file is a series of TUI commands stored in a text file. The file can be written in a text editor or generated by Fluent as a transcript of the commands given to Fluent during your session. + +A journal file generated by Fluent will include any GUI operations (in a TUI form, though). This is quite useful if you have a series of tasks that you need to execute, as it provides a shortcut. To record a journal file, start recording with File -> Write -> Start Journal..., perform whatever tasks you need, and then stop recording with File -> Write -> Stop Journal... + +You can also write your own journal file into a text file. The basic rule for a Fluent journal file is to reproduce the TUI commands that controlled the configuration and calculation of Fluent in their order. You can add a comment in a line starting with a `;` (semicolon). + +Here are some reasons why you should use a Fluent journal file: + +1. Using journal files with bash scripting can allow you to automate your jobs. +2. Using journal files can allow you to parameterize your models easily and automatically. +3. Using a journal file can set parameters you do not have in your case file e.g. autosaving. +4. Using a journal file can allow you to safely save, stop and restart your jobs easily. + +!!! Note + The order of your journal file commands is **highly important**. The correct sequences must be followed and some stages have multiple options e.g. different initialization methods. + +Here is a sample Fluent journal file for the demo case: + +``` + + + ;testJournal.jou + ;Set the TUI version for Fluent + /file/set-tui-version "22.1" + ;Read the case. The default folder + /file read-case /home/jin456/Fluent_files/tutorial_case1/elbow_files/dp0/FFF/Fluent/FFF-1.cas.gz + ;Initialize the case with Hybrid Initialization + /solve/initialize/hyb-initialization + ;Set Number of Iterations to 1000, Reporting Interval to 10 iterations and Profile Update Interval to 1 iteration + /solve/iterate 1000 10 1 + ;Outputting solver performance data upon completion of the simulation + /parallel timer usage + ;Write out the simulation results. + /file write-case-data /home/jin456/Fluent_files/tutorial_case1/elbow_files/dp0/FFF/Fluent/result.cas.h5 + ;After computation, exit Flent + /exit + +``` + +Before running this Fluent journal file, you need to make sure: 1) the ansys module has been loaded (it’s highly recommended to load the same version of Ansys when you built the case project); 2) the project case file (`***.cas.gz`) has been created. + +Then we can use Fluent to run this journal file by simply using:`fluent 3ddp -t$NTASKS -g -i testJournal.jou` in the terminal. Here, `3d` indicates this is a 3d model, `dp` indicates double precision, `-t$NTASKS` tells Fluent how many Solver Processes it will take (e.g. `-t4`), `-g` means to run without the GUI or graphics, `-i` testJournal.jou tells Fluent to read the specific journal file. + +Here is a table for the available command line Options for Linux/UNIX and Windows Platforms in Ansys Fluent. + +Options for Fluent TUI + +| Option | Platform | Description | +| --- | --- | --- | +| `-cc` | all | Use the classic color scheme | +| `-ccp x` | Windows only | Use the Microsoft Job Scheduler where x is the head node name. | +| `-cnf=x` | all | Specify the hosts or machine list file | +| `-driver` | all | Sets the graphics driver (available drivers vary by platform - opengl or x11 or null(Linux/UNIX) - opengl or msw or null (Windows)) | +| `-env` | all | Show environment variables | +| `-fgw` | all | Disables the embedded graphics | +| `-g` | all | Run without the GUI or graphics (Linux/UNIX); Run with the GUI minimized (Windows) | +| `-gr` | all | Run without graphics | +| `-gu` | all | Run without the GUI but with graphics (Linux/UNIX); Run with the GUI minimized but with graphics (Windows) | +| `-help` | all | Display command line options | +| `-hidden` | Windows only | Run in batch mode | +| `-host_ip=host:ip` | all | Specify the IP interface to be used by the host process | +| `-i journal` | all | Reads the specified journal file | +| `-lsf` | Linux/UNIX only | Run FLUENT using LSF | +| `-mpi=` | all | Specify MPI implementation | +| `-mpitest` | all | Will launch an MPI program to collect network performance data | +| `-nm` | all | Do not display mesh after reading | +| `-pcheck` | Linux/UNIX only | Checks all nodes | +| `-post` | all | Run the FLUENT post-processing-only executable | +| `-p` | all | Choose the interconnect = default or myr or inf | +| `-r` | all | List all releases installed | +| `-rx` | all | Specify release number | +| `-sge` | Linux/UNIX only | Run FLUENT under Sun Grid Engine | +| `-sge queue` | Linux/UNIX only | Name of the queue for a given computing grid | +| `-sgeckpt ckpt_obj` | Linux/UNIX only | Set checkpointing object to ckpt\_objfor SGE | +| `-sgepe fluent_pe min_n-max_n` | Linux/UNIX only | Set the parallel environment for SGE to fluent\_pe, min\_nand max\_n are number of min and max nodes requested | +| `-tx` | all | Specify the number of processors x | + +For more information for Fluent text user interface and journal files, please refer to [Fluent FAQ]( https://www.cfd-online.com/Wiki/Fluent_FAQ). diff --git a/docs/snippets/examples/apps/ansysfluent/preparing_case_files_for_fluent.md b/docs/snippets/examples/apps/ansysfluent/preparing_case_files_for_fluent.md new file mode 100644 index 00000000..7585fac9 --- /dev/null +++ b/docs/snippets/examples/apps/ansysfluent/preparing_case_files_for_fluent.md @@ -0,0 +1,118 @@ +# Preparing Case Files for Fluent + +## Creating a Fluent fluid analysis system + +In the Ansys Workbench, create a new fluid flow analysis by double-clicking the Fluid Flow (Fluent) option under the Analysis Systems in the Toolbox on the left panel. You can also drag-and-drop the analysis system into the Project Schematic. A green dotted outline indicating a potential location for the new system initially appears in the Project Schematic. When you drag the system to one of the outlines, it turns into a red box to indicate the chosen location of the new system. + +

+ Ansys Workbench GUI +

+ +

Ansys Workbench GUI and the Fluid Flow system for Fluent.

+ +The red rectangle indicates the Fluid Flow system for Fluent, which includes all the essential workflows from “2 Geometry” to “6 Results”. You can rename it and carry out the necessary step-by-step procedures by double-clicking the corresponding cells. + +It is important to save the project. Ansys Workbench saves the project with a `.wbpj` extension and also all the supporting files into a folder with the same name. In this case, a file named `elbow_demo.wbpj` and a folder `$Ansys_PROJECT_FOLDER/elbow_demo_files/` are created in the Ansys project folder: + +``` +$ ll +total 33 +drwxr-xr-x 7 myusername itap 9 Mar 3 17:47 elbow_demo_files +-rw-r--r-- 1 myusername itap 42597 Mar 3 17:47 elbow_demo.wbpj +``` + +!!! Note + You should always “Update Project” and save it after finishing a procedure. + +## Creating Geometry in the Ansys DesignModeler + +Create a geometry in the Ansys DesignModeler (by double-clicking “Geometry” cell in workflow), or import the appropriate geometry file (by right-clicking the Geometry cell and selecting “Import Geometry” option from the context menu). + +You can use Ansys DesignModeler to create 2D/3D geometries or even draw the objects yourself. In our example, we created only half of the elbow pipe because the symmetry of the structure is taken into account to reduce the computation intensity. + +

+ DesignModeler +

+ +

Elbow pipe created in Ansys DesignModeler.

+ +After saving the geometry, a geometry file `FFF.agdb` will be created in the folder: `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/DM/`. The project in Workbench will be updated automatically. + +!!! Note + If you import a pre-existing geometry into Ansys DesignModeler, it will also generate this file with the same filename at this location. + +## Creating mesh in the Ansys Meshing + +Now that we have created the elbow pipe geometry, a computational mesh can be generated by the Meshing application throughout the flow volume. + +With the successful creation of the geometry, there should be a green check showing the completion of “Geometry” in the Ansys Workbench. A Refresh Required icon within the “Mesh” cell indicates the mesh needs to be updated and refreshed for the system. + +

+ AnsysWorkbenchCells +

+ +

Status for different cells shown in Ansys Workbench.

+ +Then it’s time to open the Ansys Meshing application by double-clicking the “Mesh” cell and editing the mesh for the project. Generally, there are several steps we need to take to define the mesh: + +1. Create names for all geometry boundaries such as the inlets, outlets and fluid body. Note: You can use the strings “velocity inlet” and “pressure outlet” in the named selections (with or without hyphens or underscore characters) to allow Ansys Fluent to automatically detect and assign the corresponding boundary types accordingly. Use “Fluid” for the body to let Ansys Fluent automatically detect that the volume is a fluid zone and treat it accordingly. +2. Set basic meshing parameters for the Ansys Meshing application. Here are several important parameters you may need to assign: Sizing, Quality, Body Sizing Control, Inflation. +3. Select “Generate” to generate the mesh and “Update” to update the mesh into the system. Note: Once the mesh is generated, you can view the mesh statistics by opening the Statistics node in the Details of “Mesh” view. This will display information such as the number of nodes and the number of elements, which gives you a general idea for the future computational resources and time. + +After generation and updating the mesh, a mesh file `FFF.msh` will be generated in folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/MECH/` and a mesh database file `FFF.mshdb` will be generated in folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/global/MECH/`. + +Parameters used in demo case (use default if not assigned): + +1. Length Unit=”mm” +2. Names defined for geometry: + * velocity-inlet-large (large inlet on pipe); + * velocity-inlet-small (small inlet on pipe); + * pressure-outlet (outlet on pipe); + * symmetry (symmetry surface); + * Fluid (body); +3. Mesh: + * Quality: Smoothing=”high”; + * Inflation: Use Automatic Inflation=“Program Controlled”, Inflation Option=”Smooth Transition”; +4. Statistics: + * Nodes=29371; + * Elements=87647. + +## Calculation with Fluent + +Now all the preparations have been ready for the numerical calculation in Ansys Fluent. Both “Geometry” and “Mesh” cells should have green checks on. We can set up the CFD simulation parameters in Ansys Fluent by double-clicking the “Setup” cell. + +When Ansys Fluent is first started or by selecting “editing” on the “Setup” cell, the Fluent Launcher is displayed, enabling you to view and/or set certain Ansys Fluent start-up options (e.g. Precision, Parallel, Display). Note that “Dimension” is fixed to “3D” because we are using a 3D model in this project. + +After the Fluent is opened, an Ansys Fluent settings file `FFF.set` is written under the folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`. + +Then we are going to set up all the necessary parameters for Fluent computation. Here are the key steps for the setup: + +1. Setting up the domain: + * Change the units for length to be consistent with the Mesh; + * Check the mesh statistics and quality; +2. Setting up physics: + * Solver: “Energy”, “Viscous Model”, “Near-Wall Treatment”; + * Materials; + * Zones; + * Boundaries: Inlet, Outlet, Internal, Symmetry, Wall; +3. Solving: + * Solution Methods; + * Reports; + * Initialization; + * Iterations and output frequency. + +Then the calculation will be carried out and the results will be written out into `FFF-1.cas.gz` under folder `$Ansys_PROJECT_FOLDER/elbow_demo_file/dp0/FFF/Fluent/`. + +This file contains all the settings and simulation results which can be loaded for post analysis and re-computation (more details will be introduced in the following sections). If only configurations and settings within the Fluent are needed, we can open independent Fluent or submit Fluent jobs with bash commands by loading the existing case in order to facilitate the computation process. + +Parameters used in demo case (use default if not assigned): + +1. Domain Setup: Length Units=”mm”; +2. Solver: Energy=”on”; Viscous Model=”k-epsilon”; Near-Wall Treatment=”Enhanced Wall Treatment”; +3. Materials: water (Density=1000[kg/m^3]; Specific Heat=4216[J/kg-k]; Thermal Conductivity=0.677[w/m-k]; Viscosity=8e-4[kg/m-s]); +4. Zones=”fluid (water)”; +5. Inlet=”velocity-inlet-large” (Velocity Magnitude=0.4m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=100mm; Thermal Temperature=293.15k) &”velocity-inlet-small” (Velocity Magnitude=1.2m/s, Specification Method=”Intensity and Hydraulic Diameter”, Turbulent Intensity=5%; Hydraulic Diameter=25mm; Thermal Temperature=313.15k); Internal=”interior-fluid”; Symmetry=”symmetry”; Wall=”wall-fluid”; +6. Solution Methods: Gradient=”Green-Gauss Node Based”; +7. Report: plot residual and “Facet Maximum” for “pressure-outlet” +8. Hybrid Initialization; +9. 300 iterations. diff --git a/docs/snippets/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md b/docs/snippets/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md new file mode 100644 index 00000000..7151161e --- /dev/null +++ b/docs/snippets/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md @@ -0,0 +1,28 @@ +# Submitting Fluent jobs to SLURM + +The Fluent simulations can also run in batch. In this section we provide an example script for submitting Fluent jobs to the SLURM scheduler. Please refer to the [Running Jobs](../../../../run.md) section of our user guide for detailed tutorials of submitting jobs. + +``` + + +#!/bin/bash +# Job script for submitting a FLUENT job on multiple cores on a single node + +# Apply resources via SLURM +#SBATCH --nodes=1 +#SBATCH --ntasks=4 +#SBATCH --time=01:00:00 +#SBATCH --job-name=fluent_test +#SBATCH -o fluent_test_%j.out +#SBATCH -e fluent_test_%j.err + +# Loads Ansys and sets the application up +module purge +module load ansys/2022R1 + +#Initiating Fluent and reading input journal file +fluent 3ddp -t$NTASKS -g -i testJournal.jou + +``` + +For more information about submitting Fluent jobs, please refer to [Fluent FAQ]( https://www.cfd-online.com/Wiki/Fluent_FAQ) . diff --git a/docs/snippets/examples/apps/biocontainers.md b/docs/snippets/examples/apps/biocontainers.md new file mode 100644 index 00000000..128b4970 --- /dev/null +++ b/docs/snippets/examples/apps/biocontainers.md @@ -0,0 +1,75 @@ +# BioContainers Collection + +## What is BioContainers? + +The BioContainers project came from the idea of using the containers-based technologies such as [Docker](https://www.docker.com) or [rkt](https://github.com/rkt/rkt) for bioinformatics software. Having a common and controllable environment for running software could help to deal with some of the current problems during software development and distribution. BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. . For more information, please visit [BioContainers project](https://biocontainers.pro). + +## Getting Started + +Users can download bioinformatic containers from the [BioContainers.pro](https://biocontainers.pro) and run them directly using Singularity instructions from the corresponding container’s catalog page. + +Brief Singularity guide and examples are available at the [Bell Singularity user guide](singularity.md) page. Detailed Singularity user guide is available at: [sylabs.io/guides/3.8/user-guide](https://sylabs.io/guides/3.8/user-guide/) + +In addition, a subset of pre-downloaded biocontainers wrapped into convenient software modules are provided. These modules wrap underlying complexity and provide the same commands that are expected from non-containerized versions of each application. + +On Bell, type the command below to see the lists of biocontainers we deployed. + +``` +module load biocontainers +module avail + +------------ BioContainers collection modules ------------- + bamtools/2.5.1 + beast2/2.6.3 + bedtools/2.30.0 + blast/2.11.0 + bowtie2/2.4.2 + bwa/0.7.17 + cufflinks/2.2.1 + deeptools/3.5.1 + fastqc/0.11.9 + faststructure/1.0 + htseq/0.13.5 +[....] +``` + +## Example + +This example demonstrates how to run BLASTP with the `blast` module. This `blast` module is a biocontainer wrapper for [NCBI BLAST](https://blast.ncbi.nlm.nih.gov). + +``` +module load biocontainers +module load blast +blastp -query query.fasta -db nr -out output.txt -outfmt 6 -evalue 0.01 +``` + +To run a job in batch mode, first prepare a job script that specifies the BioContainer modules you want to launch and the resources required to run it. Then, use the `sbatch` command to submit your job script to Slurm. The following example shows the job script to use [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) in bioinformatic analysis. + +``` +#!/bin/bash + +#SBATCH -A myqueuename +#SBATCH -o bowtie2_%j.txt +#SBATCH -e bowtie2_%j.err +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=1 +#SBATCH --cpus-per-task=8 +#SBATCH --time=1:30:00 +#SBATCH --job-name bowtie2 + +# Load the Bowtie module +module load biocontainers +module load bowtie2 + +# Indexing a reference genome +bowtie2-build ref.fasta ref + +# Aligning paired-end reads +bowtie2 -p 8 -x ref -1 reads_1.fq -2 reads_2.fq -S align.sam +``` + +To help users get started, we provided detailed user guides for each containerized bioinformatics module on the [ReadTheDocs platform](https://biocontainer-doc.readthedocs.io/) + +

+ RCAC Biocontainers one ReadTheDocs +

diff --git a/docs/snippets/examples/apps/gaussian.md b/docs/snippets/examples/apps/gaussian.md new file mode 100644 index 00000000..34586188 --- /dev/null +++ b/docs/snippets/examples/apps/gaussian.md @@ -0,0 +1,115 @@ +# Gaussian + +Gaussian is a computational chemistry software package which works on electronic structure. This section illustrates how to submit a small Gaussian job to a Slurm queue. This Gaussian example runs the Fletcher-Powell multivariable optimization. + +Prepare a Gaussian input file with an appropriate filename, here named `myjob.com`. The final blank line is necessary: + +``` + +#P TEST OPT=FP STO-3G OPTCYC=2 + +STO-3G FLETCHER-POWELL OPTIMIZATION OF WATER + +0 1 +O +H 1 R +H 1 R 2 A + +R 0.96 +A 104. +``` + +To submit this job, load Gaussian then run the provided script, named `subg16`. This job uses one compute node with 128 processor cores: + +``` + +module load gaussian16 +subg16 myjob -N 1 -n 128 +``` + +View job status: + +``` + +squeue -u myusername +``` + +View results in the file for Gaussian output, here named `myjob.log`. Only the first and last few lines appear here: + +``` + + + Entering Gaussian System, Link 0=/apps/cent7/gaussian/g16-A.03/g16-haswell/g16/g16 + Initial command: + + /apps/cent7/gaussian/g16-A.03/g16-haswell/g16/l1.exe /scratch/bell/myusername/gaussian/Gau-7781.inp -scrdir=/scratch/bell/myusername/gaussian/ + + Entering Link 1 = /apps/cent7/gaussian/g16-A.03/g16-haswell/g16/l1.exe PID= 7782. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016, + Gaussian, Inc. All Rights Reserved. + +. +. +. + + Job cpu time: 0 days 0 hours 3 minutes 28.2 seconds. + Elapsed time: 0 days 0 hours 0 minutes 12.9 seconds. + File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 2 Scr= 2 + Normal termination of Gaussian 16 at Tue May 1 17:12:00 2018. +real 13.85 +user 202.05 +sys 6.12 +Machine: +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +bell-a012.rcac.purdue.edu +``` + +## Examples of Gaussian SLURM Job Submissions + +Submit job using 128 processor cores on a single node: + + +``` + +subg16 myjob -N 1 -n 128 -t 200:00:00 -A myqueuename +``` + + +Submit job using 128 processor cores on each of 2 nodes: + + +``` + +subg16 myjob -N 2 --ntasks-per-node=128 -t 200:00:00 -A myqueuename +``` + + +To submit a bash job, a submit script sample looks like: + +``` + +#!/bin/bash + +#SBATCH -A myqueuename # Queue name(use 'slist' command to find queues' name) +#SBATCH --nodes=1 # Total # of nodes +#SBATCH --ntasks=64 # Total # of MPI tasks +#SBATCH --time=1:00:00 # Total run time limit (hh:mm:ss) +#SBATCH -J myjobname # Job name +#SBATCH -o myjob.o%j # Name of stdout output file +#SBATCH -e myjob.e%j # Name of stderr error file + +module load gaussian16 + +g16 < myjob.com +``` + +For more information about Gaussian: + +* [Gaussian Website](http://www.gaussian.com/) diff --git a/docs/snippets/examples/apps/learning.md b/docs/snippets/examples/apps/learning.md new file mode 100644 index 00000000..3182aa61 --- /dev/null +++ b/docs/snippets/examples/apps/learning.md @@ -0,0 +1,9 @@ +# Machine Learning + +Machine Learning packages are now best installed through `conda`, which has available repositories for all major machine learning frameworks. `conda` can be loaded via `module load conda`. + +## In This Section + +- [Custom ML Packages](learning/customml.md) +- [ML Batch Jobs](learning/ml_batch.md) +- [ML-Toolkit](learning/mltoolkit.md) diff --git a/docs/snippets/examples/apps/learning/customml.md b/docs/snippets/examples/apps/learning/customml.md new file mode 100644 index 00000000..0aa83d8f --- /dev/null +++ b/docs/snippets/examples/apps/learning/customml.md @@ -0,0 +1,124 @@ +# Custom ML Packages + +## Installation of Custom ML Libraries + +While we try to include as many common ML frameworks and versions as we can in ML-Toolkit, we recognize that there are also situations in which a custom installation may be preferable. We recommend using `conda-env-mod` to [install and manage Python packages](../python/packages.md). Please follow the steps carefully, otherwise you may end up with a faulty installation. The example below shows how to install TensorFlow in your home directory. + +### Install + +**Step 1:** Unload all modules and start with a clean environment. + +``` +module purge +``` + +**Step 2:** Load the anaconda module with desired Python version. + +``` +module load anaconda +``` + + +**Step 2A:** If the ML application requires Cuda and CuDNN, load the appropriate modules. Be sure to check that the versions you load are compatible with the desired ML package. + +``` +module load cuda +module load cudnn +``` + +!!! Note + Many machine-learning packages (including PyTorch and TensorFlow) now provide installation pathways that include the full *cudatoolkit* within the environment, making it unnecessary to load these modules. + + +**Step 3:** Create a custom anaconda environment. Make sure the python version matches the Python version in the anaconda module. + +``` +conda-env-mod create -n env_name_here +``` + +**Step 4:** Activate the anaconda environment by loading the modules displayed at the end of step 3. + +``` +module load use.own +module load conda-env/env_name_here-py3.6.4 +``` + +**Step 5:** Now install the desired ML application. You can install multiple Python packages at this step using either `conda` or `pip`. + + +``` +pip install --ignore-installed tensorflow==2.6 +``` + + +If the installation succeeded, you can now proceed to testing and using the installed application. You must load the environment you created as well as any supporting modules (e.g., anaconda) whenever you want to use this installation. If your installation did not succeed, please refer to the troubleshooting section below as well as documentation for the desired package you are installing. + +Note that loading the modules generated by `conda-env-mod` has different behavior than `conda create env_name_here` followed by `source activate env_name_here`. After running `source activate`, you may not be able to access any Python packages in anaconda or ml-toolkit modules. Therefore, using `conda-env-mod` is the preferred way of using your custom installations. + +### Testing the Installation + +* Verify the installation by using a simple import statement, like that listed below for TensorFlow: + + ``` + python -c "import tensorflow as tf; print(tf.__version__);" + ``` + + Note that a successful import of TensorFlow will print a variety of system and hardware information. This is expected. + + If importing the package leads to errors, be sure to verify that all dependencies for the package have been managed, and the correct versions installed. Dependency issues between python packages are the most common cause for errors. For example, in TF, conflicts with the h5py or numpy versions are common, but upgrading those packages typically solves the problem. Managing dependencies for ML libraries can be non-trivial. + +### Troubleshooting + +In most situations, dependencies among Python modules lead to errors. If you cannot use a Python package after installing it, please follow the steps below to find a workaround. + +* Unload all the modules. + + ``` + module purge + ``` + +* Clean up PYTHONPATH. + + ``` + unset PYTHONPATH + ``` + +* Next load the modules, e.g., anaconda and your custom environment. + + ``` + module load anaconda + module load use.own + module load conda-env/env_name_here-py3.6.4 + ``` + +* For GPU-enabled applications, you may also need to load the corresponding `cuda/` and `cudnn/` modules. + +* Now try running your code again. + +* A few applications only run on specific versions of Python (e.g. Python 3.6). Please check the documentation of your application if that is the case. + +* If you have installed a newer version of an `ml-toolkit` package (e.g., a newer version of PyTorch or Tensorflow), make sure that the `ml-toolkit` modules are NOT loaded. In general, we recommend that you don't mix `ml-toolkit` modules with your custom installations. + +* GPU-enabled ML applications often have dependencies on specific versions of Cuda and CuDNN. For example, Tensorflow version 1.5.0 and higher needs Cuda 9. Please check the application documentation about such dependencies. + +### Tensorboard + +* You can visualize data from a Tensorflow session using Tensorboard. For this, you need to save your session summary as described in the [Tensorboard User Guide](https://www.tensorflow.org/get_started/summaries_and_tensorboard). +* Launch Tensorboard: + + ``` + $ python -m tensorboard.main --logdir=/path/to/session/logs + ``` + +* When Tensorboard is launched successfully, it will give you the URL for accessing Tensorboard. + + ``` + <... build related warnings ...> + TensorBoard 0.4.0 at http://bell-a000.rcac.purdue.edu:6006 + ``` + +* Follow the printed URL to visualize your model. + +* Please note that due to firewall rules, the Tensorboard URL may only be accessible from Bell nodes. If you cannot access the URL directly, you can use Firefox browser in ThinLinc. + +* For more details, please refer to the [Tensorboard User Guide](https://www.tensorflow.org/get_started/summaries_and_tensorboard). diff --git a/docs/snippets/examples/apps/learning/ml_batch.md b/docs/snippets/examples/apps/learning/ml_batch.md new file mode 100644 index 00000000..11e5507f --- /dev/null +++ b/docs/snippets/examples/apps/learning/ml_batch.md @@ -0,0 +1,71 @@ +# ML Batch Jobs + +## Running ML Code in a Batch Job + +Batch jobs allow us to automate model training without human intervention. They are also useful when you need to run a large number of simulations on the clusters. In the example below, we shall run a simple `tensor_hello.py` script in a batch job. We consider two situations: in the first example, we use the [ML-Toolkit](mltoolkit.md) modules to run tensorflow, while in the second example, we use a custom installation of tensorflow (See Custom ML Packages page). + +### Using ML-Toolkit Modules + +Save the following code as `tensor_hello.sub` in the same directory where `tensor_hello.py` is located. + +``` +# filename: tensor_hello.sub + +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=128 + +#SBATCH --time=00:05:00 +#SBATCH -A accountname +#SBATCH -J hello_tensor + +module purge + +module load learning +module load ml-toolkit-gpu/tensorflow + + +module list + +python tensor_hello.py +``` + +### Using a Custom Installation + +Save the following code as `tensor_hello.sub` in the same directory where `tensor_hello.py` is located. + +``` +# filename: tensor_hello.sub + +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=1 +#SBATCH --gres=gpu:1 + +#SBATCH --time=00:05:00 +#SBATCH -A accountname +#SBATCH -J hello_tensor + +module purge +module load anaconda + +module load cuda +module load cudnn +module load use.own +module load conda-env/my_tf_env-py3.8.5 + + +module list + +echo $PYTHONPATH + +python tensor_hello.py +``` + +### Running a Job + +Now you can submit the batch job using the `sbatch` command. + +``` +sbatch tensor_hello.sub +``` + +Once the job finishes, you will find an output file (`slurm-xxxxx.out`). diff --git a/docs/snippets/examples/apps/learning/mltoolkit.md b/docs/snippets/examples/apps/learning/mltoolkit.md new file mode 100644 index 00000000..af065b28 --- /dev/null +++ b/docs/snippets/examples/apps/learning/mltoolkit.md @@ -0,0 +1,61 @@ +# ML-Toolkit + +A set of pre-installed popular machine learning (ML) libraries, called ML-Toolkit is maintained on Bell. These are Anaconda/Python-based distributions of the respective libraries. Currently, applications are supported for Python 2 and 3. Detailed instructions for searching and using the installed ML applications are presented below. + +## Instructions for using ML-Toolkit Modules + +### Find and Use Installed ML Packages + +To search or load a machine learning application, you must first load one of the `learning` modules. The `learning` module loads the prerequisites (such as anaconda and cudnn) and makes ML applications visible to the user. + +**Step 1.** Find and load a preferred `learning` module. Several `learning` modules may be available, corresponding to a specific Python version and whether the ML applications have GPU support or not. Running `module load learning` without specifying a version will load the version with the most recent python version. To see all available modules, run `module spider learning` then load the desired module. + +**Step 2.** Find and load the desired machine learning libraries + +ML packages are installed under the common application name `ml-toolkit-X`, where `X` can be `cpu` or `gpu`. + +You can use the `module spider ml-toolkit` command to see all options and versions of each library. + +Load the desired modules using the `module load` command. Note that both CPU and GPU options may exist for many libraries, so be sure to load the correct version. For example, if you wanted to load the most recent version of PyTorch for CPU, you would run `module load ml-toolkit-cpu/pytorch` + +``` +caffe cntk gym keras mxnet +opencv pytorch tensorflow tflearn theano +``` + +**Step 3.** You can list which ML applications are loaded in your environment using the command `module list` + +### Verify application import + +**Step 4.** The next step is to check that you can actually use the desired ML application. You can do this by running the `import` command in Python. The example below tests if PyTorch has been loaded correctly. + +``` +python -c "import torch; print(torch.__version__)" +``` + +If the import operation succeeded, then you can run your own ML code. Some ML applications (such as tensorflow) print diagnostic warnings while loading -- this is the expected behavior. + +If the import fails with an error, please see the troubleshooting information below. + +**Step 5.** To load a different set of applications, unload the previously loaded applications and load the new desired applications. The example below loads Tensorflow and Keras instead of PyTorch and OpenCV. + +``` +module unload ml-toolkit-cpu/opencv +module unload ml-toolkit-cpu/pytorch +module load ml-toolkit-cpu/tensorflow +module load ml-toolkit-cpu/keras +``` + +### Troubleshooting + +ML applications depend on a wide range of Python packages and mixing multiple versions of these packages can lead to error. The following guidelines will assist you in identifying the cause of the problem. + +* Check that you are using the correct version of Python with the command `python --version`. This should match the Python version in the loaded anaconda module. +* Start from a clean environment. Either start a new terminal session or unload all the modules using `module purge`. Then load the desired modules following Steps 1-2. +* Verify that PYTHONPATH does not point to undesired packages. Run the following command to print PYTHONPATH: `echo $PYTHONPATH`. Make sure that your Python environment is clean. Watch out for any locally installed packages that might conflict. +* If you don't see GPU devices in your code, make sure that you are using the `ml-toolkit-gpu/` modules and not using their cpu versions. +* ML applications often have dependency on specific versions of Cuda and CuDNN libraries. Make sure that you have loaded the required versions using the command: `module list` +* Note that Caffe has a conflicting version of PyQt5. So, if you want to use Spyder (or any GUI application that uses PyQt), then you should unload the caffe module. +* Use Google search to your advantage. Copy the error message in Google and check probable causes. + +More examples showing how to use `ml-toolkit` modules in a batch job are presented in [ML Batch Jobs](ml_batch.md) guide. diff --git a/docs/snippets/examples/apps/mathematica.md b/docs/snippets/examples/apps/mathematica.md new file mode 100644 index 00000000..31bfa0db --- /dev/null +++ b/docs/snippets/examples/apps/mathematica.md @@ -0,0 +1,79 @@ +# Mathematica + +Mathematica implements numeric and symbolic mathematics. This section illustrates how to submit a small Mathematica job to a PBS queue. This Mathematica example finds the three roots of a third-degree polynomial. + +Prepare a Mathematica input file with an appropriate filename, here named `myjob.in`: + +``` + +(* FILENAME: myjob.in *) + +(* Find roots of a polynomial. *) +p=x^3+3*x^2+3*x+1 +Solve[p==0] +Quit +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`: + +``` + +#!/bin/sh -l +# FILENAME: myjob.sub + +module load mathematica +cd $PBS_O_WORKDIR + +math < myjob.in +``` + +Submit the job: + +``` + + +$ qsub -l nodes=1:ppn=128 myjob.sub + +``` + +View job status: + +``` + +$ qstat -u myusername +``` + +View results in the file for all standard output, here named `myjob.sub.omyjobid`: + +``` + +Mathematica 5.2 for Linux x86 (64 bit) +Copyright 1988-2005 Wolfram Research, Inc. + -- Terminal graphics initialized -- + +In[1]:= +In[2]:= +In[2]:= +In[3]:= + 2 3 +Out[3]= 1 + 3 x + 3 x + x + +In[4]:= +Out[4]= {{x -> -1}, {x -> -1}, {x -> -1}} + +In[5]:= +``` +{% endraw %} + +View the standard error file, `myjob.sub.emyjobid`: + +``` + +rmdir: ./ligo/rengel/tasks: Directory not empty +rmdir: ./ligo/rengel: Directory not empty +rmdir: ./ligo: Directory not empty +``` + +For more information about Mathematica: + +* [Wolfram Research Website](http://www.wolfram.com/products/mathematica/index.html) diff --git a/docs/snippets/examples/apps/matlab.md b/docs/snippets/examples/apps/matlab.md new file mode 100644 index 00000000..96bbddc6 --- /dev/null +++ b/docs/snippets/examples/apps/matlab.md @@ -0,0 +1,23 @@ +# Matlab + +*MATLAB®* (MATrix LABoratory) is a high-level language and interactive environment for numerical computation, visualization, and programming. MATLAB is a product of [MathWorks](http://www.mathworks.com/). + +MATLAB, Simulink, Compiler, and several of the optional toolboxes are available to faculty, staff, and students. To see the kind and quantity of all MATLAB licenses plus the number that you are currently using you can use the `matlab_licenses` command: + +``` +$ module load matlab +$ matlab_licenses +``` + +The MATLAB client can be run in the front-end for application development, however, computationally intensive jobs must be run on compute nodes. + +The following sections provide several examples illustrating how to submit MATLAB jobs to a Linux compute cluster. + +## In This Section + +- [Implicit Parallelism](matlab/implicit_parallelism.md) +- [Matlab Script (.m File)](matlab/interpreter.md) +- [Distributed Computing Server (parallel job)](matlab/mdcs_parallel.md) +- [Parallel Computing Toolbox (parfor)](matlab/parfor.md) +- [Profile Manager](matlab/profile_manager.md) +- [Parallel Toolbox (spmd)](matlab/spmd.md) diff --git a/docs/snippets/examples/apps/matlab/implicit_parallelism.md b/docs/snippets/examples/apps/matlab/implicit_parallelism.md new file mode 100644 index 00000000..e8872cfe --- /dev/null +++ b/docs/snippets/examples/apps/matlab/implicit_parallelism.md @@ -0,0 +1,21 @@ +# Implicit Parallelism + +MATLAB implements *implicit parallelism* which is automatic multithreading of many computations, such as matrix multiplication, linear algebra, and performing the same operation on a set of numbers. This is different from the explicit parallelism of the Parallel Computing Toolbox. + +MATLAB offers implicit parallelism in the form of thread-parallel enabled functions. Since these processor cores, or threads, share a common memory, many MATLAB functions contain multithreading potential. Vector operations, the particular application or algorithm, and the amount of computation (array size) contribute to the determination of whether a function runs serially or with multithreading. + +When your job triggers implicit parallelism, it attempts to allocate its threads on all processor cores of the compute node on which the MATLAB client is running, including processor cores running other jobs. This competition can degrade the performance of all jobs running on the node. + +> When you know that you are coding a serial job but are unsure whether you are using thread-parallel enabled operations, run MATLAB with implicit parallelism turned off. Beginning with the R2009b, you can turn multithreading off by starting MATLAB with `-singleCompThread`: + +``` +$ matlab -nodisplay -singleCompThread -r mymatlabprogram +``` + +When you are using implicit parallelism, make sure you request exclusive access to a compute node, as MATLAB has no facility for sharing nodes. + +For more information about MATLAB's implicit parallelism: + +* [Which MATLAB functions benefit from multithreaded computation?](http://www.mathworks.com/support/solutions/en/data/1-4PG4AN/index.html?solution=1-4PG4AN) +* [What is the difference between "MATLAB as a fully-multithreaded application" versus "multithreaded computation"?](http://www.mathworks.com/support/solutions/en/data/1-3P8CC5/index.html) +* [MathWorks Website](http://www.mathworks.com/) diff --git a/docs/snippets/examples/apps/matlab/interpreter.md b/docs/snippets/examples/apps/matlab/interpreter.md new file mode 100644 index 00000000..f7b4521c --- /dev/null +++ b/docs/snippets/examples/apps/matlab/interpreter.md @@ -0,0 +1,86 @@ +# Matlab Script (.m File) + +This section illustrates how to submit a small, serial, MATLAB program as a job to a batch queue. This MATLAB program prints the name of the run host and gets three random numbers. + +Prepare a MATLAB script `myscript.m`, and a MATLAB function file `myfunction.m`: + +``` +% FILENAME: myscript.m + +% Display name of compute node which ran this job. +[c name] = system('hostname'); +fprintf('\n\nhostname:%s\n', name); + +% Display three random numbers. +A = rand(1,3); +fprintf('%f %f %f\n', A); + +quit; +``` + +``` +% FILENAME: myfunction.m + +function result = myfunction () + + % Return name of compute node which ran this job. + [c name] = system('hostname'); + result = sprintf('hostname:%s', name); + + % Return three random numbers. + A = rand(1,3); + r = sprintf('%f %f %f', A); + result=strvcat(result,r); + +end +``` + +Also, prepare a job submission file, here named `myjob.sub`. Run with the name of the script: + +``` +#!/bin/bash +# FILENAME: myjob.sub + +echo "myjob.sub" + +# Load module, and set up environment for Matlab to run +module load matlab + +unset DISPLAY + +# -nodisplay: run MATLAB in text mode; X11 server not needed +# -singleCompThread: turn off implicit parallelism +# -r: read MATLAB program; use MATLAB JIT Accelerator +# Run Matlab, with the above options and specifying our .m file +matlab -nodisplay -singleCompThread -r myscript +``` + +[Submit the job](../../../slurm/submit_script.md) + +[View job status](../../../slurm/monitoring_job.md) + +[View results of the job](../../../slurm/checking_output.md) + +``` +myjob.sub + + < M A T L A B (R) > + Copyright 1984-2011 The MathWorks, Inc. + R2011b (7.13.0.564) 64-bit (glnxa64) + August 13, 2011 + +To get started, type one of these: helpwin, helpdesk, or demo. +For product information, visit www.mathworks.com. + +hostname:bell-a001.rcac.purdue.edu +0.814724 0.905792 0.126987 +``` + +Output shows that a processor core on one compute node (bell-a001) processed the job. Output also displays the three random numbers. + +For more information about MATLAB: + +* [inv()](http://www.mathworks.com/help/techdoc/ref/inv.html) +* [Run a Batch Job](http://www.mathworks.com/help/distcomp/introduction-to-parallel-solutions.html#brjw1fx-2) +* [Archived MathWorks Documentation](http://www.mathworks.com/help/doc-archives.html) +* [MathWorks Website](http://www.mathworks.com/) diff --git a/docs/snippets/examples/apps/matlab/mdcs_parallel.md b/docs/snippets/examples/apps/matlab/mdcs_parallel.md new file mode 100644 index 00000000..ba788108 --- /dev/null +++ b/docs/snippets/examples/apps/matlab/mdcs_parallel.md @@ -0,0 +1,107 @@ +# Distributed Computing Server (parallel job) + +The MATLAB *Parallel Computing Toolbox (PCT)* enables a *parallel job* via the MATLAB *Distributed Computing Server (DCS)*. The tasks of a parallel job are identical, run simultaneously on several MATLAB workers (labs), and communicate with each other. This section illustrates an MPI-like program. + +This section illustrates how to submit a small, MATLAB *parallel job* with four workers running one MPI-like task to a batch queue. The MATLAB program broadcasts an integer to four workers and gathers the names of the compute nodes running the workers and the lab IDs of the workers. + +This example uses the job submission command to submit a Matlab script with a [user-defined cluster profile](profile_manager.md) which scatters the MATLAB workers onto different compute nodes. This method uses the MATLAB interpreter, the Parallel Computing Toolbox, and the Distributed Computing Server; so, it requires and checks out six licenses: one MATLAB license for the client running on the compute node, one PCT license, and four DCS licenses. Four DCS licenses run the four copies of the parallel job. This job is completely off the front end. + +Prepare a MATLAB script named `myscript.m` : + +``` +% FILENAME: myscript.m + +% Specify pool size. +% Convert the parallel job to a pool job. +parpool('4'); +spmd + +if labindex == 1 + % Lab (rank) #1 broadcasts an integer value to other labs (ranks). + N = labBroadcast(1,int64(1000)); +else + % Each lab (rank) receives the broadcast value from lab (rank) #1. + N = labBroadcast(1); +end + +% Form a string with host name, total number of labs, lab ID, and broadcast value. +[c name] =system('hostname'); +name = name(1:length(name)-1); +fmt = num2str(floor(log10(numlabs))+1); +str = sprintf(['%s:%d:%' fmt 'd:%d '], name,numlabs,labindex,N); + +% Apply global concatenate to all str's. +% Store the concatenation of str's in the first dimension (row) and on lab #1. +result = gcat(str,1,1); +if labindex == 1 + disp(result) +end + +end % spmd +matlabpool close force; +quit; +``` + +Also, prepare a job submission, here named `myjob.sub`. Run with the name of the script: + +``` +# FILENAME: myjob.sub + +echo "myjob.sub" + +module load matlab + +unset DISPLAY + +# -nodisplay: run MATLAB in text mode; X11 server not needed +# -r: read MATLAB program; use MATLAB JIT Accelerator +matlab -nodisplay -r myscript +``` + +Run MATLAB to set the default parallel configuration to your appropriate Profile: + +``` +$ matlab -nodisplay +>> defaultParallelConfig('myslurmprofile'); +>> quit; +$ +``` + +[Submit the job](../../../slurm/submit_script.md) as a single compute node with one processor core. + +Once this job starts, a second job submission is made. + +[View job status](../../../slurm/monitoring_job.md) + +[View results of the job](../../../slurm/checking_output.md) + +``` +myjob.sub + + < M A T L A B (R) > + Copyright 1984-2011 The MathWorks, Inc. + R2011b (7.13.0.564) 64-bit (glnxa64) + August 13, 2011 + +To get started, type one of these: helpwin, helpdesk, or demo. +For product information, visit www.mathworks.com. + +>Starting matlabpool using the 'myslurmprofile' configuration ... connected to 4 labs. +Lab 1: + bell-a006.rcac.purdue.edu:4:1:1000 + bell-a007.rcac.purdue.edu:4:2:1000 + bell-a008.rcac.purdue.edu:4:3:1000 + bell-a009.rcac.purdue.edu:4:4:1000 +Sending a stop signal to all the labs ... stopped. +Did not find any pre-existing parallel jobs created by matlabpool. +``` + +Output shows the name of one compute node (a006) that processed the job submission file `myjob.sub`. The job submission scattered four processor cores (four MATLAB labs) among four different compute nodes (a006,a007,a008,a009) that processed the four parallel regions. + +To scale up this method to handle a real application, increase the wall time in the submission command to accommodate a longer running job. Secondly, increase the wall time of `myslurmprofile` by using the `Cluster Profile Manager` in the `Parallel` menu to enter a new wall time in the property `SubmitArguments`. + +For more information about parallel jobs: + +* [MathWorks MATLAB Parallel Computing Toolbox User's Guide](http://www.mathworks.com/help/distcomp/index.html) +* [MathWorks MATLAB Distributed Computing Server User's Guide](http://www.mathworks.com/help/mdce/index.html) +* [MathWorks Website](http://www.mathworks.com/) diff --git a/docs/snippets/examples/apps/matlab/parfor.md b/docs/snippets/examples/apps/matlab/parfor.md new file mode 100644 index 00000000..38e73c2f --- /dev/null +++ b/docs/snippets/examples/apps/matlab/parfor.md @@ -0,0 +1,119 @@ +# Parallel Computing Toolbox (parfor) + +The MATLAB *Parallel Computing Toolbox (PCT)* extends the MATLAB language with high-level, parallel-processing features such as parallel for loops, parallel regions, message passing, distributed arrays, and parallel numerical methods. It offers a shared-memory computing environment running on the local cluster profile in addition to your MATLAB client. Moreover, the MATLAB *Distributed Computing Server (DCS)* scales PCT applications up to the limit of your DCS licenses. + +This section illustrates the fine-grained parallelism of a parallel for loop (`parfor`) in a *pool job*. + +The following examples illustrate a method for submitting a small, parallel, MATLAB program with a parallel loop (`parfor` statement) as a job to a queue. This MATLAB program prints the name of the run host and shows the values of variables `numlabs` and `labindex` for each iteration of the `parfor` loop. + +This method uses the job submission command to submit a MATLAB client which calls the MATLAB `batch()` function with a [user-defined cluster profile](profile_manager.md). + +Prepare a MATLAB pool program in a MATLAB script with an appropriate filename, here named `myscript.m`: + +``` +% FILENAME: myscript.m + +% SERIAL REGION +[c name] = system('hostname'); +fprintf('SERIAL REGION: hostname:%s\n', name) +numlabs = parpool('poolsize'); +fprintf(' hostname numlabs labindex iteration\n') +fprintf(' ------------------------------- ------- -------- ---------\n') +tic; + +% PARALLEL LOOP +parfor i = 1:8 + [c name] = system('hostname'); + name = name(1:length(name)-1); + fprintf('PARALLEL LOOP: %-31s %7d %8d %9d\n', name,numlabs,labindex,i) + pause(2); +end + +% SERIAL REGION +elapsed_time = toc; % get elapsed time in parallel loop +fprintf('\n') +[c name] = system('hostname'); +name = name(1:length(name)-1); +fprintf('SERIAL REGION: hostname:%s\n', name) +fprintf('Elapsed time in parallel loop: %f\n', elapsed_time) +``` + +The execution of a pool job starts with a worker executing the statements of the first serial region up to the `parfor` block, when it pauses. A set of workers (the pool) executes the `parfor` block. When they finish, the first worker resumes by executing the second serial region. The code displays the names of the compute nodes running the batch session and the worker pool. + +Prepare a MATLAB script that calls MATLAB function `batch()` which makes a four-lab pool on which to run the MATLAB code in the file `myscript.m`. Use an appropriate filename, here named `mylclbatch.m`: + +``` +% FILENAME: mylclbatch.m + +!echo "mylclbatch.m" +!hostname + +pjob=batch('myscript','Profile','myslurmprofile','Pool',4,'CaptureDiary',true); +wait(pjob); +diary(pjob); +quit; +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`: + +``` +#!/bin/bash +# FILENAME: myjob.sub + +echo "myjob.sub" +hostname + +module load matlab + +unset DISPLAY + +matlab -nodisplay -r mylclbatch +``` + +[Submit the job](../../../slurm/submit_script.md) as a single compute node with one processor core. + +One processor core runs `myjob.sub` and `mylclbatch.m`. + +Once this job starts, a second job submission is made. + +[View job status](../../../slurm/monitoring_job.md) + +[View results of the job](../../../slurm/checking_output.md) + +``` +myjob.sub + + < M A T L A B (R) > + Copyright 1984-2013 The MathWorks, Inc. + R2013a (8.1.0.604) 64-bit (glnxa64) + February 15, 2013 + +To get started, type one of these: helpwin, helpdesk, or demo. +For product information, visit www.mathworks.com. + +mylclbatch.mbell-a000.rcac.purdue.edu +SERIAL REGION: hostname:bell-a000.rcac.purdue.edu + + hostname numlabs labindex iteration + ------------------------------- ------- -------- --------- +PARALLEL LOOP: bell-a001.rcac.purdue.edu 4 1 2 +PARALLEL LOOP: bell-a002.rcac.purdue.edu 4 1 4 +PARALLEL LOOP: bell-a001.rcac.purdue.edu 4 1 5 +PARALLEL LOOP: bell-a002.rcac.purdue.edu 4 1 6 +PARALLEL LOOP: bell-a003.rcac.purdue.edu 4 1 1 +PARALLEL LOOP: bell-a003.rcac.purdue.edu 4 1 3 +PARALLEL LOOP: bell-a004.rcac.purdue.edu 4 1 7 +PARALLEL LOOP: bell-a004.rcac.purdue.edu 4 1 8 + +SERIAL REGION: hostname:bell-a001.rcac.purdue.edu + +Elapsed time in parallel loop: 5.411486 +``` + +To scale up this method to handle a real application, increase the wall time in the [submission](../../../slurm/submit_script.md) command to accommodate a longer running job. Secondly, increase the wall time of `myslurmprofile` by using the [Cluster Profile Manager](profile_manager.md) in the `Parallel` menu to enter a new wall time in the property `SubmitArguments`. + +For more information about MATLAB Parallel Computing Toolbox: + +* [MathWorks MATLAB Parallel Computing Toolbox User's Guide](http://www.mathworks.com/help/distcomp/index.html) +* [MathWorks MATLAB Distributed Computing Server User's Guide](http://www.mathworks.com/help/mdce/index.html) +* [MathWorks Website](http://www.mathworks.com/) diff --git a/docs/snippets/examples/apps/matlab/profile_manager.md b/docs/snippets/examples/apps/matlab/profile_manager.md new file mode 100644 index 00000000..462f7996 --- /dev/null +++ b/docs/snippets/examples/apps/matlab/profile_manager.md @@ -0,0 +1,17 @@ +# Profile Manager + +MATLAB offers two kinds of profiles for parallel execution: the 'local' profile and user-defined cluster profiles. The 'local' profile runs a MATLAB job on the processor core(s) of the same compute node, or front-end, that is running the client. To run a MATLAB job on compute node(s) different from the node running the client, you must define a Cluster Profile using the `Cluster Profile Manager`. + +To prepare a user-defined cluster profile, use the `Cluster Profile Manager` in the `Parallel` menu. This profile contains the scheduler details (queue, nodes, processors, walltime, etc.) of your job submission. Ultimately, your cluster profile will be an argument to MATLAB functions like `batch()`. + +For your convenience, a generic cluster profile is provided that can be downloaded: [myslurmprofile.settings](https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/matlab/myslurmprofile.settings) + +Please note that modifications are very likely to be required to make `myslurmprofile.settings` work. You may need to change values for number of nodes, number of workers, walltime, and submission queue specified in the file. As well, the generic profile itself depends on the particular job scheduler on the cluster, so you may need to download or create two or more generic profiles under different names. Each time you run a job using a Cluster Profile, make sure the specific profile you are using is appropriate for the job and the cluster. + +To import the profile, start a MATLAB session and select `Manage Cluster Profiles...` from the Parallel menu. In the Cluster Profile Manager, select `Import`, navigate to the folder containing the profile, select `myslurmprofile.settings` and click `OK`. Remember that the profile will need to be customized for your specific needs. If you have any questions, please [contact us](https://www.rcac.purdue.edu/help). + +For detailed information about MATLAB's Parallel Computing Toolbox, examples, demos, and tutorials: + +* [MATLAB - Parallel Computing Toolbox](http://www.mathworks.com/help/distcomp/index.html) +* [MATLAB Parallel Computing Toolbox: Introduction to Parallel Solutions](http://www.mathworks.com/help/distcomp/introduction-to-parallel-solutions.html) +* [MATLAB Parallel Computing Toolbox: Clusters and Cluster Profiles](https://www.mathworks.com/help/parallel-computing/discover-clusters-and-use-cluster-profiles.html) diff --git a/docs/snippets/examples/apps/matlab/spmd.md b/docs/snippets/examples/apps/matlab/spmd.md new file mode 100644 index 00000000..ca3c0f50 --- /dev/null +++ b/docs/snippets/examples/apps/matlab/spmd.md @@ -0,0 +1,113 @@ +# Parallel Toolbox (spmd) + +The MATLAB *Parallel Computing Toolbox (PCT)* extends the MATLAB language with high-level, parallel-processing features such as parallel for loops, parallel regions, message passing, distributed arrays, and parallel numerical methods. It offers a shared-memory computing environment with a maximum of eight MATLAB workers (labs, threads; versions R2009a) and 12 workers (labs, threads; version R2011a) running on the local configuration in addition to your MATLAB client. Moreover, the MATLAB *Distributed Computing Server (DCS)* scales PCT applications up to the limit of your DCS licenses. + +This section illustrates how to submit a small, parallel, MATLAB program with a parallel region (`spmd` statement) as a MATLAB pool job to a batch queue. + +This example uses the [submission command](../../../slurm/submit_script.md) to submit to compute nodes a MATLAB client which interprets a Matlab .m with a [user-defined cluster profile](profile_manager.md) which scatters the MATLAB workers onto different compute nodes. This method uses the MATLAB interpreter, the Parallel Computing Toolbox, and the Distributed Computing Server; so, it requires and checks out six licenses: one MATLAB license for the client running on the compute node, one PCT license, and four DCS licenses. Four DCS licenses run the four copies of the `spmd` statement. This job is completely off the front end. + +Prepare a MATLAB script called `myscript.m`: + +``` + +% FILENAME: myscript.m + +% SERIAL REGION +[c name] = system('hostname'); +fprintf('SERIAL REGION: hostname:%s\n', name) +p = parpool('4'); +fprintf(' hostname numlabs labindex\n') +fprintf(' ------------------------------- ------- --------\n') +tic; + +% PARALLEL REGION +spmd + [c name] = system('hostname'); + name = name(1:length(name)-1); + fprintf('PARALLEL REGION: %-31s %7d %8d\n', name,numlabs,labindex) + pause(2); +end + +% SERIAL REGION +elapsed_time = toc; % get elapsed time in parallel region +delete(p); +fprintf('\n') +[c name] = system('hostname'); +name = name(1:length(name)-1); +fprintf('SERIAL REGION: hostname:%s\n', name) +fprintf('Elapsed time in parallel region: %f\n', elapsed_time) +quit; +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`. Run with the name of the script: + +``` + +#!/bin/bash +# FILENAME: myjob.sub + +echo "myjob.sub" + +module load matlab + +unset DISPLAY + +matlab -nodisplay -r myscript +``` + +Run MATLAB to set the default parallel configuration to your job configuration: + +``` + +$ matlab -nodisplay +>> parallel.defaultClusterProfile('myslurmprofile'); +>> quit; +$ +``` + +[Submit the job](../../../slurm/submit_script.md) + +Once this job starts, a second job submission is made. + +[View job status](../../../slurm/monitoring_job.md) + +[View results for the job](../../../slurm/checking_output.md) + +``` +myjob.sub + + < M A T L A B (R) > + Copyright 1984-2011 The MathWorks, Inc. + R2011b (7.13.0.564) 64-bit (glnxa64) + August 13, 2011 + +To get started, type one of these: helpwin, helpdesk, or demo. +For product information, visit www.mathworks.com. + +SERIAL REGION: hostname:bell-a001.rcac.purdue.edu + +Starting matlabpool using the 'myslurmprofile' profile ... connected to 4 labs. + hostname numlabs labindex + ------------------------------- ------- -------- +Lab 2: + PARALLEL REGION: bell-a002.rcac.purdue.edu 4 2 +Lab 1: + PARALLEL REGION: bell-a001.rcac.purdue.edu 4 1 +Lab 3: + PARALLEL REGION: bell-a003.rcac.purdue.edu 4 3 +Lab 4: + PARALLEL REGION: bell-a004.rcac.purdue.edu 4 4 + +Sending a stop signal to all the labs ... stopped. + +SERIAL REGION: hostname:bell-a001.rcac.purdue.edu +Elapsed time in parallel region: 3.382151 +``` + +Output shows the name of one compute node (a001) that processed the job submission file `myjob.sub` and the two serial regions. The job submission scattered four processor cores (four MATLAB labs) among four different compute nodes (a001,a002,a003,a004) that processed the four parallel regions. The total elapsed time demonstrates that the jobs ran in parallel. + +For more information about MATLAB Parallel Computing Toolbox: + +* [MathWorks MATLAB Parallel Computing Toolbox User's Guide](http://www.mathworks.com/help/distcomp/index.html) +* [MathWorks MATLAB Distributed Computing Server User's Guide](http://www.mathworks.com/help/mdce/index.html) +* [MathWorks Website](http://www.mathworks.com/) diff --git a/docs/snippets/examples/apps/octave.md b/docs/snippets/examples/apps/octave.md new file mode 100644 index 00000000..6feb55b0 --- /dev/null +++ b/docs/snippets/examples/apps/octave.md @@ -0,0 +1,78 @@ +# Octave + +GNU Octave is a high-level, interpreted, programming language for numerical computations. Octave is a structured language (similar to C) and mostly compatible with MATLAB. You may use Octave to avoid the need for a MATLAB license, both during development and as a deployed application. By doing so, you may be able to run your application on more systems or more easily distribute it to others. + +This section illustrates how to submit a small Octave job to a PBS queue. This Octave example computes the inverse of a matrix. + +Prepare an Octave script file with an appropriate filename, here named `myjob.m`: + +``` + +% FILENAME: myjob.m + +% Invert matrix A. +A = [1 2 3; 4 5 6; 7 8 0] +inv(A) + +quit +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`: + +``` + +#!/bin/sh -l +# FILENAME: myjob.sub + +module load octave +cd $PBS_O_WORKDIR + +unset DISPLAY + +# Use the -q option to suppress startup messages. +# octave -q < myjob.m +octave < myjob.m +``` + +The command `octave myjob.m` (without the redirection) also works in the preceding script. + +Submit the job: + +``` + + +$ qsub -l nodes=1:ppn=128 myjob.sub + +``` + +View job status: + +``` + +$ qstat -u myusername +``` + +View results in the file for all standard output, `myjob.sub.omyjobid`: + +``` + +A = + + 1 2 3 + 4 5 6 + 7 8 0 + +ans = + + -1.77778 0.88889 -0.11111 + 1.55556 -0.77778 0.22222 + -0.11111 0.22222 -0.11111 +``` + +Any output written to standard error will appear in `myjob.sub.emyjobid`. + +For more information about Octave: + +* [GNU Octave Website](http://www.octave.org) +* [Octave Online Documentation](http://www.gnu.org/software/octave/doc/interpreter/) +* [Porting Programs from MATLAB to Octave](http://wiki.octave.org/FAQ) diff --git a/docs/snippets/examples/apps/python.md b/docs/snippets/examples/apps/python.md new file mode 100644 index 00000000..0ab22d87 --- /dev/null +++ b/docs/snippets/examples/apps/python.md @@ -0,0 +1,26 @@ +# Python + +!!! Note + Notice: Python 2.7 has reached end-of-life on Jan 1, 2020 ([announcement](https://www.anaconda.com/end-of-life-eol-for-python-2-7-is-coming-are-you-ready)). Please update your codes and your job scripts to use Python 3. + +Python is a high-level, general-purpose, interpreted, dynamic programming language. We suggest using Anaconda which is a Python distribution made for large-scale data processing, predictive analytics, and scientific computing. For example, to use the default Anaconda distribution: + +``` +$ module load conda +``` + +For a full list of available Anaconda and Python modules enter: + +``` +$ module spider conda +``` + +## In This Section + +- [Managing Environments with Conda](python/conda.md) +- [Example: Create and Use Biopython Environment with Conda](python/environment_example.md) +- [Example Python Jobs](python/examples.md) +- [Numpy Parallel Behavior](python/numpy.md) +- [Installing Packages](python/packages.md) +- [Managing Packages with Pip](python/pip.md) +- [Installing Packages from Source](python/source.md) diff --git a/docs/snippets/examples/apps/python/conda.md b/docs/snippets/examples/apps/python/conda.md new file mode 100644 index 00000000..2b63b765 --- /dev/null +++ b/docs/snippets/examples/apps/python/conda.md @@ -0,0 +1,82 @@ +# Managing Environments with Conda + +Conda is a package manager in Anaconda that allows you to create and manage multiple environments where you can pick and choose which packages you want to use. To use Conda you must load an Anaconda module: + +``` +$ module load conda +``` + +Many packages are pre-installed in the global environment. To see these packages: + +``` +$ conda list +``` + +To create your own custom environment: + +``` +$ conda create --name MyEnvName python=3.8 FirstPackageName SecondPackageName -y +``` + +The `--name` option specifies that the environment created will be named MyEnvName. You can include as many packages as you require separated by a space. Including the `-y` option lets you skip the prompt to install the package. By default environments are created and stored in the $HOME/.conda directory. + +To create an environment at a custom location: + +``` +$ conda create --prefix=$HOME/MyEnvName python=3.8 PackageName -y +``` + +To see a list of your environments: + +``` +$ conda env list +``` + +To remove unwanted environments: + +``` +$ conda remove --name MyEnvName --all +``` + + +To add packages to your environment: + +``` +$ conda install --name MyEnvName PackageNames +``` + + +To remove a package from an environment: + +``` +$ conda remove --name MyEnvName PackageName +``` + +Installing packages when creating your environment, instead of one at a time, will help you avoid dependency issues. + +To activate or deactivate an environment you have created: + +``` +$ source activate MyEnvName +$ source deactivate MyEnvName +``` + +If you created your conda environment at a custom location using `--prefix` option, then you can activate or deactivate it using the full path. + +``` +$ source activate $HOME/MyEnvName +$ source deactivate $HOME/MyEnvName +``` + +To use a custom environment inside a job you must load the module and activate the environment inside your job submission script. Add the following lines to your submission script: + +``` +$ module load conda +$ source activate MyEnvName +``` + +For more information about Python: + +* [The Python Programming Language - Official Website](http://www.python.org/) +* [Anaconda Python Distribution - Official Website](https://store.continuum.io/cshop/anaconda/) +* [Conda User Guide](https://conda.io/projects/conda/en/latest/user-guide/) diff --git a/docs/snippets/examples/apps/python/environment_example.md b/docs/snippets/examples/apps/python/environment_example.md new file mode 100644 index 00000000..3a81d8e7 --- /dev/null +++ b/docs/snippets/examples/apps/python/environment_example.md @@ -0,0 +1,51 @@ +# Example: Create and Use Biopython Environment with Conda + +## Using conda to create an environment that uses the biopython package + +To use Conda you must first load the anaconda module: + +``` +module load conda +``` + +Create an empty conda environment to install biopython: + +``` +conda-env-mod create -n biopython +``` + +Now activate the biopython environment: + +``` +module load use.own +module load conda-env/biopython-py3.12.5 +``` + +Install the biopython packages in your environment: + +``` +conda install --channel anaconda biopython -y +Fetching package metadata .......... +Solving package specifications ......... +....... +Linking packages ... +[ COMPLETE ]|################################################################ +``` + +The `--channel` option specifies that it searches the anaconda channel for the biopython package. The `-y` argument is optional and allows you to skip the installation prompt. A list of packages will be displayed as they are installed. + +Remember to add the following lines to your job submission script to use the custom environment in your jobs: + +``` +module load conda +module load use.own +module load conda-env/biopython-py3.12.5 +``` + +If you need further help or run into any issues with creating environments, [contact us](https://www.rcac.purdue.edu/about/contact) or drop by [Coffee Hour](https://www.rcac.purdue.edu/coffee) for in-person help. + +For more information about Python: + +* [The Python Programming Language - Official Website](http://www.python.org/) +* [Anaconda Python Distribution - Official Website](https://store.continuum.io/cshop/anaconda/) +* [Conda User Guide](https://conda.io/projects/conda/en/latest/user-guide/) diff --git a/docs/snippets/examples/apps/python/examples.md b/docs/snippets/examples/apps/python/examples.md new file mode 100644 index 00000000..021eae6c --- /dev/null +++ b/docs/snippets/examples/apps/python/examples.md @@ -0,0 +1,98 @@ +# Example Python Jobs + +This section illustrates how to submit a small Python job to a SLURM queue. + +## Example 1: Hello world + +Prepare a Python input file with an appropriate filename, here named `hello.py`: + +``` + +# FILENAME: hello.py + +import string, sys +print("Hello, world!") +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`: + +``` + +#!/bin/bash +# FILENAME: myjob.sub + +module load conda + +python hello.py +``` + +[Submit the job](../../../slurm/submit_script.md) + +[View job status](../../../slurm/monitoring_job.md) + +[View results of the job](../../../slurm/checking_output.md) + +``` + +Hello, world! +``` + +## Example 2: Matrix multiply + +Save the following script as matrix.py: + +``` + +# Matrix multiplication program + +x = [[3,1,4],[1,5,9],[2,6,5]] +y = [[3,5,8,9],[7,9,3,2],[3,8,4,6]] + +result = [[sum(a*b for a,b in zip(x_row,y_col)) for y_col in zip(*y)] for x_row in x] + +for r in result: + print(r) +``` + +Change the last line in the job submission file above to read: + +``` + +python matrix.py +``` + +The standard output file from this job will result in the following matrix: + +``` + +[28, 56, 43, 53] +[65, 122, 59, 73] +[63, 104, 54, 60] +``` + +## Example 3: Sine wave plot using numpy and matplotlib packages + +Save the following script as sine.py: + +``` + +import numpy as np +import matplotlib +matplotlib.use('Agg') +import matplotlib.pyplot as plt + +x = np.linspace(-np.pi, np.pi, 201) +plt.plot(x, np.sin(x)) +plt.xlabel('Angle [rad]') +plt.ylabel('sin(x)') +plt.axis('tight') +plt.savefig('sine.png') +``` + +Change your job submission file to submit this script and the job will output a png file and blank standard output and error files. + +For more information about Python: + +* [The Python Programming Language - Official Website](http://www.python.org/) +* [Anaconda Python Distribution - Official Website](https://store.continuum.io/cshop/anaconda/) +* [Conda User Guide](https://conda.io/projects/conda/en/latest/user-guide/) diff --git a/docs/snippets/examples/apps/python/numpy.md b/docs/snippets/examples/apps/python/numpy.md new file mode 100644 index 00000000..13d4c8b6 --- /dev/null +++ b/docs/snippets/examples/apps/python/numpy.md @@ -0,0 +1,29 @@ +# Numpy Parallel Behavior + +The widely available Numpy package is the best way to handle numerical computation in Python. The `numpy` package provided by our `anaconda` modules is optimized using Intel's MKL library. It will automatically parallelize many operations to make use of all the cores available on a machine. + +In many contexts that would be the ideal behavior. On the cluster however that very likely is not in fact the preferred behavior because often more than one user is present on the system and/or more than one job on a node. Having multiple processes contend for those resources will actually result in lesser performance. + +Setting the `MKL_NUM_THREADS` or `OMP_NUM_THREADS` environment variable(s) allows you to control this behavior. Our anaconda modules automatically set these variables to 1 *if and only if* you do not currently have that variable defined. + +When submitting batch jobs it is always a good idea to be explicit rather than implicit. If you are submitting a job that you want to make use of the full resources available on the node, set one or both of these variables to the number of cores you want to allow numpy to make use of. + +``` +#!/bin/bash + + +module load conda +export MKL_NUM_THREADS=128 + +... +``` + +If you are submitting multiple jobs that you intend to be scheduled together on the same node, it is probably best to restrict numpy to a single core. + +``` +#!/bin/bash + + +module load conda +export MKL_NUM_THREADS=1 +``` diff --git a/docs/snippets/examples/apps/python/packages.md b/docs/snippets/examples/apps/python/packages.md new file mode 100644 index 00000000..435adf95 --- /dev/null +++ b/docs/snippets/examples/apps/python/packages.md @@ -0,0 +1,295 @@ +# Installing Packages + +Installing Python packages in an Anaconda environment is recommended. One key advantage of Anaconda is that it allows users to install unrelated packages in separate self-contained environments. Individual packages can later be reinstalled or updated without impacting others. If you are unfamiliar with Conda environments, please check our [Conda Guide](conda.md). + +To facilitate the process of creating and using Conda environments, we support a script (`conda-env-mod`) that generates a module file for an environment, as well as an optional Jupyter kernel to use this environment in a JupyterHub notebook. + +You must load one of the `anaconda` modules in order to use this script. + +``` +$ module load conda +``` + +Step-by-step instructions for installing custom Python packages are presented below. + +## Step 1: Create a conda environment + +Users can use the `conda-env-mod` script to create an empty conda environment. This script needs either a name or a path for the desired environment. After the environment is created, it generates a module file for using it in future. Please note that `conda-env-mod` is different from the official `conda-env` script and supports a limited set of subcommands. Detailed instructions for using `conda-env-mod` can be found with the command `conda-env-mod --help`. + +* **Example 1:** Create a conda environment named `mypackages` in user's `$HOME` directory. + + ``` + $ conda-env-mod create -n mypackages + ``` + +* **Example 2:** Create a conda environment named `mypackages` at a custom location. + + ``` + $ conda-env-mod create -p /depot/mylab/apps/mypackages + ``` + + Please follow the on-screen instructions while the environment is being created. After finishing, the script will print the instructions to use this environment. + + ``` + ... ... ... + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + +------------------------------------------------------+ + | To use this environment, load the following modules: | + | module load use.own | + | module load conda-env/mypackages-py3.8.5 | + +------------------------------------------------------+ + Your environment "mypackages" was created successfully. + ``` + +Note down the module names, as you will need to load these modules every time you want to use this environment. You may also want to add the `module load` lines in your jobscript, if it depends on custom Python packages. + +By default, module files are generated in your `$HOME/privatemodules` directory. The location of module files can be customized by specifying the `-m /path/to/modules` option to `conda-env-mod`. + +**Note:** The main differences between `-p` and `-m` are: 1) `-p` will change the location of packages to be installed for the env and the module file will still be located at the `$HOME/privatemodules` directory as defined in use.own. 2) `-m` will only change the location of the module file. So the method to load modules created with `-m` and `-p` are different, see Example 3 for details. + +* **Example 3:** Create a conda environment named `labpackages` in your group's Data Depot space and place the module file at a shared location for the group to use. + + ``` + $ conda-env-mod create -p /depot/mylab/apps/labpackages -m /depot/mylab/etc/modules + ... ... ... + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + +-------------------------------------------------------+ + | To use this environment, load the following modules: | + | module use /depot/mylab/etc/modules | + | module load conda-env/labpackages-py3.8.5 | + +-------------------------------------------------------+ + Your environment "labpackages" was created successfully. + ``` + +If you used a custom module file location, you need to run the `module use` command as printed by the command output above. + +By default, only the environment and a module file are created (no Jupyter kernel). If you plan to use your environment in a JupyterHub notebook, you need to append a `--jupyter` flag to the above commands. + +* **Example 4:** Create a Jupyter-enabled conda environment named `labpackages` in your group's Data Depot space and place the module file at a shared location for the group to use. + + ``` + $ conda-env-mod create -p /depot/mylab/apps/labpackages -m /depot/mylab/etc/modules --jupyter + ... ... ... + Jupyter kernel created: "Python (My labpackages Kernel)" + ... ... ... + Your environment "labpackages" was created successfully. + ``` + +## Step 2: Load the conda environment + +* The following instructions assume that you have used `conda-env-mod` script to create an environment named `mypackages` (Examples 1 or 2 above). If you used `conda create` instead, please use `conda activate mypackages`. + + ``` + $ module load use.own + $ module load conda-env/mypackages-py3.8.5 + ``` + + Note that the `conda-env` module name includes the Python version that it supports (Python 3.8.5 in this example). This is same as the Python version in the `conda` module. +* If you used a custom module file location (Example 3 above), please use `module use` to load the `conda-env` module. + + ``` + $ module use /depot/mylab/etc/modules + $ module load conda-env/labpackages-py3.8.5 + ``` + + +## Step 3: Install packages + +Now you can install custom packages in the environment using either `conda install` or `pip install`. + +### Installing with conda + +* **Example 1:** Install OpenCV (open-source computer vision library) using conda. + + ``` + $ conda install opencv + ``` + +* **Example 2:** Install a specific version of OpenCV using conda. + + ``` + $ conda install opencv=4.5.5 + ``` + +* **Example 3:** Install OpenCV from a specific anaconda channel. + + ``` + $ conda install -c anaconda opencv + ``` + +### Installing with pip + +* **Example 4:** Install pandas using pip. + + ``` + $ pip install pandas + ``` + +* **Example 5:** Install a specific version of pandas using pip. + + ``` + $ pip install pandas==1.4.3 + ``` + + Follow the on-screen instructions while the packages are being installed. If installation is successful, please proceed to the next section to test the packages. + +!!! Note + Do **NOT** run Pip with the `--user` argument, as that will install packages in a different location and might mess up your account environment. + +## Step 4: Test the installed packages + + +To use the installed Python packages, you must load the module for your conda environment. If you have not loaded the `conda-env` module, please do so following the instructions at the end of Step 1. + +``` +$ module load use.own +$ module load conda-env/mypackages-py3.8.5 +``` + +* **Example 1:** Test that OpenCV is available. + + ``` + $ python -c "import cv2; print(cv2.__version__)" + ``` + +* **Example 2:** Test that pandas is available. + + ``` + $ python -c "import pandas; print(pandas.__version__)" + ``` + +If the commands finished without errors, then the installed packages can be used in your program. + +## Additional capabilities of conda-env-mod script + +The `conda-env-mod` tool is intended to facilitate creation of a minimal Anaconda environment, matching module file and optionally a Jupyter kernel. Once created, the environment can then be accessed via familiar `module load` command, tuned and expanded as necessary. Additionally, the script provides several auxiliary functions to help manage environments, module files and Jupyter kernels. + +General usage for the tool adheres to the following pattern: + +``` +$ conda-env-mod help +$ conda-env-mod [optional arguments] +``` + +where required arguments are one of + +* `-n|--name ENV_NAME` (name of the environment) +* `-p|--prefix ENV_PATH` (location of the environment) + +and optional arguments further modify behavior for specific actions (e.g. `-m` to specify alternative location for generated module files). + +Given a required name or prefix for an environment, the `conda-env-mod` script supports the following subcommands: + +* `create` - to create a new environment, its corresponding module file and optional Jupyter kernel. +* `delete` - to delete existing environment along with its module file and Jupyter kernel. +* `module` - to generate just the module file for a given existing environment. +* `kernel` - to generate just the Jupyter kernel for a given existing environment (note that the environment has to be created with a `--jupyter` option). +* `help` - to display script usage help. + +Using these subcommands, you can iteratively fine-tune your environments, module files and Jupyter kernels, as well as delete and re-create them with ease. Below we cover several commonly occurring scenarios. + +!!! Note + When you try to use `conda-env-mod delete`, remember to include the arguments as you create the environment (i.e. `-p package_location` and/or `-m module_location`). + +## Generating module file for an existing environment + +If you already have an existing configured Anaconda environment and want to generate a module file for it, follow appropriate examples from **Step 1** above, but use the `module` subcommand instead of the `create` one. E.g. + +``` +$ conda-env-mod module -n mypackages +``` + +and follow printed instructions on how to load this module. With an optional `--jupyter` flag, a Jupyter kernel will also be generated. + +**Note that** the module name `mypackages` should be exactly the same with the older conda environment name. **Note also that** if you intend to proceed with a Jupyter kernel generation (via the `--jupyter` flag or a `kernel` subcommand later), you will have to ensure that your environment has `ipython` and `ipykernel` packages installed into it. To avoid this and other related complications, we highly recommend making a fresh environment using a suitable `conda-env-mod create .... --jupyter` command instead. + +## Generating Jupyter kernel for an existing environment + +If you already have an existing configured Anaconda environment and want to generate a Jupyter kernel file for it, you can use the `kernel` subcommand. E.g. + +``` +$ conda-env-mod kernel -n mypackages +``` + +This will add a `"Python (My mypackages Kernel)"` item to the dropdown list of available kernels upon your next login to the JupyterHub. + +Note that generated Jupiter kernels are always personal (i.e. each user has to make their own, even for shared environments). Note also that you (or the creator of the shared environment) will have to ensure that your environment has `ipython` and `ipykernel` packages installed into it. + +## Managing and using shared Python environments + +Here is a suggested workflow for a common group-shared Anaconda environment with Jupyter capabilities: + +**The PI or lab software manager:** + +* Creates the environment and module file (once): + + ``` + $ module purge + $ module load conda + $ conda-env-mod create -p /depot/mylab/apps/labpackages -m /depot/mylab/etc/modules --jupyter + ``` + +* Installs required Python packages into the environment (as many times as needed): + + ``` + $ module use /depot/mylab/etc/modules + $ module load conda-env/labpackages-py3.8.5 + $ conda install ....... # all the necessary packages + ``` + +**Lab members:** + +* Lab members can start using the environment in their command line scripts or batch jobs simply by loading the corresponding module: + + ``` + $ module use /depot/mylab/etc/modules + $ module load conda-env/labpackages-py3.8.5 + $ python my_data_processing_script.py ..... + ``` + +* To use the environment in Jupyter notebooks, each lab member will need to create his/her own Jupyter kernel (once). This is because Jupyter kernels are private to individuals, even for shared environments. + + ``` + $ module use /depot/mylab/etc/modules + $ module load conda-env/labpackages-py3.8.5 + $ conda-env-mod kernel -p /depot/mylab/apps/labpackages + ``` + +A similar process can be devised for instructor-provided or individually-managed class software, etc. + +## Troubleshooting + +* Python packages often fail to install or run due to dependency incompatibility with other packages. More specifically, if you previously installed packages in your home directory it is safer to clean those installations. + + ``` + $ mv ~/.local ~/.local.bak + $ mv ~/.cache ~/.cache.bak + ``` + +* Unload all the modules. + + ``` + $ module purge + ``` + +* Clean up PYTHONPATH. + + ``` + $ unset PYTHONPATH + ``` + +* Next load the modules (e.g. anaconda) that you need. + + ``` + $ module load conda/2024.02-py311 + $ module load use.own + $ module load conda-env/2024.02-py311 + ``` + +* Now try running your code again. + +* Few applications only run on specific versions of Python (e.g. Python 3.6). Please check the documentation of your application if that is the case. diff --git a/docs/snippets/examples/apps/python/pip.md b/docs/snippets/examples/apps/python/pip.md new file mode 100644 index 00000000..03abe202 --- /dev/null +++ b/docs/snippets/examples/apps/python/pip.md @@ -0,0 +1,51 @@ +# Managing Packages with Pip + +Pip is a Python package manager. Many Python package documentation provide `pip` instructions that result in permission errors because by default `pip` will install in a system-wide location and fail. + +``` + +Exception: +Traceback (most recent call last): +... ... stack trace ... ... +OSError: [Errno 13] Permission denied: '/apps/cent7/anaconda/2020.07-py38/lib/python3.8/site-packages/mkl_random-1.1.1.dist-info' +``` + +If you encounter this error, it means that you cannot modify the global Python installation. We recommend installing Python packages in a conda environment. Detailed instructions for installing packages with `pip` can be found in our [Python package installation page](packages.md). + +Below we list some other useful `pip` commands. + +* Search for a package in PyPI channels: + + ``` + $ pip search packageName + ``` + +* Check which packages are installed globally: + + ``` + $ pip list + ``` + +* Check which packages you have personally installed: + + ``` + $ pip list --user + ``` + +* Snapshot installed packages: + + ``` + $ pip freeze > requirements.txt + ``` + +* You can install packages from a snapshot inside a new conda environment. Make sure to load the appropriate conda environment first. + + ``` + $ pip install -r requirements.txt + ``` + +For more information about Python: + +* [The Python Programming Language - Official Website](http://www.python.org/) +* [Anaconda Python Distribution - Official Website](https://store.continuum.io/cshop/anaconda/) +* [Conda User Guide](https://conda.io/projects/conda/en/latest/user-guide/) diff --git a/docs/snippets/examples/apps/python/source.md b/docs/snippets/examples/apps/python/source.md new file mode 100644 index 00000000..656f718a --- /dev/null +++ b/docs/snippets/examples/apps/python/source.md @@ -0,0 +1,50 @@ +# Installing Packages from Source + +We maintain several [Anaconda](https://www.anaconda.com/) installations. Anaconda maintains numerous popular scientific Python libraries in a single installation. If you need a Python library not included with normal Python we recommend first checking Anaconda. For a list of modules currently installed in the Anaconda Python distribution: + +``` +$ module load conda +$ conda list +# packages in environment at /apps/spack/bell/apps/anaconda/2020.02-py37-gcc-4.8.5-u747gsx: +# +# Name Version Build Channel +_ipyw_jlab_nb_ext_conf 0.1.0 py37_0 +_libgcc_mutex 0.1 main +alabaster 0.7.12 py37_0 +anaconda 2020.02 py37_0 +... +``` + +If you see the library in the list, you can simply import it into your Python code after loading the Anaconda module. + +If you do not find the package you need, you should be able to install the library in your own Anaconda customization. First try to install it with [Conda or Pip](packages.md). If the package is not available from either Conda or Pip, you may be able to install it from source. + +Use the following instructions as a guideline for installing packages from source. Make sure you have a download link to the software (usually it will be a `tar.gz` archive file). You will substitute it on the wget line below. + +We also assume that you have already created an empty conda environment as described in our [Python package installation guide](packages.md). + +``` +$ mkdir ~/src +$ cd ~/src +$ wget http://path/to/source/tarball/app-1.0.tar.gz +$ tar xzvf app-1.0.tar.gz +$ cd app-1.0 +$ module load conda +$ module load use.own +$ module load conda-env/mypackages-py3.8.5 +$ python setup.py install +$ cd ~ +$ python +>>> import app +>>> quit() +``` + +The "import app" line should return without any output if installed successfully. You can then import the package in your python scripts. + +If you need further help or run into any issues installing a library, [contact us](https://www.rcac.purdue.edu/help) or drop by [Coffee Hour](https://www.rcac.purdue.edu/coffee) for in-person help. + +For more information about Python: + +* [The Python Programming Language - Official Website](http://www.python.org/) +* [Anaconda Python Distribution - Official Website](https://store.continuum.io/cshop/anaconda/) +* [Conda User Guide](https://conda.io/projects/conda/en/latest/user-guide/) diff --git a/docs/snippets/examples/apps/r.md b/docs/snippets/examples/apps/r.md new file mode 100644 index 00000000..3f380c19 --- /dev/null +++ b/docs/snippets/examples/apps/r.md @@ -0,0 +1,14 @@ +# R + +R, a GNU project, is a language and environment for data manipulation, statistics, and graphics. It is an open source version of the S programming language. R is quickly becoming the language of choice for data science due to the ease with which it can produce high quality plots and data visualizations. It is a versatile platform with a large, growing community and collection of packages. + +For more general information on R visit [The R Project for Statistical Computing](https://www.r-project.org). + +## In This Section + +- [Loading Data into R](r/data.md) +- [Running R jobs](r/job.md) +- [Installing R packages](r/package.md) +- [Setting Up R Preferences with .Rprofile](r/rprofile.md) +- [RStudio](r/rstudio.md) +- [Running RStudio Server on Bell](r/server.md) diff --git a/docs/snippets/examples/apps/r/data.md b/docs/snippets/examples/apps/r/data.md new file mode 100644 index 00000000..2fbb75ec --- /dev/null +++ b/docs/snippets/examples/apps/r/data.md @@ -0,0 +1,26 @@ +# Loading Data into R + +R is an environment for manipulating data. In order to manipulate data, it must be brought into the R environment. R has a function to read any file that data is stored in. Some of the most common file types like comma-separated variable(CSV) files have functions that come in the basic R packages. Other less common file types require additional packages to be installed. To read data from a CSV file into the R environment, enter the following command in the R prompt: + +``` +> read.csv(file = "path/to/data.csv", header = TRUE) +``` + +When R reads the file it creates an object that can then become the target of other functions. By default the read.csv() function will give the object the name of the .csv file. To assign a different name to the object created by read.csv enter the following in the R prompt: + +``` +> my_variable <- read.csv(file = "path/to/data.csv", header = FALSE) +``` + +To display the properties (structure) of loaded data, enter the following: + +``` +> str(my_variable) +``` + +For more functions and tutorials: + +* [The R Manuals](http://cran.r-project.org/manuals.html) +* [Other R Examples](http://www.mayin.org/ajayshah/KB/R/index.html) +* [Software Carpentry - Programming with R](https://swcarpentry.github.io/r-novice-inflammation/) +* [Data Carpentry Lessons](http://www.datacarpentry.org/lessons/) diff --git a/docs/snippets/examples/apps/r/job.md b/docs/snippets/examples/apps/r/job.md new file mode 100644 index 00000000..77ad52e3 --- /dev/null +++ b/docs/snippets/examples/apps/r/job.md @@ -0,0 +1,41 @@ +# Running R jobs + +This section illustrates how to submit a small R job to a SLURM queue. The example job computes a Pythagorean triple. + +Prepare an R input file with an appropriate filename, here named `myjob.R`: + +``` +# FILENAME: myjob.R + +# Compute a Pythagorean triple. +a = 3 +b = 4 +c = sqrt(a*a + b*b) +c # display result +``` + +Prepare a job submission file with an appropriate filename, here named `myjob.sub`: + +``` +#!/bin/bash +# FILENAME: myjob.sub + +module load r + +# --vanilla: +# --no-save: do not save datasets at the end of an R session +R --vanilla --no-save < myjob.R +``` + +[submit the job](../../../slurm/submit_script.md) + +[View job status](../../../slurm/monitoring_job.md) + +[View results of the job](../../../slurm/checking_output.md) + +For other examples or R jobs: + +* [The R Manuals](http://cran.r-project.org/manuals.html) +* [Other R Examples](http://www.mayin.org/ajayshah/KB/R/index.html) +* [Software Carpentry - Programming with R](https://swcarpentry.github.io/r-novice-inflammation/) +* [Data Carpentry Lessons](http://www.datacarpentry.org/lessons/) diff --git a/docs/snippets/examples/apps/r/package.md b/docs/snippets/examples/apps/r/package.md new file mode 100644 index 00000000..a2c87d54 --- /dev/null +++ b/docs/snippets/examples/apps/r/package.md @@ -0,0 +1,109 @@ +# Installing R packages + +## Challenges of Managing R Packages in the Cluster Environment + +* Different clusters have different hardware and softwares. So, if you have access to multiple clusters, you must install your R packages *separately for each cluster*. +* Each cluster has multiple versions of R and packages installed with one version of R may not work with another version of R. So, libraries for *each R version* must be installed in a *separate directory*. +* You can define the directory where your R packages will be installed using the environment variable `R_LIBS_USER`. +* For your convenience, a sample [~/.Rprofile example file](https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/r/Rprofile_example) is provided that can be downloaded to your cluster account and renamed into `~/.Rprofile` (or appended to one) to customize your installation preferences. [Detailed instructions](rprofile.md). + +## Installing Packages + +* **Step 0: Set up installation preferences.** + Follow the [steps for setting up](rprofile.md) your `~/.Rprofile` preferences. This step needs to be done only once. If you have created a `~/.Rprofile` file previously on Bell, ignore this step. +* **Step 1: Check if the package is already installed.** + As part of the R installations on community clusters, a lot of R libraries are pre-installed. You can check if your package is already installed by opening an R terminal and entering the command `installed.packages()`. For example, + + ``` + module load r/4.4.1 + R + ``` + + ``` + installed.packages()["units",c("Package","Version")] + Package Version + "units" "0.8-1" + quit() + ``` + + If the package you are trying to use is already installed, simply load the library, e.g., `library('units')`. Otherwise, move to the next step to install the package. + +* **Step 2: Load required dependencies. (if needed)** + For simple packages you may not need this step. However, some R packages depend on other libraries. For example, the `sf` package depends on `gdal` and `geos` libraries. So, you will need to load the corresponding modules before installing `sf`. Read the documentation for the package to identify which modules should be loaded. + + ``` + module load gdal + module load geos + ``` + +* **Step 3: Install the package.** + Now install the desired package using the command `install.packages('package_name')`. R will automatically download the package and all its dependencies from [CRAN](https://cran.r-project.org/mirrors.html) and install each one. Your terminal will show the build progress and eventually show whether the package was installed successfully or not. + + ``` + R + ``` + + ``` + install.packages('sf', repos="https://cran.case.edu/") + Installing package into ‘/home/myusername/R/x86_64-pc-linux-gnu-library/4.4.1’ + (as ‘lib’ is unspecified) + trying URL 'https://cran.case.edu/src/contrib/sf_0.9-7.tar.gz' + Content type 'application/x-gzip' length 4203095 bytes (4.0 MB) + ================================================== + downloaded 4.0 MB + ... + ... + more progress messages + ... + ... + ** testing if installed package can be loaded from final location + ** testing if installed package keeps a record of temporary installation path + * DONE (sf) + + The downloaded source packages are in + ‘/tmp/RtmpSVAGio/downloaded_packages’ + ``` + +* **Step 4: Troubleshooting. (if needed)** + If Step 3 ended with an error, you need to investigate why the build failed. Most common reason for build failure is not loading the necessary modules. + +## Loading Libraries + +Once you have packages installed you can load them with the `library()` function as shown below: + +``` +library('packagename') +``` + +The package is now installed and loaded and ready to be used in R. + +## Example: Installing `dplyr` + +The following demonstrates installing the `dplyr` package assuming the above-mentioned custom `~/.Rprofile` is in place (note its effect in the "Installing package into" information message): + +``` +module load r +R +``` + +``` +install.packages('dplyr', repos="http://ftp.ussg.iu.edu/CRAN/") +Installing package into ‘/home/myusername/R/bell/4.4.1’ +(as ‘lib’ is unspecified) + ... +also installing the dependencies 'crayon', 'utf8', 'bindr', 'cli', 'pillar', 'assertthat', 'bindrcpp', 'glue', 'pkgconfig', 'rlang', 'Rcpp', 'tibble', 'BH', 'plogr' + ... + ... + ... +The downloaded source packages are in + '/tmp/RtmpHMzm9z/downloaded_packages' + +library(dplyr) + +Attaching package: 'dplyr' +``` + +For more information about installing R packages: + +* [Installing additional R packages on Linux](http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Installing-packages) +* [List of Packages](https://cran.r-project.org/web/packages/) diff --git a/docs/snippets/examples/apps/r/rprofile.md b/docs/snippets/examples/apps/r/rprofile.md new file mode 100644 index 00000000..4c0ecede --- /dev/null +++ b/docs/snippets/examples/apps/r/rprofile.md @@ -0,0 +1,28 @@ +# Setting Up R Preferences with .Rprofile + +For your convenience, a sample [~/.Rprofile example file](https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/r/Rprofile_example) is provided that can be downloaded to your cluster account and renamed into `~/.Rprofile` (or appended to one). Follow these steps to download our recommended `~/.Rprofile` example and copy it into place: + +``` + +curl -#LO https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/r/Rprofile_example +mv -ib Rprofile_example ~/.Rprofile +``` + +The above installation step needs to be done only once on Bell. Now load the R module and run R: + +``` + +module load r/4.4.1 +R +``` + +``` + +.libPaths() +[1] "/home/myusername/R/bell/4.1.2-gcc-6.3.0-ymdumss" +[2] "/apps/spack/bell/apps/r/4.1.2-gcc-6.3.0-ymdumss/rlib/R/library" +``` + +`.libPaths()` should output something similar to above if it is set up correctly. + +You are now ready to [install R packages](package.md) into the dedicated directory `/home/myusername/R/bell/4.1.2-gcc-6.3.0-ymdumss`. diff --git a/docs/snippets/examples/apps/r/rstudio.md b/docs/snippets/examples/apps/r/rstudio.md new file mode 100644 index 00000000..f9b9434e --- /dev/null +++ b/docs/snippets/examples/apps/r/rstudio.md @@ -0,0 +1,33 @@ +# RStudio + + +RStudio is a graphical integrated development environment (IDE) for R. RStudio is the most popular environment for developing both R scripts and packages. RStudio is provided on most Research systems. + +There are two methods to launch RStudio on the cluster: **command-line** and **application menu icon**. + +## Launch RStudio by the command-line: + +``` +module load gcc +module load r +module load rstudio +rstudio +``` + +Note that RStudio is a graphical program and in order to run it you must have a local X11 server running or use [ThinLinc](../../../../accounts.md#thinlinc) Remote Desktop environment. See the [SSH X11 Forwarding section](../../../../accounts.md#ssh-x11-forwarding) for more details. + +## Launch Rstudio by the application menu icon: + +* Log into desktop.bell.rcac.purdue.edu with web browser or [ThinLinc](../../../../accounts.md#thinlinc) client +* Click on the `Applications` drop down menu on the top left corner +* Choose `Cluster Software` and then `RStudio` + +

+ This shows where to find Rstudio under the 'Cluster Software' option in the list of Applications. +

+ +R and RStudio are free to download and run on your local machine. For more information about RStudio: + +* [RStudio the Official Website](https://www.rstudio.com/) +* [RStudio Essentials: Tutorial](https://www.rstudio.com/resources/webinars/#rstudioessentials) +* [DataCamp: Working with the RStudio IDE](https://www.datacamp.com/courses/working-with-the-rstudio-ide-part-1) diff --git a/docs/snippets/examples/apps/r/server.md b/docs/snippets/examples/apps/r/server.md new file mode 100644 index 00000000..cab867f8 --- /dev/null +++ b/docs/snippets/examples/apps/r/server.md @@ -0,0 +1,37 @@ +# Running RStudio Server on Bell + +A different version of RStudio is also installed on Bell. RStudio Server allows you to run RStudio through your web browser. + +## Projects + +One benefit of RStudio is that your work can be separated into projects. You can give each project a working directory, workspace, history and source documents. When you are creating a new project, you can start it in a new empty directory, one with code and data already present or by cloning a repository. + +RStudio Server allows easy collaboration and sharing of R projects. Just click on the project drop down menu in the top right corner and add the career account user names of those you wish to share with. + +

+ Project drop down menu +

+ +## Sessions + +Another feature is the ability to run multiple sessions at once. You can do multiple instances of the same project in parallel or work on different projects simultaneously. The sessions dropdown menu is in the upper right corner right above the project menu. Here you can kill or open sessions. Note that closing a window does not end a session, so please kill sessions when you are not using them. + +

+ Sessions drop down menu +

+ +You can view an overview of all your projects and active sessions by clicking on the blue RStudio Server Home logo in the top left corner of the window next to the file menu. + +## Packages + +You can install new packages with the install.packages() function in the console. You can also graphically select any packages you have previously installed on any cluster. Simply select packages from the tabs on the bottom right side of the window and select the package you wish to load. + +

+ Package selection from GUI +

+ +For more information about RStudio: + +* [RStudio the Official Website](https://www.rstudio.com/) +* [RStudio Essentials: Tutorial](https://www.rstudio.com/resources/webinars/#rstudioessentials) +* [DataCamp: Working with the RStudio IDE](https://www.datacamp.com/courses/working-with-the-rstudio-ide-part-1) diff --git a/docs/snippets/examples/apps/rocmcontainers.md b/docs/snippets/examples/apps/rocmcontainers.md new file mode 100644 index 00000000..4325d518 --- /dev/null +++ b/docs/snippets/examples/apps/rocmcontainers.md @@ -0,0 +1,43 @@ +# ROCm Containers Collection + +## What is ROCm Containers? + +The AMD Infinity Hub contains a collection of advanced AMD GPU software containers and deployment guides for HPC, AI & Machine Learning applications, enabling researchers to speed up their time to science. Containerized applications run quickly and reliably in the high performance computing environment with full support of AMD GPUs. A collection of Infinity Hub tools were deployed to extend cluster capabilities and to enable powerful software and deliver the fastest results. By utilizing Singularity and Infinity Hub ROCm-enabled containers, users can focus on building lean models, producing optimal solutions and gathering faster insights. For more information, please visit [AMD Infinity Hub](https://web.archive.org/web/20230902021513/https://www.amd.com/en/technologies/infinity-hub/). + +## Getting Started + +Users can download ROCm containers from the [AMD Infinity Hub](https://web.archive.org/web/20230902021513/https://www.amd.com/en/technologies/infinity-hub/) and run them directly using Singularity instructions from the corresponding container’s catalog page. + +In addition, a subset of pre-downloaded ROCm containers wrapped into convenient software modules are provided. These modules wrap underlying complexity and provide the same commands that are expected from non-containerized versions of each application. + +On Bell, type the command below to see the lists of ROCm containers we deployed. + +``` + +module load rocmcontainers +module avail + +------------ ROCm-based application container modules for AMD GPUs ------------- + cp2k/20210311--h87ec1599 + deepspeed/rocm4.2_ubuntu18.04_py3.6_pytorch_1.8.1 + gromacs/2020.3 (D) + namd/2.15a2 + openmm/7.4.2 + pytorch/1.8.1-rocm4.2-ubuntu18.04-py3.6 + pytorch/1.9.0-rocm4.2-ubuntu18.04-py3.6 (D) + specfem3d/20201122--h9c0626d1 + specfem3d_globe/20210322--h1ee10977 + tensorflow/2.5-rocm4.2-dev +[....] +``` + +Some of these modules use the container build-in MPI libraries (you may get some error messages like "Cannot load module because these module(s) are loaded: openmpi") and may require `module unload openmpi`. + +## Examples of running ROCm-based containers on AMD GPUs + +Examples below show how to run some containerized applications using `rocmcontainers` modules. In all cases, the general workflow follows the same pattern (load the `rocmcontainers` module; load specific application's module; run the application as if it was built natively). Additional information can be found in `module help` output and on each application's [AMD Infinity Hub](https://web.archive.org/web/20230902021513/https://www.amd.com/en/technologies/infinity-hub/) page. + +## In This Section + +- [GROMACS](rocmcontainers/gromacs.md) +- [Tensorflow](rocmcontainers/tensorflow.md) diff --git a/docs/snippets/examples/apps/rocmcontainers/gromacs.md b/docs/snippets/examples/apps/rocmcontainers/gromacs.md new file mode 100644 index 00000000..27f0acc6 --- /dev/null +++ b/docs/snippets/examples/apps/rocmcontainers/gromacs.md @@ -0,0 +1,41 @@ +# GROMACS + +This example demonstrates how to run GROMACS on AMD GPUs with rocmcontainers modules. + +First, download the .tpr input files for ['lysozyme in water' tutorial](http://www.mdtutorials.com/gmx/lysozyme) from [this archive](https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/rocmcontainers/gromacs/tpr-file.zip). Then unzip the folder and go to that folder by + +``` +wget https://www.rcac.purdue.edu/files/knowledge/run/examples/apps/rocmcontainers/gromacs/tpr-file.zip +unzip tpr-file.zip +cd tpr-file +``` + +Submit a Slurm job, making sure to request GPU-enabled queue and desired number of GPUs. The following example shows an Slurm job submission, asking for one node (128 cores) in the "gpu" account with and two GPUs for 6 hours: + +``` + +#!/bin/bash +#SBATCH -A gpu --gres=gpu:2 +#SBATCH -N 1 -n 128 +#SBATCH -t 6:00:00 + +module load rocmcontainers +module load gromacs/2020.3 + +gmx mdrun -v -deffnm em +gmx mdrun -deffnm nvt +gmx mdrun -deffnm npt +gmx mdrun -deffnm md_0_1 -nb gpu -pme gpu -bonded gpu +``` + +The above batch script will perform energy minimization, NVT and NPT equilibrations and production MD simulations in sequence. The .log files contain the performance of GPU nodes. For better performance, please refer to the ['Getting good performance from mdrun'](https://manual.gromacs.org/current/user-guide/mdrun-performance.html) documentation for help. + +Afterwards you can do interactive post analysis as usual: + +``` +gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center # Select 1 ("Protein") as the group to be centered and 0 ("System") for output +gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns # Select 4 ("Backbone") for both the least-squares fit and the group for RMSD calculation +gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns +``` + +To compare generated .xvg figures with reference, please see the [analysis step of the 'lysozyme in water' tutorial](http://www.mdtutorials.com/gmx/lysozyme/09_analysis.html) for help. diff --git a/docs/snippets/examples/apps/rocmcontainers/tensorflow.md b/docs/snippets/examples/apps/rocmcontainers/tensorflow.md new file mode 100644 index 00000000..06eba6ac --- /dev/null +++ b/docs/snippets/examples/apps/rocmcontainers/tensorflow.md @@ -0,0 +1,54 @@ +# Tensorflow + +This example demonstrates how to run Tensorflow on AMD GPUs with `rocmcontainers` modules. + +First, prepare the matrix multiplication example from [Tensorflow documentation](https://www.tensorflow.org/guide/gpu): + +``` +# filename: matrixmult.py +import tensorflow as tf + +# Log device placement +print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU'))) +tf.debugging.set_log_device_placement(True) + +# Create some tensors +a = tf.constant([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]) +b = tf.constant([[1.0, 2.0], [3.0, 4.0], [5.0, 6.0]]) +c = tf.matmul(a, b) + +print(c) +``` + +Submit a Slurm job, making sure to request GPU-enabled queue and desired number of GPUs. For illustration purpose, the following example shows an interactive job submission, asking for one node (128 cores) in the "gpu" account with and two GPUs for 6 hours, but the same applies to your production batch jobs as well: + +``` +sinteractive -A gpu -N 1 -n 128 -t 6:00:00 --gres=gpu:2 +salloc: Granted job allocation 5401130 +salloc: Waiting for resource configuration +salloc: Nodes bell-g000 are ready for job +``` + +Inside the job, load necessary modules: + +``` +module load rocmcontainers +module load tensorflow/2.5-rocm4.2-dev +``` + +And run the application as usual: + +``` +python matrixmult.py +Num GPUs Available: 2 +[...] +2021-09-02 21:07:34.087607: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1418] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 32252 MB memory) -> physical GPU (device: 0, name: Vega 20, pci bus id: 0000:83:00.0) +[...] +2021-09-02 21:07:36.265167: I tensorflow/core/common_runtime/eager/execute.cc:733] Executing op MatMul in device /job:localhost/replica:0/task:0/device:GPU:0 +2021-09-02 21:07:36.266755: I tensorflow/stream_executor/platform/default/dso_loader.cc:53] Successfully opened dynamic library librocblas.so +tf.Tensor( +[[22. 28.] + [49. 64.]], shape=(2, 2), dtype=float32) +``` + +For more information, see the application’s [AMD Infinity Hub page](https://web.archive.org/web/20230902021513/https://www.amd.com/en/technologies/infinity-hub/). For applications deployed as modules, see `module help` command for a direct link to the relevant page (e.g. `module help tensorflow/2.5-rocm4.2-dev` in the above example). diff --git a/docs/snippets/examples/apps/singularity.md b/docs/snippets/examples/apps/singularity.md new file mode 100644 index 00000000..b7e8ec14 --- /dev/null +++ b/docs/snippets/examples/apps/singularity.md @@ -0,0 +1,115 @@ +# Singularity + + +**Note:** Singularity was originally a project out of [Lawrence Berkeley National Laboratory](https://www.lbl.gov). It has now been spun off into a distinct offering under a new corporate entity under the name [Sylabs Inc](https://sylabs.io). This guide pertains to the open source community edition, *SingularityCE*. + +## What is Singularity? + +Singularity is a new feature of the Community Clusters allowing the portability and reproducibility of operating system and application environments through the use of Linux containers. It gives users complete control over their environment. + +Singularity is like Docker but tuned explicitly for HPC clusters. More information is available from the [project’s website](https://sylabs.io/singularity). + +## Features + +* Run the latest applications on an Ubuntu or Centos userland +* Gain access to the latest developer tools +* Launch MPI programs easily +* Much more + +Singularity’s user guide is available at: [sylabs.io/guides/3.8/user-guide](https://sylabs.io/guides/3.8/user-guide/) + +## Example + +Here is an example using an Ubuntu 16.04 image on Bell: + +``` +singularity exec /depot/itap/singularity/ubuntu1604.img cat /etc/lsb-release +DISTRIB_ID=Ubuntu +DISTRIB_RELEASE=16.04 +DISTRIB_CODENAME=xenial +DISTRIB_DESCRIPTION="Ubuntu 16.04 LTS" +``` + +Here is another example using a Centos 7 image: + +``` +singularity exec /depot/itap/singularity/centos7.img cat /etc/redhat-release +CentOS Linux release 7.2.1511 (Core) +``` + +## Purdue Cluster Specific Notes + +All service providers will integrate Singularity slightly differently depending on site. The largest customization will be which default files are inserted into your images so that routine services will work. + +Services we configure for your images include DNS settings and account information. File systems we overlay into your images are your home directory, scratch, Data Depot, and application file systems. + +Here is a list of paths: + +* /etc/resolv.conf +* /etc/hosts +* /home/$USER +* /apps +* /scratch +* /depot + +This means that within the container environment these paths will be present and the same as outside the container. The `/apps`, `/scratch`, and `/depot` directories will need to exist *inside* your container to work properly. + +## Creating Singularity Images + +Due to how singularity containers work, you must have root privileges to *build* an image. Once you have a singularity container image built on your own system, you can copy the image file up to the cluster (you do not need root privileges to *run* the container). + +You can find information and documentation for how to install and use singularity on your system: + +* [Install Singularity on Windows or MacOS](https://docs.sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac) +* [Install Singularity on Linux](https://docs.sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-linux) + +We have version `3.8.0-1.el7` on the cluster. You will most likely not be able to run any container built with any singularity past that version. So be sure to follow the installation guide for version 3.8 on your system. + +``` +singularity --version +singularity version 3.8.0-1.el7 +``` + +Everything you need on how to [build a container](https://sylabs.io/guides/3.8/user-guide/build_a_container.html) is available from their user-guide. Below are merely some quick tips for getting your own containers built for Bell. + +You can use a [Definition File](https://sylabs.io/guides/3.8/user-guide/definition_files.html) to both build your container and share its specification with collaborators (for the sake of reproducibility). Here is a simplistic example of such a file: + +``` +# FILENAME: Buildfile + +Bootstrap: docker +From: ubuntu:18.04 + +%post + apt-get update && apt-get upgrade -y + mkdir /apps /depot /scratch +``` + +To build the image itself: + +``` +sudo singularity build ubuntu-18.04.sif Buildfile +``` + +The challenge with this approach however is that it must start from scratch if you decide to change something. In order to create a container image iteratively and interactively, you can use the `--sandbox` option. + +``` +sudo singularity build --sandbox ubuntu-18.04 docker://ubuntu:18.04 +``` + +This will not create a flat image file but a directory tree (i.e., a folder), the contents of which are the container's filesystem. In order to get a shell inside the container that allows you to modify it, user the `--writable` option. + +``` +sudo singularity shell --writable ubuntu-18.04 +Singularity: Invoking an interactive shell within container... + +Singularity ubuntu-18.04.sandbox:~> +``` + +You can then proceed to install any libraries, software, etc. within the container. Then to create the final image file, `exit` the shell and call the `build` command once more on the *sandbox*. + +``` +sudo singularity build ubuntu-18.04.sif ubuntu-18.04 +``` + +Finally, copy the new image to Bell and run it. diff --git a/docs/snippets/examples/apps/spark.md b/docs/snippets/examples/apps/spark.md new file mode 100644 index 00000000..310c67fa --- /dev/null +++ b/docs/snippets/examples/apps/spark.md @@ -0,0 +1,8 @@ +# Spark + +[Apache Spark](http://spark.apache.org) is an open-source data analytics cluster computing framework. + +## In This Section + +- [Hadoop](spark/hadoop.md) +- [PBS](spark/pbs.md) diff --git a/docs/snippets/examples/apps/spark/hadoop.md b/docs/snippets/examples/apps/spark/hadoop.md new file mode 100644 index 00000000..8af7dffd --- /dev/null +++ b/docs/snippets/examples/apps/spark/hadoop.md @@ -0,0 +1,72 @@ +# Hadoop + +Spark is not tied to the two-stage MapReduce paradigm, and promises performance up to 100 times faster than Hadoop MapReduce for certain applications. Spark provides primitives for in-memory cluster computing that allows user programs to load data into a cluster's memory and query it repeatedly, making it well suited to machine learning algorithms. + +Before to submit a Spark application to a YARN cluster, export environment variables: + +``` + +$ source /etc/default/hadoop +``` + +To submit a Spark application to a YARN cluster: + +``` + +$ cd /apps/hathi/spark +$ ./bin/spark-submit --master yarn --deploy-mode cluster examples/src/main/python/pi.py 100 +``` + +Please note that there are two ways to specify the master: yarn-cluster and yarn-client. In cluster mode, your driver program will run on the worker nodes; while in client mode, your driver program will run within the spark-submit process which runs on the hathi front end. We recommand that you always use the cluster mode on hathi to avoid overloading the front end nodes. + +To write your own spark jobs, use the Spark Pi as a baseline to start. + +Spark can work with input files from both HDFS and local file system. The default after exporting the environment variables is from HDFS. To use input files that are on the cluster storage (e.g., data depot), specify: file:///path/to/file. + +Note: when reading input files from cluster storage, the files must be accessible from any node in the cluster. + +To run an interactive analysis or to learn the API with Spark Shell: + +``` + +$ cd /apps/hathi/spark +$ ./bin/pyspark +``` + +Create a Resilient Distributed Dataset (RDD) from Hadoop InputFormats (such as HDFS files): + +``` + +>>> textFile = sc.textFile("derby.log") +15/09/22 09:31:58 INFO storage.MemoryStore: ensureFreeSpace(67728) called with curMem=122343, maxMem=278302556 +15/09/22 09:31:58 INFO storage.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 66.1 KB, free 265.2 MB) +15/09/22 09:31:58 INFO storage.MemoryStore: ensureFreeSpace(14729) called with curMem=190071, maxMem=278302556 +15/09/22 09:31:58 INFO storage.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 14.4 KB, free 265.2 MB) +15/09/22 09:31:58 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on localhost:57813 (size: 14.4 KB, free: 265.4 MB) +15/09/22 09:31:58 INFO spark.SparkContext: Created broadcast 1 from textFile at NativeMethodAccessorImpl.java:-2 +``` + +Note: derby.log is a file on hdfs://hathi-adm.rcac.purdue.edu:8020/user/myusername/derby.log + +Call the count() action on the RDD: + +``` + +>>> textFile.count() +15/09/22 09:32:01 INFO mapred.FileInputFormat: Total input paths to process : 1 +15/09/22 09:32:01 INFO spark.SparkContext: Starting job: count at :1 +15/09/22 09:32:01 INFO scheduler.DAGScheduler: Got job 0 (count at :1) with 2 output partitions (allowLocal=false) +15/09/22 09:32:01 INFO scheduler.DAGScheduler: Final stage: ResultStage 0(count at :1) +...... +15/09/22 09:32:03 INFO executor.Executor: Finished task 1.0 in stage 0.0 (TID 1). 1870 bytes result sent to driver +15/09/22 09:32:04 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 2254 ms on localhost (1/2) +15/09/22 09:32:04 INFO scheduler.TaskSetManager: Finished task 1.0 in stage 0.0 (TID 1) in 2220 ms on localhost (2/2) +15/09/22 09:32:04 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool +15/09/22 09:32:04 INFO scheduler.DAGScheduler: ResultStage 0 (count at :1) finished in 2.317 s +15/09/22 09:32:04 INFO scheduler.DAGScheduler: Job 0 finished: count at :1, took 2.548350 s +93 +``` + +To learn programming in Spark, refer to [Spark Programming Guide](http://spark.apache.org/docs/latest/programming-guide.html) + +To learn submitting Spark applications, refer to [Submitting Applications](http://spark.apache.org/docs/latest/submitting-applications.html) diff --git a/docs/snippets/examples/apps/spark/pbs.md b/docs/snippets/examples/apps/spark/pbs.md new file mode 100644 index 00000000..9987e44f --- /dev/null +++ b/docs/snippets/examples/apps/spark/pbs.md @@ -0,0 +1,86 @@ +# PBS + +This section walks through how to submit and run a Spark job using PBS on the compute nodes of Bell. + +`pbs-spark-submit` launches an Apache Spark program within a PBS job, including starting the Spark master and worker processes in standalone mode, running a user supplied Spark job, and stopping the Spark master and worker processes. The Spark program and its associated services will be constrained by the resource limits of the job and will be killed off when the job ends. This effectively allows PBS to act as a Spark cluster manager. + +The following steps assume that you have a Spark program that can run without errors. + +To use Spark and pbs-spark-submit, you need to load the following two modules to setup SPARK\_HOME and PBS\_SPARK\_HOME environment variables. + +``` + +module load spark +module load pbs-spark-submit +``` + +The following example submission script serves as a template to build your customized, more complex Spark job submission. This job requests 2 whole compute nodes for 10 minutes, and submits to the default queue. + +``` + +#PBS -N spark-pi +#PBS -l nodes=2:ppn=128 + +#PBS -l walltime=00:10:00 +#PBS -q accountname +#PBS -o spark-pi.out +#PBS -e spark-pi.err + +cd $PBS_O_WORKDIR +module load spark +module load pbs-spark-submit +pbs-spark-submit $SPARK_HOME/examples/src/main/python/pi.py 1000 +``` + +In the submission script above, this command submits the `pi.py` program to the nodes that are allocated to your job. + +``` + +pbs-spark-submit $SPARK_HOME/examples/src/main/python/pi.py 1000 +``` + +You can set various environment variables in your submission script to change the setting of Spark program. For example, the following line sets the SPARK\_LOG\_DIR to $HOME/log. The default value is current working directory. + +``` + +export SPARK_LOG_DIR=$HOME/log +``` + +The same environment variables can be set via the pbs-spark-submit command line argument. For example, the following line sets the SPARK\_LOG\_DIR to $HOME/log2. + +``` + +pbs-spark-submit --log-dir $HOME/log2 +``` + +The following table summarizes the environment variables that can be set. Please note that setting them from the command line arguments overwrites the ones that are set via shell export. Setting them from shell export overwrites the system default values. + +| Environment Variable | Default | Shell Export | Command Line Args | +| --- | --- | --- | --- | +| SPAKR\_CONF\_DIR | $SPARK\_HOME/conf | export SPARK\_CONF\_DIR=$HOME/conf | --conf-dir or -C | +| SPAKR\_LOG\_DIR | Current Working Directory | export SPARK\_LOG\_DIR=$HOME/log | --log-dir or -L | +| SPAKR\_LOCAL\_DIR | /tmp | export SPARK\_LOCAL\_DIR=$RCAC\_SCRATCH/local | NA | +| SCRATCHDIR | Current Working Directory | export SCRATCHDIR=$RCAC\_SCRATCH/scratch | --work-dir or -d | +| SPARK\_MASTER\_PORT | 7077 | export SPARK\_MASTER\_PORT=7078 | NA | +| SPARK\_DAEMON\_JAVA\_OPTS | None | export SPARK\_DAEMON\_JAVA\_OPTS="-Dkey=value" | -D key=value | + +Note that SCRATCHDIR must be a shared scratch directory across all nodes of a job. + +In addition, `pbs-spark-submit` supports command line arguments to change the properties of the Spark daemons and the Spark jobs. For example, the --no-stop argument tells Spark to not stop the master and worker daemons after the Spark application is finished, and the --no-init argument tells Spark to not initialize the Spark master and worker processes. This is intended for use in a sequence of invocations of Spark programs within the same job. + +``` + +pbs-spark-submit --no-stop $SPARK_HOME/examples/src/main/python/pi.py 800 +pbs-spark-submit --no-init $SPARK_HOME/examples/src/main/python/pi.py 1000 +``` + +Use the following command to see the complete list of command line arguments. + +``` + +pbs-spark-submit -h +``` + +To learn programming in Spark, refer to [Spark Programming Guide](http://spark.apache.org/docs/latest/programming-guide.html) + +To learn submitting Spark applications, refer to [Submitting Applications](http://spark.apache.org/docs/latest/submitting-applications.html) diff --git a/docs/snippets/examples/apps/windows.md b/docs/snippets/examples/apps/windows.md new file mode 100644 index 00000000..641d6321 --- /dev/null +++ b/docs/snippets/examples/apps/windows.md @@ -0,0 +1,29 @@ +# Windows + +Windows virtual machines (VMs) are supported as batch jobs on HPC systems. This section illustrates how to submit a job and run a Windows instance in order to run Windows applications on the high-performance computing systems. + +The following images are pre-configured and made available by staff: + +* Windows 2016 Server Basic (minimal software pre-loaded) +* Windows 2016 Server GIS (GIS Software Stack pre-loaded) + +The Windows VMs can be launched in two fashions: + +* [Menu Launcher](windows/launcher.md) - Point and click to start +* [Command Line](windows/cmd.md) - Advanced and customized usage + +Click each of the above links for detailed instructions on using them. + +## Software Provided in Pre-configured Virtual Machines + +The Windows 2016 Base server image available on Bell has the following software packages preloaded: + +* Anaconda Python 2 and Python 3 +* JMP 13 +* Matlab R2017b +* Microsoft Office 2016 +* Notepad++ +* NVivo 12 +* Rstudio +* Stata SE 15 +* VLC Media Player diff --git a/docs/snippets/examples/apps/windows/cmd.md b/docs/snippets/examples/apps/windows/cmd.md new file mode 100644 index 00000000..934d2cdf --- /dev/null +++ b/docs/snippets/examples/apps/windows/cmd.md @@ -0,0 +1,64 @@ +# Command line + +If you wish to work with Windows VMs on the command line or work into scripted workflows you can interact directly with the Windows system: + + +* Submit an interactive PBS job, with the appropriate walltime and queue: + + ``` + $ qsub -X -I -l walltime=8:00:00 -l nodes=1:ppn=128 + ``` + +* Load the "qemu" module: + + ``` + $ module load qemu + ``` + + + +Copy a Windows 2016 Server VM image to your storage. Scratch or Research Data Depot are good locations to save a VM image. If you are using scratch, remember that [scratch spaces are temporary](https://www.rcac.purdue.edu/policies/scratchpurge), and be sure to safely back up your disk image somewhere permanent, such as Research Data Depot or Fortress. To copy a basic image: + +`$ cp /apps/external/apps/windows/images/latest.qcow2  $RCAC_SCRATCH/windows.qcow2` + +To copy a GIS image: + +``` +$ cp /depot/itap/windows/gis/2k16.qcow2 $RCAC_SCRATCH/windows.qcow2 +``` + + +To launch a virtual machine in a batch job, use the "windows" script, specifying the path to your Windows virtual machine image. With no other command-line arguments, the `windows` script will autodetect a number cores and memory for the Windows VM. A Windows network connection will be made to your home directory. To launch: + +``` + +$ windows -i $RCAC_SCRATCH/windows.qcow2 + +``` + + +## Command line options: + +``` +-i (For example, $RCAC_SCRATCH/windows-2k16.qcow2) +-m G (For example, 32G) +-c (For example, 20) +-s (UNIX Path to map as a drive, for example, $RCAC_SCRATCH) +-b (If present, launches VM in background. Use VNC to connect to Windows.) +``` + +To launch a virtual machine with 32GB of RAM, 20 cores, and a network mapping to your home directory: + +``` +$ windows -i /path/to/image.qcow2 -m 32G -c 20 -s $HOME +``` + +To launch a virtual machine with 16GB of RAM, 10 cores, and a network mapping to your Data Depot space: + +``` +$ windows -i /path/to/image.qcow2 -m 16G -c 10 -s /depot/mylab +``` + + + + The Windows 2016 server desktop will open, and automatically log in as an administrator, so that you can install any software into the Windows virtual machine that your research requires. Changes to the image will be stored in the file specified with the `-i` option. diff --git a/docs/snippets/examples/apps/windows/launcher.md b/docs/snippets/examples/apps/windows/launcher.md new file mode 100644 index 00000000..83b5b19b --- /dev/null +++ b/docs/snippets/examples/apps/windows/launcher.md @@ -0,0 +1,30 @@ +# Menu Launcher + +Windows VMs can be easily launched through the [ThinLinc](../../../../accounts.md#thinlinc) remote desktop environment. + +* Log in via [ThinLinc](../../../../accounts.md#thinlinc). +* Click on Applications menu in the upper left corner. +* Look under the Cluster Software menu. +* The "Windows 10" launcher will launch a VM directly on the front-end. +* Follow the dialogs to set up your VM. + +

+ ThinLinc Applications list +

+ + +Find Windows 10 under the 'Cluster Software' option in the list of Applications. + +The dialog menus will walk you through setting up and loading your VM. + + +* You can choose to create a new image or load a saved image. +* New VMs should be saved on Scratch or Research Data Depot as they are too large for Home Directories. +* If you are using scratch, remember that [scratch spaces are temporary](https://www.rcac.purdue.edu/policies/scratchpurge), and be sure to safely back up your disk image somewhere permanent, such as Research Data Depot or Fortress. + +You will also be prompted to select a storage space to mount on your image (Home, Scratch, or Data Depot). You can only choose one to be mounted. It will appear on a shortcut on the desktop once the VM loads. + + +## Notes + +Using the menu launcher will launch automatically select reasonable CPU and memory values. If you wish to choose other options or work Windows VMs into scripted workflows see the section on [using the command line](cmd.md). diff --git a/docs/snippets/examples/hadoop/hbase.md b/docs/snippets/examples/hadoop/hbase.md new file mode 100644 index 00000000..256ed5f6 --- /dev/null +++ b/docs/snippets/examples/hadoop/hbase.md @@ -0,0 +1,3 @@ +# HBase + +[Apache HBase](http://hbase.apache.org/) is the Hadoop database, a distributed, scalable, big data store. HBase is an open-source, distributed, versioned, non-relational database modeled after Google's [Bigtable: A Distributed Storage System for Structured Data](http://research.google.com/archive/bigtable.html) by Chang et al. Just as Bigtable leverages the distributed data storage provided by the Google File System, Apache HBase provides Bigtable-like capabilities on top of Hadoop and HDFS. diff --git a/docs/snippets/examples/hadoop/hive.md b/docs/snippets/examples/hadoop/hive.md new file mode 100644 index 00000000..c9702bc0 --- /dev/null +++ b/docs/snippets/examples/hadoop/hive.md @@ -0,0 +1,75 @@ +# Hive + +[Apache Hive](https://hive.apache.org/) is a data warehouse infrastructure built on top of Hadoop for providing data summarization, query, and analysis. Hive provides a mechanism to project structure onto this data and query the data using a SQL-like language called HiveQL. At the same time this language also allows traditional map/reduce programmers to plug in their custom mappers and reducers when it is inconvenient or inefficient to express this logic in HiveQL. + +Load java module: + +``` + +$ module load java +``` + +Export environment variables: + +``` + +$ source /etc/default/hadoop +$ export HIVE_HOME=/apps/hathi/hive/ +$ export PATH=$HIVE_HOME/bin:$HIVE_HOME/hcatalog/bin:$PATH +``` + +To access Hive: + +``` + +$ hive +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.reduce.tasks is deprecated. Instead, use mapreduce.job.reduces +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.min.split.size is deprecated. Instead, use mapreduce.input.fileinputformat.split.minsize +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.reduce.tasks.speculative.execution is deprecated. Instead, use mapreduce.reduce.speculative +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.min.split.size.per.node is deprecated. Instead, use mapreduce.input.fileinputformat.split.minsize.per.node +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.input.dir.recursive is deprecated. Instead, use mapreduce.input.fileinputformat.input.dir.recursive +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.min.split.size.per.rack is deprecated. Instead, use mapreduce.input.fileinputformat.split.minsize.per.rack +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.max.split.size is deprecated. Instead, use mapreduce.input.fileinputformat.split.maxsize +15/09/10 15:14:16 INFO Configuration.deprecation: mapred.committer.job.setup.cleanup.needed is deprecated. Instead, use mapreduce.job.committer.setup.cleanup.needed + +Logging initialized using configuration in jar:file:/apps/hathi/apache-hive-0.14.0-bin/lib/hive-common-0.14.0.jar!/hive-log4j.properties +SLF4J: Class path contains multiple SLF4J bindings. +SLF4J: Found binding in [jar:file:/usr/lib/gphd/hadoop/lib/slf4j-log4j12-1.7.5.jar!/org/slf4j/impl/StaticLoggerBinder.class] +SLF4J: Found binding in [jar:file:/apps/hathi/apache-hive-0.14.0-bin/lib/hive-jdbc-0.14.0-standalone.jar!/org/slf4j/impl/StaticLoggerBinder.class] +SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. +SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory] +hive> +``` + +To create and browse Hive tables: + +``` + +$ hive> CREATE TABLE pokes_user (foo INT, bar STRING); +OK +Time taken: 1.56 seconds +$ hive> CREATE TABLE invites_user (foo INT, bar STRING) PARTITIONED BY (ds STRING); +OK +Time taken: 0.125 seconds +$ hive> SHOW TABLES; +OK +invites_user +pokes_user +Time taken: 0.114 seconds, Fetched: 2 row(s) +``` + +To browse Hive tables from hdfs: + +* Go to +* Click on "Browse the filesystem" +* Navigate to "/user/hive/warehouse" + +To run the HCatalog Server from the command-line: + +``` + +$ cd /apps/hathi/hive +$ hcatalog/bin/hcat +``` + +For more information, refer to [GettingStarted - Apache Hive - Apache Software Foundation.](https://cwiki.apache.org/confluence/display/Hive/GettingStarted#GettingStarted-SimpleExampleUseCases) diff --git a/docs/snippets/examples/hadoop/pig.md b/docs/snippets/examples/hadoop/pig.md new file mode 100644 index 00000000..d23a6a51 --- /dev/null +++ b/docs/snippets/examples/hadoop/pig.md @@ -0,0 +1,60 @@ +# Pig + +[Apache Pig](http://pig.apache.org/) is a platform for analyzing large data sets that consists of a high-level language for expressing data analysis programs, coupled with infrastructure for evaluating these programs. + +Before to use Pig, setup environment variables: + +``` +$ module load java +$ export PATH=/apps/hathi/pig/bin:$PATH +``` + +The following steps walk through how to run Pig in interactive mode. Before to run, you should put the `/etc/passwd` file from you local system to `hdfs:///user/yourusername/`. These Pig Latin statements extract all user IDs from the `/etc/passwd` file. + +First, invoke the Grunt shell: + +``` +$ pig -x mapreduce +15/10/06 16:32:01 INFO pig.ExecTypeProvider: Trying ExecType : LOCAL +15/10/06 16:32:01 INFO pig.ExecTypeProvider: Trying ExecType : MAPREDUCE +15/10/06 16:32:01 INFO pig.ExecTypeProvider: Picked MAPREDUCE as the ExecType +2015-10-06 16:32:01,856 [main] INFO org.apache.pig.Main - Apache Pig version 0.15.0 (r1682971) compiled Jun 01 2015, 11:44:35 +2015-10-06 16:32:01,857 [main] INFO org.apache.pig.Main - Logging error messages to: /path/to/pig/pig_1444163521852.log +2015-10-06 16:32:01,908 [main] INFO org.apache.pig.impl.util.Utils - Default bootup file /path/to/.pigbootup not found +2015-10-06 16:32:02,808 [main] INFO org.apache.hadoop.conf.Configuration.deprecation - mapred.job.tracker is deprecated. Instead, use mapreduce.jobtracker.address +2015-10-06 16:32:02,808 [main] INFO org.apache.hadoop.conf.Configuration.deprecation - fs.default.name is deprecated. Instead, use fs.defaultFS +2015-10-06 16:32:02,809 [main] INFO org.apache.pig.backend.hadoop.executionengine.HExecutionEngine - Connecting to hadoop file system at: hdfs://hathi-adm.rcac.purdue.edu:8020 +2015-10-06 16:32:02,816 [main] INFO org.apache.hadoop.conf.Configuration.deprecation - mapred.used.genericoptionsparser is deprecated. Instead, use mapreduce.client.genericoptionsparser.used +2015-10-06 16:32:04,362 [main] INFO org.apache.hadoop.conf.Configuration.deprecation - fs.default.name is deprecated. Instead, use fs.defaultFS +grunt> +``` + +Then, enter the Pig Latin statements interactively at the grunt prompt: + +``` +$ grunt> A = load 'passwd' using PigStorage(':'); +$ grunt> B = foreach A generate $0 as id; +$ grunt> dump B; +``` + +The following steps walk through how to run Pig in batch mode. + +First, save the following statements in the Pig script (id.pig): + +``` +/* id.pig */ + +A = load 'passwd' using PigStorage(':'); -- load the passwd file +B = foreach A generate $0 as id; -- extract the user IDs +store B into 'id.out'; -- write the results to a file name id.out +``` + +Then, run the Pig script in batch mode: + +``` +$ pig -x mapreduce id.pig +``` + +This is generate output in `hdfs:///user/yourusername/id.put/`. + +To learn programming in Pig, refer to: [Pig Overview](http://pig.apache.org/docs/r0.15.0/) diff --git a/docs/snippets/examples/slurm/batch.md b/docs/snippets/examples/slurm/batch.md new file mode 100644 index 00000000..1ea843f3 --- /dev/null +++ b/docs/snippets/examples/slurm/batch.md @@ -0,0 +1,49 @@ +# Simple Job + +Every SLURM job consists of a job submission file. A job submission file contains a list of commands that run your program and a set of resource (nodes, walltime, queue) requests. The resource requests can appear in the [job submission file](directives.md) or can be specified at submit-time as shown below. + +This simple example submits the job submission file `hello.sub` to the `accountname` account on Bell and requests a single node: + +``` + +#!/bin/bash +# FILENAME: hello.sub + +# Show this ran on a compute node by running the hostname command. +hostname + +echo "Hello World" +``` + + +``` + +sbatch -A accountname --nodes=1 --ntasks=1 --cpus-per-task=1 --time=00:01:00 hello.sub +Submitted batch job 3521 +``` + + +For a real job you would replace `echo "Hello World"` with a command, or sequence of commands, that run your program. + +After your job finishes running, the `ls` command will show a new file in your directory, the `.out` file: + +``` + +ls -l +hello.sub +slurm-3521.out +``` + +The file `slurm-3521.out` contains the output and errors your program would have written to the screen if you had typed its commands at a command prompt: + +``` + +cat slurm-3521.out + + +bell-a001.rcac.purdue.edu + +Hello World +``` + +You should see the hostname of the compute node your job was executed on. Following should be the "Hello World" statement. diff --git a/docs/snippets/examples/slurm/directives.md b/docs/snippets/examples/slurm/directives.md new file mode 100644 index 00000000..80209a8c --- /dev/null +++ b/docs/snippets/examples/slurm/directives.md @@ -0,0 +1,39 @@ +# Directives + +So far these examples have shown submitting jobs with the resource requests on the `sbatch` command line such as: + + +``` + +sbatch -A accountname --nodes=1 --time=00:01:00 hello.sub +``` + + +The resource requests can also be put into job submission file itself. Documenting the resource requests in the job submission is desirable because the job can be easily reproduced later. Details left in your command history are quickly lost. Arguments are specified with the `#SBATCH` syntax: + +``` + +#!/bin/bash + +# FILENAME: hello.sub + +#SBATCH -A accountname + + +#SBATCH --nodes=1 --time=00:01:00 + + +# Show this ran on a compute node by running the hostname command. +hostname + +echo "Hello World" +``` + +The `#SBATCH` directives **must** appear at the top of your submission file. SLURM will stop parsing directives as soon as it encounters a line that does not start with '#'. If you insert a directive in the middle of your script, it will be ignored. + +This job can be then submitted with: + +``` + +sbatch hello.sub +``` diff --git a/docs/snippets/examples/slurm/interactive.md b/docs/snippets/examples/slurm/interactive.md new file mode 100644 index 00000000..fbef21b3 --- /dev/null +++ b/docs/snippets/examples/slurm/interactive.md @@ -0,0 +1,22 @@ +# Interactive Jobs + +Interactive jobs are run on compute nodes, while giving you a shell to interact with. They give you the ability to type commands or use a graphical interface in the same way as if you were on a front-end login host. + +To submit an interactive job, use `sinteractive` to run a login shell on allocated resources. + +`sinteractive` accepts most of the same resource requests as `sbatch`, so to request a login shell on the `accountname` account while allocating 2 nodes and 128 total cores, you might do: + + + +``` + +sinteractive -A accountname -N2 -n256 +``` + + + +To quit your interactive job: + +`exit` or `Ctrl-D` + +The above example will allocate the total of 256 CPU cores across 2 nodes. Note that if your multi-node job requests fewer than each node's full 128 cores per node, by default Slurm provides no guarantee with respect to how this total is distributed between assigned nodes (i.e. the cores may not necessarily be split evenly). If you need specific arrangements of your tasks and cores, you can use `--cpus-per-task=` and/or `--ntasks-per-node=` flags. See [Slurm documentation](https://slurm.schedmd.com/salloc.html) or `man salloc` for more options. diff --git a/docs/snippets/examples/slurm/monitor.md b/docs/snippets/examples/slurm/monitor.md new file mode 100644 index 00000000..0affc6f0 --- /dev/null +++ b/docs/snippets/examples/slurm/monitor.md @@ -0,0 +1,86 @@ +# Monitoring Resources + +## Collecting System Resource Utilization Data + +Knowing the precise resource utilization an application had during a job, such as CPU load or memory, can be incredibly useful. This is especially the case when the application isn't performing as expected. + +One approach is to run a program like `htop` during an interactive job and keep an eye on system resources. You can get precise time-series data from nodes associated with your job using [XDmod](https://xdmod.rcac.purdue.edu) as well, online. But these methods don't gather telemetry in an automated fashion, nor do they give you control over the resolution or format of the data. + +As a matter of course, a robust implementation of some HPC workload would include resource utilization data as a diagnostic tool in the event of some failure. + +The `monitor` utility is a simple command line system resource monitoring tool for gathering such telemetry and is available as a module. + +``` +module load monitor +``` + +Complete documentation is available online at [resource-monitor.readthedocs.io](https://resource-monitor.readthedocs.io). A full manual page is also available for reference, `man monitor`. + +In the context of a SLURM job you will need to put this monitoring task in the background to allow the rest of your job script to proceed. Be sure to interrupt these tasks at the end of your job. + + +``` +#!/bin/bash +# FILENAME: monitored_job.sh + + module load monitor + +# track per-code CPU load +monitor cpu percent --all-cores >cpu-percent.log & +CPU_PID=$! + +# track memory usage +monitor cpu memory >cpu-memory.log & +MEM_PID=$! + +# your code here + +# shut down the resource monitors +kill -s INT $CPU_PID $MEM_PID +``` + + +A particularly elegant solution would be to include such tools in your *prologue* script and have the tear down in your *epilogue* script. + +For large distributed jobs spread across multiple nodes, `mpiexec` can be used to gather telemetry from all nodes in the job. The hostname is included in each line of output so that data can be grouped as such. A concise way of constructing the needed list of hostnames in SLURM is to simply use `srun hostname | sort -u`. + + +``` +#!/bin/bash +# FILENAME: monitored_job.sh + +module load monitor + +# track all CPUs (one monitor per host) +mpiexec -machinefile <(srun hostname | sort -u) \ + monitor cpu percent --all-cores >cpu-percent.log & +CPU_PID=$! + +# track memory on all hosts (one monitor per host) +mpiexec -machinefile <(srun hostname | sort -u) \ + monitor cpu memory >cpu-memory.log & +MEM_PID=$! + +# your code here + +# shut down the resource monitors +kill -s INT $CPU_PID $MEM_PID +``` + + +To get resource data in a more readily computable format, the `monitor` program can be told to output in CSV format with the `--csv` flag. + + +``` +monitor cpu memory --csv >cpu-memory.csv +``` + + +For a distributed job you will need to suppress the header lines otherwise one will be created by each host. + + +``` +monitor cpu memory --csv | head -1 >cpu-memory.csv +mpiexec -machinefile <(srun hostname | sort -u) \ + monitor cpu memory --csv --no-header >>cpu-memory.csv +``` diff --git a/docs/snippets/examples/slurm/mpi.md b/docs/snippets/examples/slurm/mpi.md new file mode 100644 index 00000000..653c8f36 --- /dev/null +++ b/docs/snippets/examples/slurm/mpi.md @@ -0,0 +1,88 @@ +# MPI + +An MPI job is a set of processes that take advantage of multiple compute nodes by communicating with each other. OpenMPI and Intel MPI (IMPI) are implementations of the MPI standard. + +This section shows how to submit one of the MPI programs compiled in the section [Compiling MPI Programs](../../../compile/mpi.md). + +Use `module load` to set up the paths to access these libraries. Use `module avail` to see all MPI packages installed on Bell. + +Create a job submission file: + + +``` +#!/bin/bash +# FILENAME: mpi_hello.sub +#SBATCH --nodes=2 +#SBATCH --ntasks-per-node=128 +#SBATCH --time=00:01:00 +#SBATCH -A accountname + +srun -n 256 ./mpi_hello +``` + + +SLURM can run an MPI program with the `srun` command. The number of processes is requested with the `-n` option. If you do not specify the `-n` option, it will default to the total number of processor cores you request from SLURM. + +If the code is built with OpenMPI, it can be run with a simple `srun -n` command. If it is built with Intel IMPI, then you also need to add the `--mpi=pmi2` option: `srun --mpi=pmi2 -n 256 ./mpi_hello` in this example. + +Submit the MPI job: + +``` +sbatch ./mpi_hello.sub +``` + +View results in the output file: + +``` +cat slurm-myjobid.out +Runhost:bell-a010.rcac.purdue.edu Rank:0 of 256 ranks hello, world +Runhost:bell-a010.rcac.purdue.edu Rank:1 of 256 ranks hello, world +... +Runhost:bell-a011.rcac.purdue.edu Rank:128 of 256 ranks hello, world +Runhost:bell-a011.rcac.purdue.edu Rank:129 of 256 ranks hello, world +... +``` + +If the job failed to run, then view error messages in the output file. + +If an MPI job uses a lot of memory and 128 MPI ranks per compute node use all of the memory of the compute nodes, request more compute nodes, while keeping the total number of MPI ranks unchanged. + +Submit the job with double the number of compute nodes and modify the resource request to halve the number of MPI ranks per compute node. + +``` +#!/bin/bash +# FILENAME: mpi_hello.sub + +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=64 +#SBATCH -t 00:01:00 + +#SBATCH -A accountname + +srun -n 256 ./mpi_hello +``` + +``` +sbatch ./mpi_hello.sub +``` + +View results in the output file: + +``` +cat slurm-myjobid.out +Runhost:bell-a10.rcac.purdue.edu Rank:0 of 256 ranks hello, world +Runhost:bell-a010.rcac.purdue.edu Rank:1 of 256 ranks hello, world +... +Runhost:bell-a011.rcac.purdue.edu Rank:64 of 256 ranks hello, world +... +Runhost:bell-a012.rcac.purdue.edu Rank:128 of 256 ranks hello, world +... +Runhost:bell-a013.rcac.purdue.edu Rank:192 of 256 ranks hello, world +... +``` + +**Notes** + +* Use `slist` to determine which queues (`--account` or `-A` option) are available to you. The name of the queue you should use depends on the Bell allocation you are charging. +* Invoking an MPI program on Bell with `./program` is typically wrong, since this will use only one MPI process and defeat the purpose of using MPI. Unless that is what you want (rarely the case), you should use `srun` or `mpiexec` to invoke an MPI program. +* In general, the exact order in which MPI ranks output similar write requests to an output file is random. diff --git a/docs/snippets/examples/slurm/multiple.md b/docs/snippets/examples/slurm/multiple.md new file mode 100644 index 00000000..69636fa2 --- /dev/null +++ b/docs/snippets/examples/slurm/multiple.md @@ -0,0 +1,28 @@ +# Multiple Node + +In some cases, you may want to request multiple nodes. To utilize multiple nodes, you will need to have a program or code that is specifically programmed to use multiple nodes such as with MPI. Simply requesting more nodes will not make your work go faster. Your code must support this ability. + +This example shows a request for multiple compute nodes. The job submission file contains a single command to show the names of the compute nodes allocated: + +``` + +# FILENAME: myjobsubmissionfile.sub +#!/bin/bash +echo "$SLURM_JOB_NODELIST" +``` + + +``` + +sbatch --nodes=2 --ntasks=256 --time=00:10:00 -A accountname myjobsubmissionfile.sub +``` + + +Compute nodes allocated: + +``` + +bell-a[014-015] +``` + +The above example will allocate the total of 256 CPU cores across 2 nodes. Note that if your multi-node job requests fewer than each node's full 128 cores per node, by default Slurm provides no guarantee with respect to how this total is distributed between assigned nodes (i.e. the cores may not necessarily be split evenly). If you need specific arrangements of your tasks and cores, you can use `--cpus-per-task=` and/or `--ntasks-per-node=` flags. See [Slurm documentation](https://slurm.schedmd.com/sbatch.html) or `man sbatch` for more options. diff --git a/docs/snippets/examples/slurm/openmp.md b/docs/snippets/examples/slurm/openmp.md new file mode 100644 index 00000000..c857f0fb --- /dev/null +++ b/docs/snippets/examples/slurm/openmp.md @@ -0,0 +1,61 @@ +# OpenMP + +A shared-memory job is a single process that takes advantage of a multi-core processor and its shared memory to achieve parallelization. + +This example shows how to submit an OpenMP program compiled in the section [Compiling OpenMP Programs](../../../compile/openmp.md). + +!!! Note + When running OpenMP programs, all threads must be on the same compute node to take advantage of shared memory. The threads cannot communicate between nodes. + +To run an OpenMP program, set the environment variable OMP\_NUM\_THREADS to the desired number of threads: + +In csh: + +``` +setenv OMP_NUM_THREADS 128 +``` + +In bash: + +``` +export OMP_NUM_THREADS=128 +``` + +This should almost always be equal to the number of cores on a compute node. You may want to set to another appropriate value if you are running several processes in parallel in a single job or node. + +Create a job submissionfile: + + +``` +#!/bin/bash +# FILENAME: omp_hello.sub +#SBATCH --nodes=1 +#SBATCH --ntasks=128 +#SBATCH --time=00:01:00 + +export OMP_NUM_THREADS=128 +./omp_hello +``` + + +Submit the job: + +``` +sbatch omp_hello.sub +``` + +View the results from one of the sample OpenMP programs about task parallelism: + + +``` +cat omp_hello.sub.omyjobid +SERIAL REGION: Runhost:bell-a003.rcac.purdue.edu Thread:0 of 1 thread hello, world +PARALLEL REGION: Runhost:bell-a003.rcac.purdue.edu Thread:0 of 128 threads hello, world +PARALLEL REGION: Runhost:bell-a003.rcac.purdue.edu Thread:1 of 128 threads hello, world + ... +``` + + +If the job failed to run, then view error messages in the file `slurm-myjobid.out`. + +If an OpenMP program uses a lot of memory and 128 threads use all of the memory of the compute node, use fewer processor cores (OpenMP threads) on that compute node. diff --git a/docs/snippets/examples/slurm/serial.md b/docs/snippets/examples/slurm/serial.md new file mode 100644 index 00000000..bc277eda --- /dev/null +++ b/docs/snippets/examples/slurm/serial.md @@ -0,0 +1,35 @@ +# Serial Jobs + +This shows how to submit one of the serial programs compiled in the section [Compiling Serial Programs](../../../compile/serial.md). + +Create a job submission file: + +``` + +#!/bin/bash +# FILENAME: serial_hello.sub + +./serial_hello +``` + +Submit the job: + + +``` + +sbatch --nodes=1 --ntasks=1 --time=00:01:00 serial_hello.sub +``` + + +After the job completes, view results in the output file: + +``` + +cat slurm-myjobid.out + +Runhost:bell-a009.rcac.purdue.edu +hello, world + +``` + +If the job failed to run, then view error messages in the file `slurm-myjobid.out`. diff --git a/docs/snippets/examples/slurm/specific.md b/docs/snippets/examples/slurm/specific.md new file mode 100644 index 00000000..1ada39ab --- /dev/null +++ b/docs/snippets/examples/slurm/specific.md @@ -0,0 +1,23 @@ +# Specific Types of Nodes + +SLURM allows running a job on [specific types of compute nodes](../../../overview.md) to accommodate special hardware requirements (e.g. a certain CPU or GPU type, etc.) + +Cluster nodes have a set of descriptive features assigned to them, and users can specify which of these features are required by their job by using the constraint option at submission time. Only nodes having features matching the job constraints will be used to satisfy the request. + +**Example:** a job requires a compute node in an "A" sub-cluster: + + +``` +sbatch --nodes=1 --ntasks=128 --constraint=A myjobsubmissionfile.sub +``` + + +Compute node allocated: + +``` +bell-a003 +``` + +Feature constraints can be used for both batch and interactive jobs, as well as for individual job steps inside a job. Multiple constraints can be specified with a predefined syntax to achieve complex request logic (see detailed description of the '--constraint' option in `man sbatch` or online Slurm documentation). + +Refer to the [Detailed Hardware Specification](../../../overview.md#bell-specifications) section for the list of available sub-cluster labels, their respective per-node memory sizes, and other hardware details. You could also use `sfeatures` command to list available constraint feature names for different node types. diff --git a/docs/snippets/monitoring_job.md b/docs/snippets/monitoring_job.md new file mode 100644 index 00000000..8f96b525 --- /dev/null +++ b/docs/snippets/monitoring_job.md @@ -0,0 +1,69 @@ +# Checking Job Status + +Once a job is [submitted](submit_script.md) there are several commands you can use to monitor the progress of the job. + +To see your jobs, use the `squeue -u` command and specify your username: + +(Remember, in our SLURM environment a queue is referred to as an 'Account') + +``` + + + +squeue -u myusername + + JOBID ACCOUNT NAME USER ST TIME NODES NODELIST(REASON) + 182792 accountname job1 myusername R 20:19 1 bell-a000 + 185841 accountname job2 myusername R 20:19 1 bell-a001 + 185844 accountname job3 myusername R 20:18 1 bell-a002 + 185847 accountname job4 myusername R 20:18 1 bell-a003 + + +``` + +To retrieve useful information about your queued or running job, use the `scontrol show job` command with your job's ID number. The output should look similar to the following: + +``` + + +scontrol show job 3519 + +JobId=3519 JobName=t.sub + UserId=myusername GroupId=mygroup MCS_label=N/A + Priority=3 Nice=0 Account=(null) QOS=(null) + JobState=PENDING Reason=BeginTime Dependency=(null) + Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 + RunTime=00:00:00 TimeLimit=7-00:00:00 TimeMin=N/A + SubmitTime=2019-08-29T16:56:52 EligibleTime=2019-08-29T23:30:00 + AccrueTime=Unknown + StartTime=2019-08-29T23:30:00 EndTime=2019-09-05T23:30:00 Deadline=N/A + PreemptTime=None SuspendTime=None SecsPreSuspend=0 + LastSchedEval=2019-08-29T16:56:52 + Partition=workq AllocNode:Sid=mack-fe00:54476 + ReqNodeList=(null) ExcNodeList=(null) + NodeList=(null) + NumNodes=1 NumCPUs=2 NumTasks=2 CPUs/Task=1 ReqB:S:C:T=0:0:*:* + TRES=cpu=2,node=1,billing=2 + Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=* + MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0 + Features=(null) DelayBoot=00:00:00 + OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null) + Command=/home/myusername/jobdir/myjobfile.sub + WorkDir=/home/myusername/jobdir + StdErr=/home/myusername/jobdir/slurm-3519.out + StdIn=/dev/null + StdOut=/home/myusername/jobdir/slurm-3519.out + Power= + + +``` + +There are several useful bits of information in this output. + +* `JobState` lets you know if the job is Pending, Running, Completed, or Held. +* `RunTime and TimeLimit` will show how long the job has run and its maximum time. +* `SubmitTime` is when the job was submitted to the cluster. +* `NumNodes`, `NumCPUs`, `NumTasks` and `CPUs/Task` are the number of Nodes, CPUs, Tasks, and CPUs per Task are shown. +* `WorkDir` is the job's working directory. +* `StdOut` and `Stderr` are the locations of stdout and stderr of the job, respectively. +* `Reason` will show why a `PENDING` job isn't running. The above error says that it has been requested to start at a specific, later time. diff --git a/docs/snippets/purdue_login.md b/docs/snippets/purdue_login.md index 40a49ade..a4335e03 100644 --- a/docs/snippets/purdue_login.md +++ b/docs/snippets/purdue_login.md @@ -3,8 +3,8 @@ - When asked for a password, type your Purdue password. - Your Purdue MFA client will receive a notification to approve the login. -### Thinlinc Web/Client +**Thinlinc Web/Client** - When asked for a password, type your Purdue password. - Your Purdue MFA client will receive a notification to approve the login. - The native Thinlinc client will prompt for MFA approval **twice** due to the way Thinlinc works. -- The native Thinlinc client also supports key-based authentication. \ No newline at end of file +- The native Thinlinc client also supports key-based authentication. diff --git a/docs/userguides/bell/accounts.md b/docs/userguides/bell/accounts.md new file mode 100644 index 00000000..c56a75d3 --- /dev/null +++ b/docs/userguides/bell/accounts.md @@ -0,0 +1,30 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: bell +search: + boost: 2 +--- + +{% set host = "bell.rcac.purdue.edu" %} +{% set cluster = "Bell" %} +{% set resource = "bell" %} + +{{ accounts_md_snippet(resource) }} + +## SSH Keys +{{ ssh_keys_snippet(resource) }} + +## SSH X11 Forwarding +{{ ssh_x11_snippet(resource) }} + +## Thinlinc +{{ thinlinc_snippet(resource) }} + +## Purchasing Nodes + +--8<-- "docs/snippets/purchase_nodes.md" + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/accounts/purchase.md b/docs/userguides/bell/accounts/purchase.md new file mode 100644 index 00000000..52c8bfdd --- /dev/null +++ b/docs/userguides/bell/accounts/purchase.md @@ -0,0 +1,33 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Purchasing Nodes + +RCAC operates a significant shared cluster computing infrastructure developed over several years through focused acquisitions using funds from grants, faculty startup packages, and institutional sources. These "community clusters" are now at the foundation of Purdue's research cyberinfrastructure. + +We strongly encourage any Purdue faculty or staff with computational needs to join this growing community and enjoy the enormous benefits this shared infrastructure provides: + +* **Peace of Mind** + + RCAC system administrators take care of security patches, attempted hacks, operating system upgrades, and hardware repair so faculty and graduate students can concentrate on research. + +* **Low Overhead** + + RCAC data centers provide infrastructure such as networking, racks, floor space, cooling, and power. + +* **Cost Effective** + + RCAC works with vendors to obtain the best price for computing resources by pooling funds from different disciplines to leverage greater group purchasing power. + +Through the Community Cluster Program, Purdue affiliates have invested several million dollars in computational and storage resources from Q4 2006 to the present with great success in both the research accomplished and the money saved on equipment purchases. + +For more information or to purchase access to our latest cluster today, see the [Purchase](https://www.rcac.purdue.edu/purchase) page. Have questions? contact us at [rcac-cluster-purchase@lists.purdue.edu](mailto:rcac-cluster-purchase@lists.purdue.edu) to discuss. + +[**Back to the Accounts section**](../accounts.md) diff --git a/docs/userguides/bell/biography.md b/docs/userguides/bell/biography.md new file mode 100644 index 00000000..68d39d7b --- /dev/null +++ b/docs/userguides/bell/biography.md @@ -0,0 +1,32 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Clara Bell Sessions +![Portrait of Clara Bell Sessions](/assets/images/userguides/bell/bell-bio.png){ align=right width="260" } + +Clara Bell Sessions was a nursing professor and director of continuing education in nursing at Purdue University. While at Purdue, she helped establish the Minority Student Nurses' Association (MSNA) and Minority Faculty Fellows program. Bell attended Indiana State University where she earned her bachelor of science in nursing, followed by Indiana University where she earned her master's and doctoral degrees in their School of Education. + +In 1981, Purdue University hired Bell as a professor of nursing and she later became the director of continuing education in nursing. Bell was dedicated to improving the experience for minority students and faculty at Purdue. She was integral in the creation of the Minority Student Nurses' Association (MSNA), now Diversity in Nursing Association, and the Minority Faculty Fellows program, the precursor of the Office of Diversity and Multicultural Affairs. + +Bell was also active in national organizations. In 1992 and 1993, she co-chaired the National Congress of Black Faculty Council on Research and Education, served as a cabinet member on the Human Rights Committee of the American Nurses Association, and was a charter member of the Association of Black Nursing Faculty in Higher Education. She earned numerous service awards for her work, including service awards from the Indiana Diabetes Association, Indiana State Nurses Association's board of directors, Delta Omicron Chapter of the Nursing Honor Society of Sigma Theta Tau, and Indiana Department of Aging and Community Services. + +Clara Bell Sessions died on March 3, 1996 in Terre Haute, Indiana. After her death, the Black Caucus of Faculty and Staff created the annual Clara E. Bell Academic Achievement Award for the senior in nursing or health sciences with the highest grade point average. In 2013, she was posthumously awarded the Title IX Distinguished Service Award for her contributions to gender equity in education. + +## Citations + +Archives and Special Collections. (2020, July 28). Bell, Clara E., 1934-. Purdue University. Retrieved from: + +Klink, A. (2020, February 4). Clara E. Bell was a trailblazing African American professor of nursing. Purdue University. Retrieved from: + +Lythgoe, D. (2001-2020). Clara E. Stewart. The Lost Creek Settlement of Vigo County, Indiana. Retrieved from: https://www.lost-creek.org/genealogy/getperson.php?personID=I72&tree=tree2 + +Purdue Today. (2013, April 19). Purdue Today presenting profiles on Title IX service awardees. Purdue University. Retrieved from: + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/compile.md b/docs/userguides/bell/compile.md new file mode 100644 index 00000000..daaf2754 --- /dev/null +++ b/docs/userguides/bell/compile.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Compiling Source Code + +Documentation on compiling source code on Bell. + +## In This Section + +- [Compiling Serial Programs](compile/serial.md) +- [Compiling MPI Programs](compile/mpi.md) +- [Compiling OpenMP Programs](compile/openmp.md) +- [Compiling Hybrid Programs](compile/hybrid.md) +- [Intel MKL Library](compile/intel_mkl.md) + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/compile/hybrid.md b/docs/userguides/bell/compile/hybrid.md new file mode 100644 index 00000000..fb3e2c3b --- /dev/null +++ b/docs/userguides/bell/compile/hybrid.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/compile_hybrid.md" + +[**Back to the Compiling Source Code section**](../compile.md) diff --git a/docs/userguides/bell/compile/intel_mkl.md b/docs/userguides/bell/compile/intel_mkl.md new file mode 100644 index 00000000..4040275b --- /dev/null +++ b/docs/userguides/bell/compile/intel_mkl.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/compile_intel_mkl.md" + +[**Back to the Compiling Source Code section**](../compile.md) diff --git a/docs/userguides/bell/compile/mpi.md b/docs/userguides/bell/compile/mpi.md new file mode 100644 index 00000000..61c9b3d8 --- /dev/null +++ b/docs/userguides/bell/compile/mpi.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/compile_mpi.md" + +[**Back to the Compiling Source Code section**](../compile.md) diff --git a/docs/userguides/bell/compile/openmp.md b/docs/userguides/bell/compile/openmp.md new file mode 100644 index 00000000..af8894f2 --- /dev/null +++ b/docs/userguides/bell/compile/openmp.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/compile_openmp.md" + +[**Back to the Compiling Source Code section**](../compile.md) diff --git a/docs/userguides/bell/compile/serial.md b/docs/userguides/bell/compile/serial.md new file mode 100644 index 00000000..ad1c5ca1 --- /dev/null +++ b/docs/userguides/bell/compile/serial.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/compile_serial.md" + +[**Back to the Compiling Source Code section**](../compile.md) diff --git a/docs/userguides/bell/faqs.md b/docs/userguides/bell/faqs.md new file mode 100644 index 00000000..2e8b0bde --- /dev/null +++ b/docs/userguides/bell/faqs.md @@ -0,0 +1,24 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Frequently Asked Questions + +Some common questions, errors, and problems are categorized below. + +## In This Section + +- [About Bell](faqs/about.md) +- [Logging In & Accounts](faqs/login.md) +- [Jobs](faqs/jobs.md) +- [Data](faqs/data.md) +- [Software](faqs/software.md) +- [About Research Computing](faqs/researchcomputing.md) + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/faqs/about.md b/docs/userguides/bell/faqs/about.md new file mode 100644 index 00000000..65d32936 --- /dev/null +++ b/docs/userguides/bell/faqs/about.md @@ -0,0 +1,22 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# About Bell + +Frequently asked questions about Bell. + +## In This Section + +- [Can you remove me from the Bell mailing list?](about/removemailinglist.md) +- [How is Bell different than other Community Clusters?](about/different.md) +- [Do I need to do anything to my firewall to access Bell?](about/firewall.md) +- [Does Bell have the same home directory as other clusters?](about/selfhome.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/about/different.md b/docs/userguides/bell/faqs/about/different.md new file mode 100644 index 00000000..d66e14ed --- /dev/null +++ b/docs/userguides/bell/faqs/about/different.md @@ -0,0 +1,34 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# How is Bell different than other Community Clusters? + +Bell differs from the previous Community Clusters in several significant aspects: + +* Bell home directories are entirely separate from other Community Clusters home directories. There is no automatic copying or synchronization between the two. At their discretion, users can copy parts or all of the Community Clusters home directory into Bell. [Instructions are provided](../../storage/transfer/copyhome.md). +* Users of `hsi` and `htar` commands may encounter Fortress keytab- and authentication-related error messages due to the dedicated nature of Bell home directories. A [temporary workaround is provided](../data/transferkeytab.md) while a permanent solution is being developed. +* Bell contains the latest generation of AMD EPYC processors, codenamed "Rome". These CPUs support AVX2 vector instructions set. When compiling your code, use of `-march=znver2` flag (for latest GCC, Clang and AOCC compilers) or `-march=core-avx2` (for Intel compilers and GCC prior to 9.3) is recommended. +* If your application heavily uses Intel MKL routines, setting the following environment variable is beneficial: + + ``` + export MKL_DEBUG_CPU_TYPE=5 + ``` + + When using FFTW interface from MKL, please also set: + + ``` + export MKL_CBWR=AUTO + ``` + +* If you use Jupyter notebooks, JupyterHub on Bell will only be available via the [OnDemand Gateway](https://gateway.bell.rcac.purdue.edu) rather than the freestanding version as on previous systems. Other RCAC systems will transition to OnDemand as well, following Bell. +* A subset of Bell compute nodes contain AMD Instinct MI50 accelerator cards which can significantly improve performance of compute-intensive workloads. These can be utilized by submitting jobs to the `gpu` partition. +* A selection of GPU-enabled ROCm application containers from the AMD InfinityHub collection is installed. + +[**Back to the About Bell section**](../about.md) diff --git a/docs/userguides/bell/faqs/about/firewall.md b/docs/userguides/bell/faqs/about/firewall.md new file mode 100644 index 00000000..0ff6d644 --- /dev/null +++ b/docs/userguides/bell/faqs/about/firewall.md @@ -0,0 +1,16 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Do I need to do anything to my firewall to access Bell? + + +No firewall changes are needed to access Bell. However, to access data through Network Drives (i.e., CIFS, "Z: Drive"), you must be on a Purdue campus network or connected through [VPN](http://www.itap.purdue.edu/connections/vpn/). + +[**Back to the About Bell section**](../about.md) diff --git a/docs/userguides/bell/faqs/about/removemailinglist.md b/docs/userguides/bell/faqs/about/removemailinglist.md new file mode 100644 index 00000000..b15261af --- /dev/null +++ b/docs/userguides/bell/faqs/about/removemailinglist.md @@ -0,0 +1,18 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Can you remove me from the Bell mailing list? + + +Your subscription in the Bell mailing list is tied to your account on Bell. If you are no longer using your account on Bell, your account can be deleted from the [My Accounts](https://www.rcac.purdue.edu/account/myinfo) page. Hover over the resource you wish to remove yourself from and click the red 'X' button. Your account and mailing list subscription will be removed overnight. Be sure to make a copy of any data you wish to keep first. + +[**Back to the About Bell section**](../about.md) + + diff --git a/docs/userguides/bell/faqs/about/selfhome.md b/docs/userguides/bell/faqs/about/selfhome.md new file mode 100644 index 00000000..b708b110 --- /dev/null +++ b/docs/userguides/bell/faqs/about/selfhome.md @@ -0,0 +1,20 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Does Bell have the same home directory as other clusters? + +The Bell home directory and its contents are exclusive to Bell cluster front-end hosts and compute nodes. This home directory is not available on other RCAC machines but Bell. There is no automatic copying or synchronization between home directories. + + +At your discretion you can manually copy all or parts of your main research computing home to Bell using one of the [suggested methods](../../storage/transfer/copyhome.md). + +If you plan to use `hsi` or `htar` commands to access Fortress tape archive from Bell, please see also the [keytab generation question](../data/transferkeytab.md) for a temporary workaround to a potential caveat, while a permanent mitigation is being developed. + +[**Back to the About Bell section**](../about.md) diff --git a/docs/userguides/bell/faqs/data.md b/docs/userguides/bell/faqs/data.md new file mode 100644 index 00000000..a37e1f08 --- /dev/null +++ b/docs/userguides/bell/faqs/data.md @@ -0,0 +1,24 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Data + +Frequently asked questions about data and data management. + +## In This Section + +- [How is my Data Secured on Bell?](data/security.md) +- [Does Bell have the same home directory as other clusters?](data/selfhome.md) +- [Can I share data with outside collaborators?](data/sharingdata.md) +- [HSI/HTAR: Unable to authenticate user with remote gateway (error 2 or 9)](data/transferkeytab.md) +- [HSI/HTAR: put: Error -5 on transfer](data/puterror.md) +- [Can I access Fortress from Bell?](data/xmountfortress.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/data/puterror.md b/docs/userguides/bell/faqs/data/puterror.md new file mode 100644 index 00000000..e0b053d2 --- /dev/null +++ b/docs/userguides/bell/faqs/data/puterror.md @@ -0,0 +1,29 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# HSI/HTAR: put: Error -5 on transfer + +First, check your firewall settings, and ensure that there are no firewall rules interfering with connecting to Fortress. For firewall configuration, please see "[Do I need to do anything to my firewall to access Fortress?](../about/firewall.md)" **If firewalls are not responsible:** + +Open the file named /etc/hosts on your workstation, especially if you run a Debian or Ubuntu Linux distribution. Look for a line like: + +``` + +127.0.1.1 hostname.dept.purdue.edu hostname +``` + +Replace the IP address 127.0.1.1 with the real IP address for your system. If you don't know your IP address, you can find it with the command: + +``` + +host `hostname --fqdn` +``` + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/data/security.md b/docs/userguides/bell/faqs/data/security.md new file mode 100644 index 00000000..dead7064 --- /dev/null +++ b/docs/userguides/bell/faqs/data/security.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# How is my Data Secured on Bell? + + +Bell is operated in line with policies, standards, and best practices as described within [Secure Purdue](https://www.purdue.edu/securepurdue), and specific to [RCAC Resources](https://www.rcac.purdue.edu/policies). + +Security controls for Bell are based on ones defined in NIST cybersecurity standards. + +Bell supports research at the L1 fundamental and L2 sensitive levels. +Bell is not approved for storing data at the L3 restricted (covered by HIPAA) or L4 Export Controlled (ITAR), or any Controlled Unclassified Information (CUI). + +For resources designed to support research with heightened security requirements, please look for resources within the [REED+ Ecosystem](https://www.rcac.purdue.edu/services/reedplus). + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/data/selfhome.md b/docs/userguides/bell/faqs/data/selfhome.md new file mode 100644 index 00000000..099f7a65 --- /dev/null +++ b/docs/userguides/bell/faqs/data/selfhome.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Does Bell have the same home directory as other clusters? + +The Bell home directory and its contents are exclusive to Bell cluster front-end hosts and compute nodes. This home directory is not available on other RCAC machines but Bell. There is no automatic copying or synchronization between home directories. + +At your discretion you can manually copy all or parts of your main research computing home to Bell using one of the [suggested methods](../../storage/transfer/copyhome.md). + +If you plan to use `hsi` or `htar` commands to access Fortress tape archive from Bell, please see also the [keytab generation question](transferkeytab.md) for a temporary workaround to a potential caveat, while a permanent mitigation is being developed. + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/data/sharingdata.md b/docs/userguides/bell/faqs/data/sharingdata.md new file mode 100644 index 00000000..6fc45454 --- /dev/null +++ b/docs/userguides/bell/faqs/data/sharingdata.md @@ -0,0 +1,18 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Can I share data with outside collaborators? + + +Yes! Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other institutions. See the Globus documentation on how to share data: + +* + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/data/transferkeytab.md b/docs/userguides/bell/faqs/data/transferkeytab.md new file mode 100644 index 00000000..d86f1940 --- /dev/null +++ b/docs/userguides/bell/faqs/data/transferkeytab.md @@ -0,0 +1,47 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# HSI/HTAR: Unable to authenticate user with remote gateway (error 2 or 9) + +There could be a variety of such errors, with wordings along the lines of + +``` + +Could not initialize keytab on remote server. +result = -2, errno = 2rver connection +*** hpssex_OpenConnection: Unable to authenticate user with remote gateway at 128.211.138.40.1217result = -2, errno = 9 +Unable to setup communication to HPSS... +ERROR (main) unable to open remote gateway server connection +HTAR: HTAR FAILED +``` + +and + +``` + +*** hpssex_OpenConnection: Unable to authenticate user with remote gateway at 128.211.138.40.1217result = -11000, errno = 9 +Unable to setup communication to HPSS... +*** HSI: error opening logging +Error - authentication/initialization failed +``` + +The root cause for these errors is an expired or non-existent keytab file (a special authentication token stored in your home directory). These keytabs are valid for 90 days and on most RCAC resources they are usually automatically checked and regenerated when you execute `hsi` or `htar` commands. However, if the keytab is invalid, or fails to generate, Fortress may be unable to authenticate you and you would see the above errors. This is especially common on those RCAC clusters that have their own dedicated home directories (such as Bell), or on standalone installations (such as if you downloaded and installed HSI and HTAR on your non-RCAC computer). + +*This is a temporary problem and a permanent system-wide solution is being developed.* In the interim, the recommended workaround is to generate a new valid keytab file in your main research computing home directory, and then copy it to your home directory on Bell. The `fortresskey` command is used to generate the keytab and can be executed on another cluster or a dedicated data management host `data.rcac.purdue.edu`: + +``` + +$ ssh myusername@data.rcac.purdue.edu fortresskey +$ scp -pr myusername@data.rcac.purdue.edu:~/.private $HOME +``` + +With a valid keytab in place, you should then be able to use `hsi` and `htar` commands to access Fortress from Bell. Note that only one keytab can be valid at any given time (i.e. if you regenerated it, you may have to copy the new keytab to all systems that you intend to use `hsi` or `htar` from if they do not share the main research computing home directory). + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/data/xmountfortress.md b/docs/userguides/bell/faqs/data/xmountfortress.md new file mode 100644 index 00000000..d08599a5 --- /dev/null +++ b/docs/userguides/bell/faqs/data/xmountfortress.md @@ -0,0 +1,15 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Can I access Fortress from Bell? + +Yes. While Fortress directories are not directly mounted on Bell for performance and archival protection reasons, they can be accessed from Bell front-ends and nodes using any of the recommended methods of [HSI, HTAR or Globus](https://www.rcac.purdue.edu/knowledge/fortress/storage/transfer). + +[**Back to the Data section**](../data.md) diff --git a/docs/userguides/bell/faqs/jobs.md b/docs/userguides/bell/faqs/jobs.md new file mode 100644 index 00000000..de947eaa --- /dev/null +++ b/docs/userguides/bell/faqs/jobs.md @@ -0,0 +1,20 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Jobs + +Frequently asked questions related to running jobs. + +## In This Section + +- [Errors](jobs/errors.md) +- [Questions](jobs/questions.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/jobs/errors.md b/docs/userguides/bell/faqs/jobs/errors.md new file mode 100644 index 00000000..6b8f3b77 --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Errors + +Common errors and potential solutions/workarounds for them. + +## In This Section + +- [cannot connect to X server / cannot open display](errors/cannotconnectxserver.md) +- [bash: command not found](errors/commandnotfound.md) +- [bash: module command not found](errors/couldnotloadmodules.md) +- [Close Firefox / Firefox is already running but not responding](errors/firefoxalreadyrunning.md) +- [Jupyter: database is locked / can not load notebook format](errors/jupyterdatabaselocked.md) + +[**Back to the Jobs section**](../jobs.md) diff --git a/docs/userguides/bell/faqs/jobs/errors/cannotconnectxserver.md b/docs/userguides/bell/faqs/jobs/errors/cannotconnectxserver.md new file mode 100644 index 00000000..e2f2f526 --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors/cannotconnectxserver.md @@ -0,0 +1,35 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# cannot connect to X server / cannot open display + +## Problem + +You receive the following message after entering a command to bring up a graphical window + +`cannot connect to X server` `cannot open display` + +## Solution + +This can happen due to multiple reasons: + +1. Reason: Your SSH client software does not support graphical display by itself (e.g. SecureCRT or PuTTY). + * Solution: Try using a client software like ThinLinc or MobaXterm as described in the [SSH X11 Forwarding guide](../../../accounts.md#ssh-x11-forwarding). +2. Reason: You did not enable X11 forwarding in your SSH connection. + + * Solution: If you are in a Windows environment, make sure that X11 forwarding is enabled in your connection settings (e.g. in MobaXterm or PuTTY). If you are in a Linux environment, try + + `ssh -Y -l username hostname` + + +3. Reason: If you are trying to open a graphical window within an interactive PBS job, make sure you are using the `-X` option with `qsub` after following the previous step(s) for connecting to the front-end. Please see the example in the [Interactive Jobs guide](../../../run/examples/slurm/interactive.md). +4. Reason: If none of the above apply, make sure that you are [within quota of your home directory](../../login/errors/errorlockingauthfile.md). + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/jobs/errors/commandnotfound.md b/docs/userguides/bell/faqs/jobs/errors/commandnotfound.md new file mode 100644 index 00000000..3668fa5d --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors/commandnotfound.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# bash: command not found + +## Problem + +You receive the following message after typing a command + +`bash: command not found` + +## Solution + +This means the system doesn't know how to find your command. Typically, you need to load a module to do it. + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/jobs/errors/couldnotloadmodules.md b/docs/userguides/bell/faqs/jobs/errors/couldnotloadmodules.md new file mode 100644 index 00000000..2cdbb8ac --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors/couldnotloadmodules.md @@ -0,0 +1,29 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# bash: module command not found + +## Problem + +You receive the following message after typing a command, e.g. module load intel + +`bash: module command not found` + +## Solution + +The system cannot find the module command. You need to source the modules.sh file as below + +`source /etc/profile.d/modules.sh` + +or + +`#!/bin/bash -i` + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/jobs/errors/firefoxalreadyrunning.md b/docs/userguides/bell/faqs/jobs/errors/firefoxalreadyrunning.md new file mode 100644 index 00000000..f1bf44e3 --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors/firefoxalreadyrunning.md @@ -0,0 +1,16 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Close Firefox / Firefox is already running but not responding + + +--8<-- "docs/snippets/firefox_lock.md" + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/jobs/errors/jupyterdatabaselocked.md b/docs/userguides/bell/faqs/jobs/errors/jupyterdatabaselocked.md new file mode 100644 index 00000000..a67c5c5e --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/errors/jupyterdatabaselocked.md @@ -0,0 +1,15 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Jupyter: database is locked / can not load notebook format + +--8<-- "docs/snippets/jupyter_lock.md" + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/jobs/questions.md b/docs/userguides/bell/faqs/jobs/questions.md new file mode 100644 index 00000000..ac0461c3 --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/questions.md @@ -0,0 +1,21 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Questions + +Frequently asked questions about jobs. + +## In This Section + +- [How do I know Non-uniform Memory Access (NUMA) layout on Bell?](questions/numainfo.md) +- [Why cannot I use --mem=0 when submitting jobs?](questions/no_--mem0.md) +- [Can I extend the walltime on a job?](questions/extendwalltime.md) + +[**Back to the Jobs section**](../jobs.md) diff --git a/docs/userguides/bell/faqs/jobs/questions/extendwalltime.md b/docs/userguides/bell/faqs/jobs/questions/extendwalltime.md new file mode 100644 index 00000000..85c86d90 --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/questions/extendwalltime.md @@ -0,0 +1,27 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Can I extend the walltime on a job? + +In some circumstances, yes. Walltime extensions must be requested of and completed by staff. Walltime extension requests will be considered on named (your advisor or research lab) queues. **Standby or debug queue jobs cannot be extended**. + +Extension requests are at the discretion of staff based on factors such as any upcoming maintenance or resource availability. Extensions can be made past the normal maximum walltime on named queues but these jobs are subject to early termination should a conflicting maintenance downtime be scheduled. + +Please be mindful of time remaining on your job when making requests and make requests at least 24 hours before the end of your job AND during business hours. We cannot guarantee jobs will be extended in time with less than 24 hours notice, after-hours, during weekends, or on a holiday. + +We ask that you make accurate walltime requests during job submissions. Accurate walltimes will allow the job scheduler to efficiently and quickly schedule jobs on the cluster. Please consider that extensions can impact scheduling efficiency for all users of the cluster. + +Requests can be made by [contacting support](https://www.rcac.purdue.edu/help). We ask that you: + +* Provide numerical job IDs, cluster name, and your desired extension amount. +* Provide at least 24 hours notice before job will end (more if request is made on a weekend or holiday). +* Consider making requests during business hours. We may not be able to respond in time to requests made after-hours, on a weekend, or on a holiday. + +[**Back to the Questions section**](../questions.md) diff --git a/docs/userguides/bell/faqs/jobs/questions/no_--mem0.md b/docs/userguides/bell/faqs/jobs/questions/no_--mem0.md new file mode 100644 index 00000000..be6b729a --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/questions/no_--mem0.md @@ -0,0 +1,26 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Why cannot I use --mem=0 when submitting jobs? + +## Question + +Why can't I specify `--mem=0` for my job? + +## Answer + +We no longer support requesting unlimited memory (`--mem=0`) as it has an adverse effect on the way scheduler allocates job, and could lead to large amount of nodes being blocked from usage. + +!!! note + Most often we suggest relying on default memory allocation (cluster-specific). But if you have to request custom amounts of memory, you can do it explicitly. For example `--mem=20G`. + +If you want to use the entire node's memory, you can submit the job with the `--exclusive` option. + +[**Back to the Questions section**](../questions.md) diff --git a/docs/userguides/bell/faqs/jobs/questions/numainfo.md b/docs/userguides/bell/faqs/jobs/questions/numainfo.md new file mode 100644 index 00000000..d9b7ceaa --- /dev/null +++ b/docs/userguides/bell/faqs/jobs/questions/numainfo.md @@ -0,0 +1,27 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# How do I know Non-uniform Memory Access (NUMA) layout on Bell? + +* You can learn about processor layout on Bell nodes using the following command: + + ``` + bell-a003:~$ lstopo-no-graphics + ``` + +* For detailed IO connectivity: + + ``` + bell-a003:~$ lstopo-no-graphics --physical --whole-io + ``` + +* Please note that NUMA information is useful for advanced MPI/OpenMP/GPU optimizations. For most users, using default NUMA settings in MPI or OpenMP would give you the best performance. + +[**Back to the Questions section**](../questions.md) diff --git a/docs/userguides/bell/faqs/login.md b/docs/userguides/bell/faqs/login.md new file mode 100644 index 00000000..cb2a47b7 --- /dev/null +++ b/docs/userguides/bell/faqs/login.md @@ -0,0 +1,20 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Logging In & Accounts + +Frequently asked questions about logging in & accounts. + +## In This Section + +- [Errors](login/errors.md) +- [Questions](login/questions.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/login/errors.md b/docs/userguides/bell/faqs/login/errors.md new file mode 100644 index 00000000..d9bca82b --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Errors + +Common errors and solutions/work-arounds for them. + +## In This Section + +- [/usr/bin/xauth: error in locking authority file](errors/errorlockingauthfile.md) +- [My SSH connection hangs](errors/sshsessionhangs.md) +- [ThinLinc session frozen](errors/thinlinc_session_frozen.md) +- [ThinLinc session unreachable](errors/thinlinc-session-is-unreachable.md) +- [How to disable ThinLinc screensaver](errors/thinlinc-disable-screensaver.md) + +[**Back to the Logging In & Accounts section**](../login.md) diff --git a/docs/userguides/bell/faqs/login/errors/errorlockingauthfile.md b/docs/userguides/bell/faqs/login/errors/errorlockingauthfile.md new file mode 100644 index 00000000..17c8d429 --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors/errorlockingauthfile.md @@ -0,0 +1,36 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# /usr/bin/xauth: error in locking authority file + +## Problem + +I receive this message when logging in: + +`/usr/bin/xauth: error in locking authority file` + +## Solution + +Your home directory disk quota is full. You may check your quota with `myquota`. + +You will need to free up space in your home directory. + +`ncdu` command is a convenient interactive tool to examine disk usage. Consider running `ncdu $HOME` to analyze where the bulk of the usage is. With this knowledge, you could then archive your data elsewhere (e.g. your research group's Data Depot space, or Fortress tape archive), or delete files you no longer need. + +There are several common locations that tend to grow large over time and are merely cached downloads.  The following are safe to delete if you see them in the output of `ncdu $HOME`: + +``` +/home/myusername/.local/share/Trash +/home/myusername/.cache/pip +/home/myusername/.conda/pkgs +/home/myusername/.singularity/cache +``` + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/login/errors/sshsessionhangs.md b/docs/userguides/bell/faqs/login/errors/sshsessionhangs.md new file mode 100644 index 00000000..13ee7a5d --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors/sshsessionhangs.md @@ -0,0 +1,27 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# My SSH connection hangs + +## Problem + +Your console hangs while trying to connect to a RCAC Server. + +## Solution + +This can happen due to various reasons. Most common reasons for hanging SSH terminals are: + +* **Network:** If you are connected over wifi, make sure that your Internet connection is fine. +* **Busy front-end server:** When you connect to a cluster, you SSH to one of the front-end login nodes. Due to transient user loads, one or more of the front-ends may become unresponsive for a short while. To avoid this, try reconnecting to the cluster or wait until the login node you have connected to has reduced load. +* **File system issue:** If a server has issues with one or more of the file systems (`home`, `scratch`, or `depot`) it may freeze your terminal. To avoid this you can connect to another front-end. + +If neither of the suggestions above work, please [contact support](https://www.rcac.purdue.edu/help) specifying the name of the server where your console is hung. + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/login/errors/thinlinc-disable-screensaver.md b/docs/userguides/bell/faqs/login/errors/thinlinc-disable-screensaver.md new file mode 100644 index 00000000..b2940685 --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors/thinlinc-disable-screensaver.md @@ -0,0 +1,53 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# How to disable ThinLinc screensaver + +## Problem + +Your ThinLinc desktop is locked after being idle for a while, and it asks for a password to refresh it. It means the "screensaver" and "lock screen" functions are turned on, but you want to disable these functions. + +## Solution + +If your screen is locked, close the ThinLinc client, reopen the client login popup, and select `End existing session`. + +

+ ThinLinc Login Popup +

+ + +Select "End existing session" and try "Connect" again. + +To permanently avoid screen lock issue, right click desktop and select `Applications`, then `settings`, and select `Screensaver`. + +

+ ThinLinc Screensaver +

+ + +Select "Applications", then "settings", and select "Screensaver". + +Under **Screensaver**, turn off the `Enable Screensaver`, then under **Lock Screen**, turn off the `Enable Lock Screen`, and close the window. + +

+ ThinLinc Disable Screensaver +

+ + +Under "Screensaver" tab, turn off the "Enable Screensaver" option. + +

+ ThinLinc Disable Lock Screen +

+ + +Under "Lock Screen" tab, turn off the "Enable Lock Screen" option. + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/login/errors/thinlinc-session-is-unreachable.md b/docs/userguides/bell/faqs/login/errors/thinlinc-session-is-unreachable.md new file mode 100644 index 00000000..6493ecd4 --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors/thinlinc-session-is-unreachable.md @@ -0,0 +1,38 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# ThinLinc session unreachable + +## Problem + +When trying to login to ThinLinc and re-connect to your existing session, you receive an error *"Your ThinLinc session is currently unreachable"*. + +## Solution + +This can happen if the specific login node your existing remote desktop session was residing on is currently offline or down, so ThinLinc can not reconnect to your existing session.  Most often the session is non-recoverable at this point, so the solution is to terminate your existing ThinLinc desktop session and start a new one. + +* **If you are using a web-version ThinLinc remote desktop (inside the browser):** + + The web version does not have the capability to kill the existing session, only the standalone client does. Please install the standalone client and follow the steps below: + + [ThinLinc](../../../accounts.md#thinlinc) + +* **If you are using a ThinLinc client:** + + Close the ThinLinc client, reopen the client login popup, and select `End existing session`. + +

+ ThinLinc Login Popup +

+ + + Select "End existing session" and try "Connect" again. + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/login/errors/thinlinc_session_frozen.md b/docs/userguides/bell/faqs/login/errors/thinlinc_session_frozen.md new file mode 100644 index 00000000..f65b08a1 --- /dev/null +++ b/docs/userguides/bell/faqs/login/errors/thinlinc_session_frozen.md @@ -0,0 +1,38 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# ThinLinc session frozen + +## Problem + +Your ThinLinc session is frozen and you can not launch any commands or close the session. + +## Solution + +This can happen due to various reasons. The most common reason is that you ran something memory-intensive inside that ThinLinc session on a front-end, so parts of the ThinLinc session got killed by Cgroups, and the entire session got stuck. + +* **If you are using a web-version ThinLinc remote desktop (inside the browser):** + + The web version does not have the capability to kill the existing session, only the standalone client does. Please install the standalone client and follow the steps below: + + [ThinLinc](../../../accounts.md#thinlinc) + +* **If you are using a ThinLinc client:** + + Close the ThinLinc client, reopen the client login popup, and select `End existing session`. + +

+ ThinLinc Login Popup +

+ + + Select "End existing session" and try "Connect" again. + +[**Back to the Errors section**](../errors.md) diff --git a/docs/userguides/bell/faqs/login/questions.md b/docs/userguides/bell/faqs/login/questions.md new file mode 100644 index 00000000..5dbd1211 --- /dev/null +++ b/docs/userguides/bell/faqs/login/questions.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Questions + +Frequently asked questions about logging in & accounts. + +## In This Section + +- [I worked on Bell after I graduated/left Purdue, but can not access it anymore](questions/expiredaccount.md) + +[**Back to the Logging In & Accounts section**](../login.md) diff --git a/docs/userguides/bell/faqs/login/questions/expiredaccount.md b/docs/userguides/bell/faqs/login/questions/expiredaccount.md new file mode 100644 index 00000000..3df23a12 --- /dev/null +++ b/docs/userguides/bell/faqs/login/questions/expiredaccount.md @@ -0,0 +1,28 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# I worked on Bell after I graduated/left Purdue, but can not access it anymore + +## Problem + +You have graduated or left Purdue but continue collaboration with your Purdue colleagues. You find that your access to Purdue resources has suddenly stopped and your password is no longer accepted. + +## Solution + +Access to all resources depends on having a valid Purdue Career Account. Expired Career Accounts are removed twice a year, during Spring and October breaks (more details at the [official page](https://www.purdue.edu/apps/account/IAMO/Purdue_CareerAccount_Expiration.jsp)). If your Career Account was purged due to expiration, you will not be be able to access the resources. + +To provide remote collaborators with valid Purdue credentials, the University provides a special procedure called [Request for Privileges (R4P)](https://www.purdue.edu/apps/account/r4p). If you need to continue your collaboration with your Purdue PI, the PI will have to submit or renew an R4P request on your behalf. + +After your R4P is completed and Career Account is restored, please note two additional necessary steps: + +* **Access:** Restored Career Accounts by default do **not** have any RCAC resources enabled for them. **Your PI will have to login to the [Manage Users](https://www.rcac.purdue.edu/account/groups) tool and explicitly re-enable your access by un-checking and then ticking back checkboxes for desired queues/Unix groups resources.** +* **Email:** Restored Career Accounts by default do **not** have their *@purdue.edu* email service enabled. While this does not preclude you from using RCAC resources, any email messages (be that generated on the clusters, or any service announcements) would not be delivered - which may cause inconvenience or loss of compute jobs. To avoid this, we recommend setting your restored *@purdue.edu* email service to "Forward" (to an actual address you read). The easiest way to ensure it is to go through the [Account Setup process](https://www.purdue.edu/apps/account/AccountSetup). + +[**Back to the Questions section**](../questions.md) diff --git a/docs/userguides/bell/faqs/researchcomputing.md b/docs/userguides/bell/faqs/researchcomputing.md new file mode 100644 index 00000000..e2f7713a --- /dev/null +++ b/docs/userguides/bell/faqs/researchcomputing.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# About Research Computing + +Frequently asked questions about RCAC. + +## In This Section + +- [Can I get a private server from RCAC?](researchcomputing/vps.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/researchcomputing/vps.md b/docs/userguides/bell/faqs/researchcomputing/vps.md new file mode 100644 index 00000000..dc3c9402 --- /dev/null +++ b/docs/userguides/bell/faqs/researchcomputing/vps.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Can I get a private server from RCAC? + +## Question + +Can I get a private (virtual or physical) server from RCAC? + +## Answer + +Often, researchers may want a private server to run databases, web servers, or other software. RCAC currently has [Geddes](https://www.rcac.purdue.edu/compute/geddes), a Community Composable Platform optimized for composable, cloud-like workflows that are complementary to the batch applications run on Community Clusters. Funded by the National Science Foundation under grant OAC-2018926, Geddes consists of Dell Compute nodes with two 64-core AMD Epyc 'Rome' processors (128 cores per node). + +To purchase access to Geddes today, go to the [Cluster Access Purchase](https://www.rcac.purdue.edu/purchase) page. Please subscribe to our Community Cluster Program Mailing List to stay informed on the latest purchasing developments or contact us (rcac-cluster-purchase@lists.purdue.edu) if you have any questions. + +[**Back to the About Research Computing section**](../researchcomputing.md) diff --git a/docs/userguides/bell/faqs/software.md b/docs/userguides/bell/faqs/software.md new file mode 100644 index 00000000..49ae5cb7 --- /dev/null +++ b/docs/userguides/bell/faqs/software.md @@ -0,0 +1,21 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Software + +Frequently asked questions about software. + +## In This Section + +- [Cannot use pip after loading ml-toolkit modules](software/pip.md) +- [How can I get access to Sentaurus software?](software/sentaurus.md) +- [Julia package installation](software/julia_package.md) + +[**Back to the Frequently Asked Questions section**](../faqs.md) diff --git a/docs/userguides/bell/faqs/software/julia_package.md b/docs/userguides/bell/faqs/software/julia_package.md new file mode 100644 index 00000000..eee389ce --- /dev/null +++ b/docs/userguides/bell/faqs/software/julia_package.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Julia package installation + + +Users do not have write permission to the default julia package installation destination. However, users can install packages into home directory under `~/.julia`. + +Users can side step this by explicitly defining where to put julia packages: + +``` +$ export JULIA_DEPOT_PATH=$HOME/.julia +$ julia -e 'using Pkg; Pkg.add("PackageName")' +``` + +[**Back to the Software section**](../software.md) diff --git a/docs/userguides/bell/faqs/software/pip.md b/docs/userguides/bell/faqs/software/pip.md new file mode 100644 index 00000000..294b46c9 --- /dev/null +++ b/docs/userguides/bell/faqs/software/pip.md @@ -0,0 +1,36 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Cannot use pip after loading ml-toolkit modules + + +## Question + +Pip throws an error after loading the machine learning modules. How can I fix it? + +## Answer + +Machine learning modules (tensorflow, pytorch, opencv etc.) include a version of `pip` that is newer than the one installed with Anaconda. As a result it will throw an error when you try to use it. + +``` +$ pip --version +Traceback (most recent call last): + File "/apps/cent7/anaconda/5.1.0-py36/bin/pip", line 7, in + from pip import main +ImportError: cannot import name 'main' +``` + +The preferred way to use `pip` with the machine learning modules is to invoke it via Python as shown below. + +``` +$ python -m pip --version +``` + +[**Back to the Software section**](../software.md) diff --git a/docs/userguides/bell/faqs/software/sentaurus.md b/docs/userguides/bell/faqs/software/sentaurus.md new file mode 100644 index 00000000..5393f042 --- /dev/null +++ b/docs/userguides/bell/faqs/software/sentaurus.md @@ -0,0 +1,28 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# How can I get access to Sentaurus software? + + +## Question + +How can I get access to Sentaurus tools for micro- and nano-electronics design? + +## Answer + +Sentaurus software license requires a signed NDA. Please contact [Dr. Mark Johnson, Director of ECE Instructional Laboratories](https://engineering.purdue.edu/Mark-Johnson) to complete the process. + +Once the licensing process is complete and you have been added into a `cae2` Unix group, you could use Sentaurus on RCAC community clusters by loading the corresponding environment module: + +``` +module load sentaurus +``` + +[**Back to the Software section**](../software.md) diff --git a/docs/userguides/bell/gateway.md b/docs/userguides/bell/gateway.md new file mode 100644 index 00000000..7f9d2ba8 --- /dev/null +++ b/docs/userguides/bell/gateway.md @@ -0,0 +1,33 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Gateway (Open OnDemand) + +Bell's Gateway is an [open-source HPC portal](http://openondemand.org/) developed by the [Ohio Supercomputing Center](https://www.osc.edu/). Open OnDemand allows one to interact with HPC resources through a web browser and easily manage files, submit jobs, and interact with graphical applications directly in a browser, all with no software to install. Bell has an instance of OnDemand available that can be accessed via [gateway.bell.rcac.purdue.edu](https://gateway.bell.rcac.purdue.edu). + +## Logging In + +To log into Gateway: + +* Navigate to [gateway.bell.rcac.purdue.edu](https://gateway.bell.rcac.purdue.edu) +* Log in using your Career account username and Purdue Login Duo client. + +On the splash page you will see a quota usage report. If you are over 90% on any of your quotas a warning will be displayed. This information will update every 10-15 minutes while you are active on Gateway. + +## Apps + +There are a number of built-in apps in Gateway that can be accessed from the top menu bar. Below are links to documentation on each app. + +- [Interactive Apps](gateway/interactive.md) +- [Files](gateway/files.md) +- [Jobs](gateway/jobs.md) +- [Cluster Tools](gateway/cluster.md) + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/gateway/cluster.md b/docs/userguides/bell/gateway/cluster.md new file mode 100644 index 00000000..8039bcc4 --- /dev/null +++ b/docs/userguides/bell/gateway/cluster.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Cluster Tools + +The Cluster Tools menu contains cluster utilities. At the moment, only a terminal app is provided. Additional apps may be developed and provided in the future. + +## Shell Access + +Launching the shell app will provide you with a web-based terminal session on the cluster front-end. This is equivalent to using a standalone SSH client to connect to `bell.rcac.purdue.edu` where you are connected to one several front-ends. The normal acceptable [front-end use policy](https://www.rcac.purdue.edu/policies/frontenduse) applies to access through the web-app. X11 Forwarding is not supported. Use of one of the [interactive apps](interactive.md) is recommended for graphical applications. + +[**Back to the Gateway (Open OnDemand) section**](../gateway.md) diff --git a/docs/userguides/bell/gateway/files.md b/docs/userguides/bell/gateway/files.md new file mode 100644 index 00000000..a89f528a --- /dev/null +++ b/docs/userguides/bell/gateway/files.md @@ -0,0 +1,41 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Files + +The Files app will let you access your files in your [Home Directory](../storage/options/home.md), [Scratch](../storage/options/scratch.md), and [Data Depot](https://www.rcac.purdue.edu/storage/depot) spaces. The app lets you manage create, manage, and delete files and directories from your web browser. Navigate by double clicking on folders in the file explorer or by using the file tree on the left. + +

+ Open OnDemand file browser +

+ + +The browser-based file explorer. Navigate by double clicking on folders in the file explorer or by using the file tree on the left. + +On the top row, there are buttons to: + +* Go To: directly input a directory to navigate to +* Open in Terminal: launches the Shell app and navigates you to the current directory in the terminal +* New File: creates a new, empty file +* New Dir: creates a new, empty directory +* Upload: upload a file from your computer + +**Note:** File uploads from your browser are limited to 100 GB per file. Be mindful that uploads over a few gigabytes may be unreliable through your browser, especially from off-campus connections. For very large files or off-campus transfers alternative methods such as [Globus](../storage/transfer/globus.md) are highly recommended. + +The second row of buttons lets you perform typical file management operations. The Edit button will open files in a fully fledged browser based text editor - it features syntax highlighting and vim and Emacs key bindings. + +

+ Open OnDemand file editor +

+ + +The browser-based text editor interface, shown here editing a Bash script, includes syntax highlighting, font-size adjustments, and various key bindings. + +[**Back to the Gateway (Open OnDemand) section**](../gateway.md) diff --git a/docs/userguides/bell/gateway/interactive.md b/docs/userguides/bell/gateway/interactive.md new file mode 100644 index 00000000..c94137b8 --- /dev/null +++ b/docs/userguides/bell/gateway/interactive.md @@ -0,0 +1,24 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Interactive Apps + +There are several interactive apps available through Gateway that can be accessed through the Interactive Apps dropdown menu. These apps are provided with a basic node and software configuration as a 'quick-launch' option to get your work up and running quickly. For simplicity, minimal options are provided - these apps are not intended for complex configuration/customization scenarios. + +After you a submit an interactive app to the queue, Gateway will track and manage the session. Once it starts, you may connect and disconnect from the session in your browser, leaving the job running while you log out of your browser. + +Each of the available apps are documented through the following links. + +- [Compute Node Desktop](interactive/desktop.md) +- [Jupyter Notebook](interactive/notebook.md) +- [MATLAB](interactive/matlab.md) +- [RStudio Server](interactive/rstudio.md) + +[**Back to the Gateway (Open OnDemand) section**](../gateway.md) diff --git a/docs/userguides/bell/gateway/interactive/desktop.md b/docs/userguides/bell/gateway/interactive/desktop.md new file mode 100644 index 00000000..f8b42f1f --- /dev/null +++ b/docs/userguides/bell/gateway/interactive/desktop.md @@ -0,0 +1,21 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Compute Node Desktop + +The Compute Node Desktop app will launch a graphical desktop session on a compute node. This is similar to using [ThinLinc](/userguides/bell/accounts/#thinlinc), however, this gives you a desktop directly on a compute node instead on a front-end. This app is useful if you have a custom application or application not directly available as an interactive app you would like to run inside Gateway. + +To launch a desktop session on a compute node, select the Bell Compute Desktop app. From the submit form, select from the available options - the queue to which you wish to submit and the number of wallclock hours you wish to have job running. There is also a checkbox that enable a notification to your email when the job starts. + +After the interactive job is submitted you will be taken to your list of active interactive app sessions. You can monitor the status of the job from here until it starts, or if you enabled the email notification, watch your Purdue email for the notification the job has started. + +Once it is indicated the job has started you can connect to the desktop with the "Launch noVNC in New Tab" button. The session will be terminated after the wallclock hours you specified have elapsed or you terminate the session early with the "Delete" button from the list of sessions. Deleting the session when you are finished will free up queue resources for your lab mates and other users on the system. + +[**Back to the Interactive Apps section**](../interactive.md) diff --git a/docs/userguides/bell/gateway/interactive/matlab.md b/docs/userguides/bell/gateway/interactive/matlab.md new file mode 100644 index 00000000..e8901efd --- /dev/null +++ b/docs/userguides/bell/gateway/interactive/matlab.md @@ -0,0 +1,24 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# MATLAB + +The MATLAB app will launch a MATLAB session on a compute node and allow you to connect directly to it in a web browser. + +To launch a MATLAB session on a compute node, select the MATLAB app. From the submit form, select from the available options - the version of MATLAB you are interested in running, the queue to which you wish to submit, and the number of wallclock hours you wish to have job running. There is also a checkbox that enable a notification to your email when the job starts. + +After the interactive job is submitted you will be taken to your list of active interactive app sessions. You can monitor the status of the job from here until it starts, or if you enabled the email notification, watch your Purdue email for the notification the job has started. + +Once it is indicated the job has started you can connect to the desktop with the "Launch noVNC in New Tab" button. The session will be terminated after the wallclock hours you specified have elapsed or you terminate the session early with the "Delete" button from the list of sessions. Deleting the session when you are finished will free up queue resources for your lab mates and other users on the system. + +!!! Warning + There are known issues with running Matlab in this way and resizing your web browser. Graphical corruption may occur if you resize the browser. Fixes for this are being investigated. + +[**Back to the Interactive Apps section**](../interactive.md) diff --git a/docs/userguides/bell/gateway/interactive/notebook.md b/docs/userguides/bell/gateway/interactive/notebook.md new file mode 100644 index 00000000..4deeb31b --- /dev/null +++ b/docs/userguides/bell/gateway/interactive/notebook.md @@ -0,0 +1,31 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Jupyter Notebook + +The Notebook app will launch a Notebook session on a compute node and allow you to connect directly to it in a web browser. + +To launch a Notebook session on a compute node, select the Notebook app. From the submit form, select from the available options: + +1. **Queue:**This is a dropdown menu from which you can select a queue from all of the queues to which you have permission to submit. +2. **Walltime:**This is a field which expects a number and represents how many hours you want to keep the session running. Note that this value should not exceed the maximum value given next to the selected queue name from the queue dropdown menu. +3. **Number of Cores/GPUs:** This is a field which expects a number and represents the number of your resources your session is requesting. Note that the amount of memory allocated for your session is proportional to the number of cores or GPUs that you request for your job, so if your session is running out of memory, consider increasing this value. +4. **Use Jupyter Lab:**This is a checkbox which, when checked, will run Jupyter Lab instead of Jupyter Notebook. Both of these applications are interfaces to Jupyter, and you can launch Jupyter notebooks from within Jupyter Lab. Jupyter Notebook is more "barebones" while Jupyter Lab has additional features such as the ability to interact with additional file types. +5. **E-mail Notice:**This is a checkbox which, when checked, will send you an e-mail notification to your Purdue e-mail that your session is ready when the scheduler has found resources to dedicate to your session. + +After the interactive job is submitted you will be taken to your list of active interactive app sessions. You can monitor the status of the job from here until it starts, or if you enabled the email notification, watch your Purdue email for the notification the job has started. + +Once it is indicated the job has started you can connect to the desktop with the "Connect to Jupyter" button. Once connected, you can create new notebooks, selecting the currently available Anaconda versions available as modules, and any personally created Notebook kernels. + +Often times you may want to use one of your existing Anaconda environments within your Jupyter session to use libraries specific to your workflow. In order to do so, you must ensure that the Anaconda environment you want to use contains the Python packages "IPyKernel" and "IPython" which are packages that are required by Jupyter. When you create a Jupyter session, Open OnDemand will check through your existing Anaconda environments and create a Jupyter kernel for any Anaconda environment that contains these two packages, and you will be able to select to use that kernel from within the application. + +The session will be terminated after the number of hours you specified have elapsed or you terminate the session early with the "Delete" button from the list of sessions. Deleting the session when you are finished will free up queue resources for your lab mates and other users on the system. + +[**Back to the Interactive Apps section**](../interactive.md) diff --git a/docs/userguides/bell/gateway/interactive/rstudio.md b/docs/userguides/bell/gateway/interactive/rstudio.md new file mode 100644 index 00000000..19f20ed3 --- /dev/null +++ b/docs/userguides/bell/gateway/interactive/rstudio.md @@ -0,0 +1,21 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# RStudio Server + +The RStudio app will launch a RStudio session on a compute node and allow you to connect directly to it in a web browser. + +To launch a RStudio session on a compute node, select the RStudio app. From the submit form, select from the available options - the queue to which you wish to submit, and the number of wallclock hours you wish to have job running. There is also a checkbox that enable a notification to your email when the job starts. + +After the interactive job is submitted you will be taken to your list of active interactive app sessions. You can monitor the status of the job from here until it starts, or if you enabled the email notification, watch your Purdue email for the notification the job has started. + +Once it is indicated the job has started you can connect to the desktop with the "Connect to RStudio Server" button. The session will be terminated after the wallclock hours you specified have elapsed or you terminate the session early with the "Delete" button from the list of sessions. Deleting the session when you are finished will free up queue resources for your lab mates and other users on the system. + +[**Back to the Interactive Apps section**](../interactive.md) diff --git a/docs/userguides/bell/gateway/jobs.md b/docs/userguides/bell/gateway/jobs.md new file mode 100644 index 00000000..e3cfb91c --- /dev/null +++ b/docs/userguides/bell/gateway/jobs.md @@ -0,0 +1,102 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Jobs + +There are two apps under the Jobs apps: Active Jobs and Job Composer. These are detailed below. + +## Active Jobs + +This shows you active SLURM jobs currently on the cluster. The default view will show you your current jobs, similar to `squeue -u rices`. Using the button labeled "Your Jobs" in the upper right allows you to select different filters by queue (account). All accounts output by `slist` will appear for you here. Using the arrow on the left hand side will expand the full job details. + + +

+ A table of active jobs +

+ + +The table of active jobs shows useful information such as queue, status, cluster, and ID. It can be sorted by clicking the headers of each column or searched with the "Filter" box above it. + + +### Job Composer + +The Job Composer app allows you to create and submit jobs to the cluster. You can select from pre-defined templates (most of these are taken from the User Guide examples) or you can create your own templates for frequently used workflows. + +### Creating Job from Existing Template + +Click "New Job" menu, then select "From Template": + +

+ The job composer interface +

+ + +When clicking the 'New Job' button a drop-down will show a few options. "From Template" is usually the second item in the list. + +Then select from one of the available templates. + + +

+ A sortable data table containing a list of all the available templates. +

+ + +Select one of the templates by clicking its row in the table of available templates. + + +Click 'Create New Job' in second pane. + + +

+ The 'Create New Job' pane +

+ + +The "Create New Job" pane will show form options for "Job Name", "Cluster", and "Script Name" with the "Create New Job" button below. + + +Your new job should be selected in your list of jobs. In the 'Submit Script' pane you can see the job script that was generated with an 'Open Editor' link to open the script in the built-in editor. Open the file in the editor and edit the script as necessary. By default the job will specify standby queue - this should be changed as appropriate, along with the node and walltime requests. + + +

+ The 'Submit Script' pane +

+ + +The "Submit Script" pane will show a preview of the contents of the script file and action buttons below. + + +When you are finished with editing the job and are ready to submit, click the green 'Submit' button at the top of the job list. You can monitor progress from here or from the Active Jobs app. Once completed, you should see the output files appear: + +

+ A list of files found in the output folder +

+ + +The folder contents will be listed, showing the resulting output files from running the submitted script. + +Clicking on one of the output files will open it in the file editor for your viewing. + +## Creating New Template + +First, prepare a template directory containing a template submission script along with any input files. Then, to import the job into the Job Composer app, click the 'Create New Template' button. Fill in the directory containing your template job script and files in the first box. Give it an appropriate name and notes. + + +

+ The 'Create New Template' form +

+ + +The "Create New Template" form has inputs for "Path", "Name", "Cluster", and "Notes". If "Path" is left blank, a default job script will be added to the new template. + + +This template will now appear in your list of templates to choose from when composing jobs. You can now go create and submit a job from this new template. + +[**Back to the Gateway (Open OnDemand) section**](../gateway.md) diff --git a/docs/userguides/bell/index.md b/docs/userguides/bell/index.md new file mode 100644 index 00000000..bb11625b --- /dev/null +++ b/docs/userguides/bell/index.md @@ -0,0 +1,20 @@ +--- +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Bell User Guide +Bell is a Community Cluster optimized for communities running traditional, tightly-coupled science and engineering applications. + +- [**Bell Overview**](overview.md) +- [**Biography of Bell**](biography.md) +- [**Accounts**](accounts.md) +- [**Software**](software.md) +- [**Running Jobs**](run.md) +- [**File Storage and Transfer**](storage.md) +- [**Gateway (Open OnDemand)**](gateway.md) +- [**Compiling Source Code**](compile.md) +- [**Frequently Asked Questions**](faqs.md) diff --git a/docs/userguides/bell/overview.md b/docs/userguides/bell/overview.md new file mode 100644 index 00000000..a44da812 --- /dev/null +++ b/docs/userguides/bell/overview.md @@ -0,0 +1,47 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Overview of Bell + +Bell is a Community Cluster optimized for communities running traditional, tightly-coupled science and engineering applications. Bell was built through a partnership with Dell and AMD over the summer of 2020. Bell consists of Dell compute nodes with two 64-core AMD Epyc 7662 "Rome" processors (128 cores per node) and 256 GB of memory. All nodes have 100 Gbps HDR Infiniband interconnect and a 6-year warranty. + +Bell access is offered on the basis of each 64-core Rome processor, or a half-node share. To purchase access to Bell today, go to the [Cluster Access Purchase](https://www.rcac.purdue.edu/purchase) page. Please subscribe to our Community Cluster Program Mailing List to stay informed on the latest purchasing developments or contact us via email at [rcac-cluster-purchase@lists.purdue.edu](mailto:rcac-cluster-purchase@lists.purdue.edu) if you have any questions. + +## Bell Namesake + +Bell is named in honor of Clara Bell Sessions, minority advocate and Professor and Director of Continuing Education of Nursing. More information about her life and impact on Purdue is available in a [Biography of Bell](biography.md). + +## Bell Specifications + +All Bell compute nodes have 128 processor cores and 100 Gbps Infiniband interconnects. + +Bell Front-Ends + +| Front-Ends | Number of Nodes | Processors per Node | Cores per Node | Memory per Node | Retires in | +| --- | --- | --- | --- | --- | --- | +| | 8 | One Rome CPU @ 2.0GHz | 32 | 512 GB | 2026 | + +Bell Sub-Clusters + +| Sub-Cluster | Number of Nodes | Processors per Node | Cores per Node | Memory per Node | Retires in | +| --- | --- | --- | --- | --- | --- | +| A | 448 | Two Rome CPUs @ 2.0GHz | 128 | 256 GB | 2026 | +| B | 8 | Two Rome CPUs @ 2.0GHz | 128 | 1 TB | 2026 | +| G | 4 | Two Rome CPUs @ 2.0GHz, two MI50 AMD GPUs (32GB) | 128 | 256 GB | 2026 | +| G | 1 | Two Cascade Lake CPUs @ 2.90 GHz, six MI50 AMD GPUs (32GB) | 48 | 384 GB | 2026 | + +Bell nodes run Rocky Linux 8 and use Slurm (Simple Linux Utility for Resource Management) as the batch scheduler for resource and job management. The application of operating system patches occurs as security needs dictate. All nodes allow for unlimited stack usage, as well as unlimited core dump size (though disk space and server quotas may still be a limiting factor). + +On Bell, the following set of compiler and message-passing library for parallel code are recommended: + +* GCC 9.3.0 +* OpenMPI + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/run.md b/docs/userguides/bell/run.md new file mode 100644 index 00000000..4d617b83 --- /dev/null +++ b/docs/userguides/bell/run.md @@ -0,0 +1,52 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Running Jobs + +Jobs are submitted on {{ resource }} via the SLURM (Simple Linux Utility for Resource Management) scheduler, which is responsible for allocating resources and scheduling the start time of a job. You may use either the batch or interactive mode to run your jobs. The batch mode is ideal for finished programs, and the interactive mode is useful for debugging your job. + +!!! important + Do NOT run large, long, multi-threaded, parallel, or CPU-intensive jobs on a front-end login host. All users share the front-end hosts, and running anything but the smallest test job will negatively impact everyone's ability to use Bell. Always use SLURM to submit your work as a job. + +Before creating your submission script, learn more about how to use Slurm accounts, partitions, and QOS options: + +- [**Basics of using Slurm accounts, partitions, and QOS options**](run/slurm/queues.md) + +Batch jobs submitted via SLURM have four main steps: + +* [Create job submission script](run/slurm/creating_the_submission_script.md) +* [Submit job script](run/slurm/submit_script.md) +* [Monitor job status](run/slurm/monitoring_job.md) +* [Check output](run/slurm/checking_output.md) + +## Other useful topics + +- [Canceling a Job](run/slurm/cancelling_job.md) +- [Job Dependencies](run/slurm/job_dependencies.md) +- [Holding a Job](run/slurm/holding_job.md) + + +## Example Jobs + +A number of example jobs are available for you to look over and adapt to your own needs. The first few are generic examples, and latter ones go into specifics for particular software packages. + +- [Specific Applications](run/examples/apps.md) +- [Hadoop](run/examples/hadoop.md) +- [Generic SLURM Jobs](run/examples/slurm.md) + + +## PBS to Slurm + +This is a reference for the most common command, environment variables, and job specification options used by the workload management systems and their equivalents. + +- [Notable Differences](run/rosetta/differences.md) +- [Quick Guide](run/rosetta/stone.md) + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/run/examples/apps.md b/docs/userguides/bell/run/examples/apps.md new file mode 100644 index 00000000..10d6f506 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps.md @@ -0,0 +1,31 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Specific Applications + +The following examples demonstrate job submission files for some common real-world applications. See the [Generic SLURM Examples](slurm.md) section for more examples on job submissions that can be adapted for use. + +## In This Section + +- [Ansys Fluent](apps/ansysfluent.md) +- [BioContainers Collection](apps/biocontainers.md) +- [Gaussian](apps/gaussian.md) +- [Machine Learning](apps/learning.md) +- [Mathematica](apps/mathematica.md) +- [Matlab](apps/matlab.md) +- [Octave](apps/octave.md) +- [Python](apps/python.md) +- [R](apps/r.md) +- [ROCm Containers Collection](apps/rocmcontainers.md) +- [Singularity](apps/singularity.md) +- [Spark](apps/spark.md) +- [Windows](apps/windows.md) + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/examples/apps/ansysfluent.md b/docs/userguides/bell/run/examples/apps/ansysfluent.md new file mode 100644 index 00000000..7ad99aea --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/ansysfluent.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/ansysfluent.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/ansysfluent/case_calculating_with_fluent.md b/docs/userguides/bell/run/examples/apps/ansysfluent/case_calculating_with_fluent.md new file mode 100644 index 00000000..c9104f93 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/ansysfluent/case_calculating_with_fluent.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/ansysfluent/case_calculating_with_fluent.md" + +[**Back to the Ansys Fluent section**](../ansysfluent.md) diff --git a/docs/userguides/bell/run/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md b/docs/userguides/bell/run/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md new file mode 100644 index 00000000..ac6d5f05 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/ansysfluent/fluent_text_user_interface_and_journal_file.md" + +[**Back to the Ansys Fluent section**](../ansysfluent.md) diff --git a/docs/userguides/bell/run/examples/apps/ansysfluent/preparing_case_files_for_fluent.md b/docs/userguides/bell/run/examples/apps/ansysfluent/preparing_case_files_for_fluent.md new file mode 100644 index 00000000..afc2980a --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/ansysfluent/preparing_case_files_for_fluent.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/ansysfluent/preparing_case_files_for_fluent.md" + +[**Back to the Ansys Fluent section**](../ansysfluent.md) diff --git a/docs/userguides/bell/run/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md b/docs/userguides/bell/run/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md new file mode 100644 index 00000000..d96a5f92 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/ansysfluent/submit_fluent_jobs_to_slurm.md" + +[**Back to the Ansys Fluent section**](../ansysfluent.md) diff --git a/docs/userguides/bell/run/examples/apps/biocontainers.md b/docs/userguides/bell/run/examples/apps/biocontainers.md new file mode 100644 index 00000000..c52d9dbb --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/biocontainers.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/biocontainers.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/gaussian.md b/docs/userguides/bell/run/examples/apps/gaussian.md new file mode 100644 index 00000000..00c379cb --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/gaussian.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/gaussian.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/learning.md b/docs/userguides/bell/run/examples/apps/learning.md new file mode 100644 index 00000000..72834806 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/learning.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/learning.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/learning/customml.md b/docs/userguides/bell/run/examples/apps/learning/customml.md new file mode 100644 index 00000000..5afdd24e --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/learning/customml.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/learning/customml.md" + +[**Back to the Machine Learning section**](../learning.md) diff --git a/docs/userguides/bell/run/examples/apps/learning/ml_batch.md b/docs/userguides/bell/run/examples/apps/learning/ml_batch.md new file mode 100644 index 00000000..eb34c01c --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/learning/ml_batch.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/learning/ml_batch.md" + +[**Back to the Machine Learning section**](../learning.md) diff --git a/docs/userguides/bell/run/examples/apps/learning/mltoolkit.md b/docs/userguides/bell/run/examples/apps/learning/mltoolkit.md new file mode 100644 index 00000000..dea3a78a --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/learning/mltoolkit.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/learning/mltoolkit.md" + +[**Back to the Machine Learning section**](../learning.md) diff --git a/docs/userguides/bell/run/examples/apps/mathematica.md b/docs/userguides/bell/run/examples/apps/mathematica.md new file mode 100644 index 00000000..80b537a2 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/mathematica.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/mathematica.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab.md b/docs/userguides/bell/run/examples/apps/matlab.md new file mode 100644 index 00000000..ad8f9a4c --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/implicit_parallelism.md b/docs/userguides/bell/run/examples/apps/matlab/implicit_parallelism.md new file mode 100644 index 00000000..e2a55996 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/implicit_parallelism.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/implicit_parallelism.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/interpreter.md b/docs/userguides/bell/run/examples/apps/matlab/interpreter.md new file mode 100644 index 00000000..d48226ad --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/interpreter.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/interpreter.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/mdcs_parallel.md b/docs/userguides/bell/run/examples/apps/matlab/mdcs_parallel.md new file mode 100644 index 00000000..748984e2 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/mdcs_parallel.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/mdcs_parallel.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/parfor.md b/docs/userguides/bell/run/examples/apps/matlab/parfor.md new file mode 100644 index 00000000..653a0ec4 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/parfor.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/parfor.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/profile_manager.md b/docs/userguides/bell/run/examples/apps/matlab/profile_manager.md new file mode 100644 index 00000000..3158c831 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/profile_manager.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/profile_manager.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/matlab/spmd.md b/docs/userguides/bell/run/examples/apps/matlab/spmd.md new file mode 100644 index 00000000..d112ca21 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/matlab/spmd.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/matlab/spmd.md" + +[**Back to the Matlab section**](../matlab.md) diff --git a/docs/userguides/bell/run/examples/apps/octave.md b/docs/userguides/bell/run/examples/apps/octave.md new file mode 100644 index 00000000..95739239 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/octave.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/octave.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/python.md b/docs/userguides/bell/run/examples/apps/python.md new file mode 100644 index 00000000..091e88bc --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/python/conda.md b/docs/userguides/bell/run/examples/apps/python/conda.md new file mode 100644 index 00000000..b997581b --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/conda.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/conda.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/environment_example.md b/docs/userguides/bell/run/examples/apps/python/environment_example.md new file mode 100644 index 00000000..0de3ef52 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/environment_example.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/environment_example.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/examples.md b/docs/userguides/bell/run/examples/apps/python/examples.md new file mode 100644 index 00000000..15e8b2e8 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/examples.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/examples.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/numpy.md b/docs/userguides/bell/run/examples/apps/python/numpy.md new file mode 100644 index 00000000..d7de5f61 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/numpy.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/numpy.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/packages.md b/docs/userguides/bell/run/examples/apps/python/packages.md new file mode 100644 index 00000000..2d2caf11 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/packages.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/packages.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/pip.md b/docs/userguides/bell/run/examples/apps/python/pip.md new file mode 100644 index 00000000..acfc8380 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/pip.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/pip.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/python/source.md b/docs/userguides/bell/run/examples/apps/python/source.md new file mode 100644 index 00000000..0bf24d37 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/python/source.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/python/source.md" + +[**Back to the Python section**](../python.md) diff --git a/docs/userguides/bell/run/examples/apps/r.md b/docs/userguides/bell/run/examples/apps/r.md new file mode 100644 index 00000000..b6218b33 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/r/data.md b/docs/userguides/bell/run/examples/apps/r/data.md new file mode 100644 index 00000000..e327eb66 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/data.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/data.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/r/job.md b/docs/userguides/bell/run/examples/apps/r/job.md new file mode 100644 index 00000000..86129a3d --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/job.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/job.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/r/package.md b/docs/userguides/bell/run/examples/apps/r/package.md new file mode 100644 index 00000000..5a7865b0 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/package.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/package.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/r/rprofile.md b/docs/userguides/bell/run/examples/apps/r/rprofile.md new file mode 100644 index 00000000..653c9d96 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/rprofile.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/rprofile.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/r/rstudio.md b/docs/userguides/bell/run/examples/apps/r/rstudio.md new file mode 100644 index 00000000..b033909a --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/rstudio.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/rstudio.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/r/server.md b/docs/userguides/bell/run/examples/apps/r/server.md new file mode 100644 index 00000000..2a82ace1 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/r/server.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/r/server.md" + +[**Back to the R section**](../r.md) diff --git a/docs/userguides/bell/run/examples/apps/rocmcontainers.md b/docs/userguides/bell/run/examples/apps/rocmcontainers.md new file mode 100644 index 00000000..2fdb61b0 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/rocmcontainers.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/rocmcontainers.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/rocmcontainers/gromacs.md b/docs/userguides/bell/run/examples/apps/rocmcontainers/gromacs.md new file mode 100644 index 00000000..2b315d03 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/rocmcontainers/gromacs.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/rocmcontainers/gromacs.md" + +[**Back to the ROCm Containers Collection section**](../rocmcontainers.md) diff --git a/docs/userguides/bell/run/examples/apps/rocmcontainers/tensorflow.md b/docs/userguides/bell/run/examples/apps/rocmcontainers/tensorflow.md new file mode 100644 index 00000000..aad40e4f --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/rocmcontainers/tensorflow.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/rocmcontainers/tensorflow.md" + +[**Back to the ROCm Containers Collection section**](../rocmcontainers.md) diff --git a/docs/userguides/bell/run/examples/apps/singularity.md b/docs/userguides/bell/run/examples/apps/singularity.md new file mode 100644 index 00000000..8aa354ad --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/singularity.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/singularity.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/spark.md b/docs/userguides/bell/run/examples/apps/spark.md new file mode 100644 index 00000000..3d4d1417 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/spark.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/spark.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/spark/hadoop.md b/docs/userguides/bell/run/examples/apps/spark/hadoop.md new file mode 100644 index 00000000..d11e6783 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/spark/hadoop.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/spark/hadoop.md" + +[**Back to the Spark section**](../spark.md) diff --git a/docs/userguides/bell/run/examples/apps/spark/pbs.md b/docs/userguides/bell/run/examples/apps/spark/pbs.md new file mode 100644 index 00000000..e4a9c635 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/spark/pbs.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/spark/pbs.md" + +[**Back to the Spark section**](../spark.md) diff --git a/docs/userguides/bell/run/examples/apps/windows.md b/docs/userguides/bell/run/examples/apps/windows.md new file mode 100644 index 00000000..fdb720a8 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/windows.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/windows.md" + +[**Back to the Specific Applications section**](../apps.md) diff --git a/docs/userguides/bell/run/examples/apps/windows/cmd.md b/docs/userguides/bell/run/examples/apps/windows/cmd.md new file mode 100644 index 00000000..188592ad --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/windows/cmd.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/windows/cmd.md" + +[**Back to the Windows section**](../windows.md) diff --git a/docs/userguides/bell/run/examples/apps/windows/launcher.md b/docs/userguides/bell/run/examples/apps/windows/launcher.md new file mode 100644 index 00000000..44a37a56 --- /dev/null +++ b/docs/userguides/bell/run/examples/apps/windows/launcher.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/apps/windows/launcher.md" + +[**Back to the Windows section**](../windows.md) diff --git a/docs/userguides/bell/run/examples/hadoop.md b/docs/userguides/bell/run/examples/hadoop.md new file mode 100644 index 00000000..13b9295e --- /dev/null +++ b/docs/userguides/bell/run/examples/hadoop.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Hadoop + +## In This Section + +- [HBase](hadoop/hbase.md) +- [Hive](hadoop/hive.md) +- [Pig](hadoop/pig.md) + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/examples/hadoop/hbase.md b/docs/userguides/bell/run/examples/hadoop/hbase.md new file mode 100644 index 00000000..e38752ee --- /dev/null +++ b/docs/userguides/bell/run/examples/hadoop/hbase.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/hadoop/hbase.md" + +[**Back to the Hadoop section**](../hadoop.md) diff --git a/docs/userguides/bell/run/examples/hadoop/hive.md b/docs/userguides/bell/run/examples/hadoop/hive.md new file mode 100644 index 00000000..c60636e9 --- /dev/null +++ b/docs/userguides/bell/run/examples/hadoop/hive.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/hadoop/hive.md" + +[**Back to the Hadoop section**](../hadoop.md) diff --git a/docs/userguides/bell/run/examples/hadoop/pig.md b/docs/userguides/bell/run/examples/hadoop/pig.md new file mode 100644 index 00000000..e2854f2d --- /dev/null +++ b/docs/userguides/bell/run/examples/hadoop/pig.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/hadoop/pig.md" + +[**Back to the Hadoop section**](../hadoop.md) diff --git a/docs/userguides/bell/run/examples/slurm.md b/docs/userguides/bell/run/examples/slurm.md new file mode 100644 index 00000000..bf731f65 --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm.md @@ -0,0 +1,27 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Generic SLURM Jobs + +The following examples demonstrate the basics of SLURM jobs, and are designed to cover common job request scenarios. These example jobs will need to be modified to run your application or code. + +## In This Section + +- [Simple Job](slurm/batch.md) +- [Multiple Node](slurm/multiple.md) +- [Directives](slurm/directives.md) +- [Specific Types of Nodes](slurm/specific.md) +- [Interactive Jobs](slurm/interactive.md) +- [Serial Jobs](slurm/serial.md) +- [OpenMP](slurm/openmp.md) +- [MPI](slurm/mpi.md) +- [Monitoring Resources](slurm/monitor.md) + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/examples/slurm/batch.md b/docs/userguides/bell/run/examples/slurm/batch.md new file mode 100644 index 00000000..623ce96c --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/batch.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/batch.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/directives.md b/docs/userguides/bell/run/examples/slurm/directives.md new file mode 100644 index 00000000..6227fd2a --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/directives.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/directives.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/interactive.md b/docs/userguides/bell/run/examples/slurm/interactive.md new file mode 100644 index 00000000..9dc5bf74 --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/interactive.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/interactive.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/monitor.md b/docs/userguides/bell/run/examples/slurm/monitor.md new file mode 100644 index 00000000..46f269cd --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/monitor.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/monitor.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/mpi.md b/docs/userguides/bell/run/examples/slurm/mpi.md new file mode 100644 index 00000000..b6b7e260 --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/mpi.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/mpi.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/multiple.md b/docs/userguides/bell/run/examples/slurm/multiple.md new file mode 100644 index 00000000..770b64ac --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/multiple.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/multiple.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/openmp.md b/docs/userguides/bell/run/examples/slurm/openmp.md new file mode 100644 index 00000000..ab597503 --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/openmp.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/openmp.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/serial.md b/docs/userguides/bell/run/examples/slurm/serial.md new file mode 100644 index 00000000..9f2566a2 --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/serial.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/serial.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/examples/slurm/specific.md b/docs/userguides/bell/run/examples/slurm/specific.md new file mode 100644 index 00000000..391731ce --- /dev/null +++ b/docs/userguides/bell/run/examples/slurm/specific.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/examples/slurm/specific.md" + +[**Back to the Generic SLURM Jobs section**](../slurm.md) diff --git a/docs/userguides/bell/run/rosetta/differences.md b/docs/userguides/bell/run/rosetta/differences.md new file mode 100644 index 00000000..2bd52f8d --- /dev/null +++ b/docs/userguides/bell/run/rosetta/differences.md @@ -0,0 +1,33 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Notable Differences + +* **Separate commands for Batch and Interactive jobs** + + Unlike PBS, in Slurm interactive jobs and batch jobs are launched with completely distinct commands. + Use `sbatch [allocation request options] script` to submit a job to the batch scheduler, and `sinteractive [allocation request options]` to launch an interactive job. `sinteractive` accepts most of the same allocation request options as `sbatch` does. + +* **No need for `cd $PBS_O_WORKDIR`** + + In Slurm your batch job starts to run in the directory from which you submitted the script whereas in PBS/Torque you need to explicitly move back to that directory with `cd $PBS_O_WORKDIR`. + +* **No need to manually export environment** + + + The environment variables that are defined in your shell session at the time that you submit the script are exported into your batch job, whereas in PBS/Torque you need to use the `-V` flag to export your environment. + +* **Location of output files** + + The output and error files are created in their final location immediately that the job begins or an error is generated, whereas in PBS/Torque temporary files are created that are only moved to the final location at the end of the job. Therefore in Slurm you can examine the output and error files from your job during its execution. + +See the official [Slurm Documentation](http://slurm.schedmd.com/documentation.html) for further details. + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/rosetta/stone.md b/docs/userguides/bell/run/rosetta/stone.md new file mode 100644 index 00000000..34a80321 --- /dev/null +++ b/docs/userguides/bell/run/rosetta/stone.md @@ -0,0 +1,74 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Quick Guide + +This table lists the most common command, environment variables, and job specification options used by the workload management systems and their equivalents (adapted from ). + +Common commands across workload management systems + +| User Commands | PBS/Torque | Slurm | +| --- | --- | --- | +| Job submission | `qsub [script_file]` | `sbatch [script_file]` | +| Interactive Job | `qsub -I` | `sinteractive` | +| Job deletion | `qdel [job_id]` | `scancel [job_id]` | +| Job status (by job) | `qstat [job_id]` | `squeue [-j job_id]` | +| Job status (by user) | `qstat -u [user_name]` | `squeue [-u user_name]` | +| Job hold | `qhold [job_id]` | `scontrol hold [job_id]` | +| Job release | `qrls [job_id]` | `scontrol release [job_id]` | +| Queue info | `qstat -Q` | `squeue` | +| Queue access | `qlist` | `slist` | +| Node list | `pbsnodes -l` | `sinfo -N` `scontrol show nodes` | +| Cluster status | `qstat -a` | `sinfo` | +| GUI | `xpbsmon` | `sview` | +| Environment | PBS/Torque | Slurm | +| --- | --- | --- | +| Job ID | `$PBS_JOBID` | `$SLURM_JOB_ID` | +| Job Name | `$PBS_JOBNAME` | `$SLURM_JOB_NAME` | +| Job Queue/Account | `$PBS_QUEUE` | `$SLURM_JOB_ACCOUNT` | +| Submit Directory | `$PBS_O_WORKDIR` | `$SLURM_SUBMIT_DIR` | +| Submit Host | `$PBS_O_HOST` | `$SLURM_SUBMIT_HOST` | +| Number of nodes | `$PBS_NUM_NODES` | `$SLURM_JOB_NUM_NODES` | +| Number of Tasks | `$PBS_NP` | `$SLURM_NTASKS` | +| Number of Tasks Per Node | `$PBS_NUM_PPN` | `$SLURM_NTASKS_PER_NODE` | +| Node List (Compact) | n/a | `$SLURM_JOB_NODELIST` | +| Node List (One Core Per Line) | `LIST=$(cat $PBS_NODEFILE)` | `LIST=$(srun hostname)` | +| Job Array Index | `$PBS_ARRAYID` | `$SLURM_ARRAY_TASK_ID` | +| Job Specification | PBS/Torque | Slurm | +| --- | --- | --- | +| Script directive | `#PBS` | `#SBATCH` | +| Queue | `-q [queue]` | `-A [queue]` | +| Node Count | `-l nodes=[count]` | `-N [min[-max]]` | +| CPU Count | `-l ppn=[count]` | `-n [count]` Note: total, not per node | +| Wall Clock Limit | `-l walltime=[hh:mm:ss]` | `-t [min]` OR `-t [hh:mm:ss]` OR `-t [days-hh:mm:ss]` | +| Standard Output FIle | `-o [file_name]` | `-o [file_name]` | +| Standard Error File | `-e [file_name]` | `-e [file_name]` | +| Combine stdout/err | `-j oe` (both to stdout) OR `-j eo` (both to stderr) | `(use -o without -e)` | +| Copy Environment | `-V` | `--export=[ALL | NONE | variables]` Note: default behavior is `ALL` | +| Copy Specific Environment Variable | `-v myvar=somevalue` | `--export=NONE,myvar=somevalue` OR `--export=ALL,myvar=somevalue` | +| Event Notification | `-m abe` | `--mail-type=[events]` | +| Email Address | `-M [address]` | `--mail-user=[address]` | +| Job Name | `-N [name]` | `--job-name=[name]` | +| Job Restart | `-r [y|n]` | `--requeue` OR `--no-requeue` | +| Working Directory | | `--workdir=[dir_name]` | +| Resource Sharing | `-l naccesspolicy=singlejob` | `--exclusive` OR `--shared` | +| Memory Size | `-l mem=[MB]` | `--mem=[mem][M|G|T]` OR `--mem-per-cpu=[mem][M|G|T]` | +| Account to charge | `-A [account]` | `-A [account]` | +| Tasks Per Node | `-l ppn=[count]` | `--tasks-per-node=[count]` | +| CPUs Per Task | | `--cpus-per-task=[count]` | +| Job Dependency | `-W depend=[state:job_id]` | `--depend=[state:job_id]` | +| Job Arrays | `-t [array_spec]` | `--array=[array_spec]` | +| Generic Resources | `-l other=[resource_spec]` | `--gres=[resource_spec]` | +| Licenses | | `--licenses=[license_spec]` | +| Begin Time | `-A "y-m-d h:m:s"` | `--begin=y-m-d[Th:m[:s]]` | + +See the official [Slurm Documentation](http://slurm.schedmd.com/documentation.html) for further details. + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/cancelling_job.md b/docs/userguides/bell/run/slurm/cancelling_job.md new file mode 100644 index 00000000..ee32958e --- /dev/null +++ b/docs/userguides/bell/run/slurm/cancelling_job.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/cancelling_job.md" + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/checking_output.md b/docs/userguides/bell/run/slurm/checking_output.md new file mode 100644 index 00000000..5bbe2d30 --- /dev/null +++ b/docs/userguides/bell/run/slurm/checking_output.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/checking_output.md" + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/creating_the_submission_script.md b/docs/userguides/bell/run/slurm/creating_the_submission_script.md new file mode 100644 index 00000000..d188adb4 --- /dev/null +++ b/docs/userguides/bell/run/slurm/creating_the_submission_script.md @@ -0,0 +1,45 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Job Submission Script + +To submit work to a SLURM queue, you must first create a *job submission file*. This job submission file is essentially a simple shell script. It will set any required environment variables, load any necessary modules, create or modify files and directories, and run any applications that you need: + +``` +#!/bin/bash +# FILENAME: myjobsubmissionfile + +# Loads Matlab and sets the application up +module load matlab + +# Change to the directory from which you originally submitted this job. +cd $SLURM_SUBMIT_DIR + +# Runs a Matlab script named 'myscript' +matlab -nodisplay -singleCompThread -r myscript +``` + +Once your script is prepared, you are ready to [submit your job](submit_script.md). + +## Job Script Environment Variables + +SLURM sets several potentially useful environment variables which you may use within your job submission files. Here is a list of some: + +| Name | Description | +| --- | --- | +| SLURM\_SUBMIT\_DIR | Absolute path of the current working directory when you submitted this job | +| SLURM\_JOBID | Job ID number assigned to this job by the batch system | +| SLURM\_JOB\_NAME | Job name supplied by the user | +| SLURM\_JOB\_NODELIST | Names of nodes assigned to this job | +| SLURM\_CLUSTER\_NAME | Name of the cluster executing the job | +| SLURM\_SUBMIT\_HOST | Hostname of the system where you submitted this job | +| SLURM\_JOB\_PARTITION | Name of the original queue to which you submitted this job | + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/holding_job.md b/docs/userguides/bell/run/slurm/holding_job.md new file mode 100644 index 00000000..c2e2f280 --- /dev/null +++ b/docs/userguides/bell/run/slurm/holding_job.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/holding_job.md" + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/job_dependencies.md b/docs/userguides/bell/run/slurm/job_dependencies.md new file mode 100644 index 00000000..ba4c2b0f --- /dev/null +++ b/docs/userguides/bell/run/slurm/job_dependencies.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/job_dependencies.md" + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/monitoring_job.md b/docs/userguides/bell/run/slurm/monitoring_job.md new file mode 100644 index 00000000..f3e91924 --- /dev/null +++ b/docs/userguides/bell/run/slurm/monitoring_job.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/monitoring_job.md" + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/queues.md b/docs/userguides/bell/run/slurm/queues.md new file mode 100644 index 00000000..7ee221be --- /dev/null +++ b/docs/userguides/bell/run/slurm/queues.md @@ -0,0 +1,125 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Queues + +On Bell, the required options for job submission deviates from some of the other community clusters you might have experience using. In general every job submission will have four parts: “`sbatch --ntasks=1 --cpus-per-task=4 --partition=cpu --account=rcac --qos=standby`” + +1. The number and type of resources you want (`--ntasks=1 --cores-per-task=4`) +2. The partition where the resources are located (`--partition=cpu`) +3. The account the resources should come out of ( `--account=rcac`) +4. The quality of service (QOS) this job expects from the resources (`--qos=standby`) + +Table Summary of Changes + +| Use Case | Old Syntax | New Syntax | +| --- | --- | --- | +| Submit a job to your group's account | `sbatch -A mygroup` | `sbatch -A mygroup -p cpu` | +| Submit a standby job | `sbatch -A standby` | `sbatch -A mygroup -p cpu -q standby` | +| Submit a highmem job | `sbatch -A highmem` | `sbatch -A mygroup -p highmem` | +| Submit a gpu job | `sbatch -A gpu` | `sbatch -A mygroup -p gpu` | +| Submit a multigpu job | `sbatch -A multigpu` | `sbatch -A mygroup -p multigpu` | + +If you have used other clusters, you will be familiar with the first item. If you have not, you can read about how to format the request [on our job submission page.](submit_script.md) The rest of this page will focus on the last three items. + +## Partitions + +On Bell, the various types of nodes on the cluster are organized into distinct partitions. This allows jobs to different node types to be charged separately and differently. This also means that Instead of only needing to specify the account name in the job script, the desired partition must also be specified. Each of these partitions is subject to different limitations and has a specific use case that will be described below.  + +### CPU Partition + +This partition contains the resources a group purchases access to when they purchase CPU resources on Bell and is made up of 488 Bell-A nodes. Each of these nodes contains two Zen 2 AMD EPYC 7662 64-core processors for a total of 128 cores and 256 GB of memory for a total of more than 62,000 cores in the partition. Memory in this partition is allocated proportional to your core request such that each core is given about 2 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p cpu` or `--partition=cpu`. + +The purchasing model for this partition allows groups to purchase high priority access to some number of cores. When an account uses resources in this account by submitting a job tagged with the `normal` QOS, the cores used by that job are withdrawn from the account and deposited back into the account when the job terminates. + +When using the CPU partition, jobs are tagged by the `normal` QOS by default, but they can be tagged with the `standby` QOS if explicitly submitted using the `-q standby` or `--qos=standby` option. + +1. Jobs tagged with the `normal` QOS are subject to the following policies: + 1. Jobs have a high priority and should not need to wait very long before starting. + 2. Any cores requested by these jobs are withdrawn from the account until the job terminates. + 3. These jobs can run for up to two weeks at a time. +2. Jobs tagged with the `standby` QOS are subject to the following policies: + 1. Jobs have a low priority and there is no expectation of job start time. If the partition is very busy with jobs using the `normal` QOS or if you are requesting a very large job, then jobs using the `standby` QOS may take hours or days to start. + 2. These jobs can use idle resources on the cluster and as such cores requested by these jobs are not withdrawn from the account to which they were submitted. + 3. These jobs can run for up to four hours at a time. + +Available QOSes: `normal`, `standby` + +### Highmem Partition + +This partition is made up of 8 Bell-B nodes which have four times as much memory as a standard Bell-A node, and access to this partition is given to all accounts on the cluster to enable work that has higher memory requirements. Each of these nodes contains two Zen 2 AMD EPYC 7662 64-core processors for a total of 128 cores and 1 TB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 8 GB of memory per core requested. Submission to this partition can be accomplished by using the option: `-p highmem` or `--partition=highmem`. + +When using the Highmem partition, jobs are tagged by the `normal` QOS by default, and this is the only QOS that is available for this partition, so there is no need to specify a QOS when using this partition. Additionally jobs are tagged by a highmem partition QOS that enforces the following policies + +1. There is no expectation of job start time as these nodes are a shared resources that are given as a bonus for purchasing access to high priority access to resources on Bell +2. You can have 2 jobs running in this partition at once +3. You can have 8 jobs submitted to thie partition at once +4. Your jobs must use more than 64 of the 128 cores on the node otherwise your memory footprint would fit on a standard Bell-A node +5. These jobs can run for up to 24 hours at a time. + +Available QOSes: `normal` + +### GPU Partition + +This partition is made up of 4 Bell-G nodes. Each of these nodes contains two AMD MI50s and two Zen 2 AMD EPYC 7662 64-core processors for a total of 128 cores and 256GB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 3 GB of memory per core requested. You should request cores proportional to the number of GPUs you are using in this partition (i.e. if you only need one of the two GPUs, you should request half of the cores on the node) Submission to this partition can be accomplished by using the option: `-p gpu` or `--partition=gpu`. + +When using the gpu partition, jobs are tagged by the `normal` QOS by default, and this is the only QOS that is available for this partition, so there is no need to specify a QOS when using this partition. Additionally jobs are tagged by a gpu partition QOS that enforces the following policies + +1. There is no expectation of job start time as these nodes are a shared resources that are given as a bonus for purchasing access to high priority access to resources on Bell +2. You can use up to 2 GPUs in this partition at once +3. You can have 8 jobs submitted to thie partition at once +4. These jobs can run for up to 24 hours at a time. + +Available QOSes: `normal` + +### Multi-GPU Partition + +This partition is made up of a single Bell-X node. Each of these nodes contains six AMD MI60s and two Intel Xeon 8268 48-core processors for a total of 96 cores and 354GB of memory. Memory in this partition is allocated proportional to your core request such that each core is given about 3.5 GB of memory per core requested. You should request cores proportional to the number of GPUs you are using in this partition (i.e. if you only need one of the six GPUs, you should request 16 of the cores on the node) Submission to this partition can be accomplished by using the option: `-p multigpu` or `--partition=multigpu`. + +When using the gpu partition, jobs are tagged by the `normal` QOS by default, and this is the only QOS that is available for this partition, so there is no need to specify a QOS when using this partition. Additionally jobs are tagged by a multigpu partition QOS that enforces the following policies + +1. There is no expectation of job start time as these nodes are a shared resources that are given as a bonus for purchasing access to high priority access to resources on Bell +2. You can use up to 6 GPUs in this partition at once +3. You can have 1 jobs submitted to thie partition at once +4. These jobs can run for up to 24 hours at a time. + +Available QOSes: `normal` + +## Accounts + +On the Bell community cluster, users will have access to one or more accounts, also known as queues. These accounts are dedicated to and named after each partner who has purchased access to the cluster, and they provide partners and their researchers with priority access to their portion of the cluster. These accounts can be thought of as bank accounts that contain the resources a group has purchased access to which may include some number of cores. To see the list of accounts that you have access to on Bell as well as the resources they contain, you can use the command `slist`. + +On Bell, you must explicitly define the account that you want to submit to using the `-A`or`--account=` option. + +## Quality of Service (QOS) + +On Bell, we use a Slurm concept called a Quality of Service or a QOS. A QOS can be thought of as a tag for a job that tells the scheduler how that job should be treated with respect to limits, priority, etc. The cluster administrators define the available QOSes as well as the policies for how each QOS should be treated on the cluster. A toy example of such a policy may be "no single user can have more than 200 jobs that has been tagged with a QOS named *highpriority*". + +There are two classes of QOSes and a job can have both: + +1. Partition QOSes: A partition QOS is a tag that is automatically added to your job when you submit to a partition that defines a partition QOS. +2. Job QOSes: A Job QOS is a tag that you explicitly give to a job using the option `-q`or`--qos=`. By explicitly tagging your jobs this way, you can choose the policy that each one of your jobs should abide by. We will describe the policies for the available job QOSes in the partition section below. + +As an extended metaphor, if we think of a job as a package that we need to have shipped to some destination, then the partition can be thought of as the carrier we decide to ship our package with. That carrier is going to have some company policies that dictate how you need to label/pack that package, and that company policy is like the partition QOS. It is the policy that is enforced for simply deciding to use that carrier, or in this case, deciding to submit to a particular partition. + +The Job QOS can then be thought of as the various different types of shipping options that carrier might offer. You might pay extra to have that package shipped overnight. On the other hand you may choose to pay less and have your package arrive as available. Once we decide to go with a particular carrier, we are subject to their company policy, but we also have some degree of control through choosing one of their available shipping options. In the same way, when you choose to submit to a partition, you are subject to the limits enforced by the partition QOS, but you may be able to ask for your job to be handled a particular way by specifying a job QOS offered by the partition. + +In order for a job to use a Job QOS, the user submitting the job must have access to the QOS, the account the job is being submitted to must accept the QOS, and the partition the job is being submitted to must accept the QOS. The below list of job QOSes are QOSes that every user and every account of Bell has access to: + +1. `normal`: The `normal` QOS is the default job QOS on the cluster meaning if you do not explicitly list an alternative job QOS, your job will be tagged with this QOS. The policy for this QOS provides a high priority and does not add any additional limits. +2. `standby`: The `standby` QOS must be explicitly used if desired by using the option `-q standby` or `--qos=standby`. The policy for this QOS gives access to idle resources on the cluster. Jobs tagged with this QOS are "low priority" jobs and are only allowed to run for up to four hours at a time, however the resources used by these jobs do not count against the resources in your Account. For users of our previous clusters, usage of this QOS replaces the previous `-A standby` style of submission. + +Some of these QOSes may not be available in every partition. Each of the partitions in the following section will enumerate which of these QOSes are allowed in the partition. + +## In This Section + +- [Job Submission Matrix](queues/job-submission-matrix.md) + +[**Back to the Running Jobs section**](../../run.md) diff --git a/docs/userguides/bell/run/slurm/queues/job-submission-matrix.md b/docs/userguides/bell/run/slurm/queues/job-submission-matrix.md new file mode 100644 index 00000000..09d49bc9 --- /dev/null +++ b/docs/userguides/bell/run/slurm/queues/job-submission-matrix.md @@ -0,0 +1,24 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Job Submission Matrix + +| Job Type | Partition | QoS | Job Submission Options | Number of Cores Per Account | Number of Jobs Per Account | Priority Accrual | Max Walltime | +| --- | --- | --- | --- | --- | --- | --- | --- | +| PI Queue | cpu | normal | `-A "mygroup" -p cpu` | Limited to purchased cores | No limit | No Limit | 2 weeks | +| Standby Job | cpu | standby | `-A "mygroup" -p cpu -q standby` | 15360 Cores | 5000 | No Limit | 4 hours | +| Highmem Job | highmem | normal | `-A "mygroup" -p highmem` | 128 Cores | 2 | 1 | 24 hours | +| GPU Job | gpu | normal | `-A "mygroup" -p gpu` | 128 cores | 1 | 1 | 24 hours | +| Multi GPU Job | multigpu | normal | `-A "mygroup" -p multigpu` | 48 cores | 1 | 1 | 24 hours | + +!!! Note + The normal QOS is the default and does not need to be specified. + +[**Back to the Queues section**](../queues.md) diff --git a/docs/userguides/bell/run/slurm/submit_script.md b/docs/userguides/bell/run/slurm/submit_script.md new file mode 100644 index 00000000..af0e703d --- /dev/null +++ b/docs/userguides/bell/run/slurm/submit_script.md @@ -0,0 +1,109 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Submitting a Job + +Once you have a [job submission file](creating_the_submission_script.md), you may submit this script to SLURM using the `sbatch` command. SLURM will find, or wait for, available resources matching your request and run your job there. + + +​On Bell, in order to submit jobs, you need to specify the partition, account and Quality of Service (QoS) name to which you want to submit your jobs. To familiarize yourself with the partitions and QoS available on Bell, visit [Bell Queues and Partitions](queues.md). To check the available partitions on Bell, you can use the `showpartitions` , and to check your available accounts you can use `slist` commands. Slurm uses the term "Account" with the option `-A` or `--account=` to specify different batch accounts, the option `-p` or `--partition=` to select a specific partition for job submission, and the option `-q` or `--qos=` . + +``` +Partition statistics for cluster bell at Wed Jul 30 13:07:27 EDT 2025 + Partition #Nodes #CPU_cores Cores_pending Job_Nodes MaxJobTime Cores Mem/Node + Name State Total Idle Total Idle Resorc Other Min Max Day-hr:mn /node (GB) +bell-nodes up$ 488 476 62464 61376 0 0 1 infin infinite 128 257+ + cpu up 480 476 61440 60928 0 0 1 infin infinite 128 257 + highmem up$ 8 0 1024 448 0 0 1 infin infinite 128 1031 + gpu up$ 4 0 512 512 0 0 1 infin infinite 128 257 + multigpu up$ 1 0 48 48 0 0 1 infin infinite 48 353 +``` + +## CPU Partition + +The CPU partition on Bell has two Quality of Service (QoS) levels: **normal** and **standby**. To submit your job to one compute node on `cpu` partition and 'normal' QoS which has "high priority": + +``` +$ sbatch --nodes=1 --ntasks=1 --partition=cpu --account=accountname --qos=normal myjobsubmissionfile +$ sbatch -N1 -n1 -p cpu -A accountname -q normal myjobsubmissionfile +``` + + To submit your job to one compute node on `cpu` partition and 'standby' QoS which is has "low priority": + +``` +$ sbatch --nodes=1 --ntasks=1 --partition=cpu --account=accountname --qos=standby myjobsubmissionfile +$ sbatch -N1 -n1 -p cpu -A accountname -q standby myjobsubmissionfile +``` + +## GPU Partition + +On the GPU partition on **Bell** you don’t need to specify the QoS name because only one QoS exists for this partition, and the default is **normal**. To submit your job to one compute node requesting one GPU on the `gpu` partition under the 'normal' QoS which has "high priority": + +``` +$ sbatch --nodes=1 --gpus-per-node=1 --ntasks=1 --cpus-per-task=64 --partition=gpu --account=accountname myjobsubmissionfile +$ sbatch -N1 --gpus-per-node=1 -n1 -c64 -p gpu -A accountname -q normal myjobsubmissionfile +``` + +## Highmem Partition + +To submit your job to a compute node in the highmem partition, you don’t need to specify the QoS name because only one QoS exists for this partition, and the default is **normal**. However, the **highmem** partition is *only* suitable for jobs with memory requirements that exceed the capacity of a standard node, so the number of requested tasks should be appropriately high. + +``` +$ sbatch --nodes=1 --ntasks=1 --cpus-per-task=64 --partition=highmem --account=accountname myjobsubmissionfile +$ sbatch -N1 -n1 -c64 -p highmem -A accountname myjobsubmissionfile +``` + +## General Information + +By default, each job receives 30 minutes of *wall time*, or clock time. If you know that your job will not need more than a certain amount of time to run, request less than the maximum wall time, as this may allow your job to run sooner. To request 1 hour and 30 minutes of wall time: + +``` +$ sbatch -t 01:30:00 -N=1 -n=1 -p=cpu -A=accountname -q=standby myjobsubmissionfile +``` + +The `--nodes=` or `-N` value indicates how many compute nodes you would like for your job, and `--ntasks=` or `-n` value indicates the number of tasks you want to run. + +In some cases, you may want to request multiple nodes. To utilize multiple nodes, you will need to have a program or code that is specifically programmed to use multiple nodes such as with MPI. Simply requesting more nodes will not make your work go faster. Your code must support this ability. + +To request 2 compute nodes: + +``` +$ sbatch -t 01:30:00 -N=2 -n=16 -p=cpu -A=accountname -q=standby myjobsubmissionfile +``` + +By default, jobs on Bell will share nodes with other jobs. + +If more convenient, you may also specify any command line options to `sbatch` from within your job submission file, using a special form of comment: + +``` +#!/bin/sh -l +# FILENAME: myjobsubmissionfile + +#SBATCH --account=accountname +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --partition=cpu +#SBATCH --qos=normal +#SBATCH --time=1:30:00 +#SBATCH --job-name myjobname + +# Print the hostname of the compute node on which this job is running. +/bin/hostname +``` + +If an option is present in both your job submission file and on the command line, the option on the command line will take precedence. + +After you submit your job with `SBATCH`, it may wait in queue for minutes, hours, or even weeks. How long it takes for a job to start depends on the specific queue, the resources and time requested, and other jobs already waiting in that queue requested as well. It is impossible to say for sure when any given job will start. For best results, request no more resources than your job requires. + +Once your job is submitted, you can [monitor the job status](monitoring_job.md), wait for the job to complete, and [check the job output](checking_output.md). + +[**Back to the Running Jobs section**](../../run.md) + +​ diff --git a/docs/userguides/bell/software.md b/docs/userguides/bell/software.md new file mode 100644 index 00000000..62f7f40b --- /dev/null +++ b/docs/userguides/bell/software.md @@ -0,0 +1,69 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Software + +## Software Catalog + +A comprehensive list of centrally installed software applications can be found here: + +[Software Catalog](../../software/app_catalog.md) + +Software can also be explored by popular domains and categories on the main [Software](../../software/index.md) page. + +## Module system + +{% set resource = "bell" %} + +{{ module_system(resource) }} + +## Running the Apps +### Find available apps in the terminal +In addition to searching the software catalog for available applications, one can generate a list via the terminal: + +``` bash +$ module avail +---------------------- Core Applications --------------------- + amduprof/5.1.701 hypershell/2.5.2 ngc/default + anaconda/2024.10-py312 hypershell/2.6.5 oclfpga/2024.1.0 + anaconda/2025.06-py313 (D) hypershell/2.7.0 (D) openblas/0.3.27 +[MORE...] +``` +### View module prequisites and license information +After finding the module that you want to load, use 'module spider' to find any prerequisites or license information, if applicable: + +``` bash +$ module spider hypershell + +------------------------------------------------------------- + hypershell: +------------------------------------------------------------- + Description: + A cross-platform, high-throughput computing utility for processing shell commands over a + distributed, asynchronous queue. + + Versions: + hypershell/2.5.2 + hypershell/2.6.5 + hypershell/2.7.0 + + +``` +### Load the module +Use the command specified in the 'module spider' output to load your software module: + +``` bash +module load hypershell/2.7.0 +``` + +### Running GUI versions of apps +If the app you want to use has a GUI, you can also login to {{ resource }} via Thinlinc. More information on this process can be found [here](accounts.md#thinlinc). + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/storage.md b/docs/userguides/bell/storage.md new file mode 100644 index 00000000..00736cc2 --- /dev/null +++ b/docs/userguides/bell/storage.md @@ -0,0 +1,25 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# File Storage and Transfer + +Learn more about file storage transfer for Bell. + +## In This Section + +- [Archive and Compression](storage/archive_and_compression.md) +- [Storage Environment Variables](storage/env.md) +- [Storage Options](storage/options.md) +- [Storage Quota / Limits](storage/quota.md) +- [Sharing](storage/sharing.md) +- [File Transfer](storage/transfer.md) +- [Lost File Recovery](storage/recover.md) + +[**Back to Bell User Guide**](index.md) diff --git a/docs/userguides/bell/storage/archive_and_compression.md b/docs/userguides/bell/storage/archive_and_compression.md new file mode 100644 index 00000000..7a99478c --- /dev/null +++ b/docs/userguides/bell/storage/archive_and_compression.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/archive_and_compression.md" + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/env.md b/docs/userguides/bell/storage/env.md new file mode 100644 index 00000000..971a1ccd --- /dev/null +++ b/docs/userguides/bell/storage/env.md @@ -0,0 +1,62 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Storage Environment Variables + +Several environment variables are automatically defined for you to help you manage your storage. Use environment variables instead of actual paths whenever possible to avoid problems if the specific paths to any of these change. + +Some of the environment variables you should have are: + +| Name | Description | +| --- | --- | +| HOME | /home/myusername | +| PWD | path to your current directory | +| RCAC\_SCRATCH | /scratch/bell/myusername | + +By convention, environment variable names are all uppercase. You may use them on the command line or in any scripts in place of and in combination with hard-coded values: + +``` +$ ls $HOME +... + +$ ls $RCAC_SCRATCH/myproject +... +``` + +To find the value of any environment variable: + +``` +$ echo $RCAC_SCRATCH +/scratch/bell/myusername +``` + +To list the values of all environment variables: + +``` +$ env +USER=myusername +HOME=/home/myusername +RCAC_SCRATCH=/scratch/bell/myusername +... +``` + +You may create or overwrite an environment variable. To pass (export) the value of a variable in bash: + +``` +$ export MYPROJECT=$RCAC_SCRATCH/myproject +``` + +To assign a value to an environment variable in either tcsh or csh: + +``` +$ setenv MYPROJECT value +``` + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/options.md b/docs/userguides/bell/storage/options.md new file mode 100644 index 00000000..45751eff --- /dev/null +++ b/docs/userguides/bell/storage/options.md @@ -0,0 +1,22 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Storage Options + + File storage options on RCAC systems include long-term storage (home directories, depot, Fortress) and short-term storage (scratch directories, /tmp directory). Each option has different performance and intended uses, and some options vary from system to system as well. Daily snapshots of home directories are provided for a limited time for accidental deletion recovery. Scratch directories and temporary storage are not backed up and old files are regularly purged from scratch and /tmp directories. More details about each storage option appear below. + +## In This Section + +- [Home Directory](options/home_directory.md) +- [Long-Term Storage](options/long_term_storage.md) +- [Scratch Space](options/scratch.md) +- [/tmp Directory](options/tmp_directory.md) + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/options/home_directory.md b/docs/userguides/bell/storage/options/home_directory.md new file mode 100644 index 00000000..2d012911 --- /dev/null +++ b/docs/userguides/bell/storage/options/home_directory.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/home_directory.md" + +[**Back to the Storage Options section**](../options.md) diff --git a/docs/userguides/bell/storage/options/long_term_storage.md b/docs/userguides/bell/storage/options/long_term_storage.md new file mode 100644 index 00000000..b8c5e3cf --- /dev/null +++ b/docs/userguides/bell/storage/options/long_term_storage.md @@ -0,0 +1,13 @@ +--- +tags: + - Gautschi +authors: + - jin456 +resource: Gautschi +search: + boost: 2 +--- + +--8<-- "docs/snippets/long_term_storage.md" + +[**Back to the Storage Options section**](../options.md) diff --git a/docs/userguides/bell/storage/options/scratch.md b/docs/userguides/bell/storage/options/scratch.md new file mode 100644 index 00000000..36e429cb --- /dev/null +++ b/docs/userguides/bell/storage/options/scratch.md @@ -0,0 +1,46 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Scratch Space + + +*Scratch directories* are provided for short-term file storage only. The quota of your scratch directory is much greater than the quota of your home directory. You should use your scratch directory for storing temporary input files which your job reads or for writing temporary output files which you may examine after execution of your job. You should use your home directory and Fortress for longer-term storage or for holding critical results. The `hsi` and `htar` commands provide easy-to-use interfaces into the archive and can be used to copy files into the archive interactively or even automatically at the end of your regular job submission scripts. + +!!! Warning + Files in scratch directories are not recoverable. Files in scratch directories are not backed up. If you accidentally delete a file, a disk crashes, or old files are purged, they cannot be restored. + +**Files are purged from scratch directories not accessed or had content modified in 30 days.** Owners of these files receive a notice one week before removal via email. Be sure to regularly check your Purdue email account or [set up mail forwarding](https://www.purdue.edu/apps/account/ChangeMailbox) to an email account you do regularly check. For more information, please refer to our [Scratch File Purging Policy](https://www.rcac.purdue.edu/policies/scratchpurge). + + +All users may access scratch directories on Bell. To find the path to your scratch directory: + +``` +$ findscratch +/scratch/bell/myusername +``` + +The value of variable $RCAC\_SCRATCH is your scratch directory path. Use this variable in any scripts. Your actual scratch directory path may change without warning, but this variable will remain current. + +``` +$ echo $RCAC_SCRATCH +/scratch/bell/myusername +``` + +!!! Note + Scratch directories are specific per cluster. I.e. only the /scratch/bell directory is available on Bell front-end and compute nodes. No other scratch directories are available on Bell. + + +**Your scratch directory has a quota capping the total size and number of files you may store in it.** For more information, refer to the section [Storage Quotas / Limits](../quota.md). + +## Performance + +Your scratch directory is located on a high-performance, large-capacity parallel filesystem engineered to provide work-area storage optimized for a wide variety of job types. It is designed to perform well with data-intensive computations, while scaling well to large numbers of simultaneous connections. + +[**Back to the Storage Options section**](../options.md) diff --git a/docs/userguides/bell/storage/options/tmp_directory.md b/docs/userguides/bell/storage/options/tmp_directory.md new file mode 100644 index 00000000..65f6bf39 --- /dev/null +++ b/docs/userguides/bell/storage/options/tmp_directory.md @@ -0,0 +1,13 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +--8<-- "docs/snippets/temp_directory.md" + +[**Back to the Storage Options section**](../options.md) diff --git a/docs/userguides/bell/storage/quota.md b/docs/userguides/bell/storage/quota.md new file mode 100644 index 00000000..b197bdf9 --- /dev/null +++ b/docs/userguides/bell/storage/quota.md @@ -0,0 +1,72 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Storage Quota / Limits + +Some limits are imposed on your disk usage on research systems. A quota is implemented on each filesystem. Each filesystem (home directory, scratch directory, etc.) may have a different limit. If you exceed the quota, you will not be able to save new files or new data to the filesystem until you delete or move data to long-term storage. + +## Checking Quota + +To check the current quotas of your home and scratch directories check the [My Quota](https://www.rcac.purdue.edu/account/myquota) page or use the `myquota` command: + +``` +$ myquota +Type Filesystem Size Limit Use Files Limit Use +============================================================================== +home myusername 5.0GB 25.0GB 20% - - - +scratch bell 220.7GB 100.0TB 0.22% 8k 2,000k 0.43% +``` + +The columns are as follows: + +* Type: indicates home or scratch directory or your depot space. +* Filesystem: name of storage option. +* Size: sum of file sizes in bytes. +* Limit: allowed maximum on sum of file sizes in bytes. +* Use: percentage of file-size limit currently in use. +* Files: number of files and directories (not the size). +* Limit: allowed maximum on number of files and directories. It is possible, though unlikely, to reach this limit and not the file-size limit if you create a large number of very small files. +* Use: percentage of file-number limit currently in use. + +If you find that you reached your quota in either your home directory or your scratch file directory, obtain estimates of your disk usage. Find the top-level directories which have a high disk usage, then study the subdirectories to discover where the heaviest usage lies. + +To see in a human-readable format an estimate of the disk usage of your top-level directories in your home directory: + +``` +$ du -h --max-depth=1 $HOME >myfile +32K /home/myusername/mysubdirectory_1 +529M /home/myusername/mysubdirectory_2 +608K /home/myusername/mysubdirectory_3 +``` + +The second directory is the largest of the three, so apply command `du` to it. + +To see in a human-readable format an estimate of the disk usage of your top-level directories in your scratch file directory: + +``` +$ du -h --max-depth=1 $RCAC_SCRATCH >myfile +160K /scratch/bell/myusername +``` + +This strategy can be very helpful in figuring out the location of your largest usage. Move unneeded files and directories to long-term storage to free space in your home and scratch directories. + +## Increasing Quota + +### Home Directory + + +If you find you need additional disk space in your home directory, please consider archiving and compressing old files and moving them to long-term storage on the [Fortress HPSS Archive](https://www.rcac.purdue.edu/storage/fortress), or purchase the [Depot](https://www.rcac.purdue.edu/storage/depot) space for long-term storage. Unfortunately, it is not possible to increase your home directory quota beyond it's current level. + +### Scratch Space + + +If you find you need additional disk space in your scratch space, please first consider archiving and compressing old files and moving them to long-term storage on the [Fortress HPSS Archive](https://www.rcac.purdue.edu/storage/fortress). If you are unable to do so, you may ask for a quota increase by [contacting support](https://www.rcac.purdue.edu/help). + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/recover.md b/docs/userguides/bell/storage/recover.md new file mode 100644 index 00000000..8695fde2 --- /dev/null +++ b/docs/userguides/bell/storage/recover.md @@ -0,0 +1,31 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Lost File Recovery + +Bell is protected against accidental file deletion through a series of snapshots taken every night just after midnight. Each snapshot provides the state of your files at the time the snapshot was taken. It does so by storing only the files which have changed between snapshots. A file that has not changed between snapshots is only stored once but will appear in every snapshot. This is an efficient method of providing snapshots because the snapshot system does not have to store multiple copies of every file. + +These snapshots are kept for a limited time at various intervals. RCAC keeps nightly snapshots for 7 days, weekly snapshots for 4 weeks, and monthly snapshots for 3 months. This means you will find snapshots from the last 7 nights, the last 4 Sundays, and the last 3 first of the months. Files are available going back between two and three months, depending on how long ago the last first of the month was. Snapshots beyond this are not kept. + +**Only files which have been saved during an overnight snapshot are recoverable.** If you lose a file the same day you created it, the file is **not** recoverable because the snapshot system has not had a chance to save the file. + +**Snapshots are not a substitute for regular backups.** It is the responsibility of the researchers to back up any important data to the [Fortress Archive](https://www.rcac.purdue.edu/storage/fortress). Bell **does** protect against hardware failures or physical disasters through other means however these other means are also **not** substitutes for backups. + +!!! Warning + Files in scratch directories are not recoverable. Files in scratch directories are not backed up. If you accidentally delete a file, a disk crashes, or old files are purged, they cannot be restored. + +Bell offers several ways for researchers to access snapshots of their files. + +- [flost](recover/flost.md) +- [Manual Browsing](recover/manual.md) +- [Windows](recover/windows.md) +- [Mac OS X](recover/mac.md) + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/recover/flost.md b/docs/userguides/bell/storage/recover/flost.md new file mode 100644 index 00000000..1c3d7a23 --- /dev/null +++ b/docs/userguides/bell/storage/recover/flost.md @@ -0,0 +1,28 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# flost + +If you know when you lost the file, the easiest way is to use the `flost` command. This tool is available from any RCAC resource. If you do not have access to a compute cluster, any Data Depot user may use an SSH client to connect to `bell.rcac.purdue.edu` and run this command. + +To run the tool you will need to specify the location where the lost file was with the `-w` argument: + +``` +$ flost -w /depot/mylab +``` + +Replace `mylab` with the name of your lab's Bell directory. If you know more specifically where the lost file was you may provide the full path to that directory. + +This tool will prompt you for the date on which you lost the file or would like to recover the file from. If the tool finds an appropriate snapshot it will provide instructions on how to search for and recover the file. + + +If you are not sure what date you lost the file you may try entering different dates into the `flost` to try to find the file or you may also [manually browse](manual.md) the snapshots as described below. + +[**Back to the Lost File Recovery section**](../recover.md) diff --git a/docs/userguides/bell/storage/recover/mac.md b/docs/userguides/bell/storage/recover/mac.md new file mode 100644 index 00000000..5dd6dbb7 --- /dev/null +++ b/docs/userguides/bell/storage/recover/mac.md @@ -0,0 +1,35 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Mac OS X + +Mac OS X does not provide any way to access the Bell snapshots directly. To access the snapshots there are two options: browse the snapshots by hand through a network drive mount or use an automated command-line based tool. + + +To browse the snapshots by hand, follow the directions outlined in the [Manual Browsing](manual.md) section. + +To use the automated command-line tool, log into a compute cluster or into the host `bell.rcac.purdue.edu` (which is available to all Bell users) and use the [flost](flost.md) tool. On Mac OS X you can use the built-in SSH terminal application to connect. + + +* Open the Applications folder from Finder. +* Navigate to the Utilities folder. +* Double click the Terminal application to open it. +* Type the following command when the terminal opens. + + ``` + $ ssh myusername@bell.rcac.purdue.edu + ``` + + Replace `myusername` with your Purdue career account username and provide your password when prompted. + + +Once logged in use the [flost](flost.md) tool as described above. The tool will guide you through the process and show you the commands necessary to retrieve your lost file. + +[**Back to the Lost File Recovery section**](../recover.md) diff --git a/docs/userguides/bell/storage/recover/manual.md b/docs/userguides/bell/storage/recover/manual.md new file mode 100644 index 00000000..5c8fafcd --- /dev/null +++ b/docs/userguides/bell/storage/recover/manual.md @@ -0,0 +1,68 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Manual Browsing + +You may also search through the snapshots by hand on the Bell filesystem if you are not sure what date you lost the file or would like to browse by hand. Snapshots can be browsed from any RCAC resource. If you do not have access to a compute cluster, any Bell user may use an SSH client to connect to `bell.rcac.purdue.edu` and browse from there. The snapshots are located at `/depot/.snapshots` on these resources. + +You can also mount the snapshot directory over Samba (or SMB, CIFS) on Windows or Mac OS X. Mount (or map) the snapshot directory in the [same way](../transfer/cifs.md) as you did for your main Bell space substituting the server name and path for `\\datadepot.rcac.purdue.edu\depot\.winsnaps` (Windows) or `smb://datadepot.rcac.purdue.edu/depot/.winsnaps` (Mac OS X). + +Once connected to the snapshot directory through SSH or Samba, you will see something similar to this: + +Snapshots folders may look slightly differently when accessed via SSH on `bell.rcac.purdue.edu` or via Samba on `datadepot.rcac.purdue.edu`. Here are examples of both. + + + + + + + + + + + + + + +
SSH to bell.rcac.purdue.eduSamba mount on datadepot.rcac.purdue.edu
+ +```text +$ cd /depot/.snapshots +$ ls -1 +daily_20190129000501 +daily_20190130000501 +daily_20190131000502 +daily_20190201000501 +daily_20190202000501 +daily_20190203000501 +daily_20190204000501 +monthly_20181101001501 +monthly_20181201001501 +monthly_20190101001501 +monthly_20190201001501 +weekly_20190113002501 +weekly_20190120002501 +weekly_20190127002501 +weekly_20190203002501 +``` + + + Bell snapshots via Samba +
+ +Each of these directories is a snapshot of the entire Bell filesystem at the timestamp encoded into the directory name. The format for this timestamp is year, two digits for month, two digits for day, followed by the time of the day. + +You may `cd` into any of these directories where you will find the entire Bell filesystem. Use `cd` to continue into your lab's Bell space and then you may browse the snapshot as normal. + +If you are browsing these directories over a Samba network drive you can simply drag and drop the files over into your live Data Depot folder. + +Once you find the file you are looking for, use `cp` to copy the file back into your lab's live Bell space. **Do not attempt to modify files directly in the snapshot directories.** + +[**Back to the Lost File Recovery section**](../recover.md) diff --git a/docs/userguides/bell/storage/recover/windows.md b/docs/userguides/bell/storage/recover/windows.md new file mode 100644 index 00000000..badfb512 --- /dev/null +++ b/docs/userguides/bell/storage/recover/windows.md @@ -0,0 +1,25 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Windows + +If you use Bell through "network drives" on Windows you may recover lost files directly from within Windows: + +* Open the folder that contained the lost file. +* Right click inside the window and select "Properties". +* Click on the "Previous Versions" tab. +* A list of snapshots will be displayed. +* Select the snapshot from which you wish to restore. +* In the new window, locate the file you wish to restore. +* Simply drag the file or folder to their correct locations. + +In the "Previous Versions" window the list contains two columns. The first column is the timestamp on which the snapshot was taken. The second column is the date on which the selected file or folder was last modified in that snapshot. This may give you some extra clues to which snapshot contains the version of the file you are looking for. + +[**Back to the Lost File Recovery section**](../recover.md) diff --git a/docs/userguides/bell/storage/sharing.md b/docs/userguides/bell/storage/sharing.md new file mode 100644 index 00000000..91198628 --- /dev/null +++ b/docs/userguides/bell/storage/sharing.md @@ -0,0 +1,19 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Sharing Files from Bell + +Bell supports several methods for file sharing. Use the links below to learn more about these methods. + +## In This Section + +- [Globus](sharing/globus.md) + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/sharing/globus.md b/docs/userguides/bell/storage/sharing/globus.md new file mode 100644 index 00000000..a7ef0f15 --- /dev/null +++ b/docs/userguides/bell/storage/sharing/globus.md @@ -0,0 +1,21 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Sharing Data with Globus + +Data on any RCAC resource can be shared with other users within Purdue or with collaborators at other institutions. Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other institutions. + +To share files, login to [https://transfer.rcac.purdue.edu](https://transfer.rcac.purdue.edu/), navigate to the endpoint (collection) of your choice, and follow instructions as described in Globus documentation on how to share data: + +* + +See also [RCAC Globus presentation](https://www.rcac.purdue.edu/training/globus). + +[**Back to the Sharing Files from Bell section**](../sharing.md) diff --git a/docs/userguides/bell/storage/transfer.md b/docs/userguides/bell/storage/transfer.md new file mode 100644 index 00000000..b377a6fc --- /dev/null +++ b/docs/userguides/bell/storage/transfer.md @@ -0,0 +1,23 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# File Transfer + + Bell supports several methods for file transfer. Use the links below to learn more about these methods. + +## In This Section + +- [SCP](transfer/scp.md) +- [Globus](transfer/globus.md) +- [Windows Network Drive / SMB](transfer/cifs.md) +- [FTP / SFTP](transfer/sftp.md) +- [Copying files from Purdue IT research computing home directory to Bell](transfer/copyhome.md) + +[**Back to the Storage section**](../storage.md) diff --git a/docs/userguides/bell/storage/transfer/cifs.md b/docs/userguides/bell/storage/transfer/cifs.md new file mode 100644 index 00000000..9ab4bfea --- /dev/null +++ b/docs/userguides/bell/storage/transfer/cifs.md @@ -0,0 +1,62 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Windows Network Drive / SMB + +*SMB* (Server Message Block), also known as CIFS, is an easy-to-use file transfer protocol that is useful for transferring files between RCAC systems and a desktop or laptop. You may use SMB to connect to your home, scratch, and Fortress storage directories. The SMB protocol is available on Windows, Linux, and Mac OS X. It is primarily used as a graphical means of transfer, but it can also be used over the command line. + +!!! Note + To access Bell through SMB file sharing, you must be on a Purdue campus network or connected through [VPN](http://www.itap.purdue.edu/connections/vpn/). + +## Windows: + +* Windows 7: Click Windows menu > Computer, then click Map Network Drive in the top bar +* Windows 8 & 10: Tap the Windows key, type `computer`, select This PC, click Computer > Map Network Drive in the top bar +* Windows 11: Tap the Windows key, type `File Explorer`, select This PC, click Computer > Map Network Drive in the top bar +* In the folder location, enter the following information and click Finish: + + To access your Bell home directory, enter `\\home.bell.rcac.purdue.edu\bell-home`. + + To access your scratch space on Bell, enter `\\scratch.bell.rcac.purdue.edu\bell-scratch`. Once mapped, you will be able to navigate to your scratch directory. + +* Note: Use your career account login name and password when prompted. (You will **not** need to add "`,push`" nor use your Purdue Duo client.) +* Your home or scratch directory should now be mounted as a drive in the Computer window. +* If you have issues mapping the drive check Credential Manager. + + In the Search bar, type "Credential Manager" + + Inside Credential Manager, click "Windows Credentials" and "Add New Credential" + + Servername: `\\home.bell.rcac.purdue.edu` + + Username: `boilerad\PurdueLogin` + + Then save it and try mapping again. + - If there's already an entry for the server you are trying to map delete it. + +## Mac OS X: + +* In the Finder, click Go > Connect to Server +* In the Server Address enter the following information and click Connect: + + To access your Bell home directory, enter `smb://home.bell.rcac.purdue.edu/bell-home`. + + To access your scratch space on Bell, enter `smb://scratch.bell.rcac.purdue.edu/bell-scratch`. Once mapped, you will be able to navigate to your scratch directory. + +* Note: Use your career account login name and password when prompted. (You will **not** need to add "`,push`" nor use your Purdue Duo client.) +* Your home or scratch directory should now be mounted as a drive in the Computer window. + +## Linux: + +* There are several graphical methods to connect in Linux depending on your desktop environment. Once you find out how to connect to a network server on your desktop environment, choose the Samba/SMB protocol and adapt the information from the Mac OS X section to connect. +* If you would like access via samba on the command line you may install `smbclient` which will give you FTP-like access and can be used as shown below. For all the possible ways to connect look at the Mac OS X instructions. + + ``` + smbclient //home.bell.rcac.purdue.edu/bell-home -U boilerad/myusername + ``` + ``` + smbclient //scratch.bell.rcac.purdue.edu/bell-scratch -U boilerad/myusername + ``` + +!!! Note + Use your career account login name and password when prompted. (You will **not** need to add "`,push`" nor use your Purdue Duo client.) + +[**Back to the File Transfer section**](../transfer.md) diff --git a/docs/userguides/bell/storage/transfer/copyhome.md b/docs/userguides/bell/storage/transfer/copyhome.md new file mode 100644 index 00000000..5e7fc132 --- /dev/null +++ b/docs/userguides/bell/storage/transfer/copyhome.md @@ -0,0 +1,59 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Copying files from Purdue IT research computing home directory to Bell + +The Bell home directory and its contents are specific to the Bell cluster, and are not available on other RCAC machines. For people having access to other Community Clusters and Bell, *there is no automatic copying or synchronization between main and Bell home directories*. At your discretion, you can manually copy all or parts of your main research computing home to Bell using one of the methods described below. + +Please note that copying may fail if the size of your research computing home directory is larger than the Bell one's quota. Please [check](../quota.md) usage and limits before proceeding! + +## Complete copy + +For your convenience, a custom tool `copy-rcac-home` is provided to simplify at-will duplication of your main research computing home directory into Bell. The tool performs a complete 1-to-1 copy using `rsync -auH` (with exception of a narrow subset of system-specific service files). + +To use the tool, simply type `copy-rcac-home` in a terminal window on a Bell front-end or compute node: + +``` + +$ copy-rcac-home + + This script will copy entire contents of your main RCAC + home directory into your Bell cluster's $HOME. + + Note: copying may fail if the size of your RCAC home directory + is larger than your quota on the Bell one (25GB). + BEFORE PROCEEDING, please run 'myquota' command on another + cluster to see your usage there and judge whether it would fit! + +Would you like to proceed? [Y/n]: +``` + +At this stage answering `yes` will proceed with copying, or you can respond with a `no` (or `Ctrl-C`) to cancel. See `copy-rcac-home --help` for more details on the tool. + +## Partial copy + +Desired parts (or whole) of your research computing home directories can be copied to Bell via any of the home directories' supported [transfer methods](../transfer.md), such as SCP, SFTP, rsync, or Globus. + +* **Example:** recursive copying of a subdirectory from RCAC home directory into Bell home using `scp`. + + ``` + + (if you are on Bell, use other cluster name for the remote part) + $ scp -pr myothercluster.rcac.purdue.edu:somedirectory/ ~/ + + (if you are on another cluster, use Bell for the remote part) + $ scp -pr somedirectory/ myusername@bell.rcac.purdue.edu:~/ + ``` + +* **Example:** copying using Globus. + + Search collections for *"Purdue Research Computing - Home Directories"* and * "Purdue Bell Cluster - Home" * endpoints, respectively, then transfer desired files and/or directories as usual. + +[**Back to the File Transfer section**](../transfer.md) diff --git a/docs/userguides/bell/storage/transfer/globus.md b/docs/userguides/bell/storage/transfer/globus.md new file mode 100644 index 00000000..73e8bbe1 --- /dev/null +++ b/docs/userguides/bell/storage/transfer/globus.md @@ -0,0 +1,57 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# Globus + +*Globus*, previously known as Globus Online, is a powerful and easy to use file transfer service for transferring files virtually anywhere. It works within RCAC's various research storage systems; it connects between RCAC and remote research sites running Globus; and it connects research systems to personal systems. You may use Globus to connect to your home, scratch, and Fortress storage directories. Since Globus is web-based, it works on any operating system that is connected to the internet. The Globus Personal client is available on Windows, Linux, and Mac OS X. It is primarily used as a graphical means of transfer but it can also be used over the command line. + +## Globus Web + +* Navigate to +* Click "Proceed" to log in with your Purdue Career Account. +* On your first login it will ask to make a connection to a Globus account. Accept the conditions. +* Now you are at the main screen. Click "File Transfer" which will bring you to a two-panel interface (if you only see one panel, you can use selector in the top-right corner to switch the view). +* You will need to select one collection and file path on one side as the source, and the second collection on the other as the destination. This can be one of several Purdue endpoints, or another University, or even your personal computer (see the [Globus Personal Client Setup](#globus-personal-client-setup) section below). + +The RCAC collections are as follows. A search for "Purdue" will give you several suggested results you can choose from, or you can give a more specific search. + +* Home Directory storage: *"Purdue Research Computing - Home Directories"*, however, you can start typing "Purdue" and "Home Directories" and it will suggest appropriate matches. +* Bell scratch storage: *"Purdue Bell Cluster"*, however, you can start typing "Purdue" and "Bell" and it will suggest appropriate matches. From here you will need to navigate into your username. +* **Research Data Depot:** *"Purdue Research Computing - Data Depot"*, a search for "Depot" should provide appropriate matches to choose from. +* **Fortress:** *"Purdue Fortress HPSS Archive"*, a search for "Fortress" should provide appropriate matches to choose from. + +From here, select a file or folder in either side of the two-pane window, and then use the arrows in the top-middle of the interface to instruct Globus to move files from one side to the other. You can transfer files in either direction. You will receive an email once the transfer is completed. + +## Globus Personal Client Setup + +Globus Connect Personal is a small software tool you can install to make your own computer a Globus endpoint on its own. It is useful if you need to transfer files via Globus to and from your computer directly. + +* On the "Collections" page from earlier, click *"Get Globus Connect Personal"* or download a version for your operating system it from here: [Globus Connect Personal](https://www.globus.org/globus-connect-personal) +* Name this particular personal system and follow the setup prompts to create your Globus Connect Personal endpoint. +* Your personal system is now available as a collection within the Globus transfer interface. + +## Globus Command Line + +Globus supports command line interface, allowing advanced automation of your transfers. + +To use the recommended standalone Globus CLI application (the `globus` command): + +* First time use: issue the `globus login` command and follow instructions for initial login. +* Commands for interfacing with the CLI can be found via [Using the Command Line Interface](https://docs.globus.org/cli/), as well as the [Globus CLI Examples](https://docs.globus.org/cli/examples/) pages. + +## Sharing Data with Outside Collaborators + +Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other institutions. See the Globus documentation on how to share data: + +* + +For links to more information, please see [Globus Support](https://support.globus.org/home) page and [RCAC Globus presentation](https://www.rcac.purdue.edu/training/globus). + +[**Back to the File Transfer section**](../transfer.md) diff --git a/docs/userguides/bell/storage/transfer/scp.md b/docs/userguides/bell/storage/transfer/scp.md new file mode 100644 index 00000000..4037335a --- /dev/null +++ b/docs/userguides/bell/storage/transfer/scp.md @@ -0,0 +1,80 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# SCP + +*SCP* (Secure CoPy) is a simple way of transferring files between two machines that use the SSH protocol. SCP is available as a protocol choice in some graphical file transfer programs and also as a command line program on most Linux, Unix, and Mac OS X systems. SCP can copy single files, but will also recursively copy directory contents if given a directory name. + +!!! Note + After Aug 17, 2020, the community clusters will not support password-based authentication for login. Methods that can be used include two-factor authentication ([Purdue Login](/userguides/bell/accounts/#logging-in-to-bell)) or [SSH keys](/userguides/bell/accounts/#ssh-keys). If you do not have SSH keys installed, you would need to type your Purdue Login response into the SFTP's "Password" prompt. + + +## Command-line usage: + +You can transfer files both to and from Bell while initiating an SCP session on either some other computer or on Bell (in other words, directionality of connection and directionality of data flow are independent from each other). The `scp` command appears somewhat similar to the familiar `cp` command, with an extra `user@host:file` syntax to denote files and directories on a remote host. Either Bell or another computer can be a remote. + +* **Example:** Initiating SCP session on some other computer (i.e. you are on some other computer, connecting to Bell): + + ``` + (transfer TO Bell) + (Individual files) + $ scp sourcefile myusername@bell.rcac.purdue.edu:somedir/destinationfile + $ scp sourcefile myusername@bell.rcac.purdue.edu:somedir/ + (Recursive directory copy) + $ scp -pr sourcedirectory/ myusername@bell.rcac.purdue.edu:somedir/ + + (transfer FROM Bell) + (Individual files) + $ scp myusername@bell.rcac.purdue.edu:somedir/sourcefile destinationfile + $ scp myusername@bell.rcac.purdue.edu:somedir/sourcefile somedir/ + (Recursive directory copy) + $ scp -pr myusername@bell.rcac.purdue.edu:sourcedirectory somedir/ + ``` + + The **-p** flag is optional. When used, it will cause the transfer to preserve file attributes and permissions. The **-r** flag is required for recursive transfers of entire directories. + +* **Example:** Initiating SCP session on Bell (i.e. you are on Bell, connecting to some other computer): + + ``` + (transfer TO Bell) + (Individual files) + $ scp myusername@$another.computer.example.com:sourcefile somedir/destinationfile + $ scp myusername@$another.computer.example.com:sourcefile somedir/ + (Recursive directory copy) + $ scp -pr myusername@$another.computer.example.com:sourcedirectory/ somedir/ + + (transfer FROM Bell) + (Individual files) + $ scp somedir/sourcefile myusername@$another.computer.example.com:destinationfile + $ scp somedir/sourcefile myusername@$another.computer.example.com:somedir/ + (Recursive directory copy) + $ scp -pr sourcedirectory myusername@$another.computer.example.com:somedir/ + ``` + + The **-p** flag is optional. When used, it will cause the transfer to preserve file attributes and permissions. The **-r** flag is required for recursive transfers of entire directories. + +## Software (SCP clients) + +Linux and other Unix-like systems: + +* The `scp` command-line program should already be installed. + +Microsoft Windows: + +* [MobaXterm](https://mobaxterm.mobatek.net/download.html) + Free, full-featured, graphical Windows SSH, SCP, and SFTP client. +* Command-line `scp` program can be installed as part of Windows Subsystem for Linux (WSL), or Git-Bash. + +Mac OS X: + +* The `scp` command-line program should already be installed. You may start a local terminal window from "Applications->Utilities". +* [Cyberduck](https://cyberduck.io/) is a full-featured and free graphical SFTP and SCP client. + +[**Back to the File Transfer section**](../transfer.md) diff --git a/docs/userguides/bell/storage/transfer/sftp.md b/docs/userguides/bell/storage/transfer/sftp.md new file mode 100644 index 00000000..78ca11a4 --- /dev/null +++ b/docs/userguides/bell/storage/transfer/sftp.md @@ -0,0 +1,79 @@ +--- +tags: + - Bell +authors: + - mahlawat +resource: Bell +search: + boost: 2 +--- + +# FTP / SFTP + +!!! Warning + FTP is not supported on any research systems because it does not allow for secure transmission of data. Use SFTP instead, as described below. + +*SFTP* (Secure File Transfer Protocol) is a reliable way of transferring files between two machines. SFTP is available as a protocol choice in some graphical file transfer programs and also as a command-line program on most Linux, Unix, and Mac OS X systems. SFTP has more features than SCP and allows for other operations on remote files, remote directory listing, and resuming interrupted transfers. Command-line SFTP cannot recursively copy directory contents; to do so, try using SCP or graphical SFTP client. + +!!! Note + After Aug 17, 2020, the community clusters will not support password-based authentication for login. Methods that can be used include two-factor authentication ([Purdue Login](/userguides/bell/accounts/#logging-in-to-bell)) or [SSH keys](/userguides/bell/accounts/#ssh-keys). If you do not have SSH keys installed, you would need to type your Purdue Login response into the SFTP's "Password" prompt. + + +## Command-line usage + +You can transfer files both to and from Bell while initiating an SFTP session on either some other computer or on Bell (in other words, directionality of connection and directionality of data flow are independent from each other). Once the connection is established, you use `put` or `get` subcommands between "local" and "remote" computers. Either Bell or another computer can be a remote. + +* **Example:** Initiating SFTP session on some other computer (i.e. you are on another computer, connecting to Bell): + + ``` + $ sftp myusername@bell.rcac.purdue.edu + + (transfer TO Bell) + sftp> put sourcefile somedir/destinationfile + sftp> put -P sourcefile somedir/ + + (transfer FROM Bell) + sftp> get sourcefile somedir/destinationfile + sftp> get -P sourcefile somedir/ + + sftp> exit + ``` + + The **-P** flag is optional. When used, it will cause the transfer to preserve file attributes and permissions. + +* **Example:** Initiating SFTP session on Bell (i.e. you are on Bell, connecting to some other computer): + + ``` + $ sftp myusername@$another.computer.example.com + + (transfer TO Bell) + sftp> get sourcefile somedir/destinationfile + sftp> get -P sourcefile somedir/ + + (transfer FROM Bell) + sftp> put sourcefile somedir/destinationfile + sftp> put -P sourcefile somedir/ + + sftp> exit + ``` + + The **-P** flag is optional. When used, it will cause the transfer to preserve file attributes and permissions. + +## Software (SFTP clients) + +Linux and other Unix-like systems: + +* The `sftp` command-line program should already be installed. + +Microsoft Windows: + +* [MobaXterm](https://mobaxterm.mobatek.net/download.html) + Free, full-featured, graphical Windows SSH, SCP, and SFTP client. +* Command-line `sftp` program can be installed as part of Windows Subsystem for Linux (WSL), or Git-Bash. + +Mac OS X: + +* The `sftp` command-line program should already be installed. You may start a local terminal window from "Applications->Utilities". +* [Cyberduck](https://cyberduck.io/) is a full-featured and free graphical SFTP and SCP client. + +[**Back to the File Transfer section**](../transfer.md) diff --git a/main.py b/main.py index f5d1e45e..32096d64 100644 --- a/main.py +++ b/main.py @@ -517,7 +517,7 @@ def accounts_md_snippet(resource): #### SSH Client Software Linux / Solaris / AIX / HP-UX / Unix: -- The `ssh` command is pre-installed. Log in using `ssh username@gautschi.rcac.purdue.edu` from a terminal. +- The `ssh` command is pre-installed. Log in using `ssh username@{resource}` from a terminal. Microsoft Windows: @@ -725,4 +725,4 @@ def scratch_purge(resource): "\n**Recommendations**\n\nRCAC recommends that important data, research results, and other important files be permanently stored in the [Fortress HPSS Archive](https://www.rcac.purdue.edu/storage/fortress), and copied to scratch spaces while being actively worked on. The hsi and htar commands provide easy-to-use interfaces into the archive and can be used to copy files into the archive interactively or even automatically at the end of your regular job submission scripts. Making frequent copies of your files will minimize work required when these files eventually become subject to purge, as well as protect your work in the unlikely event of a scratch system failure.\n\nPlease [contact us](https://www.rcac.purdue.edu/help) if you have questions or need assistance in copying your files to a more permanent location such as the [Fortress HPSS Archive](https://www.rcac.purdue.edu/storage/fortress).", "" ) - return content \ No newline at end of file + return content diff --git a/mkdocs.yml b/mkdocs.yml index 2be6b5a9..718a77b2 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -123,6 +123,17 @@ nav: - Gateway (Open OnDemand): userguides/gautschi/gateway.md - Compiling Source Code: userguides/gautschi/compile.md - Frequently Asked Questions: userguides/gautschi/faqs.md + - Bell: + - userguides/bell/index.md + - Overview of Bell: userguides/bell/overview.md + - Biography of Bell: userguides/bell/biography.md + - Accounts: userguides/bell/accounts.md + - Software: userguides/bell/software.md + - Running Jobs: userguides/bell/run.md + - File Storage and Transfer: userguides/bell/storage.md + - Gateway (Open OnDemand): userguides/bell/gateway.md + - Compiling Source Code: userguides/bell/compile.md + - Frequently Asked Questions: userguides/bell/faqs.md - Gilbreth: - userguides/gilbreth/index.md - Gilbreth Overview: userguides/gilbreth/overview.md @@ -134,7 +145,6 @@ nav: - Gateway (Open OnDemand): userguides/gilbreth/gateway.md - Compiling Source Code: userguides/gilbreth/compile.md - Frequently Asked Questions: userguides/gilbreth/faqs.md - - Bell: https://www.rcac.purdue.edu/knowledge/bell - Negishi: https://www.rcac.purdue.edu/knowledge/negishi - Scholar: https://www.rcac.purdue.edu/knowledge/scholar - Geddes: https://www.rcac.purdue.edu/knowledge/geddes diff --git a/tools/generate_breadcrumbs.py b/tools/generate_breadcrumbs.py index 6aa820c2..2d27b3ca 100644 --- a/tools/generate_breadcrumbs.py +++ b/tools/generate_breadcrumbs.py @@ -39,6 +39,8 @@ def handle_env_tag(loader, node): BREADCRUMB_TITLE_OVERRIDES = { "Anvil": "Anvil User Guide", "Gautschi": "Gautschi User Guide", + "Bell": "Bell User Guide", + "Gilbreth": "Gilbreth User Guide", } # ----------------------------