Merge pull request #25729 from easybuilders/5.3.x

release EasyBuild v5.3.0

Author: boegel

.github/workflows/tagbot.py

@@ -146,6 +146,7 @@ def pr_ecs(pr_diff):
     '13.3': '2024a',
     '14.2': '2025a',
     '14.3': '2025b',
+    '15.2': '2026.1',
 }
 
 ic_tc_gen_map = {
@@ -157,11 +158,13 @@ def pr_ecs(pr_diff):
     '2024.2.0': '2024a',
     '2025.1.1': '2025a',
     '2025.2.0': '2025b',
+    '2025.3.3': '2026.1',
 }
 
 llvm_tc_gen_map = {
     '20.1.5': '2023b',
     '20.1.8': '2025b',
+    '21.1.8': '2026.1',
 }
 
 toolchain_names = ['foss', 'gompi', 'gfbf', 'iimpi', 'iimkl', 'intel', 'llvm-compilers', 'lfbf',

.github/workflows/unit_tests.yml

@@ -13,9 +13,13 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python: ['3.7', '3.11']
-        modules_tool: [Lmod-8.6.8]
-        module_syntax: [Lua, Tcl]
+        include:
+          - python: '3.7'
+            modules_tool: Lmod-8.6.8
+            module_syntax: Tcl
+          - python: '3.11'
+            modules_tool: Lmod-8.6.8
+            module_syntax: Lua
       fail-fast: false
     steps:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
@@ -45,7 +49,8 @@ jobs:
         # for testing OpenMPI-system*eb we need to have Open MPI installed
         sudo apt-get install libopenmpi-dev openmpi-bin
         # required for test_dep_graph
-        pip install pycodestyle python-graph-core python-graph-dot
+        sudo apt-get install graphviz
+        pip install pycodestyle graphviz
 
     - name: install EasyBuild framework
       run: |

RELEASE_NOTES

@@ -3,9 +3,107 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/release-notes .
 
-The latest version of easybuild-easyconfig provides 11,063 easyconfig files, for 3,049 different software packages,
+The latest version of easybuild-easyconfig provides 10,284 easyconfig files, for 2,993 different software packages,
 incl. 29 different (compiler) toolchains.
 
+
+v5.3.0 (10 Apr 2026)
+--------------------
+
+feature release
+
+- add easyconfigs for update of (common) toolchains: `foss/2026.1` (#25615), `intel/2026.1` (#25621), `lfoss/2026.1` (#25634)
+- added example easyconfig files for 85 new software packages:
+  - ADIOS2 (#24194), ADOL-C (#24357), ArmComputeLibrary (#21309, #25566, #25670, #25671, #25672), ASTER (#25405), BamQuery (#25650),
+    CaDiCaL (#25404), CasADi (#23463, #24453), cascadia (#25299), coremltools (#25432), cvc5 (#25404), docopt.cpp (#23464), DRAM (#25635),
+    EasyOCR (#25604), ekg-intervaltree (#24616), Entwine (#25151), Eww (#25143), fastobo (#25299), fMRIPrep (#22732), FSL (#25383, #22914),
+    giotto-tda (#24743), git-lfs-s3 (#25397), gnome-common (#25143), hwdata (#25123), IDR (#25168), Ipopt (#23462), JPype (#19880),
+    jupyter-bash-kernel (#25464, #25521), JupyterLab-NVdashboard (#25497), kraken-OCR (#25432), k-Wave-python (#25149), labwc (#25123),
+    LDhelmet (#25516), LDpop (#25517), libdbusmenu (#25143), libdisplay-info (#25123), libevdev (#25123), libinput (#25123), libliftoff (#25123),
+    libsfdo (#25123), mango-auth (#25575), MDBM (#19536, #20677), mycotools (#25212), Nipype (#22732, #25400), OpenLB (#24334),
+    OpenSim (#23464, #24676), pb-CpG-tools (#25462), Polyscope (#23108), PyCBC (#25187), pyNVML (#25395), pyrho (#25517), pyteomics (#25299),
+    pytest-forked (#25574), python-bidi (#25432), pytmatrix (#25502), qibo (#19843), qibojit (#19843), ratarmount (#25555), RGI (#25480),
+    s9s (#25559), scikit-multimodallearn (#25438), SCONE (#23464), seatd (#25123), Sentaurus (#24699), sentieon-genomics (#25119),
+    SHAPEIT5 (#25515), Simbody (#23464), SOD (#25322, #25684), SPAM (#25156), SPH-EXA (#25606, #25584, #25585, #25693), STREAmS (#25219),
+    SvABA (#25561), SWASH (#25638), sway (#25412), SymFPU (#25404), SYSMOIC (#25298), table2asn (#25039), tangram-sc (#25622),
+    TIDDIT (#25583), tllist (#25412), treePL (#24357), trove-classifiers (#25526), VCF2Dis (#25460), verifyBamID (#25164), xraylib (#25491),
+    Xwayland (#25123)
+- added additional easyconfigs for various supported software packages, including (but not limited to):
+  - Alfred 0.5.3, ASAP3 3.13.11, AOCL-BLAS 5.2, BEDOPS 2.4.42, bin2cell 0.3.4, Braindecode 1.2.0, bx-python 0.14.0, Cantera 3.2.0,
+    CapnProto 1.4.0, Cassiopeia 2.1.0-2025-10-9, CellRank 2.0.7, CellTypist 1.7.1, Clarabel.rs 0.11.1, ColabFold 1.5.5, COBRApy 0.30.0,
+    code-cli 1.108.1, code-server 4.108.1, COLMAP 3.13.0, CPLEX 22.1.2, cramjam 2.11.0, CSBDeep 0.8.2, CUDA 13.1.1 + 13.2.0, CUTLASS 4.3.5,
+    CVXPY 1.5.1, cython-cmake 0.2.2, Dalton 2026, DFT-D4 4.0.2, DIA-NN 2.3.2, DIRAC 26.0, dm-haiku 0.0.16, DMTCP 4.1.0, Emacs 30.2,
+    Faiss 1.13.2, fastp 1.1.0, fastparquet 2026.3.0, Filtlong 0.3.1, fio 3.41, FlexiBLAS 3.5.0, GD 2.77, gemmi 0.7.4, gflags 2.3.0,
+    HF-Datasets 4.5.0, hwloc 2.13.0, igraph 1.0.0, inferCNV 1.22.0, infercnvpy 0.6.1, jax 0.8.1, json-fortran 9.2.1, jq 1.8.1, libdap 3.21.1,
+    libfabric 2.5.0, libgpg-error 1.59, libpciaccess 0.19, libxc 7.0.0, libzip 1.11.4, llama.cpp b8354, lpsolve 5.5.2.14, LLVM 21.1.8,
+    MAQAO 2026.0.0-b, MATLAB 2025b-r2, MEME 5.5.9, Meson 1.10.2, Miller 6.17.0, msprime 1.4.1, multicharge 0.5.0, nauty 2.9.3, ncdu 1.22,
+    NCO 5.3.6, NiBabel 5.3.3, Ninja 1.13.2, nvtop 3.3.2, Octave 11.1.0, ollama 0.15.6, OpenBLAS 0.3.32, OpenMolcas 26.02, OrfM 1.4.0,
+    panaroo 1.6.0, Parsnp 2.1.5, PMIx 6.1.0. pod5-file-format 0.3.23, PRANK 251117, prokka 1.15.6, PRRTE 4.1.0, psutil 7.2.1,
+    PyCharm 2025.3.2.1, pybedtools 0.12.0, pybind11-stubgen 2.5.5, pycocotools 2.0.11, pydot 4.0.1, pyfaidx 0.9.0.3, PyFrag 1.0.0,
+    Pylint 3.3.9, Pyomo 6.10.0, pyperf 2.10.0, PyQtGraph 0.14.0, PyRosetta 4.r420, pySCENIC 0.12.1-20250109, pyseer 1.4.0, python-docx 1.2.0,
+    python-igraph 1.0.0, python-irodsclient 3.2.0, python-isal 1.8.0, python-libsbml 5.21.0, QtPy 2.4.3,
+    QuantumESPRESSO 7.5 w/ NVHPC 25.3 + CUDA 12.8.0, QUAST 5.3.0, ReFrame 4.9.1, rioxarray 0.21.0, robin-map 1.4.1, rpy2 3.6.4, scib 1.1.7,
+    scib-metrics 0.5.9, scikit-bio 0.7.1.post1, scikit-misc 0.5.1, scVelo 0.3.4, SeqAn 2.5.2, Seurat 5.4.0, snpEff 5.4c, Spack 1.1.1,
+    Squidpy 1.6.6, STAR-CCM+ 2602, stardist 0.9.1, SUNDIALS 7.6.0, Transformers 5.0.0, TurboVNC 3.3, UCC 1.7.0, UCX 1.20.0, Umpire 2025.12.0,
+    unixODBC 2.3.14, vsc-mympirun 5.5.1, VTune 2025.9.0, waLBerla 7.2, wandb 0.25.1, XeniumRanger 4.0.0, XML-Compile 1.64, Z3 4.15.4
+- various bug fixes, including:
+  - avoid test failures for netCDF with `iimpi` toolchain, by setting `$I_MPI_HYDRA_BOOTSTRAP` to `ssh` (#24735)
+  - fix mpirun patch for CRYSTAL 23.1.0.1 (#25023)
+  - don't specify KIND for search paths in RUSTFLAGS in easyconfig for librsvg 2.61.0 (#25332)
+  - make sure that ReFrame script has executable permissions (#25338)
+  - add (post-install) patch for libtool v2.5.4 to improve support for LLVM flang (#25345)
+  - make libdisplay-info proper dependency for Xfce 4.20, add Wayland build dependency to VTE 0.82.2 (#25365)
+  - add patch to UCX v1.18.0 and v1.19.0 to fix build failure with glibc v2.43 (#25399)
+  - fix wrong source URL for python-parasail 1.3.4 (#25403)
+  - fix source URL in git-annex easyconfigs (#25426)
+  - make Python, Meson, Ninja, and CMake build dependencies in easyconfigs for btllib 1.7.0 + 1.7.5 (#25456)
+  - add back patch to fix hardcoded paths in setup.py for libxml2-python 2.12.10 + 2.14.3 (#25465)
+  - use `-fno-tree-ter` compiler option when building libaom and SVT-AV1 on Arm with GCC 14.2.0, to work around bug causing segmentation fault (#25466)
+  - fix extension name for SMC++-1.15.4 (#25468)
+  - fix pyiron 0.5.2-20251013 extension version (#25473)
+  - use `NETCDF_ENABLE_DAP_REMOTE_TESTS` instead of `ENABLE_DAP_REMOTE_TESTS` and prevent use of `srun` in netCDF 4.9.3 easyconfigs (#25490)
+  - add additional patches for PyTorch 2.9.1 to fix problems with the tests + exclude `inductor/test_flex*` tests (#25492)
+  - add patch to reduce the number of used resources in scipy 1.16.1 test `test_import_cycles` + patch to disable failing test on RISC-V (#25495)
+  - don't depend on ScaFaCos in LAMMPS easyconfigs when building on Arm + add patch to disable failing test on Arm due to bug in kim-api (#25133)
+  - add patch to Mesa in 2025a and OpenGL in 2025b to fix build for glibc v2.43 (#25505)
+  - add patch for DMTCP 4.0.0 to fix build on RHEL8 (#25530)
+  - add patch to fix using wrong OpenMP library in easyconfigs for PyTorch 2.3.0 + 2.6.0 + 2.7.1 (#25541, #25542, #25543, #25544)
+  - add SQLite dependency to NSS 3.114 to avoid internal SQLite (#25551)
+  - add pkconf build dependency to cargo-c 0.10.13 (#25571)
+  - remove PyTorch (and CUDA) dependency for CellRank 2.0.2, since they're not actually needed (#25580)
+  - add patch to LAMMPS v22Jul2025 to fix failing test + make sure patches of CUDA version are consistent (#25593)
+  - correct homepage for Underworld 2.16.4 (#25594)
+  - use gompi/2023b toolchain instead of gompi/2024a for ORCA v6.1.1 w/ avx2, since it doesn't work correctly on top of OpenMPI 5.x (#25607, #25691)
+  - add patch to pybind11 v3.0.0 to fix build failure with CUDA nvcc (#25620)
+  - fix VESTA-gui by adding installation dir to `$LD_LIBRARY_PATH` (#25633)
+  - add patch to fix implicit function declaration in OpenMPI 4.1.4 (#25663)
+  - fix locale-dependent test failure in RCall 0.13.17 (#25666)
+  - move netCDF to last dependency in `2022*` GDAL easyconfigs, to make sure correct `netcdf.h` is picked up (not the one included in HDF dependency) (#25683)
+  - fix reported version for kiwisolver 1.4.5 extension in matplotlib easyconfigs (#25685)
+  - avoid requiring `glibc-static` for BEDOPS 2.4.41 by removing `-static` flag from `Makefile`s (#25686)
+  - add alternate checksum for VSURF extension in R-bundle-CRAN 2023.12 (#25687)
+  - fix homepage + description in lfoss easyconfigs (#25695)
+- minor enhancements, including:
+  - add jupyter-bash-kernel v0.9.3 dependency to recent Jupyter-bundle versions (#25464)
+  - add patch to support `$TRITON_HOME` In Triton 3.1 (#25557) and Triton 2.3.1 (#25582)
+  - enable Wayland support in Qt6 6.9.3 (#25611)
+  - also build serial library in recent easyconfigs for Wannier90 3.1.0 (#25660)
+- enhancements and fixes for test suite:
+  - improve reported errors in easyconfigs test suite (#23969)
+  - add GCC/GCCcore 15.2 based toolchains as 2026.1 to tagbot workflow (#24990)
+  - fix binutils build dependency test for BinariesTarball (#25305)
+  - reduce combinations for CI unit tests (#25413)
+  - add tagbot mapping for `2026.1` and add LLVM to toolchain map tests (#25639)
+  - install `graphviz` in CI workflow for easyconfigs test suite, required for `test_dep_graph` (#25696)
+  - disable `test_dep_graph` for now, since it takes excessively long (#25699)
+- other changes:
+  - remove default PyPI URL from PythonBundle easyconfigs (#21291)
+  - disable building BOLT in LLVM 20.1.x on RISC-V (#25218)
+  - bump OpenBLAS to v0.3.32 as dependency for FlexiBLAS 3.5.0 w/ GCC 15.2.0 (#25603)
+- archiving of old easyconfigs:
+  - archive easyconfigs from 2021b generation (#25697, #25698, #25716)
+
+
 v5.2.1 (20 Feb 2026)
 --------------------
 

easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb

@@ -0,0 +1,108 @@
+easyblock = "CMakeMake"
+
+name = "ADIOS2"
+version = "2.10.2"
+
+homepage = 'https://github.com/ornladios/ADIOS2/'
+description = """This is ADIOS2: The Adaptable Input/Output (I/O) System.
+ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing
+Project. It is a framework for scientific data I/O to publish and subscribe to data when
+and where required.
+ADIOS2 transports data as groups of self-describing variables and attributes across different
+media types (such as files, wide-area-networks, and remote direct memory access) using a
+common application programming interface for all transport modes. ADIOS2 can be used on
+supercomputers, cloud systems, and personal computers. """
+
+toolchain = {'name': 'foss', 'version': '2025b'}
+
+source_urls = ['https://github.com/ornladios/ADIOS2/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_include_iomanip.patch']
+checksums = [
+    {'v2.10.2.tar.gz': '14cf0bcd94772194bce0f2c0e74dba187965d1cffd12d45f801c32929158579e'},
+    {'ADIOS2-2.10.2_include_iomanip.patch': '9e3a094f43c21a254fedc4305ae1dc646c084fd6a85448e7dc8e7df7ef4eb031'},
+]
+
+builddependencies = [
+    ('CMake', '3.31.8'),  # Bug in ADIOS2 with CMake 4
+    ('pkgconf', '2.4.3'),
+    ('googletest', '1.17.0'),
+    ('SciPy-bundle', '2025.07'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('HDF5', '1.14.6'),
+    ('Python', '3.13.5'),
+    ('mpi4py', '4.1.0'),
+    ('pybind11', '3.0.0'),
+    ('Blosc2', '2.19.0'),
+    ('bzip2', '1.0.8'),
+    ('libpng', '1.6.50'),
+    ('ZeroMQ', '4.3.5'),
+    ('nlohmann_json', '3.12.0'),
+    ('yaml-cpp', '0.8.0'),
+    ('pugixml', '1.15'),
+    ('SQLite', '3.50.1'),
+    ('libsodium', '1.0.20'),
+    ('zfp', '1.0.1'),
+    ('MGARD', '1.6.0'),
+    ('UCX', '1.19.0'),
+    # ('libfabric', '2.0.0'), # optional
+]
+
+configopts = ' '.join([
+    '-DBUILD_TESTING=ON',
+    '-DBUILD_EXTERNAL_GTEST=ON',
+    '-DADIOS2_USE_EXTERNAL_PYBIND11=ON',
+    '-DADIOS2_USE_EXTERNAL_YAMLCPP=ON',
+    '-DADIOS2_USE_EXTERNAL_NLOHMANN_JSON=ON',
+    '-DADIOS2_USE_EXTERNAL_PUGIXML=ON',
+    '-DADIOS2_USE_EXTERNAL_GTEST=ON',
+    # MPI tests could fail depending on the system and environment configuration
+    '-DADIOS2_RUN_MPI_MPMD_TESTS=OFF',
+    '-DMPIEXEC_MAX_NUMPROCS=2'
+])
+
+
+# Taken from https://github.com/ornladios/ADIOS2/blob/master/scripts/ci/gh-actions/run.sh
+pretestopts = ' && '.join([
+    'export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe',
+    'export OMPI_MCA_hwloc_base_binding_policy=none',
+    'export ADIOS2_IP=127.0.0.1',
+    'export OMP_NUM_THREADS=1',
+    '',  # Trailing &&
+])
+
+_skip_tests = [
+    'Unit.FileTransport.FailOnEOF.Serial',  # Fails due to not throwing an expected exception
+]
+_skip_tests_str = '|'.join(_skip_tests)
+
+test_cmd = 'ctest'
+testopts = ' '.join([
+    '-VV',  # Verbose output
+    '--output-on-failure',
+    '-j %(parallel)s',
+    f'-E "{_skip_tests_str}"',
+
+    # https://github.com/ornladios/ADIOS2/blob/v2.10.2/scripts/dashboard/adios_common.cmake#L94
+    '--repeat until-pass:5',
+])
+
+sanity_check_paths = {
+    'files': [
+        'bin/adios2-config', 'include/adios2.h', 'include/adios2_c.h',
+        f'lib/libadios2_c.{SHLIB_EXT}', f'lib/libadios2_c_mpi.{SHLIB_EXT}',
+        f'lib/libadios2_c_mpi.{SHLIB_EXT}', f'lib/libadios2_c_mpi.{SHLIB_EXT}',
+    ],
+    'dirs': ['bin', 'include', 'lib64']
+}
+
+sanity_check_commands = [
+    'adios2-config -v',
+    'bpls --help',
+]
+
+moduleclass = 'lib'