Re: [easybuild] [ANN] EasyBuild v4.9.1
As can be seen in the description of the PR that added this: https://github.com/easybuilders/easybuild-easyconfigs/pull/19940 the problem was detected on ARM only, but I would recommend rebuilding regardless of arch. It is a bug that might cause problems if not fixed. From: easybuild-requ...@lists.ugent.be on behalf of Ehsan Moravveji Sent: Tuesday, April 9, 2024 12:01 To: easybuild@lists.ugent.be Subject: RE: [easybuild] [ANN] EasyBuild v4.9.1 Dear Kenneth et al. Thanks for all the new () features and improvements. Among the whole list, I came across the recommended reinstallation for OpenMPI/4.1.x. I looked up the new patch file OpenMPI-4.1.x_add_atomic_wmb.patch<https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch>. There is a new function call "atomic_wmb()" added there, and apparently the new patched installation is tested successfully on arm64 cpus (only?) without a failure. OK, great. Now, I wonder whether this patch/reinstallation is recommended for the x86 Intel and AMD CPUs, too? Thanks in advance Ehsan -Original Message- From: easybuild-requ...@lists.ugent.be On Behalf Of Kenneth Hoste Sent: vrijdag 5 april 2024 22:32 To: easybuild@lists.ugent.be Subject: [easybuild] [ANN] EasyBuild v4.9.1 Dear EasyBuilders, We're pleased to announce the release of EasyBuild v4.9.1 [1]. We had to bump the version for this one, because it's the best EasyBuild release so far! EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements. The executive summary for this release: - Support for --from-commit and --include-easyblocks-from-commit; - 1 new sofware-specific easyblocks for DualSPHysics; - Support for installing 101 (!) new software applications, tools, and libraries; - Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more; - Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below); Highlights for this release are listed below. More details are available in the release notes [2] which includes links to the respective pull requests for more detailed information. (this information is also available at https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.1<https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.1>) ## Highlighted enhancements & updates [enhancements or updates that (may) warrant updating existing installations are marked with (***)] - new software-specific easyblock for DualSPHysics; - enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage; - updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k; - (***) significant improvements to QuantumESPRESSO easyblock, incl. running the test suite; - enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems; - (***) add extensions to R-bundle-CRAN v2023.12 (use '--rebuild --skip' [3]); - (***) add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency; - (***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use '--rebuild --skip' [3]); ## Prominent bug fixes & changes [bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***)] - bug fixes for generic easyblocks: Cargo, CMakeMake, - bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision; - (***) fix link order in PETSc easyblock for SCOTCH >= 7.x; - (***) do not rename GCC's include-fixed directory by default + add script to regenerate it; Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0, see easyblocks PR #3254 for more info. - (***) add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component; We recommend re-installing OpenMPI 4.1.x to pick up this fix. - (***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support; - (***) add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin; - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs; - (***) move setuptools_scm extension from hatchling to Python easyconfig; We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.3-GCCcore-12.3.0 using "eb --rebuid --skip&q
RE: [easybuild] [ANN] EasyBuild v4.9.1
Dear Kenneth et al. Thanks for all the new () features and improvements. Among the whole list, I came across the recommended reinstallation for OpenMPI/4.1.x. I looked up the new patch file OpenMPI-4.1.x_add_atomic_wmb.patch<https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch>. There is a new function call "atomic_wmb()" added there, and apparently the new patched installation is tested successfully on arm64 cpus (only?) without a failure. OK, great. Now, I wonder whether this patch/reinstallation is recommended for the x86 Intel and AMD CPUs, too? Thanks in advance Ehsan -Original Message- From: easybuild-requ...@lists.ugent.be On Behalf Of Kenneth Hoste Sent: vrijdag 5 april 2024 22:32 To: easybuild@lists.ugent.be Subject: [easybuild] [ANN] EasyBuild v4.9.1 Dear EasyBuilders, We're pleased to announce the release of EasyBuild v4.9.1 [1]. We had to bump the version for this one, because it's the best EasyBuild release so far! EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements. The executive summary for this release: - Support for --from-commit and --include-easyblocks-from-commit; - 1 new sofware-specific easyblocks for DualSPHysics; - Support for installing 101 (!) new software applications, tools, and libraries; - Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more; - Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below); Highlights for this release are listed below. More details are available in the release notes [2] which includes links to the respective pull requests for more detailed information. (this information is also available at https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.1) ## Highlighted enhancements & updates [enhancements or updates that (may) warrant updating existing installations are marked with (***)] - new software-specific easyblock for DualSPHysics; - enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage; - updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k; - (***) significant improvements to QuantumESPRESSO easyblock, incl. running the test suite; - enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems; - (***) add extensions to R-bundle-CRAN v2023.12 (use '--rebuild --skip' [3]); - (***) add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency; - (***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use '--rebuild --skip' [3]); ## Prominent bug fixes & changes [bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***)] - bug fixes for generic easyblocks: Cargo, CMakeMake, - bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision; - (***) fix link order in PETSc easyblock for SCOTCH >= 7.x; - (***) do not rename GCC's include-fixed directory by default + add script to regenerate it; Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0, see easyblocks PR #3254 for more info. - (***) add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component; We recommend re-installing OpenMPI 4.1.x to pick up this fix. - (***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support; - (***) add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin; - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs; - (***) move setuptools_scm extension from hatchling to Python easyconfig; We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.3-GCCcore-12.3.0 using "eb --rebuid --skip" (or the reinstall these modules) [3]. - add patches for PyTorch v2.1.2 to fix test failures; - add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+; - (***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency; ## Supported software Support for installing 101 (!) new software packages has been added, including (but not limited to): AMICA Circlator Clarabel.rs DeepLoc devbio-napari EpiSCORE ExtremeLy GenomeComb GRASP-suite IDG IonQuant libspectre MLflow
[easybuild] [ANN] EasyBuild v4.9.1
Dear EasyBuilders, We're pleased to announce the release of EasyBuild v4.9.1 [1]. We had to bump the version for this one, because it's the best EasyBuild release so far! EasyBuild v4.9.1 is primarily a bugfix & update release, but it also includes various enhancements. The executive summary for this release: - Support for --from-commit and --include-easyblocks-from-commit; - 1 new sofware-specific easyblocks for DualSPHysics; - Support for installing 101 (!) new software applications, tools, and libraries; - Easyconfigs for various recent software versions, including CuPy 13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more; - Fixes/changes to easyblocks/easyconfigs that require reinstallation, including for GCC, OpenMPI, and Python (more info below); Highlights for this release are listed below. More details are available in the release notes [2] which includes links to the respective pull requests for more detailed information. (this information is also available at https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.1) ## Highlighted enhancements & updates [enhancements or updates that (may) warrant updating existing installations are marked with (***)] - new software-specific easyblock for DualSPHysics; - enhancement to generic easyblocks: Conda, GoPackage, PerlModule, PythonPackage; - updated & enhancements to custom easyblocks for Clang-AOMP, GCC, Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k; - (***) significant improvements to QuantumESPRESSO easyblock, incl. running the test suite; - enhancements to GCC easyblock and additional patch for recent GCC versions to support installation on RISC-V systems; - (***) add extensions to R-bundle-CRAN v2023.12 (use '--rebuild --skip' [3]); - (***) add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency; - (***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use '--rebuild --skip' [3]); ## Prominent bug fixes & changes [bug fixes or changes that (may) warrant re-installing easyconfigs are marked with (***)] - bug fixes for generic easyblocks: Cargo, CMakeMake, - bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, SLEPc, torchvision; - (***) fix link order in PETSc easyblock for SCOTCH >= 7.x; - (***) do not rename GCC's include-fixed directory by default + add script to regenerate it; Re-installing GCC 13.2.0 is required to ensure compatibility with CUDA 12.4.0, see easyblocks PR #3254 for more info. - (***) add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs, to bug in smcuda component; We recommend re-installing OpenMPI 4.1.x to pick up this fix. - (***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support; - (***) add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin; - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs; - (***) move setuptools_scm extension from hatchling to Python easyconfig; We strongly recommend to install the missing extensions for Python/3.11.3-GCCcore-12.3.0 and Python/3.11.3-GCCcore-12.3.0 using "eb --rebuid --skip" (or the reinstall these modules) [3]. - add patches for PyTorch v2.1.2 to fix test failures; - add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+; - (***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency; ## Supported software Support for installing 101 (!) new software packages has been added, including (but not limited to): AMICA Circlator Clarabel.rs DeepLoc devbio-napari EpiSCORE ExtremeLy GenomeComb GRASP-suite IDG IonQuant libspectre MLflow MSFragger noise PAGAN2 phyluce python-casacore QuPath RHEIA SemiBin Sentence-Transformers SQLAlchemy Vamb zUMIs => This brings the total number of supported software packages to 3,470 (excluding extensions)! An up-to-date list of supported software is available at [4]. Various software updates have been added, including (but not limited to): anvio 8 arrow-R 14.0.0.2 BerkeleyGW 3.1.0 + 4.0 Cartopy 0.22.0 Clang-Python-bindings 16.0.6 CUDA 12.3.2 + 12.4.0 CuPy 13.0.0 CVXPY 1.4.2 DeepLabCut 2.3.6 EggLib 3.3.0 ESMF 8.4.2 FDS 6.8.0 Flask 3.0.0 FLINT 3.1.1 GATK 4.5.0.0 GLFW 3.4 GROMACS 2024.1 Gurobi 11.0.0 HeFFTe 2.4.0 LAMMPS 2Aug2023_update2 likwid 5.3.0 matplotlib 3.8.2 medaka 1.11.3 MOABB 1.0.0 MONAI 1.3.0 NCCL 2.20.5 NGSpeciesID 0.3.0 NLTK 3.8.1 NVHPC 24.1 OCaml 4.14.0 ONNX 1.15.0 OpenFOAM v2306 + v2312 OpenSSL/3 (wrapper) PAPI 7.1.0 ParaView 5.12.0 PETSc 3.20.3 plotly.py 5.18.0 PyQt5 5.15.10
