From a2f9360850d8628f74885e2e61ed7a204d3b35d1 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Mon, 14 Apr 2025 19:55:31 +0200 Subject: [PATCH 1/4] {2023.06}[2023a,a64fx] apps originally built with EB 4.8.2 --- .../a64fx/eessi-2023.06-eb-4.9.4-2023a.yml | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml index 170a639064..082c3331f0 100644 --- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml @@ -9,3 +9,74 @@ easyconfigs: options: # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21600 from-commit: 9b12318bcff1749781d9eb71c23e21bc3a79ed01 +# from here continuing building up the stack; first apps originally built with EB +# 4.8.2 +# originally built with EB 4.8.2; PR 19270 included since EB 4.9.0 +# - pybind11-2.11.1-GCCcore-12.3.0.eb: +# # avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency; +# # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19270 +# options: +# from-pr: 19270 + - pybind11-2.11.1-GCCcore-12.3.0.eb +# the package SciPy-bundle itself has to be rebuilt; here we use the commit to add the dependency +# Cython; PR 21693 is included since EB 5.0.0 +# - SciPy-bundle-2023.07-gfbf-2023a.eb: +# options: +# from-pr: 21693 + - SciPy-bundle-2023.07-gfbf-2023a.eb: + options: + from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0 +# originally built with EB 4.8.2; PR 19268 included since EB 4.9.0 +# - TensorFlow-2.13.0-foss-2023a.eb: +# # patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot; +# # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19268 +# options: +# from-pr: 19268 + - TensorFlow-2.13.0-foss-2023a.eb + - X11-20230603-GCCcore-12.3.0.eb +# originally built with EB 4.8.2; PR 19339 included since EB 4.9.0 +# - HarfBuzz-5.3.1-GCCcore-12.3.0.eb: +# options: +# from-pr: 19339 + - HarfBuzz-5.3.1-GCCcore-12.3.0.eb + - Qt5-5.15.10-GCCcore-12.3.0.eb + - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb +# originally built with EB 4.8.2; PR 19363 included since EB 4.9.0 +# - LHAPDF-6.5.4-GCC-12.3.0.eb: +# options: +# from-pr: 19363 + - LHAPDF-6.5.4-GCC-12.3.0.eb +# originally built with EB 4.8.2; PR 19397 included since EB 4.9.0 +# - LoopTools-2.15-GCC-12.3.0.eb: +# options: +# from-pr: 19397 + - LoopTools-2.15-GCC-12.3.0.eb +# originally built with EB 4.8.2; PR 19185 included since EB 4.9.0 +# - R-4.3.2-gfbf-2023a.eb: +# options: +# from-pr: 19185 + - R-4.3.2-gfbf-2023a.eb +# originally built with EB 4.8.2; source URL has changed recently +# - Boost-1.82.0-GCC-12.3.0.eb + - Boost-1.82.0-GCC-12.3.0.eb: + options: + # source URLs for Boost have changed, corresponding PR is + # https://github.com/easybuilders/easybuild-easyconfigs/pull/22157 + from-commit: 5bebccf792ccf35a8ee3250bc8fed86dff5d5df9 + - netCDF-4.9.2-gompi-2023a.eb + - FFmpeg-6.0-GCCcore-12.3.0.eb +# originally built with EB 4.8.2; PR 19455 included since EB 4.9.0 +# - ALL-0.9.2-foss-2023a.eb: +# options: +# from-pr: 19455 + - ALL-0.9.2-foss-2023a.eb +# originally built with EB 4.8.2; PR 19735 included since EB 4.9.1 +# - CDO-2.2.2-gompi-2023a.eb: +# options: +# from-pr: 19735 + - CDO-2.2.2-gompi-2023a.eb +# originally built with EB 4.8.2; PR 19820 included since EB 4.9.1 +# - BWA-0.7.17-20220923-GCCcore-12.3.0.eb: +# options: +# from-pr: 19820 + - BWA-0.7.17-20220923-GCCcore-12.3.0.eb From adce1f956df5c116d7a6994f133cd728ff95672b Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Tue, 15 Apr 2025 18:37:19 +0200 Subject: [PATCH 2/4] install dependencies of TensorFlow --- .../a64fx/eessi-2023.06-eb-4.9.4-2023a.yml | 116 ++++++++++-------- 1 file changed, 63 insertions(+), 53 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml index 082c3331f0..d0ae1fb23f 100644 --- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml @@ -26,57 +26,67 @@ easyconfigs: - SciPy-bundle-2023.07-gfbf-2023a.eb: options: from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0 -# originally built with EB 4.8.2; PR 19268 included since EB 4.9.0 -# - TensorFlow-2.13.0-foss-2023a.eb: -# # patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot; -# # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19268 +# first install dependencies of TensorFlow + - Bazel-6.3.1-GCCcore-12.3.0.eb + - dill-0.3.7-GCCcore-12.3.0.eb + - flatbuffers-23.5.26-GCCcore-12.3.0.eb + - h5py-3.9.0-foss-2023a.eb + - flatbuffers-python-23.5.26-GCCcore-12.3.0.eb + - JsonCpp-1.9.5-GCCcore-12.3.0.eb + - nsync-1.26.0-GCCcore-12.3.0.eb + - RE2-2023-08-01-GCCcore-12.3.0.eb + - protobuf-python-4.24.0-GCCcore-12.3.0.eb +## originally built with EB 4.8.2; PR 19268 included since EB 4.9.0 +## - TensorFlow-2.13.0-foss-2023a.eb: +## # patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot; +## # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19268 +## options: +## from-pr: 19268 +# - TensorFlow-2.13.0-foss-2023a.eb +# - X11-20230603-GCCcore-12.3.0.eb +## originally built with EB 4.8.2; PR 19339 included since EB 4.9.0 +## - HarfBuzz-5.3.1-GCCcore-12.3.0.eb: +## options: +## from-pr: 19339 +# - HarfBuzz-5.3.1-GCCcore-12.3.0.eb +# - Qt5-5.15.10-GCCcore-12.3.0.eb +# - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb +## originally built with EB 4.8.2; PR 19363 included since EB 4.9.0 +## - LHAPDF-6.5.4-GCC-12.3.0.eb: +## options: +## from-pr: 19363 +# - LHAPDF-6.5.4-GCC-12.3.0.eb +## originally built with EB 4.8.2; PR 19397 included since EB 4.9.0 +## - LoopTools-2.15-GCC-12.3.0.eb: +## options: +## from-pr: 19397 +# - LoopTools-2.15-GCC-12.3.0.eb +## originally built with EB 4.8.2; PR 19185 included since EB 4.9.0 +## - R-4.3.2-gfbf-2023a.eb: +## options: +## from-pr: 19185 +# - R-4.3.2-gfbf-2023a.eb +## originally built with EB 4.8.2; source URL has changed recently +## - Boost-1.82.0-GCC-12.3.0.eb +# - Boost-1.82.0-GCC-12.3.0.eb: # options: -# from-pr: 19268 - - TensorFlow-2.13.0-foss-2023a.eb - - X11-20230603-GCCcore-12.3.0.eb -# originally built with EB 4.8.2; PR 19339 included since EB 4.9.0 -# - HarfBuzz-5.3.1-GCCcore-12.3.0.eb: -# options: -# from-pr: 19339 - - HarfBuzz-5.3.1-GCCcore-12.3.0.eb - - Qt5-5.15.10-GCCcore-12.3.0.eb - - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb -# originally built with EB 4.8.2; PR 19363 included since EB 4.9.0 -# - LHAPDF-6.5.4-GCC-12.3.0.eb: -# options: -# from-pr: 19363 - - LHAPDF-6.5.4-GCC-12.3.0.eb -# originally built with EB 4.8.2; PR 19397 included since EB 4.9.0 -# - LoopTools-2.15-GCC-12.3.0.eb: -# options: -# from-pr: 19397 - - LoopTools-2.15-GCC-12.3.0.eb -# originally built with EB 4.8.2; PR 19185 included since EB 4.9.0 -# - R-4.3.2-gfbf-2023a.eb: -# options: -# from-pr: 19185 - - R-4.3.2-gfbf-2023a.eb -# originally built with EB 4.8.2; source URL has changed recently -# - Boost-1.82.0-GCC-12.3.0.eb - - Boost-1.82.0-GCC-12.3.0.eb: - options: - # source URLs for Boost have changed, corresponding PR is - # https://github.com/easybuilders/easybuild-easyconfigs/pull/22157 - from-commit: 5bebccf792ccf35a8ee3250bc8fed86dff5d5df9 - - netCDF-4.9.2-gompi-2023a.eb - - FFmpeg-6.0-GCCcore-12.3.0.eb -# originally built with EB 4.8.2; PR 19455 included since EB 4.9.0 -# - ALL-0.9.2-foss-2023a.eb: -# options: -# from-pr: 19455 - - ALL-0.9.2-foss-2023a.eb -# originally built with EB 4.8.2; PR 19735 included since EB 4.9.1 -# - CDO-2.2.2-gompi-2023a.eb: -# options: -# from-pr: 19735 - - CDO-2.2.2-gompi-2023a.eb -# originally built with EB 4.8.2; PR 19820 included since EB 4.9.1 -# - BWA-0.7.17-20220923-GCCcore-12.3.0.eb: -# options: -# from-pr: 19820 - - BWA-0.7.17-20220923-GCCcore-12.3.0.eb +# # source URLs for Boost have changed, corresponding PR is +# # https://github.com/easybuilders/easybuild-easyconfigs/pull/22157 +# from-commit: 5bebccf792ccf35a8ee3250bc8fed86dff5d5df9 +# - netCDF-4.9.2-gompi-2023a.eb +# - FFmpeg-6.0-GCCcore-12.3.0.eb +## originally built with EB 4.8.2; PR 19455 included since EB 4.9.0 +## - ALL-0.9.2-foss-2023a.eb: +## options: +## from-pr: 19455 +# - ALL-0.9.2-foss-2023a.eb +## originally built with EB 4.8.2; PR 19735 included since EB 4.9.1 +## - CDO-2.2.2-gompi-2023a.eb: +## options: +## from-pr: 19735 +# - CDO-2.2.2-gompi-2023a.eb +## originally built with EB 4.8.2; PR 19820 included since EB 4.9.1 +## - BWA-0.7.17-20220923-GCCcore-12.3.0.eb: +## options: +## from-pr: 19820 +# - BWA-0.7.17-20220923-GCCcore-12.3.0.eb From 2ce57eed85edb7618bab62f47b6e61bb7f3df0a1 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Tue, 15 Apr 2025 21:08:28 +0200 Subject: [PATCH 3/4] install Cython --- .../2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml index d0ae1fb23f..9d4e2abd16 100644 --- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml @@ -26,7 +26,12 @@ easyconfigs: - SciPy-bundle-2023.07-gfbf-2023a.eb: options: from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0 -# first install dependencies of TensorFlow +# install Cython (new dependency of SciPy-bundle) + - Cython-3.0.8-GCCcore-12.3.0.eb: + options: + # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20578 + from-commit: c4c2826ed8afe83885bba113b0aee36477d2948c +# install dependencies of TensorFlow - Bazel-6.3.1-GCCcore-12.3.0.eb - dill-0.3.7-GCCcore-12.3.0.eb - flatbuffers-23.5.26-GCCcore-12.3.0.eb From ed0e345b92b7a051ea76996178466b9c9b689bd0 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 16 Apr 2025 21:04:36 +0200 Subject: [PATCH 4/4] use slightly older version for Cython ec --- .../2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml index 9d4e2abd16..fe1e7d3631 100644 --- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml +++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.4-2023a.yml @@ -26,11 +26,15 @@ easyconfigs: - SciPy-bundle-2023.07-gfbf-2023a.eb: options: from-commit: 7c5144d2c1a061cd9f08b5901970b7f6ec5eb5c0 -# install Cython (new dependency of SciPy-bundle) - - Cython-3.0.8-GCCcore-12.3.0.eb: - options: - # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20578 - from-commit: c4c2826ed8afe83885bba113b0aee36477d2948c +# install Cython (new dependency of SciPy-bundle), PR 20578 is included since +# EB 5.0.0; try a little older version from PR 20525 that is included since EB +# 4.9.2 +# - Cython-3.0.8-GCCcore-12.3.0.eb: +# options: +# # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20578 +# from-commit: c4c2826ed8afe83885bba113b0aee36477d2948c +# for the version from EB 4.9.2 we don't need any options because we use EB 4.9.4 + - Cython-3.0.8-GCCcore-12.3.0.eb # install dependencies of TensorFlow - Bazel-6.3.1-GCCcore-12.3.0.eb - dill-0.3.7-GCCcore-12.3.0.eb