From a51357d888a0c731dba1ed339564865398df2b68 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 13:45:18 +0100 Subject: [PATCH 01/23] adding easyconfigs: snakemake-8.27.0-foss-2024a.eb --- .../snakemake/snakemake-8.27.0-foss-2024a.eb | 153 ++++++++++++++++++ 1 file changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb new file mode 100644 index 00000000000..9e09a6ceb82 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -0,0 +1,153 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '8.27.0' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('poetry', '1.8.3'), +] +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('GitPython', '3.1.43'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0.2'), + ('wrapt', '1.15.0'), + ('PuLP', '2.8.0'), + ('Cython', '3.0.10', '', {'name': 'GCCcore', 'version': '13.3.0'}), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('plac', '1.4.3', { + 'checksums': ['d4cb3387b2113a28aebd509433d0264a4e5d9bb7c1a86db4fbd0a8f11af74eb3'], + }), + ('dpath', '2.2.0', { + 'checksums': ['34f7e630dc55ea3f219e555726f5da4b4b25f2200319c8e6902c394258dd6a3e'], + }), + ('yte', '1.5.5', { + 'checksums': ['2c49831859f3216f313a17688900690872e05f8fbe77cb5d151bdb896357d57e'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('throttler', '1.2.2', { + 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('ConfigArgParse', '1.7', { + 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], + }), + ('argparse-dataclass', '2.0.0', { + 'modulename': 'argparse_dataclass', + 'source_tmpl': 'argparse_dataclass-%(version)s.tar.gz', + 'checksums': ['09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f'], + }), + ('snakemake-interface-common', '1.17.4', { + 'modulename': 'snakemake_interface_common', + 'source_tmpl': 'snakemake_interface_common-%(version)s.tar.gz', + 'checksums': ['c2142e1b93cbc18c2cf41d15968ba8688f60b077c8284e5de057cccfc215d4d3'], + }), + ('reretry', '0.11.8', { + 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], + }), + ('snakemake-interface-storage-plugins', '3.3.0', { + 'modulename': 'snakemake_interface_storage_plugins', + 'source_tmpl': 'snakemake_interface_storage_plugins-%(version)s.tar.gz', + 'checksums': ['203d8f794dfb37d568ad01a6c375fa8beac36df8e488c0f9b9f75984769c362a'], + }), + ('snakemake-interface-report-plugins', '1.1.0', { + 'modulename': 'snakemake_interface_report_plugins', + 'source_tmpl': 'snakemake_interface_report_plugins-%(version)s.tar.gz', + 'checksums': ['b1ee444b2fca51225cf8a102f8e56633791d01433cd00cf07a1d9713a12313a5'], + }), + ('snakemake-interface-executor-plugins', '9.3.3', { + 'modulename': 'snakemake_interface_executor_plugins', + 'source_tmpl': 'snakemake_interface_executor_plugins-%(version)s.tar.gz', + 'checksums': ['11e59af04bf00e9aaee7f0b99f9358910becfccdad7b18a455d37601f6d8d2ea'], + }), + ('smart-open', '7.1.0', { + 'sources': ['smart_open-%(version)s.tar.gz'], + 'checksums': ['a4f09f84f0f6d3637c6543aca7b5487438877a21360e7368ccf1f704789752ba'], + }), + ('jupyter-core', '5.7.2', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('nbformat', '5.10.4', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b'], + }), + ('Jinja2', '3.1.4', { + 'sources': ['jinja2-%(version)s.tar.gz'], + 'checksums': ['4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369'], + }), + ('immutables', '0.21', { + 'checksums': ['b55ffaf0449790242feb4c56ab799ea7af92801a0a43f9e2f4f8af2ab24dfc4a'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('connection-pool', '0.0.3', { + 'sources': ['connection_pool-%(version)s.tar.gz'], + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('conda-inject', '1.3.2', { + 'sources': ['conda_inject-%(version)s.tar.gz'], + 'checksums': ['0b8cde8c47998c118d8ff285a04977a3abcf734caf579c520fca469df1cd0aac'], + }), + (name, version, { + 'checksums': ['7bee7e4f255fd75738b6840c3453c9b5a4f33c628705c38a5a462db008f0334d'], + }), + ('snakemake-executor-plugin-slurm-jobstep', '0.2.1', { + 'modulename': 'snakemake_executor_plugin_slurm_jobstep', + 'source_tmpl': 'snakemake_executor_plugin_slurm_jobstep-%(version)s.tar.gz', + 'checksums': ['58894d52b5998a34fa6f60ec511ff0bfde4a9ec96714bcaa3cd2f46cf8a33859'], + }), + ('snakemake-executor-plugin-flux', '0.1.1', { + 'modulename': 'snakemake_executor_plugin_flux', + 'source_tmpl': 'snakemake_executor_plugin_flux-%(version)s.tar.gz', + 'checksums': ['26655bd1cf5d7db5dfcfdfbd006c1db35968c0ad1772e0b010e64e6f71b00163'], + }), + ('snakemake-executor-plugin-slurm', '0.12.0', { + 'modulename': 'snakemake_executor_plugin_slurm', + 'source_tmpl': 'snakemake_executor_plugin_slurm-%(version)s.tar.gz', + 'checksums': ['7069590060e914afcd608c75aee8ccf1128f662dda3e258a84f3c83302232763'], + }), + ('snakemake-executor-plugin-cluster-sync', '0.1.4', { + 'modulename': 'snakemake_executor_plugin_cluster_sync', + 'source_tmpl': 'snakemake_executor_plugin_cluster_sync-%(version)s.tar.gz', + 'checksums': ['6a6dcb2110d4c2ee74f9a48ea68e0fd7ddd2800672ebef00a01faa4affa835ad'], + }), + ('snakemake-executor-plugin-cluster-generic', '1.0.9', { + 'modulename': 'snakemake_executor_plugin_cluster_generic', + 'source_tmpl': 'snakemake_executor_plugin_cluster_generic-%(version)s.tar.gz', + 'checksums': ['ad0dc2d8bde7d4f336364bebe11a3b2209653c481ce8fbb0ae8bec81016a9a14'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'tools' From b811390d672eb702ad4da32961c1a1c9abc1e6f0 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 9 Jan 2025 18:48:48 +0100 Subject: [PATCH 02/23] Update easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb Co-authored-by: Alexander Grund --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index 9e09a6ceb82..f9e497ff4fb 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -95,10 +95,6 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b'], }), - ('Jinja2', '3.1.4', { - 'sources': ['jinja2-%(version)s.tar.gz'], - 'checksums': ['4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369'], - }), ('immutables', '0.21', { 'checksums': ['b55ffaf0449790242feb4c56ab799ea7af92801a0a43f9e2f4f8af2ab24dfc4a'], }), From 2d924d2f97e5ad6144b5eaf40f525d76d5ba6178 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 18:59:18 +0100 Subject: [PATCH 03/23] Removing redundant Cython from dependencies to builddependencies --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index f9e497ff4fb..bbe5c31b3c0 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2024a'} builddependencies = [ ('poetry', '1.8.3'), + ('Cython', '3.0.10'), ] dependencies = [ ('Python', '3.12.3'), @@ -20,7 +21,6 @@ dependencies = [ ('PyYAML', '6.0.2'), ('wrapt', '1.15.0'), ('PuLP', '2.8.0'), - ('Cython', '3.0.10', '', {'name': 'GCCcore', 'version': '13.3.0'}), ] sanity_pip_check = True From 71ef70e871643ae282b33d1bea10e33206f8550d Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 19:44:51 +0100 Subject: [PATCH 04/23] Upgrading dependency IPython to v8.28.0 --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index bbe5c31b3c0..b8c95d78033 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python-bundle-PyPI', '2024.06'), ('SciPy-bundle', '2024.05'), ('GitPython', '3.1.43'), - ('IPython', '8.14.0'), + ('IPython', '8.28.0'), ('PyYAML', '6.0.2'), ('wrapt', '1.15.0'), ('PuLP', '2.8.0'), From adb3420fe2e1b92d5dbc34fb0490f7548b12d8e7 Mon Sep 17 00:00:00 2001 From: andped Date: Thu, 9 Jan 2025 21:04:10 +0100 Subject: [PATCH 05/23] Upgrading dependency wrapt to v1.16.0 --- .../easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index b8c95d78033..ee1af057ebf 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -19,7 +19,7 @@ dependencies = [ ('GitPython', '3.1.43'), ('IPython', '8.28.0'), ('PyYAML', '6.0.2'), - ('wrapt', '1.15.0'), + ('wrapt', '1.16.0'), ('PuLP', '2.8.0'), ] From aec7e7ef845fabc3e4454092c01d6c6dd06b19bb Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 09:17:00 +0100 Subject: [PATCH 06/23] Adding new easyconfig PuLP-2.8.0-foss-2024a.eb --- .../p/PuLP/PuLP-2.8.0-foss-2024a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb new file mode 100644 index 00000000000..8fa2ac3a40d --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# Updated: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.8.0' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'] + +dependencies = [ + ('Python', '3.12.3'), + ('GLPK', '5.0'), + ('Cbc', '2.10.12'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From dda7ff95d77d6ac17f16ed9f0ad235dcb09e0bc9 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 11:26:51 +0100 Subject: [PATCH 07/23] Adding new easyconfig Cbc-2.10.12-foss-2024a.eb --- .../c/Cbc/Cbc-2.10.12-foss-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb new file mode 100644 index 00000000000..f205cbb1a3a --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Cbc' +version = '2.10.12' + +homepage = 'https://github.com/coin-or/Cbc' +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases'] +sources = ['%(version)s.tar.gz'] +checksums = ['9ed71e4b61668462fc3794c102e26b4bb01a047efbbbcbd69ae7bde1f04f46a8'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), + ('Cgl', '0.60.8'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' From 0fbc9cb62f3a1081d861a12053f3aac49ea7c06d Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 11:41:48 +0100 Subject: [PATCH 08/23] Adding new easyconfig SCOTCH-7.0.6-gompi-2024a.eb --- .../s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb new file mode 100644 index 00000000000..57b94076913 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb @@ -0,0 +1,25 @@ +name = 'SCOTCH' +version = '7.0.6' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['b44acd0d2f53de4b578fa3a88944cccc45c4d2961cd8cefa9b9a1d5431de8e2b'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('zlib', '1.3.1'), +] + +threadedmpi = False + +moduleclass = 'math' From 247786930e47b38e4fbb942a326bc6ad43c9134b Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 13:43:22 +0100 Subject: [PATCH 09/23] Updating Cbc-2.10.12-foss-2024a.eb --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index f205cbb1a3a..8433f8b8bfb 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -22,7 +22,7 @@ builddependencies = [ ] dependencies = [ ('METIS', '5.1.0'), - ('MUMPS', '5.6.1', '-metis'), + ('MUMPS', '5.7.2', '-metis'), ('CoinUtils', '2.11.10'), ('Osi', '0.108.9'), ('Clp', '1.17.9'), From e8b3603c7d83954b0f9f0839837cb8f23fa69533 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 13:49:41 +0100 Subject: [PATCH 10/23] Updating MUMPS-5.7.2-foss-2024a-metis.eb --- .../m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb new file mode 100644 index 00000000000..11d0f00df20 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.7.2' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps-solver.org/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8'] + +dependencies = [ + ('SCOTCH', '7.0.6'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' From 2721934aef163035e6bf5f39247fe9f90cbee299 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Fri, 10 Jan 2025 17:32:28 +0100 Subject: [PATCH 11/23] Update easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb Co-authored-by: ocaisa --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index 8433f8b8bfb..fa5a192bb78 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -32,7 +32,14 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" ' +configopts += ' --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +configopts += ' --without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += ' --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += ' --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data ' +configopts += ' --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += ' --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" ' +configopts += ' --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { From ecc83757119afba919ff1d94ac4b0af20fe55a88 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 17:57:20 +0100 Subject: [PATCH 12/23] Adding new easyconfig CoinUtils-2.11.12-GCC-13.3.0.eb --- .../CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb new file mode 100644 index 00000000000..1ba1a8733c8 --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.12' + +homepage = 'https://github.com/coin-or/CoinUtils' +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['eef1785d78639b228ae2de26b334129fe6a7d399c4ac6f8fc5bb9054ba00de64'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From bc5541e2afb2e754c43b273fbb01fefd4d98f2c9 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 18:13:13 +0100 Subject: [PATCH 13/23] Adding new easyconfig Osi-0.108.11-GCC-13.3.0.eb --- .../o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb new file mode 100644 index 00000000000..c1f3359f5ff --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.11' + +homepage = 'https://github.com/coin-or/Osi' +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1063b6a057e80222e2ede3ef0c73c0c54697e0fee1d913e2bef530310c13a670'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('CoinUtils', '2.11.12'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + + +sanity_check_paths = { + 'files': ['lib/libOsi.so', 'lib/libOsiCommonTests.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From df145eb6e5517071d34e332c09cfbbb8719c53bb Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 18:37:11 +0100 Subject: [PATCH 14/23] Adding new easyconfig Clp-1.17.10-foss-2024a.eb --- .../c/Clp/Clp-1.17.10-foss-2024a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb new file mode 100644 index 00000000000..1b57ea3358e --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.10' + +homepage = 'https://github.com/coin-or/Clp' +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['0d79ece896cdaa4a3855c37f1c28e6c26285f74d45f635046ca0b6d68a509885'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.7.2', '-metis'), + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('bzip2', '1.0.8'), + ('zlib', '1.3.1'), +] + +# Use BLAS/LAPACK from toolchain +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libClp.so', 'lib/libClpSolver.so', 'lib/libOsiClp.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' \ No newline at end of file From a7a56222be0674fff543bc46b3798d6faeffa560 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 19:17:44 +0100 Subject: [PATCH 15/23] Breaking up line for configopts in Clp-1.17.10-foss-2024a.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 1b57ea3358e..9c00b4cba8e 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -30,7 +30,13 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" --with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" --without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data --with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' +configopts = '--with-blas="$LIBBLAS" ' +configopts += '--with-lapack="$LIBLAPACK" ' +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' +configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { From 5a3effccae249c25bc55ee990eb1d19da1e9d265 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 20:48:27 +0100 Subject: [PATCH 16/23] Updating some dependencies in Cbc-2.10.12-foss-2024a.eb --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index fa5a192bb78..85661243b14 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -23,9 +23,9 @@ builddependencies = [ dependencies = [ ('METIS', '5.1.0'), ('MUMPS', '5.7.2', '-metis'), - ('CoinUtils', '2.11.10'), - ('Osi', '0.108.9'), - ('Clp', '1.17.9'), + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('Clp', '1.17.10'), ('Cgl', '0.60.8'), ('bzip2', '1.0.8'), ('zlib', '1.3.1'), From 0ccb63780a3a2f562387247ecb375d8ae57ecd21 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 21:45:17 +0100 Subject: [PATCH 17/23] Adding easyconfig for Cgl-0.60.8-foss-2024a.eb --- .../c/Cgl/Cgl-0.60.8-foss-2024a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb new file mode 100644 index 00000000000..fa9f1a86c37 --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Cgl' +version = '0.60.8' + +homepage = 'https://github.com/coin-or/Cgl' +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Doxygen', '1.11.0'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('CoinUtils', '2.11.12'), + ('Osi', '0.108.11'), + ('Clp', '1.17.10'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + + +sanity_check_paths = { + 'files': ['lib/libCgl.so'], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = 'math' From d3bf2e76bb62e9a2c60b9ebfaa3dd96327038d68 Mon Sep 17 00:00:00 2001 From: andped Date: Fri, 10 Jan 2025 23:01:25 +0100 Subject: [PATCH 18/23] Reducing line length in Clp-1.17.10-foss-2024a.eb and Osi-0.108.11-GCC-13.3.0.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 3 ++- easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 9c00b4cba8e..7631106f719 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -33,7 +33,8 @@ dependencies = [ configopts = '--with-blas="$LIBBLAS" ' configopts += '--with-lapack="$LIBLAPACK" ' configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord ' +configopts += '-lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index c1f3359f5ff..5158800b817 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -31,7 +31,8 @@ dependencies = [ ] # Disable GLPK because Osi requires GLPK<=4.48 -configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' sanity_check_paths = { From aea95f1efb05fb0df911ccc2dcd1db52e2aac4b9 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:09:04 +0100 Subject: [PATCH 19/23] Update CoinUtils-2.11.12-GCC-13.3.0.eb --- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb index 1ba1a8733c8..44817e45d52 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -33,4 +33,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 926af35e1befe891297da8a548736921d7233d05 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:11:03 +0100 Subject: [PATCH 20/23] Update Clp-1.17.10-foss-2024a.eb --- easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 7631106f719..79e1bb66dc3 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -48,4 +48,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 2b3e4b2b3fda303c96be7e6b7167c0b99fc62ea1 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Jan 2025 23:12:13 +0100 Subject: [PATCH 21/23] Update Osi-0.108.11-GCC-13.3.0.eb --- easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index 5158800b817..3c1bdfbc9f4 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -43,4 +43,4 @@ sanity_check_paths = { # other coin-or projects expect instead of modextrapaths = {'CPATH': 'include/coin'} -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From c0b48d745ae2df72b1c1806281fce9dc6ffa0c9c Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Jan 2025 15:03:17 +0100 Subject: [PATCH 22/23] Some style updates --- .../c/Cbc/Cbc-2.10.12-foss-2024a.eb | 31 ++++++++++++------- .../c/Cgl/Cgl-0.60.8-foss-2024a.eb | 6 ++-- .../c/Clp/Clp-1.17.10-foss-2024a.eb | 22 +++++++++---- .../o/Osi/Osi-0.108.11-GCC-13.3.0.eb | 9 +++--- .../snakemake/snakemake-8.27.0-foss-2024a.eb | 6 ++-- 5 files changed, 48 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb index 85661243b14..3fe2a0752e1 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb @@ -32,19 +32,28 @@ dependencies = [ ] # Use BLAS/LAPACK from toolchain -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" ' -configopts += ' --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' -configopts += ' --without-glpk --with-coinutils-lib="-lCoinUtils" ' -configopts += ' --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' -configopts += ' --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data ' -configopts += ' --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' -configopts += ' --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl" ' -configopts += ' --with-cgl-datadir=$EBROOTCGL/share/coin/Data ' - +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb index fa9f1a86c37..27b950093ca 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb @@ -31,15 +31,17 @@ dependencies = [ # Use CoinUtils from EB configopts = '--with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' +# Use Clp from EB configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['lib/libCgl.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb index 79e1bb66dc3..1ca1d91bfec 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb @@ -32,17 +32,27 @@ dependencies = [ # Use BLAS/LAPACK from toolchain configopts = '--with-blas="$LIBBLAS" ' configopts += '--with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord ' -configopts += '-lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' -configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' -configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'lib/libClp.so', 'lib/libClpSolver.so', 'lib/libOsiClp.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb index 3c1bdfbc9f4..9462fa85bc9 100644 --- a/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb @@ -31,13 +31,14 @@ dependencies = [ ] # Disable GLPK because Osi requires GLPK<=4.48 -configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' - sanity_check_paths = { - 'files': ['lib/libOsi.so', 'lib/libOsiCommonTests.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb index ee1af057ebf..2c6a8120453 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.27.0-foss-2024a.eb @@ -140,10 +140,10 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], } -sanity_check_commands = ['%(name)s --help'] +sanity_check_commands = ['snakemake --help'] moduleclass = 'tools' From f99725bbd910faff71ace487cd7f520022c04921 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Jan 2025 15:12:32 +0100 Subject: [PATCH 23/23] Final tweaks --- .../easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb | 5 ++--- easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb | 1 + 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb index 44817e45d52..8d58c97eb49 100644 --- a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb @@ -24,10 +24,9 @@ dependencies = [ ('zlib', '1.3.1'), ] - sanity_check_paths = { - 'files': ['lib/libCoinUtils.so'], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'], + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } # other coin-or projects expect instead of diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb index 57b94076913..27002098227 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb @@ -16,6 +16,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('flex', '2.6.4'), ] + dependencies = [ ('zlib', '1.3.1'), ]