{bio,numlib}[foss/2023b] openCARP v17.0, PETSc v3.22.5 by MarieHouillon · Pull Request #22696 · easybuilders/easybuild-easyconfigs

MarieHouillon · 2025-04-03T07:03:04Z

(created using eb --new-pr)

github-actions · 2025-04-03T07:03:35Z

Updated software `openCARP-17.0-foss-2023b.eb`

Diff against openCARP-8.2-foss-2021a.eb

easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb

diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb b/easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb
index 77f898e60c..2d7b157030 100644
--- a/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb
+++ b/easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb
@@ -1,34 +1,32 @@
-easyblock = 'CMakeMakeCp'
+easyblock = 'CMakeMake'
 
 name = 'openCARP'
-version = '8.2'
+version = '17.0'
 
 homepage = 'https://opencarp.org'
 description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments."
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/']
 sources = ['openCARP-v%(version)s.tar.gz']
-patches = ['openCARP-8.2_build-info.patch']
 checksums = [
-    '56263c4280787c5c7b2ddb2b5f5b5091745dbc7e25d16118071ba0110bff494a',  # openCARP-v8.2.tar.gz
-    '23c8754c749acc5f0f58ac3780ef7e202cefbcc8092e02e832ac2ff540367365',  # openCARP-8.2_build-info.patch
+    '6439b6b8e6a265cd6cfe39f59507418739d936de6f6e059b2d0f468df816d26e',  # openCARP-v17.0.tar.gz
 ]
 
 builddependencies = [
-    ('CMake', '3.20.1'),
+    ('CMake', '3.27.6'),
     ('gengetopt', '2.23'),
-    ('pkg-config', '0.29.2'),
+    ('pkgconf', '2.0.3'),
 ]
 
 dependencies = [
-    ('PETSc', '3.15.1'),
-    ('zlib', '1.2.11'),
+    ('PETSc', '3.22.5'),
+    ('zlib', '1.2.13'),
 ]
-
-files_to_copy = ['bin']
+# This option turns off irrelevant postinstall steps used for packaging
+configopts = "-DSPACK_BUILD=ON "
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']],

Diff against openCARP-6.0-foss-2020b.eb

easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb

diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb b/easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb
index 12b4155a3d..2d7b157030 100644
--- a/easybuild/easyconfigs/o/openCARP/openCARP-6.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb
@@ -1,34 +1,32 @@
-easyblock = 'CMakeMakeCp'
+easyblock = 'CMakeMake'
 
 name = 'openCARP'
-version = '6.0'
+version = '17.0'
 
 homepage = 'https://opencarp.org'
 description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments."
 
-toolchain = {'name': 'foss', 'version': '2020b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'openmp': True, 'usempi': True}
 
 source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/']
 sources = ['openCARP-v%(version)s.tar.gz']
-patches = ['openCARP-3.2_build-info.patch']
 checksums = [
-    '280f6dd2f5968e02e1f981f52cbd94da2ebb8d8fd00eb274d2fca6b566f40afb',  # openCARP-v6.0.tar.gz
-    '43004c7dee2981677c4316c32ce20080ad2e70760d53981aaaaba55ebc659e8c',  # openCARP-3.2_build-info.patch
+    '6439b6b8e6a265cd6cfe39f59507418739d936de6f6e059b2d0f468df816d26e',  # openCARP-v17.0.tar.gz
 ]
 
 builddependencies = [
-    ('CMake', '3.18.4'),
+    ('CMake', '3.27.6'),
     ('gengetopt', '2.23'),
-    ('pkg-config', '0.29.2'),
+    ('pkgconf', '2.0.3'),
 ]
 
 dependencies = [
-    ('PETSc', '3.14.4'),
-    ('zlib', '1.2.11'),
+    ('PETSc', '3.22.5'),
+    ('zlib', '1.2.13'),
 ]
-
-files_to_copy = ['bin']
+# This option turns off irrelevant postinstall steps used for packaging
+configopts = "-DSPACK_BUILD=ON "
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']],

Updated software `PETSc-3.22.5-foss-2023b.eb`

Diff against PETSc-3.20.3-foss-2023a.eb

easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
index 7c4db8a364..39c6e3439d 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
@@ -3,35 +3,35 @@
 # Author:    Jasper Grimm (UoY)
 ##
 name = 'PETSc'
-version = '3.20.3'
+version = '3.22.5'
 
 homepage = 'https://www.mcs.anl.gov/petsc'
 description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
  scalable (parallel) solution of scientific applications modeled by partial differential equations."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
 
 source_urls = [
     'https://web.cels.anl.gov/projects/petsc/download/release-snapshots',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['75a94fb44df0512f51ad093fa784e56b61f51b7ead5956fbe49185c203f8c245']
+checksums = ['984dba48bd26e7b17d42c078fc4f74d59e9cbc437ee25a8635865eeca9f5dd28']
 
-builddependencies = [('CMake', '3.26.3')]
+builddependencies = [('CMake', '3.27.6')]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('Boost', '1.82.0'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost', '1.83.0'),
     ('METIS', '5.1.0'),
-    ('SCOTCH', '7.0.3'),
+    ('SCOTCH', '7.0.4'),
     ('MUMPS', '5.6.1', '-metis'),
-    ('SuiteSparse', '7.1.0'),
-    ('Hypre', '2.29.0'),
+    ('SuiteSparse', '7.7.0'),
+    ('Hypre', '2.31.0'),
     ('ParMETIS', '4.0.3'),
-    ('SuperLU_DIST', '8.1.2'),
-    ('mpi4py', '3.1.4'),
+    ('SuperLU_DIST', '8.2.1'),
+    ('mpi4py', '3.1.5'),
 ]
 
 configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 '

Diff against PETSc-3.19.2-foss-2022b.eb

easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
index 1a49fec088..39c6e3439d 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
@@ -3,36 +3,35 @@
 # Author:    Jasper Grimm (UoY)
 ##
 name = 'PETSc'
-version = '3.19.2'
+version = '3.22.5'
 
 homepage = 'https://www.mcs.anl.gov/petsc'
 description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
  scalable (parallel) solution of scientific applications modeled by partial differential equations."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
 
 source_urls = [
-    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
-    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+    'https://web.cels.anl.gov/projects/petsc/download/release-snapshots',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['114f363f779bb16839b25c0e70f8b0ae0d947d50e72f7c6cddcb11b001079b16']
+checksums = ['984dba48bd26e7b17d42c078fc4f74d59e9cbc437ee25a8635865eeca9f5dd28']
 
-builddependencies = [('CMake', '3.24.3')]
+builddependencies = [('CMake', '3.27.6')]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('SciPy-bundle', '2023.02'),
-    ('Boost', '1.81.0'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost', '1.83.0'),
     ('METIS', '5.1.0'),
-    ('SCOTCH', '7.0.3'),
+    ('SCOTCH', '7.0.4'),
     ('MUMPS', '5.6.1', '-metis'),
-    ('SuiteSparse', '5.13.0', '-METIS-5.1.0'),
-    ('Hypre', '2.27.0'),
+    ('SuiteSparse', '7.7.0'),
+    ('Hypre', '2.31.0'),
     ('ParMETIS', '4.0.3'),
-    ('SuperLU_DIST', '8.1.2'),
-    ('mpi4py', '3.1.4'),
+    ('SuperLU_DIST', '8.2.1'),
+    ('mpi4py', '3.1.5'),
 ]
 
 configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 '

Diff against PETSc-3.18.4-intel-2021b.eb

easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
index 37ddfc1c7f..39c6e3439d 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb
@@ -1,41 +1,39 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+# Author:    Jasper Grimm (UoY)
+##
 name = 'PETSc'
-version = '3.18.4'
+version = '3.22.5'
 
 homepage = 'https://www.mcs.anl.gov/petsc'
 description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
  scalable (parallel) solution of scientific applications modeled by partial differential equations."""
 
-toolchain = {'name': 'intel', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
 
 source_urls = [
-    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
-    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+    'https://web.cels.anl.gov/projects/petsc/download/release-snapshots',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-patches = [
-    'PETSc_ranlib-fix.patch',
-]
-checksums = [
-    {'petsc-3.18.4.tar.gz': '6173d30637261c5b740c0bea14747759200ca2012c7343139f9216bc296a6394'},
-    {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'},
-]
+checksums = ['984dba48bd26e7b17d42c078fc4f74d59e9cbc437ee25a8635865eeca9f5dd28']
 
-builddependencies = [('CMake', '3.22.1')]
+builddependencies = [('CMake', '3.27.6')]
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('Boost', '1.77.0'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Boost', '1.83.0'),
     ('METIS', '5.1.0'),
-    ('SCOTCH', '6.1.2'),
-    ('MUMPS', '5.4.1', '-metis'),
-    ('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
-    ('Hypre', '2.24.0'),
+    ('SCOTCH', '7.0.4'),
+    ('MUMPS', '5.6.1', '-metis'),
+    ('SuiteSparse', '7.7.0'),
+    ('Hypre', '2.31.0'),
+    ('ParMETIS', '4.0.3'),
+    ('SuperLU_DIST', '8.2.1'),
+    ('mpi4py', '3.1.5'),
 ]
 
-# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
-# No rule to make target 'mpi4py-build'
 configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 '
 
 shared_libs = 1

easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb

@boegel

contributed through PR easybuilders#22696) as suggested by @boegel

easybuild/easyconfigs/p/PETSc/PETSc-3.22.3-foss-2023b.eb

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>

easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb

Co-authored-by: ocaisa <alan.ocais@cecam.org>

boegel · 2025-04-05T11:48:22Z

easybuild/easyconfigs/p/PETSc/PETSc-3.22.3-foss-2023b.eb

+# Author:    Jasper Grimm (UoY)
+##
+name = 'PETSc'
+version = '3.22.3'


@MarieHouillon Any particular reason you're sticking to PETSc 3.22.3 while 3.22.5 is already available for a while?

It's the version we use in our Docker image and for packaging currently, but we could certainly also use 3.22.5

I think if we are going to introduce a new PETSc into a toolchain, we should stick to including the latest version (particularly when it is patch release).

In fact 3.23.1 is available at this stage, thoughts @boegel ?

For us 3.22.5 is better, as 3.23 introduced changes that are not compatible with openCARP 17.0 without a patch.

I've updated the PETSc version to 3.22.5 as suggested, please let me know if anything else should be done.

boegel · 2025-04-05T13:19:39Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3523.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/7e884020a31098c8ac82531885928f6d for a full test report.

Co-authored-by: ocaisa <alan.ocais@cecam.org>

boegel · 2025-05-23T21:40:34Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16

boegelbot · 2025-05-23T21:50:10Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=22696 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22696 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6470

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegel · 2025-05-23T21:58:56Z

CI fails due to missing dependency:

Missing dependencies: SuiteSparse/7.7.0-foss-2023b-METIS-5.1.0 (no easyconfig file or existing module found)

@MarieHouillon I can't seem to find another PR that provides this, what am I overlooking?

easybuild/easyconfigs/p/PETSc/PETSc-3.22.5-foss-2023b.eb

boegelbot · 2025-05-23T22:31:40Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/41bfcfbf9d392b3fd25861c7f038bd29 for a full test report.

boegel · 2025-05-24T01:51:21Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3539.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/cccee44315c757b4a6dd50026d1adfcf for a full test report.

boegel

lgtm

boegel · 2025-05-24T07:10:11Z

Going in, thanks @MarieHouillon!

…ncludes 3.22.5 version)

Add openCARP v17.0 and dependencies for toolchain foss-2023b.

f922d2f

github-actions bot added the update label Apr 3, 2025

boegel mentioned this pull request Apr 4, 2025

{numlib}[foss/2023b] gmsh v4.12.2 and some dependencies #22084

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boegel added the EESSI Related to EESSI project label Apr 4, 2025

boegel added this to the release after 5.0.0 milestone Apr 4, 2025

julianmorillo added a commit to julianmorillo/easybuild-easyconfigs-jmorillo that referenced this pull request Apr 4, 2025

Upgrade PETSc version in gmsh-4.12.2-foss-2023b.eb (which is being

a3e98cd

contributed through PR easybuilders#22696) as suggested by @boegel

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MarieHouillon and others added 3 commits April 4, 2025 10:48

Use pkgconf instead of pkg-config

2981623

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>

remove pkg-config update

e247f68

remove trailing newline

f9ab1e7

MarieHouillon requested a review from boegel April 4, 2025 08:56

ocaisa reviewed Apr 4, 2025

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Remove empty line

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Co-authored-by: ocaisa <alan.ocais@cecam.org>

boegel changed the title ~~Add openCARP v17.0 and dependencies for toolchain foss-2023b.~~ {bio,numlib}[foss/2023b] openCARP v17.0, PETSc v3.22.3 Apr 5, 2025

boegel reviewed Apr 5, 2025

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boegel mentioned this pull request Apr 5, 2025

{numlib}[foss/2023b] PETSc v3.21.2 #20568

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1 task

MarieHouillon and others added 2 commits April 11, 2025 08:29

Update easybuild/easyconfigs/o/openCARP/openCARP-17.0-foss-2023b.eb

d1a7029

Co-authored-by: ocaisa <alan.ocais@cecam.org>

Add note about use of SPACK_BUILD option

08080c3

MarieHouillon requested a review from boegel April 22, 2025 12:12

Update PETSc version to 3.22.5

c96d826

MarieHouillon changed the title ~~{bio,numlib}[foss/2023b] openCARP v17.0, PETSc v3.22.3~~ {bio,numlib}[foss/2023b] openCARP v17.0, PETSc v3.22.5 May 15, 2025

Update PETSc version for openCARP-17.0

49b6590

boegel requested changes May 23, 2025

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drop versionsuffix for SuiteSparse dependency for PETSc 3.22.5

621e4b8

boegel approved these changes May 24, 2025

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boegel merged commit 1096350 into easybuilders:develop May 24, 2025
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julianmorillo added a commit to julianmorillo/easybuild-easyconfigs-jmorillo that referenced this pull request Jun 16, 2025

Remove PETSc-3.20.3-foss-2023b.eb as easybuilders#22696 got merged (i…

5272c97

…ncludes 3.22.5 version)

boegel mentioned this pull request Jul 31, 2025

{numlib}[foss/2024a] PETSc v3.22.0, ParMETIS v4.0.3, SuperLU_DIST v9.0.0 #21697

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Updated software `openCARP-17.0-foss-2023b.eb`

Updated software `PETSc-3.22.5-foss-2023b.eb`