{data,numlib}[foss/2024a] Armadillo v14.0.3, arpack-ng v3.9.1 by maxim-masterov · Pull Request #21608 · easybuilders/easybuild-easyconfigs

maxim-masterov · 2024-10-09T16:34:56Z

(created using eb --new-pr)

Depends on:

HDF5-1.14.5 {data,math,tools}[GCCcore/13.3.0,foss/2024a,gompi/2024a] gperftools v2.16, HDF5 v1.14.5, HPX v1.10.0 #21570

The following dependencies were only needed for GDAL (removed from this PR in favor of #21907):

~~Szip-2.1.1 {data,tools}[GCCcore/13.3.0,iimpi/2024a] HDF5 v1.14.5, Szip v2.1.1 #21510~~
Xerces-C++-3.2.5 {lib, data, numlib, tools, math}[GCCcore/13.3.0, foss/2024a, gfbf/2024a] libmad-0.15.1b, SoX-14.4.2, SuiteSparse-7.8.2, Szip-2.1.1, sympy-1.13.2, trimesh-4.4.9, Voro++-0.4.6, Xerces-C++-3.2.5, zsh-5.9 #21417
~~netCDF-4.9.2 {data}[gompi/2024a] netCDF-C++4 v4.3.1, netCDF-Fortran v4.6.1, netCDF v4.9.2, ... #21578~~
~~netCDF-4.9.2 {data}[gompi/2024a] netCDF-C++4 v4.3.1, netCDF-Fortran v4.6.1, netCDF v4.9.2, ... #21862~~
~~PCRE-8.45 Adding FLINT (+NTL), fmt, GEOS, LERC, libaio, libcerf, libcroco, libtirpc, libdap (+PCRE) for GCC(core) 13.3.0 #21282~~
~~GEOS-3.13.0 {math}[gfbf/2024a] Shapely v2.0.6 #21561~~
~~libtirpc-1.3.5 Adding FLINT (+NTL), fmt, GEOS, LERC, libaio, libcerf, libcroco, libtirpc, libdap (+PCRE) for GCC(core) 13.3.0 #21282~~
~~LERC-4.0.0 Adding FLINT (+NTL), fmt, GEOS, LERC, libaio, libcerf, libcroco, libtirpc, libdap (+PCRE) for GCC(core) 13.3.0 #21282~~
~~libgeotiff-1.7.3 {vis, data, tools, lib}[GCCcore/13.3.0] at-spi2-atk-2.38.0, at-spi2-core-2.54.0, exiv2-0.28.3, GraphicsMagick-1.3.45, HDF-4.3.0, IPython-8.27.0, inih-58, libgeotiff-1.7.3 #21433~~
~~HDF {vis, data, tools, lib}[GCCcore/13.3.0] at-spi2-atk-2.38.0, at-spi2-core-2.54.0, exiv2-0.28.3, GraphicsMagick-1.3.45, HDF-4.3.0, IPython-8.27.0, inih-58, libgeotiff-1.7.3 #21433~~

smoors · 2024-11-26T21:55:47Z

@maxim-masterov in the mean time v3.10.0 of GDAL has been released, see #21907
would you be ok if we dropped v3.9.2, or do you still need this version?

…asyconfigs into GDAL-2024a

github-actions · 2024-11-26T22:01:13Z

Updated software `Armadillo-14.0.3-foss-2024a.eb`

Diff against Armadillo-12.8.0-foss-2023b.eb

easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
index 2ca0b7de51..68036ea413 100644
--- a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
@@ -1,24 +1,24 @@
 name = 'Armadillo'
-version = '12.8.0'
+version = '14.0.3'
 
 homepage = 'https://arma.sourceforge.net/'
 description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
  a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
  as well as a subset of trigonometric and statistics functions."""
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://sourceforge.net/projects/arma/files']
 sources = [SOURCELOWER_TAR_XZ]
-checksums = ['a89bb6fece5ce9fdd1d01a4bc145cf7cc0b939c5777cca46de69c2f5e3412cf0']
+checksums = ['ebd6215eeb01ee412fed078c8a9f7f87d4e1f6187ebcdc1bc09f46095a4f4003']
 
 builddependencies = [
-    ('CMake', '3.27.6'),
+    ('CMake', '3.29.3'),
 ]
 dependencies = [
-    ('Boost', '1.83.0'),
-    ('HDF5', '1.14.3'),
-    ('arpack-ng', '3.9.0'),
+    ('Boost', '1.85.0'),
+    ('HDF5', '1.14.5'),
+    ('arpack-ng', '3.9.1'),
 ]

Diff against Armadillo-12.6.2-foss-2023a.eb

easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
index 9b6d74fe58..68036ea413 100644
--- a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
@@ -1,25 +1,25 @@
 name = 'Armadillo'
-version = '12.6.2'
+version = '14.0.3'
 
 homepage = 'https://arma.sourceforge.net/'
 description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
  a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
  as well as a subset of trigonometric and statistics functions."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://sourceforge.net/projects/arma/files']
 sources = [SOURCELOWER_TAR_XZ]
-checksums = ['e7efaaf29abda3448447bdf8cba2cceaa19afb802981b62f0c6384c842b01609']
+checksums = ['ebd6215eeb01ee412fed078c8a9f7f87d4e1f6187ebcdc1bc09f46095a4f4003']
 
 builddependencies = [
-    ('CMake', '3.26.3'),
+    ('CMake', '3.29.3'),
 ]
-
 dependencies = [
-    ('Boost', '1.82.0'),
-    ('HDF5', '1.14.0'),
-    ('arpack-ng', '3.9.0'),
+    ('Boost', '1.85.0'),
+    ('HDF5', '1.14.5'),
+    ('arpack-ng', '3.9.1'),
 ]
 
+
 moduleclass = 'numlib'

Diff against Armadillo-11.4.3-foss-2022a.eb

easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
index c8c874dba0..68036ea413 100644
--- a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-14.0.3-foss-2024a.eb
@@ -1,25 +1,25 @@
 name = 'Armadillo'
-version = '11.4.3'
+version = '14.0.3'
 
 homepage = 'https://arma.sourceforge.net/'
 description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
  a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
  as well as a subset of trigonometric and statistics functions."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 source_urls = ['https://sourceforge.net/projects/arma/files']
 sources = [SOURCELOWER_TAR_XZ]
-checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2']
+checksums = ['ebd6215eeb01ee412fed078c8a9f7f87d4e1f6187ebcdc1bc09f46095a4f4003']
 
 builddependencies = [
-    ('CMake', '3.24.3'),
+    ('CMake', '3.29.3'),
 ]
-
 dependencies = [
-    ('Boost', '1.79.0'),
-    ('HDF5', '1.12.2'),
-    ('arpack-ng', '3.8.0'),
+    ('Boost', '1.85.0'),
+    ('HDF5', '1.14.5'),
+    ('arpack-ng', '3.9.1'),
 ]
 
+
 moduleclass = 'numlib'

Updated software `arpack-ng-3.9.1-foss-2024a.eb`

Diff against arpack-ng-3.9.1-foss-2023b.eb

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb

diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
index 4f029ffc4f..29d5a00219 100644
--- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb
+++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
@@ -1,31 +1,35 @@
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+
 easyblock = 'ConfigureMake'
 
 name = 'arpack-ng'
 version = '3.9.1'
 
 homepage = 'https://github.com/opencollab/arpack-ng'
-description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-github_account = 'opencollab'
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
 checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('pkgconf', '2.0.3'),
-    ('Eigen', '3.4.0')
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('Eigen', '3.4.0'),
 ]
 
 preconfigopts = "sh bootstrap && "
 configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
 
+github_account = 'opencollab'
+
 sanity_check_paths = {
-    'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT,
-              'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT],
+    'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'],
     'dirs': [],
 }

Diff against arpack-ng-3.9.0-foss-2023b.eb

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
index 10d825ca22..29d5a00219 100644
--- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
@@ -3,23 +3,21 @@
 easyblock = 'ConfigureMake'
 
 name = 'arpack-ng'
-version = '3.9.0'
+version = '3.9.1'
 
 homepage = 'https://github.com/opencollab/arpack-ng'
 description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-github_account = 'opencollab'
-
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0']
+checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('pkgconf', '2.0.3'),
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
 ]
 dependencies = [
     ('Eigen', '3.4.0'),
@@ -28,9 +26,10 @@ dependencies = [
 preconfigopts = "sh bootstrap && "
 configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
 
+github_account = 'opencollab'
+
 sanity_check_paths = {
-    'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT,
-              'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT],
+    'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'],
     'dirs': [],
 }

Diff against arpack-ng-3.9.0-foss-2023a.eb

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
index bdc9b5aa64..29d5a00219 100644
--- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2024a.eb
@@ -1,34 +1,35 @@
-##
 # Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
-##
+
 easyblock = 'ConfigureMake'
 
 name = 'arpack-ng'
-version = '3.9.0'
+version = '3.9.1'
 
 homepage = 'https://github.com/opencollab/arpack-ng'
-description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-github_account = 'opencollab'
 source_urls = [GITHUB_SOURCE]
 sources = ['%(version)s.tar.gz']
-checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0']
+checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('pkgconf', '1.9.5'),
-    ('Eigen', '3.4.0')
+    ('Autotools', '20231222'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('Eigen', '3.4.0'),
 ]
 
 preconfigopts = "sh bootstrap && "
 configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
 
+github_account = 'opencollab'
+
 sanity_check_paths = {
-    'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT,
-              'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT],
+    'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'],
     'dirs': [],
 }

verdurin · 2024-11-27T15:41:44Z

There's also the giflib version issue - could it use 5.2.1 instead?

maxim-masterov · 2024-12-02T21:17:47Z

@smoors I can switch to GDAL v3.10.0, no problem. Only Fiona from #21614 needs to be updated.

@verdurin What's the problem with giflib 5.2.2? I see that #21907 also uses v5.2.2.

smoors · 2024-12-06T08:12:20Z

@verdurin What's the problem with giflib 5.2.2? I see that #21907 also uses v5.2.2.

see the failing check:

AssertionError: Should not have multiple variants of dependencies.
Found 2 variants of 'giflib' dependency in easyconfigs using '2024a' toolchain generation

version: 5.2.1; versionsuffix: as dep for {'ASE-3.23.0-gfbf-2024a.eb', 'matplotlib-3.9.2-gfbf-2024a.eb', 'modin-0.32.0-foss-2024a.eb', 'GPAW-24.6.0-foss-2024a.eb', 'Seaborn-0.13.2-gfbf-2024a.eb', 'dask-2024.9.1-gfbf-2024a.eb', 'bokeh-3.6.0-gfbf-2024a.eb', 'nf-core-2.14.1-foss-2024a.eb'}

version: 5.2.2; versionsuffix: as dep for {'GDAL-3.9.2-foss-2024a.eb'}

maxim-masterov · 2024-12-06T10:34:12Z

@smoors I see, I will remove GDAL from this PR in favour of #21907. Then #21907 needs to update giflib.

smoors · 2024-12-06T14:45:41Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-12-06T14:50:09Z

@smoors: 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=21608 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21608 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5404

Test results coming soon (I hope)...

Details

- notification for comment with ID 2523409395 processed

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).

boegelbot · 2024-12-06T14:52:04Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/7cfbc573971b1d666621f2bb935b7c85 for a full test report.

smoors · 2024-12-06T16:48:54Z

@boegelbot: please test @ generoso

boegelbot · 2024-12-06T16:50:09Z

@smoors: Request for testing this PR well received on login1

PR test command 'EB_PR=21608 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21608 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14825

Test results coming soon (I hope)...

Details

- notification for comment with ID 2523719078 processed

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).

boegelbot · 2024-12-06T16:53:08Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/8c08d5660f1d3e6323d69122c1d468c2 for a full test report.

smoors

lgtm

smoors · 2024-12-06T17:14:42Z

Going in, thanks @maxim-masterov!

Add GDAL and deps

42cc68c

maxim-masterov added the update label Oct 9, 2024

Remove HDF4

23468a0

maxim-masterov added the 2024a issues & PRs related to 2024a common toolchains label Oct 9, 2024

maxim-masterov mentioned this pull request Oct 10, 2024

{data}[foss/2024a] Fiona v1.10.1 #21614

Merged

Update GEOS version in GDAL-3.9.2-foss-2024a.eb

8dd4e0c

branfosj mentioned this pull request Nov 26, 2024

{data}[foss/2024a] GDAL v3.10.0 #21907

Merged

1 task

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

989c858

…asyconfigs into GDAL-2024a

Delete easybuild/easyconfigs/g/GDAL/GDAL-3.9.2-foss-2024a.eb

797d762

maxim-masterov changed the title ~~{data,numlib}[foss/2024a] Armadillo v14.0.3, arpack-ng v3.9.1, GDAL v3.9.2, ...~~ {data,numlib}[foss/2024a] Armadillo v14.0.3, arpack-ng v3.9.1 Dec 6, 2024

smoors added this to the release after 4.9.4 milestone Dec 6, 2024

smoors approved these changes Dec 6, 2024

View reviewed changes

smoors merged commit 173ebd9 into easybuilders:develop Dec 6, 2024

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

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Updated software Armadillo-14.0.3-foss-2024a.eb

Updated software arpack-ng-3.9.1-foss-2024a.eb

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Updated software `Armadillo-14.0.3-foss-2024a.eb`

Updated software `arpack-ng-3.9.1-foss-2024a.eb`

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