add (post-install) patch for libtool v2.5.4 to improve support for LLVM flang by Thyre · Pull Request #25345 · easybuilders/easybuild-easyconfigs

Thyre · 2026-02-19T20:00:17Z

(created using eb --new-pr)

Avoided using typical patches, as we'd otherwise need to re-bootstrap libtool, introducing builddependencies on Automake, Autoconf, XZ, makeinfo, help2man and texinfo.

Should be thoroughly tested with other applications using libtool before merging, just in case I forgot something. I explicitly did not patch %(installdir)s/share/libtool/configure, since I'm not sure if this is used at all...

Thyre · 2026-02-19T20:17:19Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb pocl-7.1-GCC-14.3.0.eb libtommath-1.3.0-GCCcore-14.3.0.eb UDUNITS-2.2.28-GCCcore-14.3.0.eb libneurosim-1.2.0-GCCcore-14.3.0.eb"

boegelbot · 2026-02-19T20:20:07Z

@Thyre: 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=25345 EB_ARGS="--installpath /tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb pocl-7.1-GCC-14.3.0.eb libtommath-1.3.0-GCCcore-14.3.0.eb UDUNITS-2.2.28-GCCcore-14.3.0.eb libneurosim-1.2.0-GCCcore-14.3.0.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9773

Test results coming soon (I hope)...

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boegelbot · 2026-02-19T20:30:56Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (total: 7 mins 55 secs) (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/9d9e770eea3bc5f459136600de86f5b1 for a full test report.

Thyre · 2026-02-19T22:50:11Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--from-pr=25281,25345 --installpath=/tmp/$USER/ecpr-25345"

boegelbot · 2026-02-19T23:00:09Z

@Thyre: 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=25345 EB_ARGS="--from-pr=25281,25345 --installpath=/tmp/$USER/ecpr-25345" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9775

Test results coming soon (I hope)...

Details

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boegelbot · 2026-02-19T23:04:35Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 4 (total: 4 mins 2 secs) (4 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/e01a02a674f469deac323372b69f4647 for a full test report.

Thyre · 2026-02-19T23:09:19Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--from-pr=25281,25345 --installpath=/tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb Autotools-20250527-GCCcore-14.3.0.eb arpack-ng-3.9.1-lfoss-2025b.eb"

boegelbot · 2026-02-19T23:10:08Z

@Thyre: 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=25345 EB_ARGS="--from-pr=25281,25345 --installpath=/tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb Autotools-20250527-GCCcore-14.3.0.eb arpack-ng-3.9.1-lfoss-2025b.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9776

Test results coming soon (I hope)...

Details

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boegelbot · 2026-02-19T23:13:38Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (total: 3 mins 10 secs) (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/5a05feeb6d1871efc03554cb229a3263 for a full test report.

Thyre · 2026-02-19T23:37:54Z

@Crivella, @boegel : What approach would you prefer, just adding this post-installation patch or patching before the installation and including all the necessary dependencies for that? The latter is probably safer I'd guess. We'd just need to make sure that we don't introduce the chance of a circular dependency.

Crivella · 2026-02-20T08:41:45Z

Would patching before result in anything different?
I think we have several instances of patching stuff after install, usually also not even with patches but using sed in postinstallcommands.

If it works it is fine with me.

Thyre · 2026-02-20T08:48:21Z

Would patching before result in anything different?

I think we have several instances of patching stuff after install, usually also not even with patches but using sed in postinstallcommands.

If it works it is fine with me.

I would guess that %(installdir)s/share/libtool/configure would be patched as well. Aside from that, I don't think that there should be any difference. libtool is generated during configure of the respective application, e.g. arpack-ng.

Lets try this on netCDF as well. arpack-ng looks better now.

Thyre · 2026-02-20T11:40:12Z

Test report by @Thyre
SUCCESS
Build succeeded for 2 out of 2 (total: 44 secs) (2 easyconfigs in total)
Framework - Linux Fedora Linux 43, x86_64, AMD Ryzen AI 7 350 w/ Radeon 860M (zen5), 1 x AMD Krackan [Radeon 840M / 860M Graphics] (device id: 0x1114, gfx: gfx1152, driver: Linuxversion6.18.9-200.fc43.x86_64(mockbuild@facc52a69fa549959e04aa067a88bdf9)(gcc(GCC)15.2.120260123(RedHat15.2.1-7),GNUldversion2.45.1-4.fc43)#1SMPPREEMPT_DYNAMICFriFeb621:43:09UTC2026), Python 3.14.2
See https://gist.github.com/Thyre/f73c386ad0cb7067c9a3c86bb8e4d742 for a full test report.

Thyre · 2026-02-20T11:41:21Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--installpath /tmp/$USER/ecpr-25345"

boegelbot · 2026-02-20T11:50:11Z

@Thyre: 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=25345 EB_ARGS="--installpath /tmp/$USER/ecpr-25345" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9783

Test results coming soon (I hope)...

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boegelbot · 2026-02-20T11:52:56Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (total: 2 mins 30 secs) (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/6ad1c0e11aa87a43d6bc91ea467ebe56 for a full test report.

Thyre · 2026-02-20T12:28:25Z

@boegelbot please test @ jsc-zen3
EB_ARGS="--from-pr=25273,25345 --installpath=/tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb Autotools-20250527-GCCcore-14.3.0.eb netCDF-4.9.3-lompi-2025b.eb netCDF-Fortran-4.6.2-lompi-2025b.eb"

boegelbot · 2026-02-20T12:30:07Z

@Thyre: 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=25345 EB_ARGS="--from-pr=25273,25345 --installpath=/tmp/$USER/ecpr-25345 libtool-2.5.4-GCCcore-14.3.0.eb Autotools-20250527-GCCcore-14.3.0.eb netCDF-4.9.3-lompi-2025b.eb netCDF-Fortran-4.6.2-lompi-2025b.eb" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9784

Test results coming soon (I hope)...

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boegelbot · 2026-02-20T13:14:08Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (total: 43 mins 39 secs) (4 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/39e5ed801bb6577d23bd25d058ba4e5f for a full test report.

boegel

lgtm

boegel · 2026-02-21T14:22:40Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (total: 1 min 44 secs) (3 easyconfigs in total)
node4208.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/boegel/9b158e2daf33d674f7de3d9083ae3b8c for a full test report.

boegel · 2026-02-23T06:55:29Z

Going in, thanks @Thyre!

Thyre · 2026-02-23T08:57:28Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-02-23T09:00:07Z

@Thyre: 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=25345 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_25345 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 9802

Test results coming soon (I hope)...

Details

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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).

boegelbot · 2026-02-23T09:03:07Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (total: 2 mins 28 secs) (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.23
See https://gist.github.com/boegelbot/e4c2da340b0b80717d39fd50f1a11b37 for a full test report.

Thyre · 2026-02-23T12:02:47Z

Test report by @Thyre
SUCCESS
Build succeeded for 3 out of 3 (total: 3 mins 11 secs) (3 easyconfigs in total)
jrc0900.jureca - Linux Rocky Linux 9.7, AArch64, ARM UNKNOWN (neoverse_v2), 1 x NVIDIA NVIDIA GH200 480GB, 590.48.01, Python 3.9.25
See https://gist.github.com/Thyre/6d652c9a99f9195c8600dfd9756d3214 for a full test report.

add postinstallpatch to libtool v2.5.4 to better support LLVM flang

5c53b38

github-actions Bot added 2025a issues & PRs related to 2025a common toolchains 2025b issues & PRs related to 2025b common toolchains change labels Feb 19, 2026

Thyre added bug fix 2026.1 issues & PRs related to 2026.1 common toolchains labels Feb 19, 2026

remove outdated comment from patch for libtool

e6ca46f

This was referenced Feb 20, 2026

{numlib}[lfoss/2025b] arpack-ng v3.9.1 #25281

Merged

{data}[lompi/2025b] netCDF v4.9.3, netCDF-C++4 v4.3.1, netCDF-Fortran v4.6.2, PnetCDF v1.14.1 #25273

Merged

Thyre added the ready-to-review label Feb 20, 2026

Thyre added this to the release after 5.2.1 milestone Feb 20, 2026

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boegel changed the title ~~add postinstallpatch to libtool v2.5.4 to better support LLVM flang~~ add (post-install) patch for libtool v2.5.4 to improve support for LLVM flang Feb 21, 2026

boegel approved these changes Feb 21, 2026

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boegel merged commit d7c99b8 into easybuilders:develop Feb 23, 2026
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Thyre removed the ready-to-review label Feb 23, 2026

boegel removed the change label Feb 25, 2026

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