Update Amber easyblock for AmberTools >= 24.x by pavelToman · Pull Request #3868 · easybuilders/easybuild-easyblocks

pavelToman · 2025-08-04T15:48:51Z

For:

{chem}[foss/2025a] AmberTools v25.2 easybuild-easyconfigs#23420

pavelToman · 2025-08-04T16:37:48Z

@boegelbot please test @ jsc-zen3 EB_ARGS="AmberTools-23.6-foss-2023a.eb Amber-24.3-foss-2023a-AmberTools-24.10.eb Amber-24.0-foss-2024a-AmberTools-24.0.eb"

boegelbot · 2025-08-04T16:53:09Z

@pavelToman: 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=3868 EB_ARGS="AmberTools-23.6-foss-2023a.eb Amber-24.3-foss-2023a-AmberTools-24.10.eb Amber-24.0-foss-2024a-AmberTools-24.0.eb" EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3868 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7486

Test results coming soon (I hope)...

Details

- notification for comment with ID 3151472262 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 · 2025-08-04T17:51:38Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

FAIL (build issue) AmberTools-23.6-foss-2023a.eb (partial log available at https://gist.github.com/boegelbot/7f194ec8a3581900d9d72ffbf1832941)
FAIL (build issue) Amber-24.3-foss-2023a-AmberTools-24.10.eb (partial log available at https://gist.github.com/boegelbot/41cfd0602a4264a05ab9785017664f13)
FAIL (build issue) Amber-24.0-foss-2024a-AmberTools-24.0.eb (partial log available at https://gist.github.com/boegelbot/7a1c14178abe93fbb159a045a28676c9)

Build succeeded for 0 out of 3 (3 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/fb82ebcde576d11815bd02778d544751 for a full test report.

pavelToman · 2025-08-05T10:21:02Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)
* **FAIL (build issue)** _AmberTools-23.6-foss-2023a.eb_ (partial log available at https://gist.github.com/boegelbot/7f194ec8a3581900d9d72ffbf1832941)

* **FAIL (build issue)** _Amber-24.3-foss-2023a-AmberTools-24.10.eb_ (partial log available at https://gist.github.com/boegelbot/41cfd0602a4264a05ab9785017664f13)

* **FAIL (build issue)** _Amber-24.0-foss-2024a-AmberTools-24.0.eb_ (partial log available at https://gist.github.com/boegelbot/7a1c14178abe93fbb159a045a28676c9)
Build succeeded for 0 out of 3 (3 easyconfigs in total) jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21 See https://gist.github.com/boegelbot/fb82ebcde576d11815bd02778d544751 for a full test report.

Second and third (Amber-24.3 and Amber 24.0) failing because it do not have sources.
First test (AmberTools-23.6-foss-2023a) failed on:

test.serial -> this should pass ( and passing on Donphan)
can not find target test.parallel.gem.pmemd - problem with sources? In our sources the file called AmberTools23.tar.bz2 but after extraction it creates amber22 dir - this is ok. Anyway, still the easyblock need to update this probably:

        # Run the tests located in the build directory
        if self.cfg['runtest']:
            if LooseVersion(self.version) >= LooseVersion('24'):
                testdir = os.path.join(self.builddir, 'test')
                testname_cs = 'test.cuda.serial'
                testname_cp = 'test.cuda.parallel'
            else:
                testdir = self.builddir
                testname_cs = 'test.cuda_serial'
                testname_cp = 'test.cuda_parallel'
            pretestcommands = 'source %s/amber.sh && cd %s' % (self.installdir, testdir)

To go to test dir before tests even for v23?
In AmberTools/23.6/foss-2023a/test/Makefile, there is test.serial.gem.pmemd target after run on Donphan.
But either in AmberTools/23.6/foss-2023a/Makefile (not in /test) there is a target test.serial and test.parallel:

test.parallel: is_amberhome_defined
        -(cd AmberTools/test && $(MAKE) test.parallel)
        @(if [ -n "$(BUILDAMBER)" ] ; then \
                cd test && $(MAKE) test.parallel; \
                echo ""; \
                echo "Summary of AmberTools parallel tests:"; \
                echo ""; cat ../logs/test_at_parallel/at_summary; \
        else \
                echo "==============================================================" ;\
                echo "$(AMBERHOME)/src/Makefile not found." ;\
                echo "This is expected if you have not installed Amber22." ;\
                echo "==============================================================" ;\
        fi ;\
        )

But no target test.parallel.gem.pmemd in AmberTools/23.6/foss-2023a/Makefile.

boegelbot · 2025-08-05T10:33:09Z

@pavelToman: 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=3868 EB_ARGS="AmberTools-23.6-foss-2023a.eb Amber-24.3-foss-2023a-AmberTools-24.10.eb Amber-24.0-foss-2024a-AmberTools-24.0.eb" EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3868 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7492

Test results coming soon (I hope)...

Details

- notification for comment with ID 3154595536 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 · 2025-08-05T11:31:59Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

FAIL (build issue) AmberTools-23.6-foss-2023a.eb (partial log available at https://gist.github.com/boegelbot/c7aa582a488f7ceb4f236b27bcc9a05d)
FAIL (build issue) Amber-24.3-foss-2023a-AmberTools-24.10.eb (partial log available at https://gist.github.com/boegelbot/b10260749b53bf3f55edbb3ccc866686)
FAIL (build issue) Amber-24.0-foss-2024a-AmberTools-24.0.eb (partial log available at https://gist.github.com/boegelbot/13d13ff398d0ca630c85bef8dbf4c53e)

Build succeeded for 0 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/d663504b62bfb305b33a17eec5da9eb2 for a full test report.

pavelToman · 2025-08-05T13:19:15Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)
* **FAIL (build issue)** _AmberTools-23.6-foss-2023a.eb_ (partial log available at https://gist.github.com/boegelbot/c7aa582a488f7ceb4f236b27bcc9a05d)

* **FAIL (build issue)** _Amber-24.3-foss-2023a-AmberTools-24.10.eb_ (partial log available at https://gist.github.com/boegelbot/b10260749b53bf3f55edbb3ccc866686)

* **FAIL (build issue)** _Amber-24.0-foss-2024a-AmberTools-24.0.eb_ (partial log available at https://gist.github.com/boegelbot/13d13ff398d0ca630c85bef8dbf4c53e)
Build succeeded for 0 out of 3 (3 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21 See https://gist.github.com/boegelbot/d663504b62bfb305b33a17eec5da9eb2 for a full test report.

Expected, before update from 6cc9da8

pavelToman · 2025-08-05T13:20:14Z

@boegelbot please test @ jsc-zen3 EB_ARGS="AmberTools-23.6-foss-2023a.eb"

boegelbot · 2025-08-05T13:33:09Z

@pavelToman: 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=3868 EB_ARGS="AmberTools-23.6-foss-2023a.eb" EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3868 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7496

Test results coming soon (I hope)...

Details

- notification for comment with ID 3155191266 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 · 2025-08-05T14:31:14Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

FAIL (build issue) AmberTools-23.6-foss-2023a.eb (partial log available at https://gist.github.com/boegelbot/2b0a26659cc68d79ed6d0c46d6566b9d)

Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/0e7b3e097469ce47f681febbfb138900 for a full test report.

pavelToman · 2025-08-05T15:00:06Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)
* **FAIL (build issue)** _AmberTools-23.6-foss-2023a.eb_ (partial log available at https://gist.github.com/boegelbot/2b0a26659cc68d79ed6d0c46d6566b9d)
Build succeeded for 0 out of 1 (1 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21 See https://gist.github.com/boegelbot/0e7b3e097469ce47f681febbfb138900 for a full test report.

There is no test.parallel.at target for older AmberTools - gonna update easyblock again

pavelToman · 2025-08-05T16:40:44Z

@boegelbot please test @ jsc-zen3 EB_ARGS="AmberTools-23.6-foss-2023a.eb"

boegelbot · 2025-08-05T16:53:09Z

@pavelToman: 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=3868 EB_ARGS="AmberTools-23.6-foss-2023a.eb" EB_REPO=easybuild-easyblocks EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_3868 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7497

Test results coming soon (I hope)...

Details

- notification for comment with ID 3155860044 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 · 2025-08-05T22:11:21Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS AmberTools-23.6-foss-2023a.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/ddd2e37231cbee2ca749d2a75a172698 for a full test report.

pavelToman · 2025-08-06T10:09:41Z

Test report by @pavelToman

Overview of tested easyconfigs (in order)

SUCCESS Amber-24.3-foss-2023a-AmberTools-24.10.eb
SUCCESS Amber-24.0-foss-2023b-AmberTools-24.0.eb
FAIL (build issue) Amber-24.0-foss-2024a-AmberTools-24.0.eb (partial log available at https://gist.github.com/pavelToman/41e31bf06c94761a5121594ee5377811)

Build succeeded for 2 out of 3 (3 easyconfigs in total)
node4305.litleo.os - Linux RHEL 9.4, x86_64, AMD EPYC 9454P 48-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/334ab2ccc71d3bee80b4ff41ea940893 for a full test report.

pavelToman · 2025-08-06T11:08:45Z

FAIL (build issue) Amber-24.0-foss-2024a-AmberTools-24.0.eb

Missing modules for dependencies (use --robot?): PnetCDF/1.14.0-gompi-2024a

pavelToman · 2025-08-06T11:51:40Z

Test report by @pavelToman

Overview of tested easyconfigs (in order)

SUCCESS Amber-24.0-foss-2024a-AmberTools-24.0.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4305.litleo.os - Linux RHEL 9.4, x86_64, AMD EPYC 9454P 48-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/1b112e222b73bcf1ee60c352c1c54ab9 for a full test report.

pavelToman · 2025-08-06T13:38:35Z

Test report by @pavelToman

Overview of tested easyconfigs (in order)

SUCCESS Amber-24.3-foss-2023a-AmberTools-24.10-CUDA-12.1.1.eb
SUCCESS Amber-24.0-foss-2023b-AmberTools-24.0-CUDA-12.4.0.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4305.litleo.os - Linux RHEL 9.4, x86_64, AMD EPYC 9454P 48-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/26c58a8615f68fdaf75ffe5bb969a0e1 for a full test report.

boegel · 2025-08-13T02:32:53Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS AmberTools-23.6-foss-2023a.eb
SUCCESS Amber-24.3-foss-2023a-AmberTools-24.10.eb
SUCCESS Amber-24.0-foss-2024a-AmberTools-24.0.eb
SUCCESS Amber-24.0-foss-2023b-AmberTools-24.0.eb

Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3508.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/3b22f065b90869f0cdab2c268442fed6 for a full test report.

boegel

lgtm

Update Amber easyblock - fix tests for AmberTools

b7368d5

pavelToman mentioned this pull request Aug 4, 2025

{chem}[foss/2025a] AmberTools v25.2 easybuilders/easybuild-easyconfigs#23420

Merged

pavelToman added 2 commits August 5, 2025 15:15

Update amber.py - update test targets for < v24

6cc9da8

Update amber.py - fix whitespace

a6bf5aa

Update amber.py

769c72a

pavelToman mentioned this pull request Aug 6, 2025

{chem}[foss/2024a] AmberTools v25.2 easybuilders/easybuild-easyconfigs#23582

Closed

boegel changed the title ~~Update Amber easyblock - fix tests for AmberTools~~ Update Amber easyblock - fix tests for AmberTools 24.x Aug 6, 2025

pavelToman changed the title ~~Update Amber easyblock - fix tests for AmberTools 24.x~~ Update Amber easyblock - fix tests for AmberTools >= 24.x Aug 6, 2025

pavelToman mentioned this pull request Aug 12, 2025

{chem}[foss/2024a] AmberTools v24.10 easybuilders/easybuild-easyconfigs#23652

Merged

boegel added the update label Aug 12, 2025

boegel added this to the next release (5.1.2) milestone Aug 12, 2025

boegel approved these changes Aug 13, 2025

View reviewed changes

boegel changed the title ~~Update Amber easyblock - fix tests for AmberTools >= 24.x~~ Update Amber easyblock for AmberTools >= 24.x Aug 13, 2025

boegel merged commit 3a33dca into easybuilders:develop Aug 13, 2025
17 checks passed

Conversation

pavelToman commented Aug 4, 2025 • edited by boegel Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

pavelToman commented Aug 4, 2025

Uh oh!

boegelbot commented Aug 4, 2025

Uh oh!

boegelbot commented Aug 4, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Overview of tested easyconfigs (in order)

Uh oh!

boegelbot commented Aug 5, 2025

Uh oh!

boegelbot commented Aug 5, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 5, 2025

Uh oh!

boegelbot commented Aug 5, 2025

Uh oh!

boegelbot commented Aug 5, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 5, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 5, 2025

Uh oh!

boegelbot commented Aug 5, 2025

Uh oh!

boegelbot commented Aug 5, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 6, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 6, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

pavelToman commented Aug 6, 2025

Overview of tested easyconfigs (in order)

Uh oh!

pavelToman commented Aug 6, 2025

Overview of tested easyconfigs (in order)

Uh oh!

boegel commented Aug 13, 2025

Overview of tested easyconfigs (in order)

Uh oh!

boegel left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

pavelToman commented Aug 4, 2025 •

edited by boegel

Loading

pavelToman commented Aug 5, 2025 •

edited

Loading

pavelToman commented Aug 5, 2025 •

edited

Loading

pavelToman commented Aug 6, 2025 •

edited

Loading