compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled #19386

bedroge · 2023-12-09T21:32:35Z

The LERC test binary was compiled in the sanity check step, but that doesn't pick up the RPATH wrappers when RPATH linking is enabled. This, in turn, leads to errors when $LD_LIBRARY_PATH is filtered as well:

./lerctest: error while loading shared libraries: libLerc.so.4: cannot open shared object file: No such file or directory

This PR fixes that by doing the compilation of the test binary as part of postinstallcmds, and also stores both the source and binary in a subdir of the installation directory. The latter should make sure that it still works if --sanity-check-only is used.

bedroge · 2023-12-09T21:43:48Z

@boegelbot please test @ generoso

bedroge · 2023-12-09T21:46:39Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/6f83e25d38ccb12dc8872e3970f70f32 for a full test report.

This was without --rpath / --filter-env-vars.

bedroge · 2023-12-09T21:48:10Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/ade660d8e538542bc47e4eb483a831a7 for a full test report.

This was with --filter-env-vars=LD_LIBRARY_PATH --rpath.

boegelbot · 2023-12-09T21:50:08Z

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

PR test command 'EB_PR=19386 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19386 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12362

Test results coming soon (I hope)...

- notification for comment with ID 1848717294 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 · 2023-12-09T21:53:43Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 5 (5 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b6511f8d4fd3338a5790db11394eb7e9 for a full test report.

bedroge · 2023-12-10T09:33:53Z

@boegelbot please test @ generoso

boegelbot · 2023-12-10T09:35:07Z

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

PR test command 'EB_PR=19386 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_19386 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12364

Test results coming soon (I hope)...

- notification for comment with ID 1848909286 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 · 2023-12-10T09:39:58Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/58ab02d91d26819aec3551f1ee259220 for a full test report.

bedroge · 2023-12-10T09:45:01Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/44b239618b446a950dff272007fa71c2 for a full test report.

bedroge · 2023-12-10T09:48:23Z

Test report by @bedroge
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/7c18e00a891993c4bcb764a1e781caae for a full test report.

This was with --filter-env-vars=LD_LIBRARY_PATH --rpath.

bedroge · 2023-12-10T09:51:48Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-12-10T09:55:07Z

@bedroge: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=19386 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_19386 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3872

Test results coming soon (I hope)...

- notification for comment with ID 1848913596 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).

boegel · 2023-12-10T18:40:32Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-12-10T18:45:08Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=19386 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_19386 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3873

Test results coming soon (I hope)...

- notification for comment with ID 1849046263 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 · 2023-12-10T18:47:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/6f59cd7fccc05976c249689ab507cfc0 for a full test report.

boegel

lgtm

boegel · 2023-12-10T19:00:18Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3139.skitty.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/1bb02c590eee5bd6570584d5be83df45 for a full test report.

boegel · 2023-12-10T19:02:04Z

Going in, thanks @bedroge!

smoors · 2024-06-14T12:15:47Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-06-14T12:20:12Z

@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=19386 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_19386 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4386

Test results coming soon (I hope)...

- notification for comment with ID 2167896184 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 · 2024-06-14T12:22:47Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/7d135457543c50d1700abd492b9853cb for a full test report.

fix for sanity check when rpath linking is enabled

5982ef6

bedroge added bug fix EESSI Related to EESSI project labels Dec 9, 2023

bedroge added 2 commits December 10, 2023 10:32

always install libraries to 'lib/'

950660d

use CXX and CXXFLAGS instead of hardcoded values

f40c6fb

boegel approved these changes Dec 10, 2023

View reviewed changes

boegel added this to the next release (4.9.0?) milestone Dec 10, 2023

boegel merged commit 1ffb092 into easybuilders:develop Dec 10, 2023
9 checks passed

bedroge deleted the fix_lerc_sanity_check branch December 10, 2023 19:30

ocaisa mentioned this pull request Jan 9, 2024

create lib -> lib64 symlink (or vice versa) *before* running postinstallcmds easybuilders/easybuild-framework#4435

Merged

smoors mentioned this pull request Jun 14, 2024

{bio}[GCCcore/12.2.0] NanoCaller v3.6.0, WFA2 v2.3.4, vcflib v1.0.9, ... w/ R 4.2.2 #20821

Merged

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compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled #19386

compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled #19386

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compile LERC test binary in postinstallcmds to fix sanity check error when RPATH linking is enabled #19386

compile LERC test binary in postinstallcmds to fix sanity check error when RPATH linking is enabled #19386

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compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled #19386

compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled #19386

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