fix link order in PETSc easyblock for SCOTCH >= 7.x #3069

boegel · 2024-01-05T20:32:05Z

(created using eb --new-pr)

When building petsc4py on top of PETSc/3.17.4-foss-2022a, I ran into the following problem during the from petsc4py import PETSc sanity check:

ImportError: /software/PETSc/3.17.4-foss-2022a/lib/libpetsc.so.3.17: undefined symbol: SCOTCH_dgraphOrderTreeDist

This is due to a change in the linking order of SCOTCH libraries to order them alphabetically, which was introduced in #2796 (on my request 🤦 ).
It's vital that libptscotch (which provides SCOTCH_dgraphOrderTreeDist) is linked in after libptscotchparmetisv3 (which requires SCOTCH_dgraphOrderTreeDist).

boegel · 2024-01-05T20:37:46Z

@boegelbot please test @ generoso
CORE_CNT=16
EB_ARGS="PETSc-3.15.1-intel-2021a.eb PETSc-3.17.4-foss-2022a.eb PETSc-3.18.4-intel-2021b.eb PETSc-3.19.2-foss-2022b.eb"

boegelbot · 2024-01-05T20:39:09Z

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

PR test command 'EB_PR=3069 EB_ARGS="PETSc-3.15.1-intel-2021a.eb PETSc-3.17.4-foss-2022a.eb PETSc-3.18.4-intel-2021b.eb PETSc-3.19.2-foss-2022b.eb" EB_CONTAINER= EB_REPO=easybuild-easyblocks /opt/software/slurm/bin/sbatch --job-name test_PR_3069 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 12516

Test results coming soon (I hope)...

- notification for comment with ID 1879230009 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).

migueldiascosta · 2024-01-05T23:58:35Z

easybuild/easyblocks/p/petsc.py

-                                   'libptscotcherr.a', 'libptscotchparmetisv3.a', 'libscotch.a',
-                                   'libscotcherr.a']
+                # which is the reason for this new code;
+                # note: order matters here, don't sort these alphabetically!


but it's much easier for human eyes! :p

lgtm

boegel · 2024-01-06T00:17:35Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS PETSc-3.17.4-foss-2022a.eb
SUCCESS PETSc-3.19.2-foss-2022b.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3123.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/73b19fe05e6b65080d4d2c8e79424ddb for a full test report.

boegelbot · 2024-01-06T01:53:03Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS PETSc-3.15.1-intel-2021a.eb
SUCCESS PETSc-3.17.4-foss-2022a.eb
FAIL (build issue) PETSc-3.18.4-intel-2021b.eb (partial log available at https://gist.github.com/boegelbot/b6a6e337a2d0cad5f7363845b7cb8bd6)
SUCCESS PETSc-3.19.2-foss-2022b.eb

Build succeeded for 3 out of 4 (4 easyconfigs in total)
cnx1 - 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/c9761e8065636243c8b2f277a49746ad for a full test report.

migueldiascosta · 2024-01-06T06:51:40Z

Hm, another issue with Intel MPI on generoso?

boegel · 2024-01-06T08:21:28Z

Hm, another issue with Intel MPI on generoso?

Hmm, yeah, maybe... I wouldn't let this block this PR though, since PETSc-3.18.4-intel-2021b.eb is actually not affected by the changes being made at all (since it uses SCOTCH 6.x < 7.x)

boegel · 2024-01-06T08:39:45Z

@boegelbot please test @ jsc-zen2
CORE_CNT=8
EB_ARGS="PETSc-3.15.1-intel-2021a.eb PETSc-3.17.4-foss-2022a.eb PETSc-3.18.4-intel-2021b.eb PETSc-3.19.2-foss-2022b.eb"

boegelbot · 2024-01-06T08:42:08Z

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

PR test command 'EB_PR=3069 EB_ARGS="PETSc-3.15.1-intel-2021a.eb PETSc-3.17.4-foss-2022a.eb PETSc-3.18.4-intel-2021b.eb PETSc-3.19.2-foss-2022b.eb" EB_REPO=easybuild-easyblocks /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_3069 --ntasks="8" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 4017

Test results coming soon (I hope)...

- notification for comment with ID 1879595628 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 · 2024-01-06T08:52:09Z

More info from configure.log for failure with PETSc-3.18.4-intel-2021b.eb on generoso:

          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
 -------------------------------------------------------------------------------
 Timeout: Unable to run MPI program with /project/boegelbot/Rocky8/haswell/software/impi/2021.4.0-intel-compilers-2021.4.0/mpi/2021.4.0/bin/mpiexec -n 1
     (1) make sure this is the correct program to run MPI jobs
     (2) your network may be misconfigured; see https://petsc.org/release/faq/#mpi-network-misconfigure
     (3) you may have VPN running whose network settings may not play nice with MPI
 *******************************************************************************
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/configure.py", line 461, in petsc_configure
     framework.configure(out = sys.stdout)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/framework.py", line 1412, in configure
     self.processChildren()
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/framework.py", line 1400, in processChildren
     self.serialEvaluation(self.childGraph)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/framework.py", line 1375, in serialEvaluation
     child.configure()
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/package.py", line 1222, in configure
     self.executeTest(self.configureLibrary)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/base.py", line 138, in executeTest
     ret = test(*args,**kargs)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/packages/MPI.py", line 881, in configureLibrary
     self.executeTest(self.configureMPIEXEC)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/base.py", line 138, in executeTest
     ret = test(*args,**kargs)
   File "/tmp/boegelbot/PETSc/3.18.4/intel-2021b/petsc-3.18.4/config/BuildSystem/config/packages/MPI.py", line 377, in configureMPIEXEC
     raise RuntimeError('Timeout: %s' % error_message)

looks like a very (very) basic MPI test: https://gitlab.com/petsc/petsc/-/blob/80f88c66aac8f9d1abe2df64bcd926bcfcc2a09a/config/BuildSystem/config/packages/MPI.py#L380

I can reproduce this issue easily when running in an interactive job started with srun -c 16 --time 600 --pty /bin/bash.

After running for x in $(env | grep SLURM| cut -f1 -d=); do unset $x; done to unset all $SLURM_* environment variables, configure works fine.

boegelbot · 2024-01-06T20:53:53Z

Test report by @boegelbot

Overview of tested easyconfigs (in order)

SUCCESS PETSc-3.17.4-foss-2022a.eb
SUCCESS PETSc-3.18.4-intel-2021b.eb
SUCCESS PETSc-3.19.2-foss-2022b.eb
FAIL (build issue) SciPy-bundle-2021.05-intel-2021a.eb (partial log available at https://gist.github.com/boegelbot/0847dbaaad8b81bc69fda90dbf22803b)
SUCCESS Boost-1.76.0-intel-compilers-2021.2.0.eb
SUCCESS SCOTCH-6.1.0-iimpi-2021a.eb
SUCCESS MUMPS-5.4.0-intel-2021a-metis.eb
SUCCESS SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
SUCCESS Hypre-2.21.0-intel-2021a.eb
FAIL (build issue) PETSc-3.15.1-intel-2021a.eb (partial log available at https://gist.github.com/boegelbot/db1551377c3d403a87d78ba535f37e5a)

Build succeeded for 8 out of 10 (4 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/b900abf19ea35a00a92f5668dbce4ac0 for a full test report.

migueldiascosta

lgtm, and failures in the test reports are not related nor affected by these changes

migueldiascosta · 2024-01-10T06:44:29Z

Going in, thanks @boegel!

migueldiascosta · 2024-01-10T06:47:39Z

@boegel SciPy-bundle/2021.05-intel-2021a at jsc-zen2 seems to be broken though, which will likely affect other tests

fix link order in PETSc easyblock for SCOTCH >= 7.x

f7c3e01

boegel added the bug fix label Jan 5, 2024

boegel added this to the release after 4.9.0 milestone Jan 5, 2024

boegel mentioned this pull request Jan 5, 2024

{bio}foss/2022a] CellRank v2.0.2, scVelo v0.2.5, slepc4py v3.17.2, petsc4py v3.17.4 easybuilders/easybuild-easyconfigs#19515

Merged

migueldiascosta reviewed Jan 5, 2024

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easybuilders deleted a comment from boegelbot Jan 6, 2024

migueldiascosta approved these changes Jan 10, 2024

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migueldiascosta merged commit c68d093 into easybuilders:develop Jan 10, 2024
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boegel deleted the 20240105213202_new_pr_petsc branch February 11, 2024 13:37

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fix link order in PETSc easyblock for SCOTCH >= 7.x #3069

fix link order in PETSc easyblock for SCOTCH >= 7.x #3069

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fix link order in PETSc easyblock for SCOTCH >= 7.x #3069

fix link order in PETSc easyblock for SCOTCH >= 7.x #3069

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