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allow oversubscription of MPI ranks to cores when running MEME test suite#15199

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jfgrimm merged 1 commit intoeasybuilders:developfrom
boegel:20220328180043_new_pr_MEME541
Mar 28, 2022
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allow oversubscription of MPI ranks to cores when running MEME test suite#15199
jfgrimm merged 1 commit intoeasybuilders:developfrom
boegel:20220328180043_new_pr_MEME541

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@boegel boegel commented Mar 28, 2022 •
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(created using eb --new-pr)

Tests fail when running in a Slurm job that only has access to some of the cores if $OMPI_MCA_rmaps_base_oversubscribe is not set...

 Test meme1 ...
 meme -p 20 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
 --------------------------------------------------------------------------
 There are not enough slots available in the system to satisfy the 20
 slots that were requested by the application:
 
   /tmp/easybuild/MEME/5.4.1/gompi-2021b-Python-2.7.18/meme-5.4.1/src/parallel/meme
 
 Either request fewer slots for your application, or make more slots
 available for use.

@boegel boegel added the bug fix label Mar 28, 2022
@boegel boegel added this to the next release (4.5.4) milestone Mar 28, 2022
@boegel boegel requested a review from jfgrimm March 28, 2022 16:03
@boegel boegel mentioned this pull request Mar 28, 2022
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jfgrimm commented Mar 28, 2022

d'oh, haven't added the Perl modules yet

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jfgrimm commented Mar 28, 2022

Test report by @jfgrimm
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node090.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/c3c536359f76ce613becc350dd0b6019 for a full test report.

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jfgrimm commented Mar 28, 2022

@boegelbot please test @ generoso

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boegelbot commented Mar 28, 2022

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

PR test command 'EB_PR=15199 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15199 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8333

Test results coming soon (I hope)...

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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).

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boegelbot commented Mar 28, 2022

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - 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/d59356edad95a4bf6c4b08150bbc32a1 for a full test report.

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jfgrimm commented Mar 28, 2022

Test report by @jfgrimm
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
login1.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/bae4424e58cd516352dda0b9842c6100 for a full test report.

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jfgrimm approved these changes Mar 28, 2022
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LGTM

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jfgrimm commented Mar 28, 2022

Going in, thanks @boegel!

@jfgrimm jfgrimm merged commit 5ffc13d into easybuilders:develop Mar 28, 2022
@boegel boegel deleted the 20220328180043_new_pr_MEME541 branch March 29, 2022 06:00
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