{bio}[GCC/10.2.0] CAFE5 v5.0.0 by sdx23 · Pull Request #14603 · easybuilders/easybuild-easyconfigs

sdx23 · 2021-12-21T11:03:20Z

(created using eb --new-pr)
New software CAFE5. Had issues when explicitly enabling openmp in toolchainopts

bedroge

Thanks for your contribution @sdx23. I've made some (minor) suggestions in my review, mostly related to some style issues, but the OpenMP issue probably requires some more work. It's caused by some hardcoded compiler flags in the Makefile, which is currently ignoring all the settings provided by Easybuild (e.g. with respect to the optimization level). This would have to be patched, would you be up for this?

Co-authored-by: Bob Dröge <[email protected]>

sdx23 · 2021-12-21T12:52:12Z

Thanks for all the suggestions for improvements and especially the explanations, @bedroge . I'd be up for writing a patch for the makefile (and suggesting this upstream). Could you perhaps point me to a project that handles openmp and CFLAGS correctly, for reference?

bedroge · 2021-12-21T13:38:19Z

@sdx23 Great! I was going to suggest to use either sed or a patch file in order to make the Makefile pick up the compiler flags provided by EB, but I had a closer look, and this is actually not necessary. You can simply override the Makefile variables by passing them as arguments to the make command, which can be done by setting buildopts. I'll make another suggestion for that.

Co-authored-by: Bob Dröge <[email protected]>

sdx23 · 2021-12-21T13:51:24Z

Thank you. I've tested the changes and with that the toolchainopts openmp setting is working fine.

Guess I should squash commits, right?

bedroge

I've given it a try myself and had one more detailed look at the easyconfig, and have two final suggestions:

Though it's not really wrong to use ConfigureMake here (bit of a corner case this installation procedure without a make install), I find MakeCp a bit cleaner, as it has an option to specify which files should be copied to the install dir. MakeCp doesn't do a ./configure, so we do have to enable that using with_configure = True, see the suggested change.
I noticed that the text files in the examples dir have execute permissions, let's remove those by adding a postinstallcmds.

After you've made these changes, I'll submit some test reports to this PR, and merge it.

bedroge · 2022-01-14T09:03:08Z

@sdx23 just a friendly reminder :-) If you could make these last small changes, we can merge your PR.

Co-authored-by: Bob Dröge <[email protected]>

sdx23 · 2022-01-18T07:41:18Z

Thank you very much @bedroge . Should I squash the commits or keep as is for maintaining history?

bedroge · 2022-01-18T08:00:44Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 20.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.8.10
See https://gist.github.com/a4ec74621096739c117b1bb0618ea299 for a full test report.

bedroge · 2022-01-18T08:01:43Z

Thank you very much @bedroge . Should I squash the commits or keep as is for maintaining history?

Thanks! No need to squash the commits. I'll upload some test reports for this easyconfig, and then merge the PR.

bedroge · 2022-01-18T08:02:04Z

@boegelbot please test @ generoso

bedroge · 2022-01-18T08:02:16Z

@boegelbot please test @ jsc-zen2

bedroge · 2022-01-18T08:03:27Z

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
pg-interactive.hpc.rug.nl - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 3.6.8
See https://gist.github.com/5b921e485896c91386be4f43da286717 for a full test report.

boegelbot · 2022-01-18T08:05:19Z

@bedroge: Request for testing this PR well received on jsfl1.int.jusuf.sebastian.cluster

PR test command 'EB_PR=14603 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14603 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 1643

Test results coming soon (I hope)...

Details

- notification for comment with ID 1015156935 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 · 2022-01-18T08:05:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsfc01.int.jusuf.sebastian.cluster - Linux rocky linux 8.4, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/836de2bdb5faf1fcb73fa9f2eff5beb3 for a full test report.

bedroge · 2022-01-18T08:12:27Z

@boegelbot please test @ generoso

boegelbot · 2022-01-18T08:15:11Z

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

PR test command 'EB_PR=14603 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14603 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7867

Test results coming soon (I hope)...

Details

- notification for comment with ID 1015164341 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 · 2022-01-18T08:16:22Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns2 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/4da0cea2ce4b6a024fe3d84767339c4a for a full test report.

bedroge

lgtm

bedroge · 2022-01-18T08:16:54Z

Going in, thanks @sdx23!

MaxVoitUP and others added 2 commits December 21, 2021 12:03

adding easyconfigs: CAFE5-5.0.0-GCC-10.2.0.eb

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Update CAFE5-5.0.0-GCC-10.2.0.eb

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sdx23 and others added 5 commits December 21, 2021 13:50

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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bedroge reviewed Dec 21, 2021

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sdx23 and others added 3 commits December 21, 2021 14:48

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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easybuilders deleted a comment from boegelbot Dec 21, 2021

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bedroge added this to the 4.x milestone Dec 21, 2021

sdx23 and others added 2 commits January 18, 2022 08:35

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb

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Co-authored-by: Bob Dröge <[email protected]>

bedroge approved these changes Jan 18, 2022

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bedroge merged commit 4c86705 into easybuilders:develop Jan 18, 2022

bedroge modified the milestones: 4.x, next release (4.5.2?) Jan 18, 2022

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