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add patch to h5py 2.8.0 easyconfigs to avoid MPI_Init on 'import h5py' #11119

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Merged
lexming merged 3 commits into from
Aug 26, 2020
Merged

add patch to h5py 2.8.0 easyconfigs to avoid MPI_Init on 'import h5py' #11119

lexming merged 3 commits into from
Aug 26, 2020

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@boegel boegel commented Aug 14, 2020

(created using eb --new-pr)

@boegel boegel added this to the next release (4.2.3?) milestone Aug 14, 2020
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boegel commented Aug 14, 2020

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node3129.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/02cb47266bcc6cf53b2d2d8c26544e1d for a full test report.

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boegel commented Aug 15, 2020

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node2492.golett.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/f606580381bcd31455565c23e88c4775 for a full test report.

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boegel commented Aug 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node3105.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/2d71f48d6e4d3df4811f4698c3bdc053 for a full test report.

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boegel commented Aug 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node3407.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/da4991cd07b616f5cb905ade982953a1 for a full test report.

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boegel commented Aug 21, 2020

Test report by @boegel
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node2560.golett.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/d758668f7e654ebec554c9fab28d2d8c for a full test report.

@easybuilders easybuilders deleted a comment from boegelbot Aug 21, 2020
@easybuilders easybuilders deleted a comment from boegelbot Aug 21, 2020
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verdurin commented Aug 24, 2020

Test report by @verdurin
SUCCESS
Build succeeded for 18 out of 18 (4 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.8.2003, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/5d59419853fec8e6d29ba59c6289c4f0 for a full test report.

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verdurin commented Aug 24, 2020

@boegelbot please test @ generoso

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boegelbot commented Aug 24, 2020

@verdurin: Request for testing this PR well received on generoso

PR test command 'EB_PR=11119 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11119 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5098

Test results coming soon (I hope)...

Details

- notification for comment with ID 679155591 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).

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boegelbot commented Aug 24, 2020

Test report by @boegelbot
FAILED
Build succeeded for 4 out of 12 (7 easyconfigs in this PR)
generoso-x-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/93b4cef2ae72ba9caf5e1046ccdacd71 for a full test report.

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verdurin commented Aug 24, 2020

Strange error on generoso:

checking size of size_t... configure: error: in `/tmp/boegelbot/Python/3.6.6/intel-2018b/Python-3.6.6':
configure: error: cannot compute sizeof (size_t)
See `config.log' for more details
 (at easybuild/easybuild-framework/easybuild/tools/run.py:533 in parse_cmd_output)

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boegel commented Aug 24, 2020

@verdurin That's because the toolchains used here are too old for CentOS 8, it's simply not worth the effort to try and fix those problems imho...

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boegelbot commented Aug 25, 2020

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
generoso - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/b57fd9c2f00f5067a18c60a61053b77b for a full test report.

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boegel commented Aug 25, 2020

@verdurin Only the intel/2018b toolchain is problematic on CentOS 8, so I submitted a test report for only the easyconfigs using foss/2018b

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verdurin commented Aug 25, 2020

@boegel is it worth noting that lack of compatibility with CentOS 8 or do we assume anyone running that will install something newer?

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lexming commented Aug 25, 2020

Test report by @lexming
FAILED
Build succeeded for 7 out of 9 (7 easyconfigs in this PR)
node373.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/c2bb82aebe3f9265117ddddb65bbae0e for a full test report.

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lexming commented Aug 25, 2020

Test report by @lexming
FAILED
Build succeeded for 7 out of 9 (7 easyconfigs in this PR)
node109.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz, Python 2.7.5
See https://gist.github.com/182162665dd41cda64b0513252e88735 for a full test report.

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boegel commented Aug 25, 2020

@boegel is it worth noting that lack of compatibility with CentOS 8 or do we assume anyone running that will install something newer?

It's probably worth documenting that somewhere, but does that imply we need to start keeping track of a compatibility matrix between different Linux distro versions and toolchains?

We can open an issue mentioning the error message, like I did for GCCcore 6.4.0 in #10950, so people will hit it when searching for the error?

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boegel commented Aug 25, 2020

@lexming It looks like your Python/2.7.15-intel-2018b installation is missing cffi?!

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lexming commented Aug 26, 2020

@boegel that's indeed the case, re-installing Python/2.7.15-intel-2018b and re-testing...

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lexming commented Aug 26, 2020

Test report by @lexming
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node321.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/7fd783c76dba0bef9526f6c6ffe24aef for a full test report.

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lexming commented Aug 26, 2020

Test report by @lexming
SUCCESS
Build succeeded for 7 out of 7 (7 easyconfigs in this PR)
node127.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz, Python 2.7.5
See https://gist.github.com/38a787708b24075c4e0a8b950207216f for a full test report.

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lexming approved these changes Aug 26, 2020
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LGTM

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lexming commented Aug 26, 2020

Since the issue with intel/2018b and CentOS8 is not a regression caused by this PR, I'm going ahead and merging.

Going in, thanks @boegel !

@lexming lexming merged commit a18cd0b into easybuilders:develop Aug 26, 2020
@boegel boegel deleted the 20200814203135_new_pr_h5py280 branch August 26, 2020 17:16
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