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Added hwloc to GROMACS dependencies#5295

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boegel merged 5 commits intoeasybuilders:developfrom
reedts:20171103151156_new_pr_GROMACS20163
Dec 6, 2017
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Added hwloc to GROMACS dependencies#5295
boegel merged 5 commits intoeasybuilders:developfrom
reedts:20171103151156_new_pr_GROMACS20163

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@reedts reedts commented Nov 3, 2017

(created using eb --new-pr)
It seems that GROMACS need hwloc to operate.

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boegel commented Nov 3, 2017

Hmm, this is the first time this has popped up...

How did you notice this exactly @reedts? Any references for it?

@boegel boegel added this to the 3.5.0 milestone Nov 3, 2017
@boegel boegel added the bug fix label Nov 3, 2017
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reedts commented Nov 17, 2017

We are currently investigating this. It is probably a problem with the Debian system in use on that machine. We had a fresh EasyBuild installation and GROMACS refused to build untils we added the hwloc dependency. I will try to reproduce and report back.

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Helios07 commented Nov 23, 2017

I see this error now on a CentOS 7.4 machine (there is no hwloc.so in /usr/lib64):

Scanning dependencies of target gmx
make[2]: Leaving directory `/home/hangenent/.local/easybuild/build/GROMACS/2016.3/intel-2017a/easybuild_obj'
make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[2]: Entering directory `/home/hangenent/.local/easybuild/build/GROMACS/2016.3/intel-2017a/easybuild_obj'
make[2]: Warning: File `src/programs/CMakeFiles/gmx.dir/depend.make' has modification time 0,32 s in the future
Scanning dependencies of target template
make[2]: Leaving directory `/home/hangenent/.local/easybuild/build/GROMACS/2016.3/intel-2017a/easybuild_obj'
make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[2]: Entering directory `/home/hangenent/.local/easybuild/build/GROMACS/2016.3/intel-2017a/easybuild_obj'
make[2]: Warning: File `share/template/CMakeFiles/template.dir/depend.make' has modification time 0,32 s in the future
make[2]: *** Keine Regel vorhanden, um das Target »/usr/lib64/libhwloc.so«, 
  benötigt von »bin/gmx«, zu erstellen.  Schluss.
make[2]: *** Warte auf noch nicht beendete Prozesse...

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boegel commented Dec 3, 2017 •
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@Helios07 And including hwloc as a dependency fixes that issue?

@reedts Please make this change consistent in at least the GROMACS 2016.3 easyconfigs (and maybe just all 2016.* ones).

Do you mind also including a SHA256 checksum in this easyconfig while you're at it?

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Helios07 commented Dec 4, 2017

@boegel Yes, in fact, it did.

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lgtm

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Comment thread easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb Outdated
checksums = ['7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27']

dependencies = [
('hwloc', '1.11.8'),
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this should be 1.11.6, since there's no hwloc easyconfig available for 1.11.8 that's compatible with foss/2017a but there is for 11.1.6, i.e. hwloc-1.11.6-GCC-6.3.0-2.28.eb

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My bad, I looked it up in the wrong toolchain. Fixing it.

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reedts commented Dec 5, 2017

@boegel Seems like we'll have to use hwloc-1.11.5 for foss-2017a as it uses GCC/6.3.0-2.27 and not GCC/6.3.0-2.28.

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boegel commented Dec 5, 2017

@reedts Ah, yes, sorry for the confusion.

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boegel commented Dec 5, 2017

@reedts

$ eb --from-pr 5295 --check-style
== temporary log file in case of crash /tmp/eb-KbrDZI/easybuild-JZ0WNQ.log

*** WARNING: Using easyconfigs from unstable (pending/failed tests or merge conflict) PR #5295 ***

Running style check on 8 easyconfig(s)...
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.2-foss-2017a.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.3-foss-2017a.eb
/tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb:35:121: E501 line too long (121 > 120 characters)
[FAIL] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb
[PASS] /tmp/eb-KbrDZI/files_pr5295/g/GROMACS/GROMACS-2016.3-intel-2017a.eb
ERROR: One or more style checks FAILED!

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Comment thread easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb Outdated
]
checksums = [
'7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27', # gromacs-2016.3.tar.gz
'6f29fde4e7d905843cccf16e4b2a341d74ef5ad8602a5cf56f3760def30816f7', # GROMACS-2016.3_amend_search_for_nvml_lib.patch
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to fix long line, use:

# GROMACS-2016.3_amend_search_for_nvml_lib.patch
'6f29fde4e7d905843cccf16e4b2a341d74ef5ad8602a5cf56f3760def30816f7',

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@reedts Ping? This is the only trivial issue blocking this PR...

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boegel commented Dec 5, 2017

Test report by @boegel
SUCCESS
Build succeeded for 20 out of 20 (8 easyconfigs in this PR)
node2548.golett.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/16f441e6abdc2a50d47b7647651a87f3 for a full test report.

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boegel commented Dec 6, 2017

Going in, thanks @reedts!

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boegel commented Dec 6, 2017

Going in, thanks @reedts!

@boegel boegel merged commit 79b6509 into easybuilders:develop Dec 6, 2017
@reedts reedts deleted the 20171103151156_new_pr_GROMACS20163 branch December 7, 2017 09:58
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