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{chem}[intel/2020a] LAMMPS v3Mar2020 w/ Python 3.8.2 #10191

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{chem}[intel/2020a] LAMMPS v3Mar2020 w/ Python 3.8.2 #10191

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@ocaisa ocaisa commented Mar 20, 2020 •
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(created using eb --new-pr)

Requires #10253, #10189, #10179, #10187 and easybuilders/easybuild-easyblocks#1997

adding easyconfigs: LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb…
1851633 
…, LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb, FFTW-3.3.8-intel-2020a.eb
@ocaisa ocaisa added update 2020a before 2020a is released labels Mar 20, 2020
@lexming lexming added this to the 2020a milestone Mar 20, 2020
@boegel boegel mentioned this pull request Mar 20, 2020
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@ocaisa ocaisa changed the title {chem}[intel/2020a] LAMMPS v3Mar2020, FFTW v3.3.8 w/ Python 3.8.2 {chem}[intel/2020a, foss/2020a] LAMMPS v3Mar2020 w/ Python 3.8.2 Mar 20, 2020
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ocaisa commented Mar 20, 2020

Test report by @ocaisa
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/d4306ea209dddb4cb459857d811d07e4 for a full test report.

@easybuilders easybuilders deleted a comment from boegelbot Mar 20, 2020
@easybuilders easybuilders deleted a comment from boegelbot Mar 20, 2020
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ocaisa commented Mar 21, 2020

Test report by @ocaisa
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/a9f9faf6cb0e6f8cfc0f98fde9bb486b for a full test report.

@easybuilders easybuilders deleted a comment from boegelbot Mar 23, 2020
@migueldiascosta migueldiascosta mentioned this pull request Mar 24, 2020
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ocaisa commented Mar 24, 2020

@Darkless012 You might be interested in looking over this one. I've added support for MKL in the easyblock and I've introduced the ScaFaCoS package.

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ocaisa commented Mar 24, 2020

Test report by @ocaisa
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/d88482b96acff78c98baea1f39670e32 for a full test report.

@easybuilders easybuilders deleted a comment from boegelbot Mar 24, 2020
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ocaisa commented Mar 24, 2020

Test report by @ocaisa
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/187fa9a8296855103f0e7c47c46df224 for a full test report.

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Test report by @migueldiascosta
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
sms - Linux centos linux 7.6.1810, AMD EPYC 7601 32-Core Processor, Python 2.7.5
See https://gist.github.com/b9c089e2c25a467f9ac22ec8ca21c477 for a full test report.

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ocaisa commented Mar 25, 2020 •
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Hold off on merging this, I will also add VTK support, waiting on #10253

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boegel commented May 2, 2020

@ocaisa The errors on generoso were lock issues, probably because the both of us were testing at the same time (we need to change our setup on generoso a bit to avoid that).

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boegel commented May 3, 2020

Test report by @boegel
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
node3149.skitty.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/0de31aeb326b0e20ea3e4d111d6120a1 for a full test report.

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Test report by @akesandgren
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
b-an03.hpc2n.umu.se - Linux ubuntu 16.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 2.7.12
See https://gist.github.com/41279425363613deabb4ab4aa7f0fb1f for a full test report.

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boegel commented May 4, 2020

The last commit I added (10dd5bc) adds a patch to fix a hang when building the LAMMPS docs that suddenly started happening. I'm still a bit puzzled as to why it didn't happen before, but fine...

The patch also avoids that the LAMMPS installation procedure pulls in Sphinx from PyPI, since it's already a part of our Python installation.

There's one more open problem when installing LAMMPS with intel/2020a: both the sphinx-build command and the sanity check commands fail because they're not run via mpirun (due to a bug in Intel MPI 2019 update 7, cfr. the discussion in #10213), which trigger an import h5py.

We've hit this problem with h5py itself (see #10246) for yaff (see #10560) and now also for LAMMPS (where it's annoying to fix it, since we need to use mpirun in the patch, in the easyblock and in the easyconfig...), so it's time to figure out a proper fix for it.
I started looking at that in h5py/h5py#1544, but I couldn't get it fully working yet...

Remove FFTW dep
1d5624d 
Picking up MKL is handled in the easyblock since easybuilders/easybuild-easyblocks#1997
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Test report by @akesandgren
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in this PR)
b-an03.hpc2n.umu.se - Linux ubuntu 16.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 2.7.12
See https://gist.github.com/9b32ff5d3f443b99a201cfd95f14c046 for a full test report.

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ocaisa commented May 4, 2020

@akesandgren Yeah, this will still fail until we resolve the h5py problem.

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Yeah, was just trying again... phase of the moon and stuff...

@boegel boegel mentioned this pull request May 12, 2020
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ocaisa commented May 12, 2020 •
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Requires #10626

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ocaisa commented May 12, 2020

Retriggering tests just in case

@ocaisa ocaisa closed this May 12, 2020
@ocaisa ocaisa reopened this May 12, 2020
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ocaisa commented May 12, 2020

Test report by @ocaisa
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, x86_64, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/778107eeeca67f41d28544a8e7ff1475 for a full test report.

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This one depends on kim-api PR #10158 which is still only in 2020a branch

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boegel commented May 13, 2020

@ocaisa I propose we close this until further notice, until we've sorted out the h5py mess that is blocking this.

We'll get rid of the 2020a branch that this PR is targeting soon-ish, so this should be reopened to target develop anyway...

The relevant fixes for LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb are included in #10537 targeting develop

@Micket Micket modified the milestones: 2020a, 4.x May 26, 2020
@ocaisa ocaisa mentioned this pull request May 28, 2020
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ocaisa commented May 28, 2020

Closing in favour of #10712

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@ocaisa You said "Closing in favour of #10712" but didn't actually close it...

@ocaisa ocaisa closed this Jun 15, 2020
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