{chem}[intel/2020a] LAMMPS v3Mar2020 w/ Python 3.8.2 by ocaisa · Pull Request #10191 · easybuilders/easybuild-easyconfigs

ocaisa · 2020-03-20T14:37:47Z

(created using eb --new-pr)

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

…, LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb, FFTW-3.3.8-intel-2020a.eb

ocaisa · 2020-03-20T17:59:36Z

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.

ocaisa · 2020-03-21T18:12:05Z

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.

ocaisa · 2020-03-24T09:10:29Z

@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.

ocaisa · 2020-03-24T09:36:22Z

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.

ocaisa · 2020-03-24T13:22:09Z

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.

migueldiascosta · 2020-03-25T10:23:09Z

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.

ocaisa · 2020-03-25T12:46:12Z

Hold off on merging this, I will also add VTK support, waiting on #10253

boegel · 2020-04-29T17:52:51Z

@ocaisa I need to make sure my impi installation is properly configured, I didn't have $I_MPI_PMI_LIBRARY set when testing this, will check again...

ocaisa · 2020-04-30T16:35:50Z

Urf, there are similar errors on generoso now...something is rotten in Denmark

boegel · 2020-05-02T18:40:53Z

@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).

boegel · 2020-05-03T07:05:03Z

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.

akesandgren · 2020-05-03T08:50:38Z

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.

…y include test script to verify installation

boegel · 2020-05-04T06:15:26Z

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...

Picking up MKL is handled in the easyblock since easybuilders/easybuild-easyblocks#1997

akesandgren · 2020-05-04T07:53:43Z

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.

ocaisa · 2020-05-04T08:19:55Z

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

akesandgren · 2020-05-04T08:24:47Z

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

ocaisa · 2020-05-12T19:07:54Z

Requires ~~#10626~~

ocaisa · 2020-05-12T19:08:22Z

Retriggering tests just in case

ocaisa · 2020-05-12T19:31:21Z

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.

akesandgren · 2020-05-12T19:54:11Z

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

boegel · 2020-05-13T18:16:24Z

@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

ocaisa · 2020-05-28T16:59:14Z

Closing in favour of #10712

akesandgren · 2020-06-08T06:15:43Z

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

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 added update 2020a before 2020a is released labels Mar 20, 2020

lexming added this to the 2020a milestone Mar 20, 2020

boegel mentioned this pull request Mar 20, 2020

wishlist for 2020a merge sprint #10000

Closed

Alan O'Cais added 3 commits March 20, 2020 17:02

Patch LAMMPS for GCC 9

58722bc

Patch LAMMPS for GCC 9

b1f5a79

Delete FFTW-3.3.8-intel-2020a.eb

bb507b0

Moved to easybuilders#10189

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

easybuilders deleted a comment from boegelbot Mar 20, 2020

easybuilders deleted a comment from boegelbot Mar 21, 2020

Use FFTW from toolchain

bb7e339

easybuilders deleted a comment from boegelbot Mar 21, 2020

easybuilders deleted a comment from boegelbot Mar 23, 2020

Alan O'Cais added 3 commits March 24, 2020 09:26

Add description and author to patch

2d27ebb

Add description and author to patch

cc44d9c

Merge branch '2020a' into 20200320153740_new_pr_LAMMPS3Mar2020

96ab2f6

migueldiascosta mentioned this pull request Mar 24, 2020

add EPYC to KOKKOS_CPU_ARCH_LIST and MAPPING in LAMMPS easyblock easybuilders/easybuild-easyblocks#1975

Merged

Bump PCRE version

8bd5172

easybuilders deleted a comment from boegelbot Mar 24, 2020

Add VTK

df87c1d

Add additional sanity check

46ef6a4

boegel requested changes May 2, 2020

View reviewed changes

Comment thread easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb

add missing FFTW dep in LAMMPS easyconfig using intel/2020a toolchain

47104ae

boegel added 2 commits May 3, 2020 11:31

Merge branch '2020a' into 20200320153740_new_pr_LAMMPS3Mar2020

b61c767

add patch for LAMMPS 3Mar2020 to fix hanging docs build + consistentl…

10dd5bc

…y include test script to verify installation

ocaisa commented May 4, 2020

View reviewed changes

Comment thread easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb Outdated

Remove FFTW dep

1d5624d

Picking up MKL is handled in the easyblock since easybuilders/easybuild-easyblocks#1997

boegel mentioned this pull request May 12, 2020

add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import #10626

Merged

ocaisa closed this May 12, 2020

ocaisa reopened this May 12, 2020

Micket modified the milestones: 2020a, 4.x May 26, 2020

ocaisa mentioned this pull request May 28, 2020

{chem}[intel/2020a] LAMMPS v3Mar2020 w/ Python 3.8.2 #10712

Merged

ocaisa closed this Jun 15, 2020

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