{math}[foss/2019b] FEniCS v2019.1.0, DOLFIN v2019.1.0.post0, FFC v2019.1.0.post0, ... w/ Python 3.7.4 by akesandgren · Pull Request #10719 · easybuilders/easybuild-easyconfigs

akesandgren · 2020-05-29T16:24:07Z

(created using eb --new-pr)

Depends on ~~#10718~~

Should try to get this to have a newer Trilinos version as dependency since the current Trilinos is hard to get built due to source no longer being available. Leaving Trilinos version change for a later PR.

…N-2019.1.0.post0-foss-2019b-Python-3.7.4.eb, FFC-2019.1.0.post0-foss-2019b-Python-3.7.4.eb, FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb, PLY-3.11-GCCcore-8.3.0-Python-3.7.4.eb, petsc4py-3.12.0-foss-2019b-Python-3.7.4.eb, slepc4py-3.12.0-foss-2019b-Python-3.7.4.eb, SUNDIALS-5.1.0-foss-2019b.eb, UFL-2019.1.0-foss-2019b-Python-3.7.4.eb

akesandgren · 2020-06-01T19:20:54Z

Test report by @akesandgren
SUCCESS
Build succeeded for 9 out of 9 (9 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/dfcf913c8d0042ee39d9f65212af39c9 for a full test report.

terjekv · 2020-06-24T16:27:35Z

Test report by @terjekv
FAILED
Build succeeded for 16 out of 23 (9 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz, Python 3.6.8
See https://gist.github.com/6ad1cb60b988269614b3804bbc9e2d12 for a full test report.

terjekv · 2020-06-24T16:59:40Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 7 (9 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz, Python 3.6.8
See https://gist.github.com/9e4a99410746284c7be7a0db9102cfbc for a full test report.

terjekv · 2020-06-24T21:47:23Z

I'm also seeing a lack of python via env for PETSc et al. Do we have a standardised way of making python3 found as python in these contexts, or should we be modifying the env call?

(This is on RHEL8, there is no python.)

== 2020-06-24 23:43:39,693 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " ./configure --prefix=/tmp/terjekv/tmp-installs/10719/software/PETSc/3.12.4-foss-2019b --LIBS="$LIBS -lrt"  --with-cc="mpicc"  --with-cxx="mpicxx" --with-c++-support  --with-fc="mpifort"  --CFLAGS="-O2 -ftree-vectorize -march=haswell -fno-math-errno -fPIC"  --CXXFLAGS="-O2 -ftree-vectorize -march=haswell -fno-math-errno -fPIC -DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX"  --FFLAGS="-O2 -ftree-vectorize -march=haswell -fno-math-errno -fPIC"  --with-mpi=1  --with-build-step-np=32  --with-shared-libraries=1  --with-debugging=0  --with-pic=1  --with-x=0 --with-windows-graphics=0  --with-fftw=1  --with-fftw-include=/opt/uio/modules/rhel8/easybuild/software/FFTW/3.3.8-gompi-2019b/include  --with-fftw-lib=[/opt/uio/modules/rhel8/easybuild/software/FFTW/3.3.8-gompi-2019b/lib/libfftw3_mpi.a,libfftw3.a]  --with-scalapack=1  --with-scalapack-include=/opt/uio/modules/rhel8/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/include  --with-scalapack-lib=[/opt/uio/modules/rhel8/easybuild/software/ScaLAPACK/2.0.2-gompi-2019b/lib/libscalapack.a,libopenblas.a,libgfortran.a]  --with-blas-lapack-lib=[/opt/uio/modules/rhel8/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas.a,libgfortran.a]  --with-boost=1 --with-boost-dir=/opt/uio/modules/rhel8/easybuild/software/Boost/1.71.0-gompi-2019b  --with-metis=1 --with-metis-dir=/opt/uio/modules/rhel8/easybuild/software/METIS/5.1.0-GCCcore-8.3.0  --with-ptscotch=1 --with-ptscotch-dir=/opt/uio/modules/rhel8/easybuild/software/SCOTCH/6.0.9-gompi-2019b  --with-mumps=1 --with-mumps-dir=/tmp/terjekv/tmp-installs/10719/software/MUMPS/5.2.1-foss-2019b-metis  --with-hypre=1 --with-hypre-dir=/tmp/terjekv/tmp-installs/10719/software/Hypre/2.18.2-foss-2019b  --with-suitesparse=1 --with-suitesparse-include=[/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/UMFPACK/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/KLU/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CHOLMOD/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/BTF/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CCOLAMD/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/COLAMD/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CAMD/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/AMD/Include,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/SuiteSparse_config] --with-suitesparse-lib=[/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/UMFPACK/Lib/libumfpack.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/KLU/Lib/libklu.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CHOLMOD/Lib/libcholmod.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/BTF/Lib/libbtf.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CCOLAMD/Lib/libccolamd.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/COLAMD/Lib/libcolamd.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/CAMD/Lib/libcamd.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/AMD/Lib/libamd.a,/tmp/terjekv/tmp-installs/10719/software/SuiteSparse/5.6.0-foss-2019b-METIS-5.1.0/SuiteSparse_config/libsuitesparseconfig.a] " exited with exit code 127 and output:
/usr/bin/env: python: No such file or directory

akesandgren · 2020-06-25T06:01:09Z

Hmm PETSc clear isn't doing the right thing. Can you open an issue on that please? something about it requiring python during build and runtime

boegel · 2020-06-25T07:16:15Z

@terjekv Like @akesandgren mentioned, that's a sign that we need to add Python as a dep for PETSc, I guess...

Our Python installation provides a python command, no matter whether it's Python 2 or 3.

akesandgren · 2020-06-25T12:10:35Z

Test report by @akesandgren
SUCCESS
Build succeeded for 9 out of 9 (9 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/c3c37ecaee5adb0c08e836ca75c10516 for a full test report.

Change implemented

smoors · 2020-06-25T14:47:57Z

Test report by @smoors
FAILED
Build succeeded for 12 out of 15 (9 easyconfigs in this PR)
node375.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 2.7.5
See https://gist.github.com/41a296217b4e11f4b0de783383ef6671 for a full test report.

smoors · 2020-06-26T10:25:38Z

(Trilinos build failed, so not related to this PR)

boegel · 2020-07-03T17:37:39Z

I would like to see #10865 dealt with before merging this, which is being dealt with via #10908...

terjekv · 2020-09-30T01:08:14Z

Test report by @terjekv
FAILED
Build succeeded for 20 out of 23 (8 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/07820398f991d6244fd57bf0a8f63116 for a full test report.

terjekv · 2020-09-30T05:20:43Z

== 2020-09-29 23:32:25,065 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd "pip check" exited with exit code 1 and output:
fenics-ffc 2019.1.0.post0 requires fenics-dijitso, which is not installed.
 (at easybuild/tools/run.py:533 in parse_cmd_output)

And add dijitso

terjekv · 2020-09-30T07:04:38Z

Test report by @terjekv
SUCCESS
Build succeeded for 4 out of 4 (9 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/a1a6962e4444308303cac52b9491e0db for a full test report.

akesandgren · 2020-09-30T07:05:42Z

@terjekv did you forget --rebuild?

terjekv · 2020-09-30T07:06:43Z

I just continued where it had failed due to the dep.

akesandgren · 2020-09-30T07:25:22Z

Test report by @akesandgren
SUCCESS
Build succeeded for 10 out of 10 (9 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/d6429af32cdb7a7dcaca440e06950900 for a full test report.

akesandgren · 2020-09-30T09:25:00Z

@boegel Now it looks fine.

terjekv · 2020-09-30T12:25:05Z

Test report by @terjekv
FAILED
Build succeeded for 90 out of 113 (9 easyconfigs in this PR)
arm1 - Linux ubuntu 18.04, AArch64, UNKNOWN (aarch64), Python 3.6.9
See https://gist.github.com/a3de0a91d9eb265a4ed4471c686be46e for a full test report.

…OURCE source URL + default sanity_check_paths for PLY, petsc4py, slepc4py, UFL

boegel · 2021-06-11T16:25:08Z

Test report by @boegel
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
node2619.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/cd71c2ebf1f735a86953166fabe468e1 for a full test report.

terjekv · 2021-06-11T17:29:35Z

Test report by @terjekv
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
ninhursaga.uio.no - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/27d8903dd8595e2fe3591fda93d6efc2 for a full test report.

…11 version restriction

boegel · 2021-06-11T18:52:04Z

@boegelbot please test @ generoso

boegelbot · 2021-06-11T18:55:07Z

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

PR test command 'EB_PR=10719 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_10719 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 17440

Test results coming soon (I hope)...

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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).

boegel · 2021-06-11T19:05:28Z

Test report by @boegel
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
node3131.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/0632342b873dcfdbff2921b5f6b7544e for a full test report.

boegelbot · 2021-06-11T19:14:01Z

Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
generoso-c1-s-5 - 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/d2730499c4901d2b42ea137dcff19418 for a full test report.

boegel · 2021-06-12T21:45:50Z

Test report by @boegel
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
node3501.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/5e32bcf8131c5514baec9bdbf9a96ec0 for a full test report.

boegel

lgtm

boegel · 2021-06-13T12:30:11Z

Going in, thanks @akesandgren!

akesandgren added new update labels May 29, 2020

akesandgren added 3 commits May 29, 2020 19:41

PLY: Add missing bilddep on binutils. Use https for hoempage.

fab9e6a

DOLFIN: Add missing checksum

7ea6839

Set sanity_pip_check to True

ece222d

FEniCS is just a bundle without code, whitelist it

63a63e6

akesandgren added this to the 4.x milestone Jun 3, 2020

easybuilders deleted a comment from boegelbot Jun 10, 2020

boegel modified the milestones: 4.x, next release (4.2.2?) Jun 18, 2020

smoors reviewed Jun 22, 2020

View reviewed changes

Comment thread easybuild/easyconfigs/f/FIAT/FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb

akesandgren changed the title ~~{math}[foss/2019b] FEniCS v2019.1.0, DOLFIN v2019.1.0.post0, FFC v2019.1.0.post0, ... w/ Python 3.7.4~~ {math}[foss/2019b] FEniCS v2019.1.0, DOLFIN v2019.1.0.post0, FFC v2019.1.0.post0, ... w/ Python 3.7.4 (WIP) Jun 24, 2020

boegel previously requested changes Jun 25, 2020

View reviewed changes

Comment thread easybuild/easyconfigs/f/FIAT/FIAT-2019.1.0-foss-2019b-Python-3.7.4.eb Outdated

FIAT: Convert to simple PythonPackage and use external sympy dependency.

756a2f5

boegel modified the milestones: 4.2.2, release after 4.2.2 (4.2.3?) Jul 3, 2020

FFC: Add missing dependency on dijitso

083ebfc

And add dijitso

boegel modified the milestones: 4.3.1 (next release), 4.x Oct 26, 2020

easybuilders deleted a comment from boegelbot Jun 11, 2021

boegel added 2 commits June 11, 2021 16:03

Merge branch 'develop' into 20200529182357_new_pr_FEniCS201910

4b5b356

add sanity check command for dijitso and FFC, clean up default PYPI_S…

5347050

…OURCE source URL + default sanity_check_paths for PLY, petsc4py, slepc4py, UFL

easybuilders deleted a comment from boegelbot Jun 11, 2021

add missing pkgconfig dependency for DOLFIN + strip out strict pybind…

4e7f009

…11 version restriction

boegel approved these changes Jun 13, 2021

View reviewed changes

boegel changed the title ~~{math}[foss/2019b] FEniCS v2019.1.0, DOLFIN v2019.1.0.post0, FFC v2019.1.0.post0, ... w/ Python 3.7.4 (WIP)~~ {math}[foss/2019b] FEniCS v2019.1.0, DOLFIN v2019.1.0.post0, FFC v2019.1.0.post0, ... w/ Python 3.7.4 Jun 13, 2021

boegel modified the milestones: 4.x, next release (4.4.1) Jun 13, 2021

boegel merged commit 621c55e into easybuilders:develop Jun 13, 2021

akesandgren deleted the 20200529182357_new_pr_FEniCS201910 branch June 14, 2021 05:56

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