{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 #12964

boegel · 2021-05-26T14:06:16Z

(created using eb --new-pr)

~~WIP because a handful of tests are still failing...~~ (failing tests fixed via easybuilders/easybuild-framework#3866 + easybuilders/easybuild-easyblocks#2606)

boegel · 2021-10-20T14:08:14Z

@boegelbot please test @ generoso

boegelbot · 2021-10-20T14:10:12Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=12964 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_12964 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7116

Test results coming soon (I hope)...

- notification for comment with ID 947703906 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).

boegelbot · 2021-10-20T14:19:09Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cnx2 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/82c4f067684b27c276262764e6df7a18 for a full test report.

akesandgren · 2021-10-21T09:25:49Z

Test report by @akesandgren
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
b-an02.hpc2n.umu.se - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 3.8.10
See https://gist.github.com/6c30d56d5ecb877aa24f0811e6c61868 for a full test report.

akesandgren · 2021-10-21T13:42:06Z

Looking at the initial part of the numpy build, it looks like it fails to find a BLAS lib completely....

  libraries -Wl,-Bstatic,-Wl,--start-group,mkl_intel_lp64,mkl_intel_thread,mkl_core,-Wl,--end-group,-Wl,-Bdynamic,iomp5 not found in ['/hpc2n/e
b/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0', '/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/include', '/hpc2n/eb/software/im
kl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib', '/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib/intel64']
  NOT AVAILABLE

...
lapack_opt_info:
lapack_mkl_info:
  libraries -Wl,-Bstatic,-Wl,--start-group,mkl_intel_lp64,mkl_intel_thread,mkl_core,-Wl,--end-group,-Wl,-Bdynamic,iomp5 not found in ['/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0', '/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/include', '/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib', '/hpc2n/eb/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib/intel64']
  NOT AVAILABLE

We might need to patch the numpy search code...

akesandgren · 2021-10-21T13:53:43Z

The numpy from SciPy-bundle 2020.11 have this instead:

  FOUND:
    libraries = ['-Wl,-Bstatic', '-Wl,--start-group', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', '-Wl,--end-group', '-Wl,-Bdynamic', 'iomp5', 'pthread']
    library_dirs = ['/hpc2n/eb/software/imkl/2020.4.304-iimpi-2020b/mkl/lib/intel64', '/hpc2n/eb/software/iccifort/2020.4.304/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/hpc2n/eb/software/imkl/2020.4.304-iimpi-2020b/mkl', '/hpc2n/eb/software/imkl/2020.4.304-iimpi-2020b/mkl/include', '/hpc2n/eb/software/imkl/2020.4.304-iimpi-2020b/mkl/lib']

akesandgren · 2021-10-21T14:42:55Z

The problem may be that intel/2021a does not add /hpc2n/eb/software/intel-compilers/2021.2.0/compiler/2021.2.0/linux/compiler/lib/intel64_lin to LDFLAGS!!!

So numpy cant find iomp5

branfosj · 2021-10-21T15:28:44Z

If I change https://github.com/easybuilders/easybuild-framework/blob/develop/easybuild/toolchains/compiler/intel_compilers.py#L53 to be:

        libpaths = [
            'lib',
            os.path.join('compiler', '2021.2.0', 'linux', 'lib', 'x64'),
            os.path.join('compiler', '2021.2.0', 'linux', 'compiler', 'lib', 'intel64_lin'),
        ]

then I get:

  FOUND:
    libraries = ['-Wl,-Bstatic', '-Wl,--start-group', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', '-Wl,--end-group', '-Wl,-Bdynamic', 'iomp5', 'pthread']
    library_dirs = ['/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib/intel64', '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/intel-compilers/2021.2.0/compiler/2021.2.0/linux/compiler/lib/intel64_lin']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0', '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/include', '/rds/bear-apps/devel/eb-sjb-up/EL8/EL8-cas/software/imkl/2021.2.0-iimpi-2021a/mkl/2021.2.0/lib']

Without that change I get similar output to #12964 (comment)

The produced Fortran code is incorrect.

akesandgren · 2021-10-21T18:04:12Z

We need easybuilders/easybuild-framework#3866 to get this moving forward.

Disable TestF90Callback since it fails with Intel.

akesandgren · 2021-10-22T16:33:11Z

We need easybuilders/easybuild-easyblocks#2606 too to get this to pass all tests.

akesandgren · 2021-10-22T17:25:14Z

Test report by @akesandgren
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2606
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
b-an02.hpc2n.umu.se - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 3.8.10
See https://gist.github.com/2c23004e84a5c918fdccfce99cbb7866 for a full test report.

branfosj · 2021-10-23T09:24:44Z

Test report by @branfosj
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2606
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/a35cc11152d71f04b51cc0db0a3d337a for a full test report.

akesandgren · 2021-10-25T08:45:37Z

@boegel Please add numpy-1.20.3_fix-target-test-ccompiler-opt.patch
It fixes a problem that shows up in my production setup but not in the test setup.

branfosj · 2021-10-25T11:10:19Z

@boegel Please add numpy-1.20.3_fix-target-test-ccompiler-opt.patch It fixes a problem that shows up in my production setup but not in the test setup.

In SciPy-bundle-2021.05-foss-2021a.eb the patches are:

numpy-1.20.3_skip-ppc-long-complex-test.patch - PPC, so not needed here
numpy-1.20.3_xfail-test-nan.patch - OpenBLAS related, so not needed here
numpy-1.20.3_fix-target-test-ccompiler-opt.patch - to add

boegel · 2021-10-26T07:50:35Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2606
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node2636.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/9ee75ba1c1cc89b1a639544d37551ab2 for a full test report.

…:boegel/easybuild-easyconfigs into 20210526160607_new_pr_SciPy-bundle202105

boegel · 2021-10-26T07:56:32Z

@boegelbot please test @ generoso

boegelbot · 2021-10-26T08:00:17Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=12964 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_12964 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7146

Test results coming soon (I hope)...

- notification for comment with ID 951658584 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).

boegelbot · 2021-10-26T08:53:39Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cnx1 - Linux rocky linux 8.4, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/f014f0f436331c63b2c18f6a08dda60a for a full test report.

SebastianAchilles · 2021-10-26T09:10:49Z

Test report by @SebastianAchilles
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
rocky8-eb - Linux rocky linux 8.4, x86_64, Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz (broadwell), Python 3.6.8
See https://gist.github.com/185c3988b3c3f7d44085689ff234148f for a full test report.

branfosj · 2021-10-26T09:41:56Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/a4eb4e5793b871292764aa75d42b2d21 for a full test report.

branfosj · 2021-10-26T10:32:12Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0104u03a.bear.cluster - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/c5e984843f062b672119bb5caafa91f2 for a full test report.

boegel · 2021-10-26T13:00:43Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2606
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3103.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/9e6b3f2197546fc2b09f1b0928690fb0 for a full test report.

branfosj

lgtm

branfosj · 2021-10-26T14:10:01Z

Going in, thanks @boegel!

{lang}[intel/2021.03] SciPy-bundle v2021.05 w/ Python 3.9.5 (WIP)

96d4198

boegel added the update label May 26, 2021

boegel marked this pull request as draft May 26, 2021 14:08

boegel added this to the 4.4.0 milestone May 26, 2021

boegel modified the milestones: 4.4.0, release after 4.4.0 May 29, 2021

update to intel/2021a

6b864d0

boegel changed the title ~~{lang}[intel/2021.03] SciPy-bundle v2021.05 w/ Python 3.9.5 (WIP)~~ {lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 (WIP) Jun 9, 2021

boegel modified the milestones: next release (4.4.1), release after 4.4.1 Jul 2, 2021

boegel modified the milestones: 4.4.2, release after 4.4.2 Sep 2, 2021

Disable TestF90Callback since it fails with Intel.

c6f73f2

The produced Fortran code is incorrect.

Merge pull request #85 from akesandgren/disable_failing_numpy_test

70cff9c

Disable TestF90Callback since it fails with Intel.

Merge branch 'develop' into 20210526160607_new_pr_SciPy-bundle202105

3dacf2a

add extra numpy patch to SciPy-bundle 2021.05 to fix problem with tests

da542bd

boegel mentioned this pull request Oct 26, 2021

fix support for recent imkl version in numexpr easyblock easybuilders/easybuild-easyblocks#2606

Merged

boegel marked this pull request as ready for review October 26, 2021 07:53

boegel changed the title ~~{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 (WIP)~~ {lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 Oct 26, 2021

Merge branch '20210526160607_new_pr_SciPy-bundle202105' of github.com…

1e36195

…:boegel/easybuild-easyconfigs into 20210526160607_new_pr_SciPy-bundle202105

branfosj approved these changes Oct 26, 2021

View reviewed changes

branfosj merged commit e195e4b into easybuilders:develop Oct 26, 2021

boegel deleted the 20210526160607_new_pr_SciPy-bundle202105 branch October 26, 2021 14:11

boegel mentioned this pull request Oct 30, 2021

failing numpy tests on AMD Rome with SciPy-bundle 2021.05 using intel/2021a #14258

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{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 #12964

{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 #12964

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{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 #12964

{lang}[intel/2021a] SciPy-bundle v2021.05 w/ Python 3.9.5 #12964

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