{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8 #16912

boegel · 2022-12-15T14:00:46Z

(created using eb --new-pr)
requires:

add gfbf as subtoolchain of foss easybuild-framework#4143
{tools}[GCCcore/12.2.0] meson-python v0.11.0 w/ Python 3.10.8 #16911
~~update scipy easyblock for scipy >= 1.9 to correctly configure BLAS/LAPACK library to use via Meson (WIP) easybuild-easyblocks#2848~~ or update scipy easyblock for scipy >= 1.9.0 to use meson/ninja easybuild-easyblocks#2862
add additional extensions to Python 3.10.8 (required for scipy test suite) #17159

…hesis v6.59.0 w/ Python 3.10.8

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb

…asyconfigs into 20221215150042_new_pr_SciPy-bundle202211

easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb

… build dependency + move mpi4py to dedicated easyconfig

boegel · 2022-12-15T22:41:53Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
fair-mastodon-c6g-2xlarge-0001 - Linux Rocky Linux 8.5, AArch64, ARM UNKNOWN (graviton2), Python 3.6.8
See https://gist.github.com/d18296751db3145f37cab3b666e03df0 for a full test report.

boegel · 2022-12-19T09:59:23Z

I've converted this back to draft, because it seems like scipy is getting linked directly to OpenBLAS rather than using FlexiBLAS, due to a switch in build procedure (now Meson-based)

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb

jfgrimm · 2023-01-17T15:58:40Z

updated easyblock is in: easybuilders/easybuild-easyblocks#2862

boegelbot · 2023-02-25T16:22:15Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2862
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/20dd522eb42319d3f091ba25156d38ef for a full test report.

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb

boegel · 2023-02-25T18:25:59Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2862
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
fair-mastodon-c6g-2xlarge-0001 - Linux Rocky Linux 8.7, AArch64, ARM UNKNOWN (graviton2), Python 3.6.8
See https://gist.github.com/9e766b49a23c1797090636b944ac392d for a full test report.

…ndle 2023.02

boegel · 2023-02-25T18:54:35Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2862 SciPy-bundle-2023.02-gfbf-2022b.eb --sanity-check-only"

boegelbot · 2023-02-25T21:25:12Z

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

PR test command 'EB_PR=16912 EB_ARGS="--include-easyblocks-from-pr 2862 SciPy-bundle-2023.02-gfbf-2022b.eb --sanity-check-only" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16912 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10367

Test results coming soon (I hope)...

- notification for comment with ID 1445181483 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 · 2023-02-25T21:26:20Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2862
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/f3867d9fb0566f6a57424b8a5a376f5c for a full test report.

branfosj · 2023-02-26T09:13:31Z

Going in, thanks @boegel!

VRehnberg · 2023-02-28T16:02:13Z

Test report by @VRehnberg
FAILED
Build succeeded for 4 out of 5 (5 easyconfigs in total)
alvis-c1 - Linux Rocky Linux 8.6, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/01664e2e8c7c85126cc92e1f6a5bc75d for a full test report.

jfgrimm · 2023-02-28T16:04:59Z

@VRehnberg you need the easyblock from easybuilders/easybuild-easyblocks#2862

VRehnberg · 2023-03-01T10:42:21Z

Test report by @VRehnberg
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2862
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
alvis-c1 - Linux Rocky Linux 8.6, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/e2d4f462977467abbc9c15844b08796e for a full test report.

verdurin · 2023-03-02T18:46:00Z

Test report by @verdurin
FAILED
Build succeeded for 4 out of 5 (5 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/f19eb34706cfb38915082fc83f7f1ae9 for a full test report.

jfgrimm · 2023-03-10T13:14:04Z

@boegelbot please test @ generoso
EB_ARGS="--include-easyblocks-from-pr 2903 SciPy-bundle-2023.02-gfbf-2022b.eb"

boegelbot · 2023-03-10T13:15:10Z

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

PR test command 'EB_PR=16912 EB_ARGS="--include-easyblocks-from-pr 2903 SciPy-bundle-2023.02-gfbf-2022b.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16912 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10419

Test results coming soon (I hope)...

- notification for comment with ID 1463788596 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 · 2023-03-10T13:55:01Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2903
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/8c04d4805ac80bb1060e6d257e58f8d2 for a full test report.

branfosj · 2023-03-10T13:56:27Z

@boegelbot please test @ jsc-zen2
EB_ARGS="--include-easyblocks-from-pr 2903 SciPy-bundle-2023.02-gfbf-2022b.eb"

boegelbot · 2023-03-10T13:57:08Z

@branfosj: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=16912 EB_ARGS="--include-easyblocks-from-pr 2903 SciPy-bundle-2023.02-gfbf-2022b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16912 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2312

Test results coming soon (I hope)...

- notification for comment with ID 1463839111 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 · 2023-03-10T14:22:55Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2903
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/d47504213f99ab3f9f4336cd3aafe91d for a full test report.

jpecar · 2023-03-16T08:10:26Z

With updated easyblocks for me this fails because of missing module "pooch".
After I add it scipy then fails in three complex64 tests, both on haswell and zen2:

FAILED ../../linalg/tests/test_decomp.py::TestQZ::test_qz_complex64 - AssertionError:
FAILED ../../linalg/tests/test_lapack.py::test_gges_tgexc[complex64] - AssertionError:
FAILED ../../linalg/tests/test_lapack.py::test_gges_tgsen[complex64] - AssertionError:

I assume no one uses that at our site so I installed it with --skip-test-step.

jfgrimm · 2023-03-16T09:22:20Z

@jpecar some extensions (including pooch) were added to the main Python easyconfig instead of this one, in PR #17159

3rdcycle · 2023-05-10T11:54:58Z

Test report by @3rdcycle
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
bigstar05 - Linux Ubuntu 20.04, x86_64, Quad-Core AMD Opteron(tm) Processor 8356 (k10), Python 3.8.10
See https://gist.github.com/3rdcycle/87cd0016a292309bd359bb251735c5e8 for a full test report.

3rdcycle · 2023-05-10T11:56:57Z

Not sure how relevant this is given my old CPU architecture (AMD Barcelona). I'm wondering if this is somehow related to #14258 and #11836. The failing tests are different but the assertions occur in connection with longdouble on AMD.

What's weird is that when I run some of these tests in isolation, they seem to succeed. E.g.

=================================== FAILURES ===================================
___________________________ TestCreation.test_zeros ____________________________

self = <numpy.core.tests.test_multiarray.TestCreation object at 0x7fa3a28b39d0>

    def test_zeros(self):
        types = np.typecodes['AllInteger'] + np.typecodes['AllFloat']
        for dt in types:
            d = np.zeros((13,), dtype=dt)
            assert_equal(np.count_nonzero(d), 0)
            # true for ieee floats
>           assert_equal(d.sum(), 0)
E           AssertionError: 
E           Items are not equal:
E            ACTUAL: nan
E            DESIRED: 0

d          = array([0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.], dtype=float128)
dt         = 'g'
self       = <numpy.core.tests.test_multiarray.TestCreation object at 0x7fa3a28b39d0>
types      = 'bBhHiIlLqQpPefdgFDG'

/tmp/eb-i46u0s0e/tmpzz3f8r08/lib/python3.10/site-packages/numpy/core/tests/test_multiarray.py:943: AssertionError

$ pytest test_multiarray.py::TestCreation::test_zeros
==================================== test session starts ====================================
platform linux -- Python 3.10.8, pytest-7.2.0, pluggy-1.0.0
rootdir: /tmp/eb-i46u0s0e/tmpzz3f8r08/lib/python3.10/site-packages/numpy/core
plugins: hypothesis-6.68.2, xdist-3.1.0
collected 1 item                                                                            

test_multiarray.py .                                                                  [100%]

===================================== 1 passed in 0.14s =====================================

boegel · 2023-05-10T14:42:17Z

@3rdcycle Please open an issue on this, we can't follow up on problems in merged PRs...

edit: see #17895

{lang}[GCCcore/12.2.0] SciPy-bundle v2022.11, pybind11 v2.10.1, hypot…

f5e911f

…hesis v6.59.0 w/ Python 3.10.8

boegel added the update label Dec 15, 2022

boegel marked this pull request as draft December 15, 2022 14:18

boegel commented Dec 15, 2022

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boegel added this to the next release (4.7.0) milestone Dec 15, 2022

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

776235b

…asyconfigs into 20221215150042_new_pr_SciPy-bundle202211

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boegel added 2 commits December 15, 2022 20:44

add easyconfig for Eigen 3.4.0 with GCCcore/12.2.0

9e2e52b

use gfbf/2022.10 toolchain for SciPy-bundle 2022.11 + drop setuptools…

1464932

… build dependency + move mpi4py to dedicated easyconfig

easybuilders deleted a comment from boegelbot Dec 15, 2022

boegel changed the title ~~{lang}[GCCcore/12.2.0] SciPy-bundle v2022.11, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8~~ {lang}[bfbf/2022.10,foss/2022.10] SciPy-bundle v2022.11, mpi4py v3.1.4, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8 Dec 15, 2022

boegel marked this pull request as ready for review December 15, 2022 19:57

boegel mentioned this pull request Dec 15, 2022

add gfbf as subtoolchain of foss easybuilders/easybuild-framework#4143

Merged

boegel marked this pull request as draft December 19, 2022 09:58

easybuilders deleted a comment from boegelbot Dec 19, 2022

jfgrimm changed the title ~~{lang}[bfbf/2022.10,foss/2022.10] SciPy-bundle v2022.11, mpi4py v3.1.4, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8~~ {lang}[gfbf/2022.10,foss/2022.10] SciPy-bundle v2022.11, mpi4py v3.1.4, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8 Dec 20, 2022

boegel commented Dec 21, 2022

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boegel modified the milestones: next release (4.7.0), release after 4.7.0 Jan 3, 2023

jfgrimm added 4 commits January 16, 2023 11:50

bump versions to latest, and use 2022b toolchain

91e5aec

remove old updated files

5f4b5e3

Switch SciPy-bundle to Bundle, use mesonninja for scipy component

0f79963

revert to PythonBundle, and update easyblock instead

987d1fa

add pooch extension to ensure scipy tests run

89f205b

boegel changed the title ~~{lang}[gfbf/2022.10,foss/2022.10] SciPy-bundle v2022.11, mpi4py v3.1.4, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8~~ {lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2022.11, mpi4py v3.1.4, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8 Jan 18, 2023

add patch for scipy 1.10.1 to xfail test_maxiter_worsening on aarch64

0b94de2

boegel commented Feb 25, 2023

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use 'import deap.base' in sanity check for deap extension in SciPy-bu…

0de78ec

…ndle 2023.02

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boegel requested a review from branfosj February 26, 2023 08:26

branfosj approved these changes Feb 26, 2023

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branfosj merged commit 76dba56 into easybuilders:develop Feb 26, 2023

boegel deleted the 20221215150042_new_pr_SciPy-bundle202211 branch February 26, 2023 18:54

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{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8 #16912

{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8 #16912

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{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8 #16912

{lang}[gfbf/2022b,foss/2022b] SciPy-bundle v2023.02, mpi4py v3.1.4, pybind11 v2.10.3, hypothesis v6.68.2 w/ Python 3.10.8 #16912

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