{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 #17467

boegel · 2023-03-03T15:45:58Z

(created using eb --new-pr)

edit: requires that numexpr in SciPy-bundle/2021.10-intel-2021b was reinstalled using fixed easyblock, see easybuilders/easybuild-easyblocks#2897

edit: now requires:

add custom easyblock for sympy to fix issue in test step when tmpdir is a symlink easybuild-easyblocks#2949

verdurin · 2023-03-03T19:22:57Z

Test report by @verdurin
FAILED
Build succeeded for 3 out of 4 (2 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/b8a77c77ec2ae9471e79b83a533b04e6 for a full test report.

boegel · 2023-03-14T14:37:38Z

@boegelbot please test @ generoso

boegelbot · 2023-03-14T14:45:11Z

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

PR test command 'EB_PR=17467 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17467 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10468

Test results coming soon (I hope)...

- notification for comment with ID 1468220772 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 · 2023-03-14T15:38:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/e1efca9c0f3eb2fadf8ef4e21a0c718a for a full test report.

boegel · 2023-03-14T16:30:14Z

@verdurin Your failing test is probably because numexpr was not rebuilt with easybuilders/easybuild-easyblocks#2897, can you try again after doing so?

boegel · 2023-03-14T16:30:58Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-03-14T16:32:08Z

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

PR test command 'EB_PR=17467 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17467 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2354

Test results coming soon (I hope)...

- notification for comment with ID 1468433523 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 · 2023-03-14T17:23:38Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/11d8f35d06477e2223463e6eb0a7639b for a full test report.

boegel · 2023-03-14T17:23:44Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3170.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/039edd73f86494d9fbfc43f0dbf9e1e2 for a full test report.

casparvl · 2023-03-15T11:24:08Z

Test report by @casparvl
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux Rocky Linux 8.7, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/b43c3e60cdabbdabfd433b85c82ec573 for a full test report.

casparvl · 2023-03-15T19:48:10Z

Test report by @casparvl
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux Rocky Linux 8.7, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/2e628795dcbd532696e2988cc3e45c0b for a full test report.

casparvl · 2023-03-16T02:48:07Z

Test report by @casparvl
SUCCESS
Build succeeded for 7 out of 7 (2 easyconfigs in total)
gcn71.local.snellius.surf.nl - Linux Rocky Linux 8.7, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz, 1 x NVIDIA NVIDIA A100-SXM4-40GB, 515.86.01, Python 3.6.8
See https://gist.github.com/f78cd648c3e2372c0d2772f295586418 for a full test report.

casparvl · 2023-03-16T09:02:34Z

So... I had this other issue with files in another PR, and it made me check if I could build this one when using a local scratch disk as build & tmpdir. That build succeeded. Still, makes me wonder if the aforementioned patch is still relevant somehow. I'll probably not be the only one who will run into this.

I will try to rebuild once more on our shared FS, see if I can indeed still reproduce the failure there after the succes on gcn71.

casparvl · 2023-03-16T09:51:25Z

Test report by @casparvl
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
tcn493.local.snellius.surf.nl - Linux Rocky Linux 8.7, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/b2c9779cab0d8523a54f006e463432c7 for a full test report.

casparvl · 2023-03-16T09:55:00Z

Yep, that's consistently failing on our GPFS, and succeeding on local scratch disks...

casparvl · 2023-03-17T09:33:37Z

I've tried to make a new quick-and-dirty patch,

diff -Nru sympy-1.9.orig/sympy/utilities/_compilation/compilation.py sympy-1.9/sympy/utilities/_compilation/compilation.py
--- sympy-1.9.orig/sympy/utilities/_compilation/compilation.py  2023-03-16 11:31:51.437345000 +0100
+++ sympy-1.9/sympy/utilities/_compilation/compilation.py       2023-03-16 22:13:33.746881742 +0100
@@ -525,7 +525,7 @@


 def _write_sources_to_build_dir(sources, build_dir):
-    build_dir = build_dir or tempfile.mkdtemp()
+    build_dir = build_dir or tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix()))
     if not os.path.isdir(build_dir):
         raise OSError("Non-existent directory: ", build_dir)

@@ -617,7 +617,7 @@
         stdout, stderr = [txt.decode('utf-8') for txt in p.communicate()]
     finally:
         if clean and os.path.isdir(build_dir):
-            shutil.rmtree(build_dir)
+            # shutil.rmtree(build_dir)
             build_dir = None
     info = dict(exit_status=exit_status, build_dir=build_dir)
     return (stdout, stderr), info

but that didn't work. I don't know exactly where the failure comes from, I just looked for the points that looked somewhat similar to what was done in the previous patch. Anyway, it didn't help, and I don't really have the time to dive deeper into this.

@boegel how do you think we can best proceed on this?

casparvl · 2023-03-22T13:32:21Z

@boegel see #17593 . Maybe you can let me know what you think of my proposition to solve it in the EasyBlock?

casparvl · 2023-07-31T14:50:49Z

Test report by @casparvl
FAILED
Build succeeded for 1 out of 2 (2 easyconfigs in total)
tcn72.local.snellius.surf.nl - Linux RHEL 8.6, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/casparvl/d66574802ed73ff6a6d2dfc441680c00 for a full test report.

casparvl · 2023-07-31T18:04:50Z

Just testing if I could still reproduce this, before making a PR for sympy's that use easybuilders/easybuild-easyblocks#2949. I've also reproduced the issue for sympy-1.11.1-foss-2022a.eb, just to get another datapoint. I guess that means I'll need to have at least all versions 1.9 and newer of sympy use the newer EasyBlock.

…anced custom ea…syblock for sympy that also takes care of sanity check & co

boegel · 2023-08-05T14:59:04Z

@boegelbot please test @ generoso

boegelbot · 2023-08-05T15:00:11Z

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

PR test command 'EB_PR=17467 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17467 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11390

Test results coming soon (I hope)...

- notification for comment with ID 1666527765 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 · 2023-08-05T15:52:06Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns8 - 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/boegelbot/21506848b1531c3ee19285dc22b189f7 for a full test report.

boegel · 2023-08-05T15:52:13Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-08-05T15:57:07Z

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

PR test command 'EB_PR=17467 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17467 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 3092

Test results coming soon (I hope)...

- notification for comment with ID 1666539521 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 · 2023-08-05T16:49:21Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/boegelbot/4e3505e9911bd206ae37cfffc3bd6c1b for a full test report.

boegel · 2023-08-05T16:49:22Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3100.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/d1666b9c3507e8c96546ea9756c3e77f for a full test report.

boegel · 2023-08-05T17:31:03Z

@casparvl Can you retest? This should be good to go now...

casparvl · 2023-08-07T11:59:50Z

Test report by @casparvl
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#2949
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
tcn440.local.snellius.surf.nl - Linux RHEL 8.6, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.6.8
See https://gist.github.com/casparvl/bcdc364b2ccb285445642de13c83eec4 for a full test report.

casparvl

Lgtm!

casparvl · 2023-08-07T13:50:07Z

Going in, thanks @boegel!

{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6

4a32038

boegel added the update label Mar 3, 2023

boegel added this to the 4.x milestone Mar 14, 2023

boegel mentioned this pull request Mar 21, 2023

sympy w/ intel/2021b vscentrum/vsc-software-stack#79

Closed

casparvl mentioned this pull request Mar 22, 2023

sympy test suite fails on FileNotFoundError because path to temporary directory has symlinks #17593

Closed

casparvl pushed a commit to sara-nl/easybuild-easyconfigs that referenced this pull request Aug 1, 2023

Replacing PR easybuilders#17467

0ca69fe

This was referenced Aug 3, 2023

add custom easyblock for sympy to fix issue in test step when tmpdir is a symlink easybuilders/easybuild-easyblocks#2949

Merged

use custom easyblock for recent sympy easyconfigs to prevent test failures #18428

Merged

Use new EasyBlock

22584db

easybuilders deleted a comment from boegelbot Aug 5, 2023

clean up easyconfig for sympy 1.9 w/ intel/2021b to fully rely on enh…

b57e2d5

…anced custom ea…syblock for sympy that also takes care of sanity check & co

easybuilders deleted a comment from casparvl Aug 5, 2023

casparvl approved these changes Aug 7, 2023

View reviewed changes

casparvl modified the milestones: 4.x, next release (4.8.1?) Aug 7, 2023

casparvl merged commit e1e07d8 into easybuilders:develop Aug 7, 2023
5 checks passed

boegel deleted the 20230303164554_new_pr_sympy19 branch August 7, 2023 19:42

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{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 #17467

{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 #17467

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{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 #17467

{math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 #17467

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