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Drop tcmalloc from SymEngine as it causes crashes with scipy #14119

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Micket
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@Micket Micket commented Oct 11, 2021

(created using eb --new-pr)
Use of tcmalloc causes some problems with SymEngine and SciPy-bundle

python3 -c "import symengine; import scipy.fft._pocketfft"

crashes. tcmalloc thinks it's a double free, so, either a bug in _pocketfft, or a but in tcmalloc I would guess. I can reproduce this with foss 2020b as well.

Since I don't know if there is a real bug in pocketfft, I propose to just drop gperftools from SymEngine instead.

(this particular bug is indirectly triggered by Qiskit 0.29 that i'm trying to add)

@Micket Micket added the bug fix label Oct 11, 2021
@Micket Micket added this to the next release (4.5.0?) milestone Oct 11, 2021
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Micket commented Oct 11, 2021

Test report by @Micket
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
alvis-c1 - Linux centos linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/319d04107a211cee499ce15715958a0b for a full test report.

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lexming commented Oct 13, 2021

Test report by @lexming
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
node300.hydra.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, Python 2.7.5
See https://gist.github.com/9816772f8542e30f89522f0b9e6d97c9 for a full test report.

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boegel commented Oct 13, 2021

@boegelbot please test @ generoso

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@Micket Why not add python -c "import symengine; import scipy.fft._pocketfft"
as a sanity check command?

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I can confirm the bug and the fix.

LGTM

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Micket commented Oct 13, 2021

SciPy isn't actually a dependency here.

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boegel commented Oct 13, 2021

SciPy isn't actually a dependency here.

Ah, ok... Nevermind then. :)

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

PR test command 'EB_PR=14119 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14119 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7071

Test results coming soon (I hope)...

- notification for comment with ID 942721363 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 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/2691f4dbc695670547e077020c79b31b for a full test report.

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boegel commented Oct 13, 2021

Going in, thanks @Micket!

@boegel boegel merged commit 77d43fa into easybuilders:develop Oct 13, 2021
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boegel commented Oct 13, 2021

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
node3520.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/7a110ae45870ecfef2add9cabd64e1d2 for a full test report.

@Micket Micket deleted the 20211011143813_new_pr_SymEngine070 branch April 21, 2023 11:14
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4 participants