{vis,math}[foss/2021a] FMPy v0.3.2, PyOpenGL v3.1.5, PyQtGraph v0.12.3 w/ Python 3.9.5 by deniskristak · Pull Request #14481 · easybuilders/easybuild-easyconfigs

deniskristak · 2021-12-01T11:32:22Z

adding easyconfigs: FMPy-0.3.2-foss-2021a.eb, PyOpenGL-3.1.5-GCCcore-10.3.0.eb, PyQtGraph-0.12.3-foss-2021a.eb, FMPy-0.3.2-foss-2021a.eb

requires:

…10.3.0.eb, PyQtGraph-0.12.3-foss-2021a.eb, FMPy-0.3.2-foss-2021a.eb

migueldiascosta · 2021-12-02T03:08:38Z

@boegelbot please test @ generoso

boegelbot · 2021-12-02T03:10:09Z

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

PR test command 'EB_PR=14481 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14481 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7417

Test results coming soon (I hope)...

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boegelbot · 2021-12-02T03:13:01Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 4 (3 easyconfigs in total)
cns1 - 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/5d20122d64dfa85b2e386eb04de3f9e5 for a full test report.

deniskristak · 2021-12-02T13:05:54Z

@boegel would you please look at the weird test result?

boegel · 2021-12-07T08:56:09Z

I tried manually compiling the QtCore utility that isn't producing any output, and I ran into this:

$ module load Qt5/5.15.2-GCCcore-10.3.0 GCC/10.3.0
$ cd /tmp/boegelbot/PyQt5/5.15.4/GCCcore-10.3.0/PyQt5-5.15.4
$ g++ -c -m64 -pipe -O2 -Wall -Wextra -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_CORE_LIB -I. -I qpy/QtCore -I/project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/include/QtCore -I. -I/project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/mkspecs/linux-g++-64 -o cfgtest_QtCore.o config-tests/cfgtest_QtCore.cpp
$ g++ -m64 -Wl,-O1 -Wl,-rpath,/project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib -o QtCore cfgtest_QtCore.o   /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so -lpthread
$ ./QtCore
Illegal instruction (core dumped)

That's... interesting. It could have something to do with generoso being a VM environment, rather than bare metal...

boegel · 2021-12-07T08:59:09Z

More info obtained via gdb:

$ gdb QtCore
(gdb) run
...
Program received signal SIGILL, Illegal instruction.
0x00007ffff78ffe0a in qRandomCpu(void*, long long) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
(gdb) bt
#0  0x00007ffff78ffe0a in qRandomCpu(void*, long long) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#1  0x00007ffff78bb6e0 in ?? () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#2  0x00007ffff78f7b3b in ?? () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#3  0x00007ffff78f84e9 in QHashData::detach_helper(void (*)(QHashData::Node*, void*), void (*)(QHashData::Node*), int, int) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#4  0x00007ffff7adf4a4 in QTextCodec::codecForName(QByteArray const&) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#5  0x00007ffff7adf7be in QTextCodec::codecForLocale() () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#6  0x00007ffff793eb26 in QString::fromLocal8Bit_helper(char const*, int) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#7  0x00007ffff7a83717 in QCoreApplicationPrivate::appName() const () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#8  0x00007ffff7a8a686 in QCoreApplicationPrivate::init() () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#9  0x00007ffff7a8ad0c in QCoreApplication::QCoreApplication(int&, char**, int) () from /project/boegelbot/Rocky8/haswell/software/Qt5/5.15.2-GCCcore-10.3.0/lib/libQt5Core.so.5
#10 0x0000000000400b1d in main ()

(gbd) disassemble
...
=> 0x00007ffff78ffe0a <+42>:    rdseed %eax

Looks very similar to https://bugs.gentoo.org/707390

boegel · 2021-12-07T09:20:39Z

From the Qt5 installation log (Aug 22nd 2021):

Checking for RDRAND instruction... yes
Checking for RDSEED instruction... yes

Perhaps we need to reinstall Qt5, it's possible that some update on generoso caused rdseed to no longer be available in the VM? I'll give that a try...

boegel · 2021-12-07T12:26:53Z

The problem indeed disappears when Qt5 is rebuilt. The log for the existing Qt5 installation shows that the build was done on an Intel Xeon E5-2660, so perhaps the VM wasn't running where it was supposed to back then (Aug 22nd 2021).

I'll ask the bot do a forced reinstall of Qt5 (I took a backup copy of the existing Qt5 install dir for debugging purposes).

boegel · 2021-12-07T12:28:21Z

@boegelbot please test @ generoso
CORE_CNT=16
EB_ARGS="Qt5-5.15.2-GCCcore-10.3.0.eb FMPy-0.3.2-foss-2021a.eb"

boegelbot · 2021-12-07T12:30:11Z

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

PR test command 'EB_PR=14481 EB_ARGS="Qt5-5.15.2-GCCcore-10.3.0.eb FMPy-0.3.2-foss-2021a.eb" /opt/software/slurm/bin/sbatch --job-name test_PR_14481 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7445

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2021-12-07T13:17:43Z

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 5 (2 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/6de5e16af05665a9ed65d2eaa7bc6d3c for a full test report.

boegel · 2021-12-07T14:40:21Z

Qt5 re-installation failed, probably due to lack of sufficient memory? I've restarted that re-installation manually on generoso...

boegel · 2021-12-07T18:52:32Z

@boegelbot please test @ generoso

boegelbot · 2021-12-07T18:55:10Z

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

PR test command 'EB_PR=14481 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14481 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7450

Test results coming soon (I hope)...

Details

- notification for comment with ID 988184803 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 · 2021-12-07T19:55:08Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 4 (3 easyconfigs in total)
cns1 - 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/63a97b746613b01caa6114cbe015c818 for a full test report.

boegel · 2021-12-16T15:41:43Z

@boegelbot please test @ generoso

boegelbot · 2021-12-16T15:45:09Z

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

PR test command 'EB_PR=14481 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_14481 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7497

Test results coming soon (I hope)...

Details

- notification for comment with ID 995935388 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).

boegel · 2021-12-16T15:48:47Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node2601.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/08164c2ea5a8a99912f69561655a7e71 for a full test report.

boegelbot · 2021-12-16T15:49:37Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
cns1 - 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/85a9efd04473ac307f1bb8b569de0567 for a full test report.

boegel · 2021-12-16T16:03:29Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3507.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/3e3fbcc191fd81cec02ea38990e7e79c for a full test report.

boegel

lgtm

boegel · 2021-12-16T16:26:31Z

Going in, thanks @deniskristak!

adding easyconfigs: FMPy-0.3.2-foss-2021a.eb, PyOpenGL-3.1.5-GCCcore-…

ccfa4a2

…10.3.0.eb, PyQtGraph-0.12.3-foss-2021a.eb, FMPy-0.3.2-foss-2021a.eb

deniskristak changed the title ~~FMPy #216~~ FMPy and deps Dec 1, 2021

migueldiascosta changed the title ~~FMPy and deps~~ {vis,math}[foss/2021a] FMPy v0.3.2, PyOpenGL v3.1.5, PyQtGraph v0.12.3 w/ Python 3.9.5 Dec 2, 2021

migueldiascosta added new update labels Dec 2, 2021

migueldiascosta added this to the 4.x milestone Dec 2, 2021

boegel added 2 commits December 16, 2021 16:40

Merge branch 'develop' into 20211201122202_new_pr_FMPy032

88a2158

add Brotli-python dependency for FMPy

feb24ec

boegel approved these changes Dec 16, 2021

View reviewed changes

boegel merged commit e53e231 into easybuilders:develop Dec 16, 2021

boegel modified the milestones: 4.x, next release (4.5.2?) Dec 16, 2021

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