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Timeout issue in hoctests::test_nrniv-launch_py #2637

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iomaganaris opened this issue Dec 11, 2023 · 0 comments
Open

Timeout issue in hoctests::test_nrniv-launch_py #2637

iomaganaris opened this issue Dec 11, 2023 · 0 comments
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bug CI Continuous Integration

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@iomaganaris
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iomaganaris commented Dec 11, 2023

Context

Intel compiler builds sometimes fail in a test with timeout issues possible related to quit() function not returning from the interpreter.
Rerunning the CI seems to fix the issue and the CI passes.

Overview of the CI issue

See the log below:

121/266 Test  #76: hoctests::test_nrniv-launch_py ...........................................***Failed   10.60 sec
['-isatty', '-nobanner', '-nogui', '-c', 'a=5', '-'] 
func square() {
  return $1*$1
}
print "a = ", a
print "square(a)=", square(a)
quit()
Traceback (most recent call last):
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P178982/J1073852/spack-build/spack-stage-neuron-develop-arr5lxib65hkgzaekzx7s3nhmkjjfyp3/spack-build-arr5lxi/test/hoctests/test_nrniv-launch_py/tests/test_nrniv-launch.py", line 34, in <module>
    r = nrniv(
  File "/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P178982/J1073852/spack-build/spack-stage-neuron-develop-arr5lxib65hkgzaekzx7s3nhmkjjfyp3/spack-build-arr5lxi/test/hoctests/test_nrniv-launch_py/tests/test_nrniv-launch.py", line 23, in nrniv
    return subprocess.run(
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py", line 505, in run
    stdout, stderr = process.communicate(input, timeout=timeout)
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py", line 1154, in communicate
    stdout, stderr = self._communicate(input, endtime, timeout)
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py", line 2006, in _communicate
    self._check_timeout(endtime, orig_timeout, stdout, stderr)
  File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_externals/install_gcc-12.2.0-skylake/python-3.10.8-rvn6l5/lib/python3.10/subprocess.py", line 1198, in _check_timeout
    raise TimeoutExpired(
subprocess.TimeoutExpired: Command '['/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P178982/J1073852/spack-build/spack-stage-neuron-develop-arr5lxib65hkgzaekzx7s3nhmkjjfyp3/spack-build-arr5lxi/bin/nrniv', '-isatty', '-nobanner', '-nogui', '-c', 'a=5', '-']' timed out after 5 seconds

Expected result/behavior

We need to make sure that there are no issues with the interpreter exiting with quit() or the Intel compilers

CI Logs

https://bbpgitlab.epfl.ch/hpc/cellular/nrn/-/jobs/1073858

@iomaganaris iomaganaris added bug CI Continuous Integration labels Dec 11, 2023
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