8000 Overlapping Freyja Runs · Issue #90 · PoonLab/gromstole · GitHub
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Overlapping Freyja Runs #90

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GopiGugan opened this issue Apr 1, 2024 · 5 comments
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Overlapping Freyja Runs #90

GopiGugan opened this issue Apr 1, 2024 · 5 comments
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@GopiGugan
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GopiGugan commented Apr 1, 2024 •
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Exception was raised even through freyja demix command ran successfully:

gromstole/freyja/trim.py

Lines 155 to 167 in cf5f290

p = subprocess.Popen(demix, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
_, error = p.communicate()
if p.returncode != 0:
if b'cvxpy.error.SolverError' in error:
sys.stderr.write(f"cvxpy.error.SolverError when running Freyja demix. Check coverage - ")
sys.stderr.write(f"{' '.join(demix)}\n")
else:
if sendemail:
send_error_notification(message="Error running {}".format(' '.join(demix)))
sys.stderr.write(f"Error running Freyja demix command - ")
sys.stderr.write(f"{' '.join(demix)}\n")
raise Exception(f"Subprocess failed with return code {p.returncode} when running {' '.join(demix)}")

Exception: Subprocess failed with return code 2 when running freyja demix
@GopiGugan GopiGugan added the bug Something isn't working label Apr 1, 2024
@GopiGugan
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Unable to reproduce:

>>> p = subprocess.Popen(demix, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
>>> _, error = p.communicate()
>>> error
b''
>>> p.returncode
0

@GopiGugan
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The job at 12:45pm started before the 10:45am one completed. This error could have come as a result of a conflict

@GopiGugan
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Solution is in place to address this for the gromstole runs (#58). Need to use a similar solution for freya runs

@ArtPoon
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ArtPoon commented Apr 2, 2024

To avoid this from happening in future runs, we should look into increasing the allocation of cores to this job so that it (hopefully) runs faster. Alternatively we can reduce the frequency of the cron job.

@GopiGugan GopiGugan changed the title Exception raised unnecessarily Overlapping Freyja Runs Apr 6, 2024
@GopiGugan
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To avoid this from happening in future runs, we should look into increasing the allocation of cores to this job so that it (hopefully) runs faster. Alternatively we can reduce the frequency of the cron job.

Script runs on 10 cores now instead of just 1 core

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@ArtPoon @GopiGugan
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