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spark-janelia out of date #24

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boazmohar opened this issue Dec 29, 2021 · 0 comments
Open

spark-janelia out of date #24

boazmohar opened this issue Dec 29, 2021 · 0 comments

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@boazmohar
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boazmohar commented Dec 29, 2021

I recently cloned and tried to run the following script with the spark-janelia version and got:

./startup-scripts/spark-janelia/n5-scale-pyramid.py 5 -n /nrs/svoboda/moharb/ExM/Basal/R3_GFP_bdv.split_output.n5 -i /GFP/s0 -f 2,2,2
/groups/spruston/home/moharb/n5-spark/startup-scripts/spark-janelia/flintstone/spark-janelia/spark-janelia:235: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if args.driveroutfile is not '':
/groups/spruston/home/moharb/n5-spark/startup-scripts/spark-janelia/flintstone/spark-janelia/spark-janelia:254: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if jobID is '':
/groups/spruston/home/moharb/n5-spark/startup-scripts/spark-janelia/flintstone/spark-janelia/spark-janelia:550: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if args.driveroutfile is '':
bsub -q spark32 -a "spark32(master,current)" -W 24:00 commandstring
This job will be billed to svoboda
spark32: No such queue. Job not submitted.
Master launch failed.
Traceback (most recent call last):
  File "/groups/spruston/home/moharb/n5-spark/startup-scripts/spark-janelia/flintstone/spark-janelia/spark-janelia", line 150, in startmaster
    rawout = subprocess.check_output(command, universal_newlines=True, shell=True)
  File "/groups/spruston/home/moharb/mambaforge/lib/python3.9/subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/groups/spruston/home/moharb/mambaforge/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'bsub -q spark32 -a "spark32(master,current)" -W 24:00 commandstring' returned non-zero exit status 255.

These is no longer a spark32 queue for example.
There is an updates script here

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