Description:
When running qunexContainer using the --scheduler
flag not scheduling the job. Issue seems to be linked to the --sessions
flag.
Call:
- FAILED - Running with the specific
--sessions
flag:
qunexContainer importDICOM \
--sessions="pb9609" \
--sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
--container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
--check=any \
--options="addImageType:1" \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"
- SUCCESS - Running without the
--sessions
flag:
qunexContainer importDICOM \
--sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
--container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
--check=any \
--options="addImageType:1" \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"
- SUCCESS - Running on a node without the
--scheduler
flag
qunexContainer importDICOM \
--sessions="pb10122" \
--sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
--container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
--check=any \
--options="addImageType:1"
- FAILED - Running qunexContainer with the
--scheduler
flag on a session (pb3924) that was already processed successfully using option 3 above.
qunexContainer importDICOM \
--sessions="pb3924" \
--sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
--container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
--check=any \
--options="addImageType:1" \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"
Logs:
-
When run with the sessions flag: No logs or terminal output created as no job is submitted.
-
When running without session flag, slurm output:
/gpfs/project/fas/n3/Studies/Longitudinal.R01/processing/logs/batchlogs/slurm-15567730.out
[job stopped because we did not want to process all the sessions folder at this time] -
Terminal output - Successful run through importDICOM. No logs created. Location of session:
/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions/pb10122
-
Output from terminal:
Quantitative Neuroimaging Environment & Toolbox (Qu|Nex) Suite Version 0.62.5
--------------------==== Qu|Nex failed! ====--------------------
ERROR: Execution of command `importDICOM` failed!
Please check documentation for the command (`qunex ?importDICOM`)!
The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)
qunex importDICOM \
--sessions=pb3924 \
--sessionsfolder=/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions \
--check=any \
--options=addImageType:1 \
--sessionids=pb3924
--------------------------------------------------------------
Here's the error as caught by python:
Traceback (most recent call last):
File "/opt/qunex/niutilities/gmri", line 558, in <module>
main()
File "/opt/qunex/niutilities/gmri", line 526, in main
runCommand(comm, opts)
File "/opt/qunex/niutilities/gmri", line 378, in runCommand
gcom.commands[command]['com'](**args)
TypeError: importDICOM() got an unexpected keyword argument 'sessionids'