--use-cluster and submit.slurm.sh

[SamuelECooper]

Hi all,

I am running HALFpipe on an HPC cluster with the --use-cluster flag and the sif from https://download.fmri.science/singularity/halfpipe-halfpipe-latest.sif. Everything goes fine in an interactive session, but once the interface exists it immediately goes into running fmriprep and there is no submit.slurm.sh scripted produced that I can use to submit this as a job. Any ideas? Thanks so much!

Best,
Sam Cooper

[HippocampusGirl]

Hi @SamuelECooper,

Could you send me the command that you use to start HALFpipe?

Thanks :-)

Best,
Lea

[SamuelECooper]

Yep, here you go @HippocampusGirl - thanks for the quick response!

singularity run --containall --bind /:/ext halfpipe-halfpipe-latest.sif --use-cluster

[HippocampusGirl]

Hi @SamuelECooper, That's odd, the same options are working for me. Could you also send me the "log.txt" file that was generated in your working directory? You can either upload it here or e-mail it to [email protected] :-)

[SamuelECooper]

Sure! I've attached it here, thanks!

log.txt

[HippocampusGirl]

Hi @SamuelECooper,

From the log file it seems like HALFpipe was cancelled before it was able to generate the submission script.

HALFpipe needs to check the metadata for all subjects to figure out which subjects actually need to be run in the cluster job (and which ones to skip because they are incomplete or not selected for processing). This usually takes a short while, and is nothing to worry about.

I would recommend trying again and letting it run a bit longer.

[SamuelECooper]

Whoops, OK, that indeed worked - I thought it was going right into fmriprep. Thanks so much for your help and glad it was only user error!

Sam