Hi Freesurfer experts,
I am trying to use the clusters to run BedpostX on a Connectome dataset.
Although the job is running now, it is running slowly. It has only got though 18 slices over the last 10 hours:
pbsubmit -n 8 -m bl744 -c "bedpostx /space/iggy/5/users/baojuan/mgh_1007/diff/preproc/mri/"
As this is the first time I am using the Center's Clusters, I have a few questions and hope someone can kindly help me or give me some suggestions.
1. How many CPUs and Vmem do you usually allocate when running BedpostX on Connectom data?
2. Which queue do you usually use? Do I need to use the extended queue?
3. I checked the jobinfo and found the Walltime is larger than the CPUtime which means the job did not use multiple processors. So could this be the reason?
Thanks a lot! Baojuan