Hi,
At the beginning of the year I processed 400 scans on a linux cluster. It had a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 and a processing time limit of 48 hours (which was fine for 99% of the scans). Most scans went through autorecon-all without problem.
I am now trying to reprocess the scans with the new version but I am running into a number of problems. On the same linux cluser processing the same scans, some scans (~30%) run without problem. The rest either fail because they exceed the memory limit or because they take much more than 48 hours (the jobs are being killed and the logs report only the left and sometimes part of the right hemisphere being processed).
Since the documentation makes clear that FS works best with 2 Gig of ram, I have switched to an Itinium cluster with 2 Gig ram limit and 48 hours processing time limit. When I compare the logs of the same scans processed on both systems the Itinium cluster seems to take longer and although I am still running tests it appears that for at least some scans autoreconall might take 70+ hours.
Here are my questions:
1. On the linux cluster can I tell freesurfer not to exceed a certain ram allocation? and if yes how?
2. Do the problems I have on the Itinium cluster suggest that FS is badly configured on this system? and if yes where should we look? (I don't have access to this system's configuration and I have to feedback to the system managers to fix eventual problems.)
Thank you very much for your help and for sharing these great tools with us.
Nic