Perhaps I am missing something stunningly obvious, but I'm not seeing a way to get FSL to use multiple cores on the same machine.
From what I can see fsl_sub is set up for SGE and Condor, but I don't see an obvious way to simply use it with multiple cores. Because of the number of users and scheduler policies, queue wait times make using any mechanism that submits another job impracticable. There is mention in fsl_sub of OMP_NUM_THREADS, but I searched the source distribution for OMP_NUM_THREADS, but I don't find it in any file but fsl_sub, so I don't think the FSL binary programs are OMP enabled.
I have access to machines with 4-56 cores on which I can run FSL, and I'd like to be able to set the number of cores that it can use. Some machines are set up to use cgroups, and the number of processors will vary from session to session, so ideally it would be possible to set a variable indicating the number of available processors. That would also help for shared but unscheduled machines.
I am very unfamiliar with the actual FSL programs themselves; I just help out when I can with Linux.
Thanks, -- bennet
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