Dear all,
I hope someone might shed a light on the problem I am having to get the
bedpostx running on a linux cluster using SGE. I have been struggling to
find the source of the problem but not exactly there, yet. I installed the
latest ver 4.1.2 on a CentOS 5 32 bit cluster and I am desperately trying to
run the bedpostx.
I made minor modifications to the bedpostx script to point to the right
directory of SGE software on this machine and changed the email address; but
nothing else. Did the same modifications in the fsl_sub, too. I had to
change the names of the queues, since they do not have them here.
When I run the bedpostx script, it puts the preprocessing and postprocessing
steps in the queue (I see bpx_prepro and bpx_postpr when I do qstat). But
there is no bedpostx task in the queue. So, it quits after preprocessing is
completed. Interestingly, if I execute the fsl_sub call from the command
line by itself, it distributes the tasks in the commands.txt, and runs fine
and I get the data processed in the cluster. Then I have to call the post
processing separately to get the final results. This is, of course, quite
tedious and I would like to do batch processing of large data.
If anyone had experienced this problem and know how to solve it, I would be
grateful if you can share your solution(s).
kind regards,
Tugan Muftuler
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