Dear all,
We recently updated our storage server which changed the paths to our
data.
Everything is up and working perfectly fine, except a problem that is
specific to submitting FEAT jobs. To be clear, we have a cluster of PPC
Mac Xserves, and use SGE to manage jobs on that cluster. If it matters,
we are still using FSL 4.1.1, but as this has been functioning fine for
a long time before the storage change, we don't think the FSL version is
the culprit.
In the command line, typing "feat design.fsf" will properly set up
the "pre" "reg" "post" and "stop" jobs in the queue. However, once
these jobs go into on of the cluster processors, each job is
terminated prematurely. No errors are found in the report_log file,
but in the preproc.feat/logs directory the following error is
reported in the feat2_pre.e file:
grep: /private/var/automount/nfs/research/data/subj1/s01/r1/
preproc.feat/design.fsf: No such file or directory
while executing
"exec sh -c "grep 'fmri(inmelodic)' $filename | tail -n 1 | awk
'{ print \$3 }'" "
(procedure "feat5:load" line 5)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(file "/common/fsl4.1/bin/feat" line 132)
I've made sure, and the design.fsf file that it is looking for does,
in fact, exist. What is interesting is that if instead of running
"feat design.fsf" in the command line, I type "fsl_sub feat
design.fsf" then the proper jobs are queued and when they get onto a
cluster node, the job runs perfectly fine. Also, if I force the jobs
to run on the head node, instead of being send into the cluster, they
also run fine.
Another potentially useful note is that, after running a job that
errors, if we log into the node that it tried to run in and check the
logs we get a different error. Here, it says that the node cannot
find a file, but it is looking in the wrong place because it is using
the *old* path that existed before the storage upgrade. This is very
strange, because nowhere in the setup of the design file (I've tried
doing this manually and with the GUI) do we input the old paths. SGE
has been updated with the new paths in the sge_aliases file and all
other FSL jobs have been running without a problem.
Any help with troubleshooting would be greatly appreciated. Thank you,
--
Lokke Highstein
Systems Manager
PICS, Columbia University
710 W.168th st.
New York, NY 10032
212-342-0293
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