Hi,
while testing an adaptor to allow using FSL in Condor pools, I found,
what I believe is, a small bug in FEAT.
diff --git a/src/feat5/feat b/src/feat5/feat
index 7953ab7..ea0cc5a 100755
--- a/src/feat5/feat
+++ b/src/feat5/feat
@@ -371,7 +371,7 @@ if { $fmri(featwatcher_yn) } {
set howlong 300
}
if { [ info exists fmri(featModelOpts) ] } {
- set jobHalt {-h featModelID}
+ set jobHalt {-h $featModelID}
}
set prestatsID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -prestats" -b $howlong $jobHalt -N feat2_pre -l logs ]
}
In SGE this doesn't seem to have a negative effect (at least when one
only runs a single FEAT pipeline per user), but Condor is more picky
regarding job ids.
I also modified the FEEDS script to survive submitting jobs to a cluster
and still be able to compute the error values (by simply waiting for the
result to be available).
--- a/RUN
+++ b/RUN
@@ -297,6 +297,9 @@
# run FEAT
fsl:exec "${FSLDIR}/bin/feat ${FEEDSDIR}/results/design.fsf"
+# wait for FEAT to finish (in case of cluster job submission)
+exec sh -c "while \[ ! -f ${FEEDSDIR}/results/fmri.feat/cluster_zfstat1_std.txt \]; do sleep 5; done"
+
puts "checking error on filtered functional data:"
perror fmri.feat/filtered_func_data 0.1
puts "checking error on raw Z stat images:"
@@ -397,6 +400,9 @@
fsl:exec "cp -r $FEEDSDIR/data/fdt_subj1 $FEEDSDIR/results"
fsl:exec "unset FSLMACHINELIST; ${FSLDIR}/bin/bedpostx $FEEDSDIR/results/fdt_subj1 -n 1"
+# wait for FEAT to finish (in case of cluster job submission)
+exec sh -c "while \[ ! -f ${FEEDSDIR}/results/fdt_subj1.bedpostX/merged_th1samples.nii.gz \]; do sleep 5; done"
+
puts "checking error on bedpost output:"
perror fdt_subj1.bedpostX/dyads1 .005
perror fdt_subj1.bedpostX/mean_f1samples .005
With these two modifications and a 'qsub'-emulation FSL seems to run
fine with Condor. If anybody is interested in trying it out, let me know.
In any case, one of the next Debian package updates will come with
out-of-the-box support for Condor. This should make it a little easier
for people to move away from SGE.
Michael
--
Michael Hanke
http://mih.voxindeserto.de
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