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Hi everybody,<br>
<br>
We have an issue trying to run FSL through Condor. The thing is
that the jobs don't start ever. Here is the output of
condor_status:<br>
<br>
Name OpSys Arch State Activity LoadAv
Mem ActvtyTime<br>
<br>
slot10@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:18<br>
slot11@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:19<br>
slot12@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:20<br>
slot13@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:21<br>
slot14@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:22<br>
slot15@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:23<br>
slot16@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:16<br>
slot17@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:17<br>
slot18@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:18<br>
slot19@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:19<br>
slot1@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+00:08:36<br>
slot20@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:20<br>
slot21@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:21<br>
slot22@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:22<br>
slot23@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:23<br>
slot24@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:16<br>
slot25@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:17<br>
slot26@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:18<br>
slot27@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:19<br>
slot28@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:20<br>
slot29@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:21<br>
slot2@srvulx01 LINUX X86_64 Unclaimed Idle 1.000
7436 0+19:25:18<br>
slot30@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:22<br>
slot31@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:23<br>
slot32@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:16<br>
slot3@srvulx01 LINUX X86_64 Unclaimed Idle 0.950
7436 0+19:25:19<br>
slot4@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:20<br>
slot5@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:21<br>
slot6@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:22<br>
slot7@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:23<br>
slot8@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:16<br>
slot9@srvulx01 LINUX X86_64 Unclaimed Idle 0.000
7436 0+19:25:17<br>
Total Owner Claimed Unclaimed Matched
Preempting Backfill<br>
<br>
X86_64/LINUX 32 0 0 32
0 0 0<br>
<br>
Total 32 0 0 32
0 0 0<br>
<br>
<br>
Here's the output of condor_q:<br>
<br>
-- Submitter: srvulx01 : <127.0.0.1:42724> : srvulx01<br>
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE
CMD <br>
<br>
0 jobs; 0 completed, 0 removed, 0 idle, 0 running, 0 held, 0
suspended<br>
<br>
This one shows that it should run even when the computer is not
idle:<br>
<br>
condor_config_val START<br>
TRUE<br>
<br>
<br>
And here is the error output:<br>
<br>
fmri.feat/log$ more design.e0<br>
/usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init
/usr/share/fsl/5.0/bin/feat
/tmp/feeds-oxford-jalapeno_linux_64-gcc4.1/feeds/results/fmri+.feat/design.fsf<br>
-D
/tmp/feeds-oxford-jalapeno_linux_64-gcc4.1/feeds/results/fmri+.feat
-I 1 -init<br>
while executing<br>
"fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session
-init" -b 10 -N feat0_init -l logs "<br>
invoked from within<br>
"if { $done_something == 0 } {<br>
<br>
if { ! $fmri(inmelodic) } {<br>
if { $fmri(level) == 1 } {<br>
#{{{ FEAT first-level analysis<br>
<br>
for { set session 1 } ..."<br>
(file "/usr/share/fsl/5.0/bin/feat" line 207)<br>
<br>
Any idea of what's going on here? One last thing, here is the
script I use for submitting:<br>
<br>
#!/bin/bash<br>
<br>
unset FSLPARALLEL # parallelization is not possible for submitted
jobs<br>
<br>
onm=allfsf.submit # submit file for condor<br>
memusg=4000 # expected memory usage for a single analysis<br>
<br>
cdir=$(pwd) # get the path to current working directory<br>
#fsflst=`ls -1 $fsfdir/*.fsf`<br>
fsflst=`ls -1 *.fsf`<br>
<br>
if [ ! -d $cdir/log ] # create directory for condor log files<br>
then<br>
mkdir $cdir/log<br>
fi<br>
<br>
# create header for the condor submit file<br>
echo "Executable = $FSLDIR/bin/feat<br>
Universe = vanilla<br>
initialdir = $cdir<br>
request_cpus = 1<br>
request_memory = $memusg<br>
getenv = True<br>
" > $onm<br>
<br>
# create a queue with each fsf file found in the current directory<br>
for cfsf in $fsflst<br>
do<br>
cstem=`basename "$cfsf" | sed -e 's/.fsf//g'`<br>
<br>
echo "arguments = $cfsf" >> $onm<br>
echo "error = $cdir/log/$cstem.e\$(Process)" >> $onm<br>
echo "output = $cdir/log/$cstem.o\$(Process)" >> $onm<br>
echo "Queue" >> $onm<br>
done<br>
<br>
condor_submit $onm # this will submit and run the analyses<br>
<br>
Thanks!!!<br>
<br>
<br>
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