Hi everybody,
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:
Name OpSys Arch State Activity LoadAv Mem
ActvtyTime
slot10@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:18
slot11@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:19
slot12@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:20
slot13@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:21
slot14@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:22
slot15@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:23
slot16@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:16
slot17@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:17
slot18@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:18
slot19@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:19
slot1@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+00:08:36
slot20@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:20
slot21@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:21
slot22@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:22
slot23@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:23
slot24@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:16
slot25@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:17
slot26@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:18
slot27@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:19
slot28@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:20
slot29@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:21
slot2@srvulx01 LINUX X86_64 Unclaimed Idle 1.000 7436
0+19:25:18
slot30@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:22
slot31@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:23
slot32@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:16
slot3@srvulx01 LINUX X86_64 Unclaimed Idle 0.950 7436
0+19:25:19
slot4@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:20
slot5@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:21
slot6@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:22
slot7@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:23
slot8@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:16
slot9@srvulx01 LINUX X86_64 Unclaimed Idle 0.000 7436
0+19:25:17
Total Owner Claimed Unclaimed Matched Preempting
Backfill
X86_64/LINUX 32 0 0 32 0 0 0
Total 32 0 0 32 0 0 0
Here's the output of condor_q:
-- Submitter: srvulx01 : <127.0.0.1:42724> : srvulx01
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD
0 jobs; 0 completed, 0 removed, 0 idle, 0 running, 0 held, 0 suspended
This one shows that it should run even when the computer is not idle:
condor_config_val START
TRUE
And here is the error output:
fmri.feat/log$ more design.e0
/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
-D /tmp/feeds-oxford-jalapeno_linux_64-gcc4.1/feeds/results/fmri+.feat
-I 1 -init
while executing
"fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -init"
-b 10 -N feat0_init -l logs "
invoked from within
"if { $done_something == 0 } {
if { ! $fmri(inmelodic) } {
if { $fmri(level) == 1 } {
#{{{ FEAT first-level analysis
for { set session 1 } ..."
(file "/usr/share/fsl/5.0/bin/feat" line 207)
Any idea of what's going on here? One last thing, here is the script I
use for submitting:
#!/bin/bash
unset FSLPARALLEL # parallelization is not possible for submitted jobs
onm=allfsf.submit # submit file for condor
memusg=4000 # expected memory usage for a single analysis
cdir=$(pwd) # get the path to current working directory
#fsflst=`ls -1 $fsfdir/*.fsf`
fsflst=`ls -1 *.fsf`
if [ ! -d $cdir/log ] # create directory for condor log files
then
mkdir $cdir/log
fi
# create header for the condor submit file
echo "Executable = $FSLDIR/bin/feat
Universe = vanilla
initialdir = $cdir
request_cpus = 1
request_memory = $memusg
getenv = True
" > $onm
# create a queue with each fsf file found in the current directory
for cfsf in $fsflst
do
cstem=`basename "$cfsf" | sed -e 's/.fsf//g'`
echo "arguments = $cfsf" >> $onm
echo "error = $cdir/log/$cstem.e\$(Process)" >> $onm
echo "output = $cdir/log/$cstem.o\$(Process)" >> $onm
echo "Queue" >> $onm
done
condor_submit $onm # this will submit and run the analyses
Thanks!!!
--
Eneko Perez
IT Manager
*BCAM -* Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao, Basque Country - Spain
Tel. +34 946 567 842
[email protected] <mailto:[email protected]> | www.bcamath.org/perez
<http://www.bcamath.org/perez>
*/
/*
*/(/*///matematika mugaz bestalde *)*/
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