hi all, for those of you more experienced in cluster computing i am
having trouble testing fsl on a cluster here at uw.
we have a sungrid 60 cpu system with alex korb's feat multithreaded tcl
plugin (thanks alex for permission to test) installed.
i wanted to test bedposting and feat to see speed gains and fsl is not
able to see the addl cpus. the FSLMACHINELIST
and FSLREMOTECALL are not being set up correctly. below is the way the
cluster admin recommended setting it up
but fsl is not happy. i would be happy to go into the gory details off
list since this is side issue for most. how do i get
fsl to see the cpus on a dynamically allocated system.
cheers jeff
feat script:
#$ -S /bin/sh
#$ -cwd
#$ -l virtual_total=5.0G
#$ -hard -l mem_total=3.0G
#$ -m bea
#$ -V
#$ -pe mpich 2-6
FSLMACHINELIST=`cat ${TMPDIR}/machines | xargs echo`
FSLREMOTECALL=${TMPDIR}/rsh
export FSLMACHINELIST FSLREMOTECALL
/mnt/local/fsl/bin/feat_model design
and for dti:
#$ -S /bin/sh
#$ -cwd
#$ -l virtual_total=5.0G
#$ -m bea
#$ -V
#$ -hard -l mem_total=3.0G
eddy_correct fM_0001 data 1
avwroi data nodif 0 1
bet nodif nodif_brain_mask1
avwmaths nodif_brain_mask1 -bin nodif_brain_mask
cat << END | qsub -pe mpich 2-10
#$ -cwd
#$ -l virtual_total=5.0G
#$ -m bea
#$ -V
FSLMACHINELIST=`cat ${TMPDIR}/machines | xargs echo`
FSLREMOTECALL=${TMPDIR}/rsh
export FSLMACHINELIST FSLREMOTECALL
bedpost ~/DTI/DTILD_3139
|