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users > RE: Running cmtk on a multi-node cluster
Apr 7, 2017 07:04 PM | Dan Xie - UCSF
RE: Running cmtk on a multi-node cluster
Hi Greg,
I have a few more questions regarding multi-threading in cmtk:
1. when building the package on a cluster, should I specify the number of threads to enable parallelization or I can just specify that number in the munger script (following the flag -T) ?
2. when submitting jobs using qsub, which parallel environment (for instance, SMP, openmpi or mpich2) should I specify?
3. To execute a parallel job, should I add "mpirun" ahead of the command line below?
"/netapp/home/danustc/cmtk-build/bin/munger" -b "/netapp/home/danustc/cmtk-build/bin" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -v -T 2 -s "refbrain/Nov012016B3ZDref.nrrd" "images"
Thanks!
Dan
I have a few more questions regarding multi-threading in cmtk:
1. when building the package on a cluster, should I specify the number of threads to enable parallelization or I can just specify that number in the munger script (following the flag -T) ?
2. when submitting jobs using qsub, which parallel environment (for instance, SMP, openmpi or mpich2) should I specify?
3. To execute a parallel job, should I add "mpirun" ahead of the command line below?
"/netapp/home/danustc/cmtk-build/bin/munger" -b "/netapp/home/danustc/cmtk-build/bin" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -v -T 2 -s "refbrain/Nov012016B3ZDref.nrrd" "images"
Thanks!
Dan
Threaded View
Title | Author | Date |
---|---|---|
Dan Xie | Mar 30, 2017 | |
Torsten Rohlfing | Mar 30, 2017 | |
Dan Xie | Mar 30, 2017 | |
Greg Jefferis | Mar 31, 2017 | |
Dan Xie | Apr 7, 2017 | |
Torsten Rohlfing | Apr 8, 2017 | |
Dan Xie | Apr 1, 2017 | |