Hello FSL Masters,
My question is how can I know the SGE and FSL is setup properly and FSL is running with multi-CPU cores. How can I monitor the parallel runing of FSL with SGE?
I'm using a 32-core 3.0GHz, 128GB RAM, Ubuntu 14.04 machine to run FSL. And I'm a HCP pipeline user. SGE was setup according to the instruction in the external link given by FSL website (http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under). FSLPARALLEL=1. SGE_ROOT has not been set.
Then when I run FSL, most of the time only 3.1% of the CPU is in usage. SInce 3.1%*32=1, most of the time only one core is occupied. With the command top and 1 to see the activity of each core in real time, almost all the time only one core is in 100% usage. With the command qstat -f, I can only see the queue configured by myself following the instruction in external link. This is the output of qstat -f, when FSL (actually PreFreeSurferPipelineBatch.sh in the HCP pipeline, which calls a bunch of FSL tools) is running.
queuename qtype resv/used/tot. load_avg arch states
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mainqueue@localhost BIP 0/0/31 -NA- -NA- au
Thanks.
Best,
Gengyan
Research Assistant
Medical Physics, UW-Madison
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