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Hi,

I think your problem is that "SGE_ROOT has not been set."
This is essential in order for the fsl_sub utility to submit jobs to the SGE cluster.
So you need to figure out the right setting for this before things are likely to work.

Also note that not all FSL jobs will be submitted to the SGE queues, so to test it you'd need to run something that explicitly invokes fsl_sub within a script or a GUI (e.g. FEAT, dual regression, bedpostx, run_first_all, and other GUIs/scripts will use SGE via the fsl_sub command).

I hope this helps.
All the best,
Mark



From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Gengyan Zhao <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, 12 May 2016 16:44
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] How to monitor FSL's running with SGE (multi-CPU cores)

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
---------------------------------------------------------------------------------
mainqueue@localhost            BIP   0/0/31         -NA-     -NA-          au

Thanks.

Best,
Gengyan

Research Assistant
Medical Physics, UW-Madison