[Neurodebian-users] unable to disable grid engine for FSL

[German Gomez-Herrero]

Hi,

This is a response to a previous list post by one of my colleagues. I 
just became a member of the neurodebian list and that is why I am 
sending this as new post rather than replying to the old one.

As Diederick said in his previous post, the environment variable 
FSLPARALLEL was having no effect for us and jobs were being submitted to 
the grid engine regardless. We tracked down the problem to script 
$FSLDIR/bin/fsl_sub (at the beginning of the script). If Michael could 
not reproduce this problem, I am guessing that it was due to the fact 
that variable SGE_ROOT was not set in his system, while it is set in 
ours. If you check the contents of script fsl_sub you can see that, if 
SGE_ROOT is set, then variable METHOD will be set to SGE, regardless of 
the value of FSLPARALLEL. The problem can be easily solved by adding the 
following lines to fsl_sub:

# Allow to override the above ...
if [ -n "$FSLPARALLEL"] ; then
     ....
# *** begins new code
else
     METHOD=NONE
# *** end of new code
fi

Best,
Germán