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

[Michael Hanke]

Hi,

thanks for tracking it down. Would you mind filing a bug report with
this information in the Debian BTS, so we can properly track this issue.

Thanks,

Michael


On Mon, Aug 13, 2012 at 10:52:13AM +0200, German Gomez-Herrero wrote:
> 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

-- 
Michael Hanke
http://mih.voxindeserto.de