[Neurodebian-users] fsl_sub error

[Michael Hanke]

Hi,

On Sat, Mar 10, 2012 at 09:48:15PM -0500, Lewis, Dave wrote:
> I believe that I found an error (a bug waiting to happen) in fsl_sub,
> and the fix is simple.  This error isn't in the original version of
> fsl_sub from the FSL website.  Our cluster has Debian 6.0 and fsl
> 4.1.9-2~nd60+1.
> 
> The person who installed FSL on our cluster (via NeuroDebian) changed
> the line 
>     #queue=long.q
> to
>     queue=all.q
> (Our cluster was installed with all.q and debug.q.)

I'm not exactly sure what is happening with your cluster, but the
solution you are proposing doesn't scale enough. There is not guarantee
that any particular SGE installation will have an 'all.q'. Meaning
always submitting to all.q will cause an error on most clusters.
Moreover, even if there is an all.q, most installations will have more
fine-grained queue configurations.

SGE is capable of selecting an appropriate queue automatically, based on
other information about a job. In the case of FSL this is mostly the
expected runtime. Removing the queue specification from fsl_sub was
necessary to make it compatible with most (apparently not all) SGE
installations.

I'd be curious to know what particular configuration aspect prevents
this from working on your cluster.

Michael


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