[Neurodebian-users] Condor parallel problem

[Eduardo Garza V.]

Hi Michael,

Thanks for the quick reply.

> If you install the 'fsl' package, in addition to 'fsl-4.1' you'll have
> that link as well, but you can also just source the versioned config
> file directly with no side-effects.


I'm fairly new to Linux, so please bare with me. 
I did what you said, source the versioned config file. Or at least I think I did that.

To source I wrote on the terminal "$. /etc/fsl/4.1/fsl.sh", which is the correct path. Is there anything else I need to do to source the config file? 
Perhaps this is the issue and I'm doing it wrong.

> FSLPARALLEL should be set to 'condor'.
> 
> Is that the case?


Inside the file "fsl.sh" there is a paragraph dedicated to parallel processing using SGE.
It says #FSLPARALLEL=1. My question is, do I have to modify the fsl.sh to say "FSLPARALLEL=condor" uncommented? 
Or do I just write in terminal "$ export FSLPARALLEL=condor" to set the variable?

Thanks again

Best regards

Eduardo 





On Aug 14, 2012, at 2:18 AM, Michael Hanke wrote:

> On Mon, Aug 13, 2012 at 11:06:15AM -0500, Eduardo Garza wrote:
>> Dear all,
>> 
>> Thanks for the great tutorial Parallelizing FSL, however I have a problem.
>> I did all the steps and exported the variable before running fsl but it's
>> not working. I'm using Ubuntu 12.04 LTS 64 bit. Condor was easily
>> installed, and the exported variable is showing in env.
>> Do I have to redirect Condor? fsl.sh is not on /etc/fsl/fsl.sh but in
>> /etc/fsl/4.1/fsl.sh.
> 
> If you install the 'fsl' package, in addition to 'fsl-4.1' you'll have
> that link as well, but you can also just source the versioned config
> file directly with no side-effects.
> 
>> Do I need to change anything in fsl.sh? Like the FSLPARALLEL=1?
> 
> FSLPARALLEL should be set to 'condor'.
> 
> Is that the case?
> 
> Michael
> 
> -- 
> Michael Hanke
> http://mih.voxindeserto.de

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