nipype and fsl_sub

[parnesh...@gmail.com]

I am currently using some workflows with FSL components in them. Some of these components use the fsl_sub command to submit subjobs (I am running on a cluster) and return. However the outputs are not available for these jobs and therefore the pipeline crashes.

Anyone else encounter this? Any solutions?

[Satrajit Ghosh]

hi parnesh,

could you please specify which interfaces are creating trouble? the simplest is to turn off fsl_sub via environment variables for those interfaces.

node_obj.inputs.environ = {'SGE_ROOT': '' }

cheers,

satra

On Sat, Sep 20, 2014 at 3:49 AM, <parnesh...@gmail.com> wrote:

I am currently using some workflows with FSL components in them. Some of these components use the fsl_sub command to submit subjobs (I am running on a cluster) and return. However the outputs are not available for these jobs and therefore the pipeline crashes.

Anyone else encounter this? Any solutions?

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[parnesh...@gmail.com]

Thanks.

I found out that this particular cluster had a modified fsl_sub for PBS/Torque that did not allow serial execution. Fixed that now.

I was hoping there was a better solution though. The interfaces causing issues are fsl first and fsl feat.