Virtualenv and Sun Grid Engine (SGE)

[Dave W]

Hi all,

I'm trying to run a pipeline that I've developed on a shared drive (so the nodes all have access to my dependencies).
Our cluster is down at the moment (not my fault ;-), so I can't experiment with it right now.  Looking at the documentation (http://nipy.sourceforge.net/nipype/users/plugins.html#sge-pbs) I'm guessing it's:

plugin_args['template'] = myEnv + "/bin/source"

Has anyone tried this before and can confirm? 

Also, can someone explain what the 'template' key does?  The Oracle web site didn't have any documentation on it at all. 

Cheers,
Dave W.

[Dave W]

Spoke too soon on the documentation:

Futher down the page:

template : submit spec template to use for job submission. The template
           all generated submit specs are appended to this template. This
           can be a str or a filename.

Could anyone clear up this?  The typos are making this even more esoteric than it was intended to be, yes?  ;-)

Dave W.

[Satrajit Ghosh]

hi dave,

here is the prebuilt SGE template that's used - fairly minimal.

https://github.com/nipy/nipype/blob/master/nipype/pipeline/plugins/sge.py#L40

the help was intended to note that other files are added to this. you can look at the batch directory in your working directory to see what the final script looked like (these would be the sh files).

and you'll get several examples if you google: SGE job script

cheers,

satra

ps. thanks for the headsup on the typo's - will fix those.

--
 
---
You received this message because you are subscribed to the Google Groups "NiPy Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nipy-user+...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.