Nipype problems with MultiCore/PBS plugins - imports & easy jobs

1

I’ve run into two issues with Nipype when running it on a cluster with either several processes (MultiCore plugin) or with separate jobs (PBS plugin).

  1. I’ve written a small interface that I’ve put into a separate file (myinterface.py). When I use parallel jobs, Python cannot find this file because the working directory is different. How can I tell nipype engine to import it or where should I put it so that it will be available?
  2. Some tasks like data grabber are very easy and it would make more sense to run them on a local machine while running other nodes in parallel. Is this possible?
2

I don’t have much experience with PBS, so hopefully someone else can help you out, there.

For question 2, check out the run_without_submitting option for Node.

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3

for question 1, you can use PYTHONPATH environment variable (assuming the path exists across your machines).

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4

Thanks, both solutions work for me.