[Nipy-devel] [nipype] better cluster support proposal

Chris Filo Gorgolewski chris.gorgolewski@gmail....
Thu Jan 27 10:32:00 CST 2011

On 26 January 2011 21:40, Michael Hanke <michael.hanke@gmail.com> wrote:
> On Wed, Jan 26, 2011 at 08:04:35PM +0000, Chris Filo Gorgolewski wrote:
>> Hi,
>> I was thinking about our (my?) problems with SGE, and after googling
>> some option I came with this very simple idea:
>> For every node submit a script with "qsub -hold_jid" specifying nodes
>> dependencies. The script will do the following things:
>> 1. Unpickle the interface it is going to run.
>> 2. Collect its inputs (we'll have to somehow pickle its connection info).
>> 3. Check the hash if incorrect run the node.
>> This should scale much better than the current ipython solution,
>> although it changes the architecture slightly.
>> What do you think? Does the cluster you use at Dartmouth support dependencies?
> There are basically two systems. One where you specify job dependencies
> after submission of previous jobs and one where you compose a DAG a
> priori. Both NiPyPE and Condor use the later paradigm.
> I think, it would be more portable to be able to export the entire DAG
> from NiPyPE into some abstract representation. If we had that, we could
> "translate" this DAG into a job array for SGE, into whatever PBS does,
> into Condor's DAGMAN format, etc... -- without having to interface with a
> particular cluster engine deep inside NiPyPE.
Good point. I'm also considering using some IPC method for passing the
inputs insdead of reading the reslts.npz files. Does your cluster
support MPI?


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