[Beowulf] Jupyter and EP HPC

Joe Landman joe.landman at gmail.com
Fri Jul 27 11:53:43 PDT 2018

On 07/27/2018 02:47 PM, Lux, Jim (337K) wrote:
> I’ve just started using Jupyter to organize my Pythonic ramblings..
> What would be kind of cool is to have a high level way to do some 
> embarrassingly parallel python stuff, and I’m sure it’s been done, but 
> my google skills appear to be lacking (for all I know there’s someone 
> at JPL who is doing this, among the 6000 people doing stuff here).
> What I’m thinking is this:
> I have a high level python script that iterates through a set of data 
> values for some model parameter, and farms out running the model to 
> nodes on a cluster, but then gathers the results back.
> So, I’d have N copies of the python model script on the nodes.
> Almost like a pythonic version of pdsh.
> Yeah, I’m sure I could use lots of subprocess() and execute() stuff 
> (heck, I could shell pdsh), but like with all things python, someone 
> has probably already done it before and has all the nice hooks into 
> the Ipython kernel.

I didn't do this with ipython or python ... but this was effectively the 
way I parallelized NCBI BLAST in 1998-1999 or so.  Wrote a perl script 
to parse args, construct jobs, move data, submit/manage jobs, recover 
results, reassemble output.  SGI turned that into a product.

Joe Landman
e: joe.landman at gmail.com
t: @hpcjoe
w: https://scalability.org
g: https://github.com/joelandman
l: https://www.linkedin.com/in/joelandman

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