Re: [modeller_usage] Unable to run parallel job

["Del Genio, Charo" <>]

OK, I figured out what the problem was. My OS installation has python3.4 as the default interpreter. Thus, to properly parallelize the job, I need to create it with

j = job(modeller_path='modpy.sh python2.7 /usr/bin/modslave.py', host='localhost')

which is the way I normally run modeller. Now it works properly. Also, thanks for the suggestion to drop SOAP and just use it later to score the models at the end!




> From: Modeller Caretaker <>
> Sent: 24 October 2016 17:15
> To: Del Genio, Charo; 
> Subject: Re: [modeller_usage] Unable to run parallel job
> 
> That's odd. I don't see anything obviously wrong with your script. But 
> the master process communicates with the slaves over the network, so may 
> be having trouble establishing a connection. You can try using 
> host='localhost' as a job() parameter. See
> https://salilab.org/modeller/9.17/manual/node459.html
> 
> I don't think soap_protein_od has ever been tried in a parallel job 
> before. I can't think of an obvious reason why it wouldn't work, 
> although note that each Modeller task runs in a separate process (there 
> is no shared memory) so at best you'll end up with 16 copies of the SOAP 
> library in memory. You could certainly run out of memory since even one 
> copy of this library is quite large. You'd probably be better off 
> skipping this assessment method here and instead rescoring your final 
> models with it in serial once the job has finished.