Re: [modeller_usage] Unable to run parallel job

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 10/21/16 5:00 AM, Del Genio, Charo wrote:
> Dear all, I'm trying to run a parallel job with modeller.
...
> a = dopehr_loopmodel(env, alnfile='OurAlignment.ali',
>     knows='2p1mB', sequence='Rece',
>     assess_methods=(assess.DOPEHR,
>         soap_protein_od.Scorer(),
>         assess.GA341),
>     loop_assess_methods=assess.DOPEHR)
...
> However, it doesn't seem to work properly. In particular, it creates 16 slave output files containing exclusively
> 'import site' failed
> and then it hangs there, doing nothing at all, until I kill it with CTRL-C.

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.

	Ben Webb, Modeller Caretaker
--
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