Subject: Re: [modeller_usage] Unable to run parallel job
From: Modeller Caretaker <>
Date: Mon, 24 Oct 2016 10:15:17 -0700
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
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.