Subject: [modeller_usage] Unable to run parallel job
From: "Del Genio, Charo" <>
Date: Fri, 21 Oct 2016 12:00:20 +0000
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Dear all, I'm trying to run a parallel job with modeller. The script is
from modeller import *
from modeller.automodel import *
from modeller import soap_protein_od
j = job()
for i in range(16)
j.append(local_slave())
log.verbose()
env.io.atom_files_directory = ['.', '../atom_files']
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)
a.starting_model = 1
a.ending_model = 16
a.loop.starting_model = 1
a.loop.ending_model = 10
a.use_parallel_job(j)
a.make()
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.
What am I doing wrong? For sake of completeness, I'm running modeller 9.17, the distribution is Gentoo Linux, and single-CPU runs of modeller work fine without problems (so far).
Thanks!