Hello:
I try to do loop refinement by loop.py using mutiple CPU, but it doesn't work. Here is the scrips and log file. Could anybody give me some advices?
scrips:
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from modeller import *
from modeller.automodel import *
from modeller.parallel import *
j = job()
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
env = environ()
log.verbose()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms (necessary)
class dope_loopmodel(loopmodel):
# This routine picks the residues to be refined by loop modeling
def select_loop_atoms(self):
# One loop from residue 19 to 28 inclusive
return selection(self.residue_range('238:', '241:'))
m = dope_loopmodel(env,
inimodel='backbone', # initial model of the target
sequence='a8') # code of the target
m.loop.starting_model= 1 # index of the first loop model
m.loop.ending_model = 100 # index of the last loop model
m.loop.md_level = refine.slow # loop refinement method
m.use_parallel_job(j)
m.make()
logfile
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Traceback (most recent call last):
File "loop.py", line 34, in ?
m.make()
File "/usr/lib64/python2.4/site-packages/modeller/aut
omodel/loopmodel.py", line 34, in make
self.build_seq(self.inimodel, 1)
File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 146, in build_seq
self.parallel_loop_models(atmsel, ini_model, num, sched)
File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 164, in parallel_loop_models
self.loop.outputs.extend(job.run_all_tasks())
File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 130, in run_all_tasks
for task in self._finish_all_tasks():
File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 163, in _finish_all_tasks
task = self._process_event(obj, s)
File "/usr/lib64/python2.4/site-packages/modeller/parallel/job.py", line 179, in _process_event
task = obj.task_results()
File "/usr/lib64/python2.4/site-packages/modeller/parallel/slave.py", line 61, in task_results
r = self.get_data(allow_heartbeat=True)
File "/usr/lib64/python2.4/site-packages/modeller/parallel/communicator.py", line 84, in get_data
(cmdtype, obj) = self._recv()
File "/usr/lib64/python2.4/site-packages/modeller/parallel/communicator.py", line 125, in _recv
raise RemoteError(obj.exc, self)
modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'MyLoop' from <Slave on localhost>