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: ------------------------------------------------------------ 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 --------------------------------------------------------------------------------------------------- Traceback (most recent call last): File "loop.py", line 34, in ? m.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/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>
Hi,
Check this link: http://www.salilab.org/archives/modeller_usage/2009/msg00222.html
Hope this helps, Rui Rodrigues
On Wed, 7 Jul 2010 15:13:03 +0800 (CST), albert wrote > 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: > ------------------------------------------------------------ > 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 > -------------------------------------------------------------------------------------- ------------- > Traceback (most recent call last): > File "loop.py", line 34, in ? > m.make() > File "/usr/lib64/python2.4/site-packages/modeller/automodel/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>
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participants (2)
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albert -
J. Rui Rodrigues