Do classes inheriting from automodel get propagated when using the sge_qsub
parallel job? I can get a parallel run to work with automodel, but not with
a new class including a cis-peptide restraint defined in special_restraints
(which I can get to run in single proc mode).
I get the following error:
# Traceback (most recent call last):
File "psamdc.py", line 77, in ?
a.make()
File "/home/namd/lib/modeller9v2/modlib/modeller/automodel/automodel.py",
line 110, in make
self.multiple_models(atmsel)
File "/home/namd/lib/modeller9v2/modlib/modeller/automodel/automodel.py",
line 214, in multiple_models
self.parallel_multiple_models(atmsel)
File "/home/namd/lib/modeller9v2/modlib/modeller/automodel/automodel.py",
line 234, in parallel_multiple_models
self.outputs.extend(job.run_all_tasks())
File "/home/namd/lib/modeller9v2/modlib/modeller/parallel/job.py", line
110, in run_all_tasks
self.finish_next_task()
File "/home/namd/lib/modeller9v2/modlib/modeller/parallel/job.py", line
127, in finish_next_task
self.process_event(obj, s)
File "/home/namd/lib/modeller9v2/modlib/modeller/parallel/job.py", line
141, in process_event
task = obj.task_results()
File "/home/namd/lib/modeller9v2/modlib/modeller/parallel/slave.py", line
54, in task_results
r = self.get_data(allow_heartbeat=True)
File
"/home/namd/lib/modeller9v2/modlib/modeller/parallel/communicator.py", line
78, in get_data
(cmdtype, obj) = self._recv()
File
"/home/namd/lib/modeller9v2/modlib/modeller/parallel/communicator.py", line
116, in _recv
raise RemoteError(obj, self)
modeller.parallel.communicator.RemoteError: AttributeError: 'module' object
has no attribute 'cismodel' from <SGE qsub slave, ID 107.1>
Is there a convenient way around this?
Thanks in advance
Regards
--
I think perhaps the most important problem is that we are trying to
understand the fundamental workings of the universe via a language devised
for telling one another when the best fruit is.
-- Terry Pratchett, alt.fan.pratchett
--
Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria