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[modeller_usage] qsub and cis restraints



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