Hi I got this output when I ran the script. Is there any python library that I have not installed. I am using python 2.6 in ubuntu 2.6 with all numpy,scipy and scitools installed. I tried to use inheritance to get my class to also import parallel.
Knut J
MODELLER 9v7, 2009/06/12, r6923
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2009 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux Human-Naa50p 2.6.31-17-generic x86_64
Date and time of compilation : 2009/06/12 12:23:44
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2010/01/21 09:51:09
read_to_681_> topology.submodel read from topology file: 3
automodel__W> Topology and/or parameter libraries already in memory. These will
be used instead of the automodel defaults. If this is not what you
want, clear them before creating the automodel object with
env.libs.topology.clear() and env.libs.parameters.clear()
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 235
atom names : C +N
atom indices : 1851 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 16 235
atom names : C CA +N O
atom indices : 1851 1848 0 1852
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16251 14565
1468 (of 1853 total) atoms selected for optimization
Running 20 tasks on 3 slaves
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.1.1:17153:0:NVOBZUNU >& build_model_single.slave0
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.1.1:17153:1:MKBZURFK >& build_model_single.slave1
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.1.1:17153:2:TGSVVIND >& build_model_single.slave2
Identified slave <Slave on localhost>
Identified slave <Slave on localhost>
Identified slave <Slave on localhost>
Traceback (most recent call last):
File "/home/knut/workspace/natAhnaa10/src/build_model_single.py", line 38, in <module>
a.make()
File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 109, in make
self.multiple_models(atmsel)
File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 212, in multiple_models
self.parallel_multiple_models(atmsel)
File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 232, in parallel_multiple_models
self.outputs.extend(job.run_all_tasks())
File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 127, in run_all_tasks
for task in self._finish_all_tasks():
File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 160, in _finish_all_tasks
task = self._process_event(obj, s)
File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 176, in _process_event
task = obj.task_results()
File "/usr/lib/python2.6/dist-packages/modeller/parallel/slave.py", line 61, in task_results
r = self.get_data(allow_heartbeat=True)
File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 84, in get_data
(cmdtype, obj) = self._recv()
File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 125, in _recv
raise RemoteError(obj.exc, self)
modeller.parallel.communicator.RemoteError: <type 'AttributeError'>: 'module' object has no attribute 'KJ' from <Slave on localhost>
> Date: Wed, 20 Jan 2010 14:26:01 -0800
> From: modeller-care@salilab.org
> To: knutjbj@hotmail.com
> CC: modeller_usage@salilab.org
> Subject: Re: [modeller_usage] muliplay cpu
>
> On 01/20/2010 01:14 PM, Knut J Bjuland wrote:
> > How do I use multiple cpu when doing loop which I have shown in a script
> > below. I am trying to use several cpus to get a faster build of a model.
>
> Your script looks fine to me, and should run in parallel, except that
> you're using the automodel class (not loopmodel) so you're doing regular
> homology modeling, not loop modeling.
>
> Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you.