Hi,
I want to run parallel job on my Quadcore. I used as a template the script provided in the examples/automodel/model-parallel.py
But I get the following error:
File "loopmodel.py", line 3, in ? from modeller.parallel import * File "/usr/lib/modeller9v5/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/usr/lib/modeller9v5/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket
Thanks for help,
Hugo
On 10/09/2009 04:31 AM, Hugo Gutiérrez de Teran wrote: > I want to run parallel job on my Quadcore. I used as a template the > script provided in the examples/automodel/model-parallel.py ... > ImportError: No module named socket
Did you read http://salilab.org/modeller/FAQ.html#19 ?
Ben Webb, Modeller Caretaker
I have python 2.5 installed, but no module named socket is found anyway ... I am not experienced in python, could you please give me some more clues?
Hugo
I have checked more carefully, I have socket in my python2.5 distribution, but still when I run my script using python (instead of mod9.5) I have a regular output at the end of which I get the following:
<< end of ENERGY. openf___224_> Open NPY2_on3eml_loop.IL00000001.pdb wrpdb___568_> Residues, atoms, selected atoms: 301 2398 2398 Running 10 tasks on 3 slaves mod9v5 -slave 127.0.0.2:17481:0:EBGHEWRT >& loopmodel.slave0 mod9v5 -slave 127.0.0.2:17481:1:GJWNQGJG >& loopmodel.slave1 mod9v5 -slave 127.0.0.2:17481:2:OJVIVOJX >& loopmodel.slave2
And the terminal stays on standby, although no process is running on my computer. If I manually try to run each of this lines, I get again the error of "no module named socket", while if I run each of this lines with python instead of mod9v5 I get again the terminal on standby, as if it was running, but with no process on my computer running.
Thanks for help,
Hugo
Modeller Caretaker wrote: > On 10/09/2009 04:31 AM, Hugo Gutiérrez de Teran wrote: >> I want to run parallel job on my Quadcore. I used as a template the >> script provided in the examples/automodel/model-parallel.py > ... >> ImportError: No module named socket > > Did you read http://salilab.org/modeller/FAQ.html#19 ? > > Ben Webb, Modeller Caretaker
Well, updating to the last version 9.7 I get one step further, but still in trouble (see bellow the log message). I also attach my script, which runs without problem in serial mode.
------- SCRIPT ----------------- from modeller import * from modeller.automodel import * from modeller.parallel import *
# Use 3 CPUs in a parallel job on this machine j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave())
log.verbose() env = environ()
# Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Two residue ranges (both will be refined simultaneously) return selection( # self.residue_range('39:', '46:'), self.residue_range('67:', '74:'), # self.residue_range('116:', '123:'), self.residue_range('141:', '170:'), # self.residue_range('214:', '228:'), self.residue_range('246:', '257:'))
################################## def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['77:'], self.residues['157:'])) env.io.atom_files_directory = ['.', '..'] env.edat.nonbonded_sel_atoms = 1
a = MyLoop(env, inimodel='NPY2_on3eml.B99990010.pdb', sequence='NPY2_on3eml_loop', loop_assess_methods=assess.DOPEHR) # assess each loop with DOPE
a.loop.starting_model = 1 # First loop model a.loop.ending_model = 10 # Last loop model a.loop.md_level = refine.slow_large # loop refinement method a.use_parallel_job(j) # Use the job for model building a.make() # do modeling and loop refinement --------------- END OF SCRIPT ------------ --------------- ERROR ------------------
<< end of ENERGY. openf___224_> Open NPY2_on3eml_loop.IL00000001.pdb wrpdb___568_> Residues, atoms, selected atoms: 301 2398 2398 Running 10 tasks on 3 slaves /usr/bin/python2.5 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.0.2:11760:0:YWJRYYUV >& loopmodel.slave0 /usr/bin/python2.5 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.0.2:11760:1:DHUJSEJZ >& loopmodel.slave1 /usr/bin/python2.5 /usr/lib/modeller9v7/bin/modslave.py -slave 127.0.0.2:11760:2:BMUFRHVN >& loopmodel.slave2 Identified slave <Slave on localhost> Identified slave <Slave on localhost> Identified slave <Slave on localhost> Traceback (most recent call last): File "loopmodel.py", line 45, in <module> a.make() # do modeling and loop refinement File "/usr/lib64/python2.5/site-packages/modeller/automodel/loopmodel.py", line 31, in make self.build_seq(self.inimodel, 1) File "/usr/lib64/python2.5/site-packages/modeller/automodel/loopmodel.py", line 143, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/lib64/python2.5/site-packages/modeller/automodel/loopmodel.py", line 161, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.5/site-packages/modeller/parallel/job.py", line 127, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.5/site-packages/modeller/parallel/job.py", line 160, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.5/site-packages/modeller/parallel/job.py", line 176, in _process_event task = obj.task_results() File "/usr/lib64/python2.5/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.5/site-packages/modeller/parallel/communicator.py", line 84, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.5/site-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 'MyLoop' from <Slave on localhost>
----------------- END OF ERROR ---------------- Modeller Caretaker wrote: > On 10/09/2009 04:31 AM, Hugo Gutiérrez de Teran wrote: >> I want to run parallel job on my Quadcore. I used as a template the >> script provided in the examples/automodel/model-parallel.py > ... >> ImportError: No module named socket > > Did you read http://salilab.org/modeller/FAQ.html#19 ? > > Ben Webb, Modeller Caretaker
Hugo Gutiérrez de Teran wrote: > Well, updating to the last version 9.7 I get one step further, but still > in trouble (see bellow the log message). I also attach my script, which > runs without problem in serial mode. ... > raise RemoteError(obj.exc, self) > modeller.parallel.communicator.RemoteError: <type 'AttributeError'>: > 'module' object has no attribute 'MyLoop' from <Slave on localhost>
Modeller's parallel support uses Python's 'pickle' module, and it's a quirk of that module that any classes you define (such as MyLoop) cannot be in the main script but must be defined in a module that you import. See examples/python/parallel-task.py for an example. So the solution is fairly straightforward - simply take the definition of the MyLoop class out of your main script and put it in a different file (say myloop.py) in the same directory as your script, then at the start of your script say "from myloop import MyLoop".
Ben Webb, Modeller Caretaker
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Hugo Gutiérrez de Teran -
Modeller Caretaker