Re: [modeller_usage] Parallel job with modeller on a machine withaltinstall python2.3

[Oscar Conchillo Solé <>]

Hi,
perhaps you can avoid using parallel modules by spliting your modell generation in several independent jobs (is not what you want but it gets the same results) check this two posts:

http://www.salilab.org/archives/modeller_usage/2013/msg00040.html
http://www.salilab.org/archives/modeller_usage/2013/msg00041.html



I use this all the time and I never had any problems with any python module, it works great for me. I run it in a rocks-cluster 5.4 (CentOS 5) using the default python installation.
I have a perl script that does everything, if you are interested I can send it to you.
it is made for running it through an SGE queue system, so perhaps you will need to change something  in order to run it in your environment, but it is just a couple of directories.

OCS

Oscar Conchillo Solé
Group of Computational Biology and Proteomics
IBB Data Center Manager and Linux Sysadmin
Institut de Biotecnologia I Biomedicina (UAB)
mail: ">
telf: 0034 93581 4431; 0034 93586 8939

On 10/20/2015 12:29 PM, ashika torikora wrote:

Hi,

I know there have been a million different and redundant questions asked concerning parallel jobs using modeller. However, after thoroughly reading through most of them (and the manual pages concerning parallel jobs) I still cannot run a modeller parallel job.

I understand that in order to run parallel modeller one has to have the python2.3 modules.

I have installed Python2.3.6 as an alternative install on my RHEL machine (the default Python for my machine is 2.7.5). However even after installing Python2.3.6 I still get the same error (no module named socket, although Python2.3.6 has the socket module --python2.7.5 does not--).

Adding a shebang with the python2.3 location in the beginning of the input changes nothing.

Here is my input:


from modeller import *
from modeller.automodel import *
from modeller.parallel import *


# Use 4 CPUs in a parallel job on this machine
j = job()
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())



log.verbose()
env = environ()

env.io.atom_files_directory = ['.', './template_struc']

# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms
class MyLoop(dopehr_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('278:', '284:'))

a = MyLoop(env,
           alnfile  = 'alignment.ali',      # alignment filename
           knowns   = '2cjf_0',               # codes of the templates
           sequence = '2cjf',               # code of the target
           loop_assess_methods=assess.DOPE) # assess each loop with DOPE

a.starting_model= 1                 # index of the first model
a.ending_model  = 1                # index of the last model

a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 1000           # Last loop model
a.loop.assess_methods=(assess.DOPE, assess.GA341, assess.normalized_dope)

a.use_parallel_job(j)               # Use the job for model building


a.make()                            # do modeling and loop refinement

And here is my error:

Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "backup.py", line 4, in ?
    from modeller.parallel import *
  File "/usr/lib/modeller9.15/modlib/modeller/parallel/__init__.py", line 1, in ?
    from modeller.parallel.job import job
  File "/usr/lib/modeller9.15/modlib/modeller/parallel/job.py", line 1, in ?
    import socket, random, os, select
ImportError: No module named socket

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