[Tutor] serial to parallel

[Bala subramanian]

Friends,
In the previous mail there was an "mistake" i was not aware of. So pls
dnt get upset.

For frame in trajectory-A:
>         cunt= str(frame.time)

It is count =str(frame.time). A counter to find frame number.

Thanks joel for letting me to know it.

Bala

On Mon, Nov 5, 2012 at 11:46 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I use a python package to analyse molecular trajectories. For those
> not familiar, I have described the the problem below.
> I have two trajectories A,B. Each trajectory has a collection of
> frames. A frame is a numpy array.
> For frame in trajectory-A:
>         cunt= str(frame.time)
>         function(trajectoryB, frame, outfile=cunt+'.txt')
> process all .txt files
>
> The function is described in the package that I use. It also has a
> built-in counter for each frame.
> I want to convert this to a parallel code in the following way. Each
> processor can take one frame from trajectory-A and applies the
> function and write the corresponding output file.
> This is the first time I am trying such parallelism. I would
> appreciate your guidance on how I can do it. The original code is
> pasted below.
> -----------------------
> #!/usr/bin/env python
> import MDAnalysis
> from MDAnalysis.analysis.align import rmsd,fasta2select, rms_fit_trj
> import argparse
> import numpy as np
>
> parser = argparse.ArgumentParser(description=info)
> # a series of  parser.add_argument definitions
>
> U1=MDAnalysis.Universe(args.rtop,args.rtrj)   # open  trajectory-A
> U2=MDAnalysis.Universe(args.ttop,args.ttrj)   # open   trajectory-B
>
>
> for fr in U1.trajectory:
>         nd='%0*d' % ( 5,fr.frame)
>         rms_fit_trj(U2,U1.selectAtoms('all'),rmsdfile=str(nd) + '.rmsd')
>
> Thanks in advance,
> Bala



-- 
C. Balasubramanian