AMBER Archive (2006)

Subject: Re: AMBER: sequential execution of number of parallel jobs

From: Petr Kulhanek (kulhanek_at_chemi.muni.cz)
Date: Tue May 02 2006 - 03:20:51 CDT

Hello,

PBS environment (both openpbs and pbspro) has capability to manage
dependencies among jobs. In your case, you should start next jobs with
following option:

qsub ... -W depend=afterany:previous_job_id ...

where previous_job_id is job id returned by qsub from previous job
submission.

Please keep in mind, that it could happen that subsequent jobs will run
on different nodes (it depends on your computer system). Therefore job
script should save final results (at least restart file) to some shared
volume to guarantee their accessibility for next job.

With regards,
        Petr

In Hee Park wrote:
> Dear Amber users:
>
> I'd like to collect trajectories not in one file, but separately several
> files as did in the AMBER Tutorial:
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section6.htm
>
> But queue job submi environment in order to use paralle sander, how to execute
> (submit the queue jobs) a number of parallel jobs one by one in sequential manner,
> i.e. after one parallel job is done, using its resulting file as input, then
> execute the next job?
>
> Could you let me know how to do that by which part should be modified in
> the script below?
>
> ===========================
> #!/usr/bin/python
> #
> import sys, posix
>
> path = "/path/dir/name"
> amber = "/amber/dir/name/exe"
>
> for i in range(2, 10+1, 1):
> j = i - 1
> jobname = """%s%d""" % ("a-dna_md", i)
> inpname = """%s%d""" % ("a-dna_md", j)
> number = """%s%d""" % ("MDINFO", i)
> command = """ echo "#PBS -N testSanderMPI
> #PBS -l walltime=00:30:00
> #PBS -l nodes=4:ppn=2:myrinet
> #PBS -S /bin/bash
> #PBS -j oe
> cd %s
> %s/sander.MPI -O -i a-dna_md_1800ps.in -o %s.out -p a-dna_wat.prmtop -c %s.rst -r %s.rst -x %s.mdcrd -inf %s" > %s.script
> chmod +x %s.script
> qsub %s.script """ % (path, amber, jobname, inpname, jobname, jobname, number, jobname, jobname, jobname)
> ++i
> posix.system(command)
> ===========================
>
> Thanks-
>
> ___________________________________________________________________________
> In Hee Park
>
>
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-- 
##################################################
   Petr Kulhanek
  ------------------------------------------------
   E-mail: kulhanek_at_chemi.muni.cz
   Phone: +420 - 549 495 459
   WWW: http://www.ncbr.chemi.muni.cz/~kulhanek
  ------------------------------------------------
   National Centre for Biomolecular Research
   Masaryk University
   Kotlarska 2, CZ-611 37 Brno
   Czech Republic
##################################################

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