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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Received on Wed May 03 2006 - 06:07:08 PDT
