Googling "tcsh help" leads you to the site
http://www.tcsh.org/Home .
That's a fairly comprehensive review of tcsh scripting.
If you're familiar with another shell (e.g. bash), then try rewriting that
script in bash instead. It'll help strengthen your scripting ability while
helping you to understand the steps that the script is actually taking.
One thing I would suggest, however, is not to run a 400 hour job before you
have a firm grasp of what you're doing. Run short jobs with small time
limits (nstlim=1000, or something) just to make sure you have a grasp of
what's happening before you dump that much computing power on the problem.
Good luck,
Jason
On Tue, Mar 29, 2011 at 2:16 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear Amber and scripting experts,
> I have very humble knowledge about script languages so I seek some help.
> I
> am running umbrella sampling calculation so I have to make sander read
> from
> sequential external files (restraint files) using some script available
> on
> ([1]
> http://projects.eml.org/mcm/people/wang/PMF/tutorial.html).Thepointis
> this script needs tcsh shell ( the scripts starts with #!/bin/tcsh) and
> that
> causes some conflict with the other commands required to run the job in
> parallel (see below the script that we use to submit the jobs on our
> cluster) so when I added the bit required for PMF calculation, the (
> PBS_NODEFILE: nproc) commands do not like this bit to be in the same file
> The added lines are highlighted in red (these lines need for PMF
> calculation
> while the rest of the script is used to submit the jobs in parallel.
> Any idea from more scripts experienced people to let me know how to avoid
> this conflict??
> #!/bin/tcsh
> ###These lines are for Moab
> #MSUB -l nodes=2:ppn=8
> #MSUB -l partition=ALL
> #MSUB -l walltime=400:00:00
> #MSUB -m be
> #MSUB -V
> #MSUB -o
> /export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/amber.our
> #MSUB -e
> /export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/amber.err
> #MSUB -d /export/home/msoliman/scratch/Amber/glycosidase_work/pmf/AM1/
> #MSUB -mb
> set number=(3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6 1.4 1.2 1.0)
> foreach N ($number)
> sed -e 's/minimum/'$N'/g' umbrella.in > input.in
> ##### Running commands
> ####nproc=`wc $PBS_NODEFILE | awk '{print $1}'`
> exe=/export/home/nmonama/amber/bin/sander.MPI
> nproc=`cat $PBS_NODEFILE | wc -l`
> mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i input.in -o
> dist_$N.out -p com_solvated.top -c com_solvated_equil.qmmm.rst -r
> dist_$N.xyz -x dist_$N.trj
>
> Thanks
> Mahmoud
>
> References
>
> 1. http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 29 2011 - 14:30:04 PDT
