On 3/29/11 11:15 PM, Jason Swails wrote:
Googling "tcsh help" leads you to the site [1]
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.
I will try
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.
I do agree with you, thanks for your advice
Best wishes
Mahmoud
Good luck,
Jason
On Tue, Mar 29, 2011 at 2:16 PM, Mahmoud Soliman [2]<mahmoudelkot.gmail.com>wro
te:
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]
[3]
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. [4]
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
_______________________________________________
AMBER mailing list
[5]AMBER.ambermd.org
[6]
http://lists.ambermd.org/mailman/listinfo/amber
--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[7]
http://people.bath.ac.uk/mess20/
[8]
http://www.bath.ac.uk/person/812559
*********************************************
Mahmoud E. Soliman
Lecturer of pharmaceutical organic chemistry
Pharmaceutical Organic Chemistry Dept.
Faculty of pharmacy
Zagazig University
Zagazig
Egypt
**********************************************
Email:
[9]mess20.bath.ac.uk
[10]meelkot.zu.edu.eg
[11]mahmoudelkot.gmail.com
References
1.
http://www.tcsh.org/Home
2. mailto:mahmoudelkot.gmail.com
3.
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
4.
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html
5. mailto:AMBER.ambermd.org
6.
http://lists.ambermd.org/mailman/listinfo/amber
7.
http://people.bath.ac.uk/mess20/
8.
http://www.bath.ac.uk/person/812559
9. mailto:mess20.bath.ac.uk
10. mailto:meelkot.zu.edu.eg
11. mailto:mahmoudelkot.gmail.com
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 29 2011 - 15:00:02 PDT
