Dear Ioana,
I wrote this script and on the machine I tested it on it runs fine (P4 3GHz
Redhat 9.0). I just tested it again on one of our cluster machines and it
also runs correctly, both on one processor or on 4 processors (using a
slightly modified script that calls mpirun). This is whether I run it
interactively or in the background (./run_a-dna_20-1820ps.x &).
Do you have sander set up in some strange way that means it immediately
backgrounds itself upon execution? If you run sander manually on the command
line does it return the command prompt straight away or after the
calculation has finished?
If you could send me the details of the exact command you are running, a
copy of the script you use (in case it is in some way different to the one
that is on the website) and a list of any screen output / error messages you
receive that would make it much easier for me to determine what is going on.
Note, if you are submitting this script to a batch queuing system such as
PBS there is no guarantee it will run correctly. This will depend on how
your queue system is set up. In this case it is probably best to speak to
the people who manage the queue so that they can advise you on the form of
run script to use.
Ps. Using crontab is a very bad idea since you have know way of knowing how
long the previous job will take. E.g if the machine gets loaded with other
jobs while yours is running you might end up starting new jobs before the
previous one finished. This would undoubtedly corrupt your results.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Ioana Cozmuta
> Sent: 08 April 2004 19:26
> To: Amber List
> Subject: AMBER: script on tutorial page
>
> Hi amber users,
>
> I think there is a mistake in the script
> run_a-dna_20-1820ps.x
> on the tutorial web site:
>
> http://amber.scripps.edu/tutorial/polyA-polyT_New/adna.html
>
> The text says that the total 1.8ns run will be executed by
> running 9 x 200
> ps simulations with each successive
> simulation continuing on from the previous one.
> The script submits all the 9 simulations at the same time and not
> successively!
>
> Ioana
>
> Here is what I would propose:
>
> use crontab to run the script.csh every 30 minutes:
> 30 * * * * $PATH/script.csh
>
> Content of:
> script.csh
>
>
> ****************************************
> #!/bin/csh
> set AMBERHOME="/usr/local/AMBER8"
> set MDSTARTJOB=2
> set MDENDJOB=10
> set MDCURRENTJOB=$MDSTARTJOB
> set MDINPUT=0
> echo -n "Starting Script at: "
> date
> echo ""
>
> set user = `whoami`
>
> while ( $MDCURRENTJOB <= $MDENDJOB )
> set chk = `ps -u $user |grep sander | wc -l`
> if ($chk == 0) then
> echo -n "Job $MDCURRENTJOB started at: "
> date
> . MDINPUT = $MDCURRENTJOB - 1
> $AMBERHOME/exe/sander -O -i a-dna_md_1800ps.in \
> -o
> a-dna_md$MDCURRENTJOB.out \
> -p a-dna_wat.prmtop \
> -c a-dna_md$MDINPUT.rst \
> -r
> a-dna_md$MDCURRENTJOB.rst \
> -x
> a-dna_md$MDCURRENTJOB.mdcrd
> gzip -9 -v a-dna_md$MDCURRENTJOB.mdcrd
> echo -n "Job $MDCURRENTJOB finished at: "
> date
> . MDCURRENTJOB = $MDCURRENTJOB + 1
> endif
> end
> echo "ALL DONE"
>
>
> ******************
> Ioana Cozmuta, PhD
> Research Scientist
> Eloret Corporation
> Mail Stop 230-3
> NASA AMES Research Center,
> Moffet Field, CA 94035-1000
> Phone: (650) 604-0993
> http://www.ipt.arc.nasa.gov/computationalpeople.html
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
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>
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Received on Fri Apr 09 2004 - 05:53:00 PDT
