Dear Ross,
Thank you very much for your detailed explanation. I'm new at TACC. Your helps made me quickly familiar with their environment. I am now about to run a benchmark with a 5ns simulation of a protein/DNA complex. Sander.MPI would be first used. I would like to use 8 cores/note as you suggested. Could you please check if my qsub script as the following is all right? Any further suggestions would be appreciated. (To shorten the message, I only show one line of the sander script as an example).
Best regards,
Lei Jia
New York University
qsub script begins-------------------------
#!/bin/csh
#$ -V # Inherit the submission environment
#$ -cwd # Start job in submission directory
#$ -N BenchMark # Job Name
#$ -j y # combine stderr & stdout into stdout
#$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID)
#$ -pe 8way 32 # Requests 8 cores/node, 32/8 = 4 nodes total (16cpu)
#$ -q normal # Queue name
#$ -l h_rt=24:00:00 # Run time (hh:mm:ss) - 24 hours
set echo #{echo cmds, use "set echo" in csh}
cd /share/home/00654/tg458141/sander/benchmarkA_int_T_ctrl0815
#...
ibrun /share/home/00654/tg458141/local/amber9/exe/sander.MPI -O -i ./prod.in -o prod1.out -p A_int_T_ctrl.top -c equil_5.restrt -x prod1.traj -r prod1.restrt
#...
qsub script ends-------------------------------
----------------------------------------
> From: ross.rosswalker.co.uk
> To: amber.scripps.edu
> Subject: RE: AMBER: Compile AMBER 9 on TACC Ranger super computer
> Date: Thu, 14 Aug 2008 17:38:30 -0700
>
> Hi Lei,
>
> Yes, sorry I made a small mistake in the qsub script - since I forgot it was
> setup for bash shell.
>
> It should read:
> -----------------------------------
>
> #!/bin/bash
> #$ -V # Inherit the submission environment
> #$ -cwd # Start job in submission directory
> #$ -N testPMEMD # Job Name
> #$ -j y # combine stderr & stdout into stdout
> #$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID)
> #$ -pe 2way 32 # Requests 2 cores/node, 32/16 = 2 nodes total (4
> cpu)
> #$ -q development # Queue name
> #$ -l h_rt=00:45:00 # Run time (hh:mm:ss) - 0.5 hours
> set -x #{echo cmds, use "set echo" in csh}
> export AMBERHOME=~/amber9
> cd $AMBERHOME/test
> export DO_PARALLEL=ibrun
> make test.pmemd
>
> -----------------------------------
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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Received on Sun Aug 17 2008 - 06:07:46 PDT
