NAMD is available for the Lemieux Alpha cluster and the T3E at PSC
NAMD 2.5b1 for Tru64-Alpha-MPI is available for
download.
NAMD 2.5b1 is installed in the directory
/usr/local/packages/namd/current
NAMD 2.4 is installed in the directory
/usr/local/packages/namd/stable
Interactive Runs
Since interactive runs are not supported on this machine, the Tru64-Alpha
version of NAMD will be installed to allow you to test your jobs before submitting them to the batch queue:
/to/be/determined/namd2 run.namd
Batch Jobs
Submit batch jobs (to run on 32 nodes, 128 processors, for 6 hours)
using the qsub command:
qsub -l walltime=6:00:00,rmsnodes=32:128 scriptfile
and use prun in your script:
prun -N ${RMS_NODES} -n ${RMS_PROCS} /usr/local/packages/namd/current/namd2 run.namd > run.log
NAMD 2.5b1 for T3E is available for
download.
NAMD 2.3 is installed as
/usr/local/bin/namd2
Interactive Runs
NAMD may be run on 1 processor trivially:
namd2 run.namd > run.log
NAMD may be run (on P processors) with the mpprun command:
mpprun -n P namd2 run.namd > run.log
Batch Jobs
Submit batch jobs (to run on P processors) using the qsub command:
qsub -l mpp_p=P -l mpp_t=time < scriptfile
and use the limit command in your script:
set -A LIMITS `limit`
NUMPES=${LIMITS[4]}
mpprun -n $NUMPES namd2 run.namd > run.log
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