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NAMD is installed on the Origin2000 and IA32 Linux cluster at NCSA
NAMD 2.5b1 for Origin2000-MPI is available for
download.
The latest version of NAMD for Origin2000-MPI is installed in the directory
/usr/apps/chemistry/namd/
Interactive Runs
Since this is an MPI
program it must be run (on P processors) with the mpirun command:
mpirun -np P /usr/local/apps/chemistry/namd/current/namd2 run.namd > run.log
Batch Jobs
Submit batch jobs (to run on P processors) using the bsub command:
bsub -nP < scriptfile
and use the $BSUB_NUMTHREADS environment variable in your script:
mpirun -np $BSUB_NUMTHREADS /usr/local/apps/chemistry/namd/current/namd2 run.namd > run.log
The latest version of NAMD for Linux-i686-VMI is installed in the directory
/usr/apps/chemistry/namd/
Interactive Runs
Since interactive runs are not yet supported on this machine, the Linux-i686
version of NAMD also installed to allow you to test your jobs before submitting them to the batch queue:
/usr/apps/chemistry/namd/current-serial/namd2 run.namd
Batch Jobs
Submit batch jobs (to run on N nodes for 1 hour) using the qsub command:
qsub -l walltime=1:00:00,nodes=N:ppn=2:pt -o run.out scriptfile
and use vmirun in your script:
vmirun "/usr/apps/chemistry/namd/current/namd2 run.namd"
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