Wayne State University

AIM HIGHER

Wayne State University

High Performance Computing Services

Running a NAMD Job

HOW TO RUN A JOB FOR NAMD

Follow these steps to run a NAMD job.

Log on to the Grid.

Create a script in nano. The one in this example is called alaajs_16.inp. Download the job script and other files in this .zip file alawsu_16.zip and put them in your home directory. Type vim alawsu_16.inp .

Input: vim alawsu_16.inp

The job script will appear in the vi text editor.

Press the I key to edit. Edit it as neccessary, typing in your access id and directory path (zz9993 is used in this example).

Job script

This is what the full jobscript looks like:

#PBS -l nodes=1:ppn=2
#PBS -q wsuq
#PBS -m ea

echo Running on host `hostname`
echo Time is `date`

cd /wsu/home/zz/zz99/zz9993/namd_test2014
echo Directory is `pwd`

module load intel-14.0.2/namd-2.9-multicore

charmrun namd2 +p2 alanin.conf > alawsu_16.log

NOTE: With NAMD jobs you do not have to work in the TMPDIR.

Press the Escape key and type :wq to save and quit.

Submit the job. Type qsub alawsu_16.inp .

Input: qsub alawsu_16.inp

The job is submitted. You can check to see what node it is running on with the qme command.

Type: qme

Input: qme
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