Running NAMD on Keeneland


There is a "namd" module provided on Keeneland. This is loaded in the usual way.

unix> module load namd

Example Input

Example input can be found at the UIUC webpage for NAMD under heh

This input will be used in the following explanations about using NAMD on Keeneland.


Once the namd module is loaded, there is a script that can be copied to the execution directory that sets up the batch job automatically. It is located at the $NAMDHOME provided by the namd module.

unix> cp $NAMDHOME/runbatch_2.9_cuda .

This script will request 3 parameters, and one optional parameter. Example usage is shown below.

unix> ./runbatch_2.9_cuda
This script requires three arguments:
 NAMD input file
 NAMD log file
 number of nodes (number of cores / 12)
 queue (defaults to "batch", other option is "test")

unix> ./runbatch_2.9_cuda apoa1.namd apoa1.log 2
Submitting NAMD run to batch queue...

 Your job uses the -V option, which requests that all of your
 current shell environment settings (4968 bytes) be exported to
 it. This is not recommended, as it causes problems for the
 batch environment in some cases. You are strongly encouraged
 to remove the -V option from your batch job. If needed,
 export individual environment variables with the -v variable_list
 directive instead. See the qsub man page for details.

 Please contact if you need assistance.

NAMD is submitted to the queue, to check on your job use this command:

 qstat -u username

Your job is running if there is an R (running) in the S (state) column.
You may monitor progress with this command:

 tail -F apao1.log

You will need to press Control-C to exit the tail command.

Additional Resources

Information about NAMD can be obtained from the website, including source code, features, benchmarks, and information about training.