Computational Cluster Programs

How to Run NAMD on ATS-Hosted Clusters

You can use any text editor to make the appropriate input files for NAMD.

How to Run NAMD in Batch

To Run NAMD from the UCLA Grid Portal

NAMD is not available from the UCLA Grid Portal.

To Run NAMD from the Cluster Login Node using the Queue Scripts

NAMD is available in batch. The easiest way to run NAMD in batch from the login node is to use the queue scripts. See Running a Batch Job on an ATS-Hosted Cluster for a discussion of the queue scripts and how they are used.

The following queue scripts are available for NAMD:

namd.q

Asks you whether you want to run in parallel or serial.

namd.q.parallel

Runs in parallel.

namd.q.serial

Runs in serial.

To Run NAMD from the Cluster Login Node Using SGE Comands

See Running a Batch Job on an ATS-Hosted Cluster for guidelines to follow to create the required SGE command file. Alternatively, you could create an SGE command file with one of the queue scripts listed above. After saving the command file, you can modify it if necessary. See Commonly-Used SGE Commands for a list of the most commonly used SGE commands.

How to Run NAMD Interactively

To run NAMD interactively you must first obtain one or more interactive nodes via qrsh (see: http://www.ats.ucla.edu/clusters/hoffman2/computing/sge_qrsh.htm). Once you obtain a prompt enter, for example:

/u/local/apps/namd/current/namd2