HPC Grid Tutorial: How to Run a NAMD Job

Follow these steps to run a NAMD job. 

NOTE: There are different versions of charmrun. Choose an appropriate version for your needs.

  • NAMD_2.9_Linux-x86_64-multicore: For one machine, does not span servers so does not need ++nodelist .
  • NAMD_2.9_Linux-x86_64-TCP: Communicates over TCP/IP network from node to node and needs the ++nodelist argument.
  • NAMD_2.9_Linux-x86_64-ibverbs: For Infiniband, currently only used on PCCQ; requires the ++nodelist argument.
  • NAMD_2.9_Linux-x86_64-ibverbs-smp : Uses SMP within a single node and IB to communicate between nodes through Infiniband, only available on PCCQ; requires the ++nodelist argument.

In this example we will only use one node, so we use the NAMD_2.9_Linux-x86_64-multicore version.

1. Login to the Grid.

2. Copy the required contents to your home directory using the following command: 

cp -R /wsu/el7/scripts/tutorial/namdtutorial .

3. Go to the namdtutorial directory: cd namdtutorial and ls to view its contents. The necessary tutorial files are in a ZIP file. 

Unzip the file: unzip namdtutorial.zip

4. The job script is called alawsu_16.inp . Edit the script to have your AccessID and directory path in vi by typing: vim alawsu_16.inp 

This is the full job script: 

#PBS-l nodes=1:ppn=2

#PBS -q wsuq

#PBS -M ea

#PBS -M xx1234@wayne.edu

echo Running on host 'hostname'

echo Time is 'date'

cd /wsu/home/xx/xx12/xx1234/namdtutorial

echo Directory is 'pwd'

ml namd/2.13-multicore

NUMPROCS='cat $PBS_NODEFILE | wc -l'

# Run job

export CONV_RSH=ssh

charmrun namd2 +p${numprocs}alanin.conf > alawsu_16.log

4. Press the Escape key. Type :wq to save and quit and hit Enter. 

5. Submit the job. Type: qsub alawsu_16.inp 

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

Type: qme