Student Login

Search our website here...

Namd

Sample job file for running Namd serial job for single CPU:

File Name : namd.cmd

#!/bin/bash

#@ output = test.out

#@ error = test.err

#@ job_type = MPICH

#@ class = Small

#@ node = 1

#@tasks_per_node = 8

#@ environment = COPY_ALL

#@ queue

Jobid=`echo $LOADL_STEP_ID | cut -f 6 -d .`

tmpdir=$HOME/scratch/job$Jobid

mkdir -p $tmpdir; cd $tmpdir

cp -R $LOADL_STEP_INITDIR/* $tmpdir

/sware/namd/NAMD_2.9_Linux-x86_64-ibverbs/charmrun ++remote-shell ssh

/sware/namd/NAMD_2.9_Linux-x86_64-ibverbs/namd2 inputfile > outfile

mv ../job$Jobid $LOADL_STEP_INITDIR

In the command prompt, type the command, llsubmit namd.cmd