questions about running namd on NCSA cluster tungsten

From: Wei Zhuang (
Date: Fri Oct 28 2005 - 17:09:22 CDT


I am trying to run the pre-compiled version of namd on NCSA cluster tungsten. I used the script "namdjob" like this:

#BSUB -n 32 # Specify 32 processes
#BSUB -W 0:10 # Specify job run time limit of 1 hour
#BSUB -o testjob.%J.o # Store the standard output and standard error of the
#BSUB -J testjob.%J # Specify job name (optional)

soft add +intel-compilers71

cmpirun -np 32 -lsf /usr/apps/chemistry/NAMD/namd2 spe3_SA_550K_conf > try.log


then I said

bsub -n 32 < namdjob

The job runs well, and it did run on 32 processors, however, the output said it will use 1.3 days for 1ns while if I ran it on 2 processors, the output said it will take 2.5 days for 1 ns. It seems to me that the cpu usage of 32-proc job is not very high. Did I do anything wrong?


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