From: Wei Zhuang (wzhuang_at_uci.edu)
Date: Fri Oct 28 2005 - 17:09:22 CDT
Hi,all:
I am trying to run the pre-compiled version of namd on NCSA cluster tungsten. I used the script "namdjob" like this:
**********************************
#!/bin/csh
#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?
Wei
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:19 CST