AMBER Archive (2008)

Subject: AMBER: parallel amber 10 sander.MPI (low cpu utilization)

From: meandme meandme (
Date: Mon Sep 15 2008 - 12:27:06 CDT

Dear amber users and makers,
I have compiled amber 10 using gfortran and -mpich2 option. MPI library used is mpich2-1.0.7 and OS used is opensuse 10.3 linux x86.
Now if i execute md simulations in parallel using 2 nodes, the cpu utilization is 91% on each node. i have connected the 2 nodes through gigabit NICS and crossover cables, without any switch/hub. My questions is that why utilization is not 99.9%. Furthermore, if i use a swtich and add additional nodes the cpu utilization further reduces to 70% on each node. Why it is so? is it because of slow network connection (10/100 in my case with 1gb nics). Or should i use additional switches/flags while compiling amber 10 or mpich2. i use this command to execute sander on 2 nodes;
mpiexec -np 2 sander.MPI -O -i md...........................bla bla bla
or is my problem because of not using a load balancer or scheduler like "openbs" etc.  i have also tried running parallel md on hard disks instead of nfs file system but there is no increase in speed. My 2 node cluster is doing 2000 steps with 28000 atoms in 10 minutes. I will be thankful for suggestions in order to maximize my cluster cpu utlization on each node.
best regards,
...................sohail. pakistan.
/life is like an english grammar.....present tense past perfect\
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