AW: running namd in parallel

From: Norman Geist (
Date: Fri Aug 02 2013 - 03:43:52 CDT



1. Can we see some benchmark timings from 1 to 8 nodes?

2. Try adding +idlepoll to the namd command.

3. What speed does your infiniband have?


Norman Geist.


Von: [] Im Auftrag
von Revthi Sanker
Gesendet: Freitag, 2. August 2013 06:39
Betreff: namd-l: running namd in parallel


Dear all,

I wish to run namd in parallel. I am using an ibverbs version. It is unable
to scale up. Kindly suggest me what has to be done to parallelize namd. The
script that I am currently using is this:

#@ output = test.out
#@ error = test.err
#@ job_type = MPICH
#@ class = Medium128
#@ node = 8
#@tasks_per_node = 16
#@ environment = COPY_ALL
#@ queue
Jobid=`echo $LOADL_STEP_ID | cut -f 6 -d .`
mkdir -p $tmpdir; cd $tmpdir
cp -R $LOADL_STEP_INITDIR/* $tmpdir
cat $LOADL_HOSTFILE | uniq >xx
/sware/namd/NAMD_2.9_Linux-x86_64-ibverbs/charmrun mpiexec.hydra -np 128 -f
$LOADL_HOSTFILE +ppn 16 /sware/namd/NAMD_2.9_Linux-x86_64-ibverbs/namd2
equ_cyca.namd > equi.log
mv ../job$Jobid $LOADL_STEP_INITDIR

Initially it does run in all 8 nodes and 16 processors but later on some
nodes have only 2 or 3 processors working (at the maximum) while most others
show no job running. I am totally new to namd. Kindly consider this request
and help me out in this regard.

Thank you so much for your help in advance.

M.S. Research Scholar
Indian Institute Of Technology, Madras


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