how to run NAMD-CUDA on multiple nodes

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Mon Nov 26 2012 - 07:57:18 CST

Greetings,

Although I can run the ibverbs binary with CUDA on a single node, on
multiple nodes I get:

Charmrun> error 0 attaching to node:
Timeout waiting for node-program to connect
Charmrun> IBVERBS version of charmrun

I use this command line in my pbs script for ibverbs binary with CUDA:

$NAMD_BIN/charmrun ++runscript ./runscript.csh ++verbose ++remote-shell ssh
++nodelist $nodefile +p24 $NAMD_BIN/namd2 +setcpuaffinity +idlepoll
prod.amber.GB.aMD.namd

runscript.csh contents are:

#!/bin/csh
CHARM_ARCH="net-linux-x86_64-ibverbs-ifort-smp-icc"
NAMD_BIN="/gpfs/home/lspro220u2/Opt/NAMD_CVS-2012-09-22_Source/charm++_$CHARM_ARCH/Linux-x86_64-icc"
setenv LD_LIBRARY_PATH "$NAMD_BIN:$LD_LIBRARY_PATH"
$*

Is this the way to run NAMD-ibverbs-cuda on multiple nodes? If not could
you please give me the right command line?

thanks,
Thomas

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