From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Nov 27 2012 - 03:20:16 CST
Hi Norman,
I've read all posts about it on the mailing list. There is no ifconfig
command on the cluster nodes to see if there is IPoIB installed. I remember
I did some other checks but didn't find IPoIB on the cluster. I don't use a
precompiled binary, I compiled charm myself using net-linux-x86_64-
ibverbs-ifort-smp-icc flags. Can I compile IPoIB driver on my own? Would I
be able then to run NAMD-CUDA on multiple nodes?
thanks,
Thomas
On 27 November 2012 10:09, Norman Geist <norman.geist_at_uni-greifswald.de>wrote:
> Hi Thomas,****
>
> ** **
>
> this problem has been posted a lot. The error you see is due the
> incompatibility of the precompiled ibverbs stuff vs. your ib installation.
> There are two possibilities to solve this:****
>
> ** **
>
> **1. **Use a non ibverbs binary with IPoIB****
>
> **2. **Compile namd with ibverbs on your own.****
>
> ** **
>
> Good luck****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Thomas Evangelidis
> *Gesendet:* Montag, 26. November 2012 14:57
> *An:* namd-l
> *Cc:* Norman Geist
> *Betreff:* namd-l: how to run NAMD-CUDA on multiple nodes****
>
> ** **
>
>
> 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****
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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