From: Alex V. (vav_at_udman.ru)
Date: Fri Jun 04 2004 - 13:46:18 CDT
When I start Namd on linux-alpha cluster with MPI + Marynet GM drivers
the queuing system provides me directory called "namd2.1" with following
# ls -la namd2.1
drwx------ 2 makaveli ipmuran 4096 May 30 18:29 .
drwxr-xr-x 13 makaveli ipmuran 4096 Jun 4 18:52 ..
-rw------- 1 makaveli ipmuran 0 May 30 18:29 errors
-rw------- 1 makaveli ipmuran 496 Jun 4 12:11 .hosts
-rw------- 1 makaveli ipmuran 217006 Jun 4 18:52 manager.log
-rw------- 1 makaveli ipmuran 9613920 Jun 4 18:51 output
-rwx--x--x 1 makaveli ipmuran 2378 Jun 4 12:11 runmvs.bat
So my running Namd program automaticly resolves nodes from ".hosts"
and runs successfully. Perhaps in your case it will be the same
> Hi all,
> I would like to start a parallel simulation with namd using charmrun
> on an linux-alpha cluster.
> The software is working perfectly for local jobs but if I want to use
> remote machines also,
> the only thing I can do is to submit my job to a queue and wait for
> free nodes.
> Then, I don't know in advance on which machines my simulation will run.
> I guess, first, that all the names of the machines in the cluster
> should be in the "nodelist" file, but is this enough to get it working ?
> I am a bit suspicious because, when I run NAMD on our smaller cluster
> (intel-linux and no queues) I have to copy the directory containing
> the starting files to an identical path in all remote nodes that are
> in my nodelist.
> Also, the executable namd2 must be in the same directory on all
> machines that I decide to use
> Any suggestion ?
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