namd on linux cluster

From: Giovanni (giovanni.bellesia_at_ucd.ie)
Date: Tue Feb 24 2004 - 13:45:44 CST

Hi everybody,
I just untar binary files on one of a 15 machines' (30 cpus) Linux cluster.
NAMD is working on simulations within the local machine using 1 and 2 cpus.
i.e. it is working with command lines

namd2 ubq_ws_eq.conf > ubq_ws_eqC.log

and

charmrun ~/bin/namd2 ++local +p2 ++verbose ubq_ws_eq.conf > ubq_ws_eqC.log

respectively.

I have charmrun and namd2 files, both in my /home/myname/bin directory.
The nodelist file is in the current working directory;
here's the content

group main
host sys15
host sys13
host sys11

I am running from sys15 with the following command

charmrun ~/bin/namd2 +p6 ++verbose ubq_ws_eq.conf > ubq_ws_eqC.log

I have rsh access without passwd to all the listed machines
and this is what I have from the screen:

Charmrun> charmrun started...
Charmrun> using ./nodelist as nodesfile
Charmrun> rsh (sys15:0d) started
Charmrun> rsh (sys13:1d) started
Charmrun> rsh (sys11:2d) started
Charmrun> rsh (sys15:3d) started
Charmrun> rsh (sys13:4d) started
Charmrun> rsh (sys11:5d) started
Charmrun> node programs all started
Charmrun> error 2 attaching to node:
Timeout waiting for node-program to connect
bash-2.05$

I am sure I am missing something really simple ... could you help me ?

Thanks in advance

Giovanni

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