AW: How can I write a log file on my cluster?

From: Norman Geist (
Date: Mon Oct 22 2012 - 09:04:29 CDT



What do you mean with logfile? If you mean the standard NAMD output during
simulation, as NAMD puts all output to stdout and stderr, you can simply
catch it on commandline like:


/path/charmrun +p40 /path/namd2 > logfile 2> errorfile


As, so I assume, only one of the processes is doing the output stuff, it is
independent from the number of used processors.


For simulations across multiple nodes you will need at least a nodelist and
passwordless login between the nodes.

As you don't seem to be very familiar with parallel computing, you should
ask your clusters admin maybe.


Norman Geist.


Von: [] Im Auftrag
von ??????? ?????????
Gesendet: Montag, 22. Oktober 2012 08:40
Betreff: namd-l: How can I write a log file on my cluster?


Hello, colleagues.

I've reached the simulation step for now, but I can't write the log-file on
my university's cluster.

It works only on 1 node with 8 cores, and I have at least 20 nodes with 160
cores on my cluster.

I think, that's a parallel programming settings problem, because nodes can't
write one log-file simultaneously.

Can you help me?


I'm using MPI-distribute of NAMD.


Best wishes
Dmitry Begovatov
master of engineering (biomedical) 
National Research University of Electronic Technology

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