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

From: Norman Geist (
Date: Wed Oct 24 2012 - 00:42:06 CDT



I’ve never used windows for that so I can only guess. Could it be possible that windows redirects the whole output after the command has finally finished and not like linux in blocks? Also, to make sure you don’t overwrite stuff, you should use >> instead of >


Norman Geist.


Von: Дмитрий Беговатов []
Gesendet: Dienstag, 23. Oktober 2012 08:42
Betreff: namd-l: How can I write a log file on my cluster?


Hello, Norman.

You wrote the answer to my question about parallel computing. Thanks a lot.


I meant the standard NAMD output file. I tried to create it with this command from the command line:

"C:\Program Files\Microsoft HPC Pack 2008 R2\Bin\job.exe" submit /numnodes:2 "C:\Program Files\Microsoft HPC Pack 2008 R2\Bin\mpiexec.exe" "D:\NAMD_2.8_Win64-MPI\NAMD_2.8_Win64-MPI\namd2.exe" "D:\NAMD_2.8_Win64-MPI\NAMD_2.8_Win64-MPI\u_zz2_bsa_wb.conf" > "D:\NAMD_2.8_Win64-MPI\NAMD_2.8_Win64-MPI\u_zz2_bsa_wb.log"


But it's only a file with the number of processes appeared instead of the log file with calculations.

I can't understand what I'm doing wrong. And my clusters admin is not so far from me.




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.


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

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