Re: problems for runing NAMD on parallel computers

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Jun 28 2006 - 22:08:02 CDT

Hi,

As the output shows, the configuration file NAMD thought was ++nodelist.
This is because ++nodelist is not an option for MPI version of NAMD
which is the one you have. Treat the NAMD binary as a normal MPI program
and run it with mpirun and -machinefile option.

Gengbin

xiaojing gong wrote:
> Dear all,
> When I run NAMD on cluster, it will becoming run at one cpu after some
> time, BUT I bsub the job on 8 cpus, and the following is the error
> messages.
> can you give me some suggestions?
> Info: NAMD 2.5 for Linux-amd64-MPI
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> <mailto:namd_at_ks.uiuc.edu>
> Info:
> Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 0143160 for mpi-linux-gm2-opteron
> Info: Built Mon Jan 17 21:19:25 CST 2005 by fgf on gbnode002
> Info: Sending usage information to NAMD developers via UDP. Sent data is:
> Info: 1 NAMD 2.5 Linux-amd64-MPI 8 ganode002 tzhang
> Info: Running on 8 processors.
> Info: 2100 kB of memory in use.
> Measuring processor speeds... Done.
> Info: Found 3 config files.
> Info: Configuration file is ++nodelist
> FATAL ERROR: Simulation config file is not accessible.
> FATAL ERROR: Simulation config file is not accessible.
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>
> ------------------------------------------------------------------------
> Ż-3.5G20M <http://cn.mail.yahoo.com/>

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