Re: Replica Exchange NAMD

From: John R. Dowdle (jrdowdle_at_gmail.com)
Date: Mon Nov 19 2007 - 20:16:43 CST

I have a similar problem.

I am having trouble getting the replica exchange script packaged with NAMD 2.6
to work on the Lonestar machine at the Texas Advanced Computing Center.

So far, I have tried using the example simulation for folding alanine with a
modified configuration file, and I have received errors regarding the
simulation configuration file being inaccessible. Here are the .conf file and
the stdout/stderr from the simulation:

http://onsager.vtmu.net:8080/tacc_remd/fold_alanin.edited.conf
http://onsager.vtmu.net:8080/tacc_remd/out.o523700
http://onsager.vtmu.net:8080/tacc_remd/fold_alanin.job0.7.log

The main error messages I am seeing are regarding the configuration file, e.g.,

From the main stderr,

"FATAL ERROR: Simulation config file is not accessible".

and from the replica log file,

"Info: Configuration file is +netpoll
FATAL ERROR: Simulation config file is not accessible."

I am asking the namd-l list about this because I think the error messages I am
getting are not specific to the system setup at TACC, but rather something more
general that I am doing wrong.

Can anyone offer help with this problem?

Thanks in advance.

-John

On Tue, Nov 13, 2007 at 12:09:52PM -0600, Dirar Homouz wrote:
>
> I'm running the replica exchange method on namd using the tcl script "replica_exchange.tcl" on a linux cluster:
>
> "Linux farnsworth1.phys.uh.edu 2.6.9-42.0.2.ELsmp #1 SMP Wed Aug 23 13:38:27 BST 2006 x86_64 x86_64 x86_64 GNU/Linux".
>
> The command in the batch file looks like this:
>
> tclsh ../replica_exchange.tcl /home/dirar/replica/example/fold_alanin.conf
>
> The run doesn't go through, I get the following error message:
>
> FATAL ERROR: Simulation config file is not accessible.
>
> The log file looks like this:
>
> Info: NAMD 2.6 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
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 50900 for mpi-linux-amd64
> Info: Built Thu Jun 28 09:51:39 CDT 2007 by root on farnsworth1.phys.uh.edu
> Info: 1 NAMD 2.6 Linux-amd64-MPI 1 compute-0-8.local dirar
> Info: Running on 1 processors.
> Info: 7896 kB of memory in use.
> Info: Memory usage based on mallinfo
> Info: Found 2 config files.
> Info: Configuration file is +netpoll
> FATAL ERROR: Simulation config file is not accessible.
> Stack Traceback:
> [0] CmiAbort+0x2b [0x75f899]
> [1] _Z8NAMD_diePKc+0x4a [0x4a630a]
> [2] main+0x1f5 [0x4a9445]
> [3] __libc_start_main+0xdb [0x345dd1c3fb]
> [4] fmod+0xaa [0x4a5c0a]
>
>
>
> Dirar
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