Re: Reading files for multiple threaded simulations

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Nov 02 2011 - 01:57:36 CDT

Also, send the log file output. It's rather hard to diagnose with just
"BUFFER OVERRUN." If there's no log file output, then send the job
scheduler output and error file, if any.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Norman Geist <norman.geist_at_uni-greifswald.de> writes:
> Date: Wed, 2 Nov 2011 07:45:32 +0100
> From: Norman Geist <norman.geist_at_uni-greifswald.de>
> To: 'Yi He' <yi.he.ustcer_at_gmail.com>
> Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
> Subject: AW: namd-l: Reading files for multiple threaded simulations
> X-Mailer: Microsoft Office Outlook 12.0
> 
> Hi
> 
>  
> 
> All mpi processes should have access to the same files under the same path,
> this is usual for any mpi application. I never observed such problems with
> mpi processes accessing the same files when they are there for everyone. Try
> to copy your stuff directly into the script and try again to see if it is
> not a problem of your config.
> 
>  
> 
> Let me know
> 
>  
> 
> Norman Geist.
> 
>  
> 
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Yi He
> Gesendet: Dienstag, 1. November 2011 18:17
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Reading files for multiple threaded simulations
> 
>  
> 
> Dear all,
> This may sounds newbie but I want to ask how to avoid errors when you let
> the script read a file (say restraints etc.) in a multiple node run.
> I had a membrane simulation that I need to constraint the head groups at a
> certain position for the whole procedure of the simulation.
> I put something like in the input file:
> 
> colvarsConfig restraints/$outputname.col
> 
> If I run this as a single node, the simulation runs without a problem.
> If I run this using MPI on the cluster 
> mpirun -np 64  -machinefile $PBS_NODEFILE
> /home/he.yi/simulation/softwares/NAMD_2.8_Linux-x86_64/namd2 eql.inp >
> eql.out
> then the simulation has a error like this:
> BUFFER OVERRUN
> This happens when namd is trying to read the restraint file under the same
> folder.
> I also have problem if I want to source a file contains parameters. 
> 
> Yi 
> 

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