From: Yi He (yi.he.ustcer_at_gmail.com)
Date: Wed Nov 02 2011 - 11:00:11 CDT
Thanks so much for the reply.
Yes, in the log file, the error I got is when namd2 was trying to read the
file step6.1_equilibration.dihe.
Info: READING EXTRA BONDS FILE
/home/he.yi/simulation/explict/dmpc/equlibrate/flat/namd/restraints/step6.1_equilibration.dihe
FATAL ERROR: BUFFER OVERRUN - buffer=**
Which is fine when I looked at this file.
Also this error will not appear if I ran namd2 using single node.
Bests,
Yi
On Wed, Nov 2, 2011 at 2:57 AM, Chris Harrison <charris5_at_gmail.com> wrote:
> 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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