AW: Reading files for multiple threaded simulations

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Nov 02 2011 - 01:45:32 CDT

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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