From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Nov 02 2011 - 01:45:32 CDT
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
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
Betreff: namd-l: Reading files for multiple threaded simulations
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:
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 >
then the simulation has a error like this:
This happens when namd is trying to read the restraint file under the same
I also have problem if I want to source a file contains parameters.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:31 CST