From: Yi He (yi.he.ustcer_at_gmail.com)
Date: Tue Nov 01 2011 - 12:16:52 CDT
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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