Hi,
I am running dynamics successfully with ONE node, using the following combination on PBS file:
#PBS -l select=1:ncpus=12:mpiprocs=12
mpirun -hostfile $PBS_NODEFILE pmemd.MPI -O -i prod.in -p 3SO6_clean.prmtop -c 3SO6_clean_prod_2.rst -o 3SO6_clean_prod_3.out -x 3SO6_clean_prod_3.mdcrd -r 3SO6_clean_prod_3.rst
But when I try to use 2 or more nodes I get an error from the system, which I think it is not connected to PBS:
That is for example:
#PBS -l select=2:ncpus=12:mpiprocs=12
Here is the error:
HYDU_create_process (./utils/launch/launch.c:94): execvp error on file 3SO6_clean_prod_3.rst (No such file or directory)
So that is one of the nodes does not find the output file?
What I am doing wrong?
Thanks!
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 16 2012 - 00:30:02 PST
