[gmx-users] parallel run errors

Ramachandra Rao Gullapalli rrg142 at psu.edu
Thu May 5 17:46:09 CEST 2005


Dear GMX ers
I have been having trouble with running the Gromacs program in parallel. I have
been trying to run the example speptide simulation of the website on a parallel
cluster as a test and am getting the same error every time. 

1) My MPI script is as follows...

#PBS -l nodes=2:myrinet:ppn=2
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxm-mcd18

# change the current working directory to the directory where
# the executable file 'foo' can be found
cd ~rrg142/gromacs/testfiles/speptide300/

# run the executable file 'foo' using the qmpirun script
mpirun /usr/global/gromacs/i686-pc-linux-gnu/bin/mdrun -v -s full.tpr -o
full.trr -c after_em.gro -np 2 -g after_md.log

2) I Grompp it for two nodes to prepare the input tpr file using the following
command

grompp -v -f full -o full -c after_em -p speptide -np 2

3) The error message i have been receving consistently is as follows

Reading file full.tpr, VERSION 3.2.1 (single precision)
Reading file full.tpr, VERSION 3.2.1 (single precision)
Fatal error: run input file full.tpr was made for 2 nodes,
             while mdrun expected it to be for 1 nodes.
Fatal error: run input file full.tpr was made for 2 nodes,
             while mdrun expected it to be for 1 nodes.
Fatal error: run input file full.tpr was made for 2 nodes,
             while mdrun expected it to be for 1 nodes.
Fatal error: run input file full.tpr was made for 2 nodes,
             while mdrun expected it to be for 1 nodes.
/var/spool/pbs/mom_priv/jobs/610948.lion.SC: full.trr: command not found


Can anyone please help me with the mistake i have been doing?
The cluster has a MPIGM kind of network

I shall be very thankful for any kind of suggestions.

Sincerely
Regards
Rama






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-Einstein 



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