[gmx-users] gmx_blast error when attempting to run in parallel

Sashank Karri sashank.karri at case.edu
Thu Jun 11 14:15:53 CEST 2009

Hi, I'm running gromacs-4.0.3 on a cluster.  I am testing gromacs on it.  We
are currently getting this error when I run with 4 nodes with one dedicated
to PME calculations.

Back Off! I just backed up md.log to ./#md.log.5#
Reading file ionsol_minim96-1.tpr, VERSION 4.0.3 (single precision)

Program mdrun, VERSION 4.0.3
Source code file: network.c, line: 357

Routine should not have been called:

"I'll Match Your DNA" (Red Hot Chili Peppers).

Here is my job that I'm submitting to the cluster.

#PBS -N ionsol_karri
#PBS -l walltime=24:00:00
#PBS -l nodes=4:ppn=4:quad
#PBS -j oe

module load mpich
module load gromacs-4.0.3
cd /home/srk18/newplcre/
mpirun -nodes 4 /usr/local/gromacs/gromacs-4.0.3/bin/mdrun -npme 1 -s
ionsol_minim96-1.tpr -o finminim96_traj.trr -x finminim96_traj.xtc -c
final_minim.g96 -e enermin_fin.edr -cpo state96.cpt

When discussing the installation of gromacs earlier with the cluster admin,
he sent the following message:

>I remember I seeing your error (not the present error) while I tried to
make the dynamic version of the GROMACS. So I used the --enable-static while
building parallel version of the GROMACS. That build the executable and most
of the inbuilt test were successful. If you think we need dynamic build let
me know, I might have to struggle a bit. Also It would be good  if you share
information you have regarding building.

Do you folks have any idea as to how to fix the above error?

Sashank Karri
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