[gmx-users] GROMACS in parallel on Dual CPU Linux machine

Pratul K. Agarwal pagarwal at linus.ornl.gov
Mon May 19 22:37:01 CEST 2003


I am having problems running GROMACS on 2 CPUs on a dual AMD 
box. The serial run is just fine but the parallel run goes 
crazy and spits garbage. In addition the lamd goes crazy and 
uses upto 99.9% of CPU for quite some time.

Any help to figure this problem would be highly appreciated.



System : 2x AMD 1800+ system running Red Hat 7.2 
GROMACS: v. 3.1.4 (installed from RPM)
FFTW   : fftw-2.1.3-2
lam    : lam-6.5.4-usysv.1

Commands used :
>grompp -f min -c input -o formin -p ../mysys -shuffle -sort -np 2
>mpirun -np 2 -lamd /usr/local/bin/mdrun_mpi -v -s formin \
 -o firstmin -c firstmin_done -g min.log

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