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

[David]

On Mon, 2003-05-19 at 22:33, Pratul K. Agarwal wrote:
> Hi,
> 
> 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.
> 
> Pratul
> 
> Information:
> 
> 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
What kernel are you running? (uname -a)

You may have to upgrade, as one of the redhat 7.x came with a broken
kernel. Other problem could be that the machine gets too hot...

> 
> Commands used :
> >grompp -f min -c input -o formin -p ../mysys -shuffle -sort -np 2
> >lamboot
> >mpirun -np 2 -lamd /usr/local/bin/mdrun_mpi -v -s formin \
>  -o firstmin -c firstmin_done -g min.log
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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