[gmx-users] Gromacs setup on dual core machine

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 12 09:27:14 CET 2008

Jens Pohl wrote:
> Hello!
> I have a similar problem with installing gromacs on a dual core machine. 
> When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't recognize the two cores and with mdrun there will be an fatal error. grompp and mdrun both were run with -np 2 and the output of mdrun says, that the file was made for two nodes but mdrun expected it to be for one node. 
> With lamnodes there is only one node on cpu0 on localhost... What to do in this case?

Read the LAM documentation to find out how to configure lam to put two 
processes on the same host. Then, restart LAM. Then use mpirun -n 2 
mdrun -n 2 and your other options.


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