[gmx-users] topol.tpr made for 2 nodes while mdrun expected 8

Guillem Plasencia guillem_pg at hotmail.com
Thu Apr 27 17:06:30 CEST 2006

Hello gmxers,

i've been struggling to make gromacs be able to use my 2 Dual CPU machines, 
without success.
I'd like to know exactly how to configure lam and how to preprocess with 
grompp (and then execute with mpirun) in order to be able to run as many 
parallel processes in my 2 Dual CPU machines that sum 4 CPUs (8 with 

My lam configuration file content is:
lead7 cpu=4 cpu=4

As a short brief, i've been able to run the same lisozyme cutoff benchmark 
in 4 parallel processes in only one node by commenting out the first line 
(the one which begins ..lead7) in my lam configuration file, and then

preprocessing as:
grompp -f cutoff.mdp -c conf.gro -p topol.top -np 4 -shuffle -sort

and running with:
mpirun C mdrun -s topol.tpr -nice 0 -np 4

So far, everything worked fine.

Problems arises when i try to include the other node (lead7).

I preprocess benchmarck lisozyme with cutoff as follows:
grompp -f cutoff.mdp -c conf.gro -p topol.top -np 8 -shuffle -sort

I include -np 8 to split into 8 processes (is that ok?)

but when i do

mpirun C mdrun -s topol.tpr -nice 0 -np 8

i get the error:

Reading file topol.tpr, VERSION 3.3.1 (single precision)
Program mdrun, VERSION 3.3.1
Source code file: init.c, line: 69

Fatal error:
run input file topol.tpr was made for 2 nodes,
             while mdrun expected it to be for 8 nodes.

How can be that, if i used grompp with option -np 8 ?

Any idea on how can i do it?

Thank you very much for your help,

Guillem Plasencia

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