[gmx-users] parallel problem

[Jithesh]

Hi,

You may try the following:

Copy "mdrun" executable to the directory where you are testing it.Then create a process group file with the name "mdrun.pg" and the contents of the file something like this:

node1 0 complete_path_of_the_mdrun_executable
node2 1 complete_path_of_the_mdrun_executable

Replace 'node1' node2' with the machine names...it can be the same on shared memory machine. complete_path_of_the_mdrun_executable may be something like:
/home/usr/myname/GROMACS/test/mdrun

Now just run:

mdrun -np 2 -s topo.tpr ...

Hope this helps!

Jithesh
--------------
Jithesh P.V. 
Bioinformatics Applications 
National PARAM Supercomputing Facility
Centre for Development of Advanced Computing,
Pune, India - 411007 



ygmu at theochem.uni-frankfurt.de wrote:




When I want to do mdrun on 2 cpu, it turns out as following, and crashs.

Fatal error: run input file mini.tpr was made for 2 nodes,
while mdrun expected it to be for 1 nodes.


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