[gmx-users] mpich/share/machines file for dual processor machine

Jeroen Mesters mesters at biochem.uni-luebeck.de
Thu Sep 29 17:06:18 CEST 2005

Looking at the md.log file, the first line states the following: *Log 
file opened: nodeid 0, nnodes = 1, host = orange, process = 7356*

Where does mdrun_mpi get the *nnodes=1* information from?

Does anyone have an *mpich/share/machines* file that shows me how a 
*dual-processor* machine is configured i.e. how do I tell mpich/gromacs 
there are two processors in one box and it should use both to run the job?


Thanx in advance, Jeroen.

Jeroen Mesters wrote:

> Machine: *dual* processor dell precision 650 with SuSE linux 9.2
> Software: *1)* mpich installed, machines file constructed, mpd started 
> *2)* compiled gromacs twice, once with and once without --enable-mpi 
> (using mpich). So, I ended up with two programmes, mdrun_mpi and 
> mdrun. The program versions are different in size which I would 
> expect... Indeed, one program was compiled with cc and the other with 
> mpicc (no errors during compilation).
> Step 1: grompp -np 2 -f full.mdp -c after_pr_CA.gro -p ph5.top -n 
> index.ndx -o 2cpu.tpr
> Step 2: mdrun_mpi -np 2 -s 2cpu.tpr  >>>> Fatal error: run input file 
> 2cpu.tpr was made for 2 nodes, while mdrun_mpi expected it to be for 1 
> nodes.
> Question 1. Are my commands correct i.e. is this the proper why to start?
> Question 2. Can this work at all or do I really need *2* computers (2 
> nodes)?
> Thanx for any hints, Jeroen.
> -- 
>Jeroen Raymundus Mesters, Ph.D.
>Institut fuer Biochemie, Universitaet zu Luebeck
>Ratzeburger Allee 160, D-23538 Luebeck
>Tel: +49-451-5004070, Fax: +49-451-5004068
>E-mail: mesters at biochem.uni-luebeck.de
>If you can look into the seeds of time and say
>which grain will grow and which will not - speak then to me  (Macbeth)
>gmx-users mailing list
>gmx-users at gromacs.org
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Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: mesters at biochem.uni-luebeck.de
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)

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