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

[MGiò]

On 9/29/05, Jeroen Mesters <mesters at biochem.uni-luebeck.de> wrote:
>
> 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?


I think that you should tell mdrun_mpi which nodes to run on, I mean you
should use the flags
-nolocal -machinefile machinefile
in the machinefile you should write something like
name of the node:number of processors for that node
in your case you have node1:2, have I understood right?

I hope this helps,
MGiò


Anybody?
>
> 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
> Http://www.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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> --
> 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
> Http://www.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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