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

[Jeroen Mesters]

Hi David,

1) during the make step it used *mpicc* instead of normal cc. The latter 
compiler was used when I left out the --enable-mpi. So, I think it is 
really compiled for mpi??!? See also my comments further below.
2) I used either *mpirun -np 2 mdrun_mpi -s new.trp* or *mpirun -np 2 
mdrun_mpi -s new.trp -np 2* and both produce the same first line in the 
md.log file.
3) Installing from the gromacs home page lamxxx.rpm and fftwxxx.rpms 
does not work properly on SuSE linux 9.2. Complains about

So my question is again, where does mdrun_mpi get the nnodes=1 
information from?
And, does anybody have an example of a machines file for dual processor!?

De groeten uit Luebeck! (Dutch for greetings from Luebeck!), Jeroen

David wrote:

>On Thu, 2005-09-29 at 17:06 +0200, Jeroen Mesters 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?
>>    
>>
>
>you sure that mdrun was compiled for mpi?
>
>try 
>ldd `which mdrun_mpi` and see whether anyhing mpi shows up. If so then
>check other commands to start mpi jobs like mpiexec or mpirun
>
>in general try to avoid mpich.
>
>  
>
>>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)
>>--
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.
>>    
>>


-- 
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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