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

[Jeroen Mesters]

Dear Omololu,
Dear Peter,
Dear David,

thanks a lot guys for not giving up on me!

Expecially the comment by Omololu and Peter "not needing to start mpd 
deamon" made me think again........
Oooops,  somehow I am running /opt/mpich/*ch-p4mpd*/bin/mpirun instead 
of /opt/mpich/*ch-p4*/bin/mpirun!!! sorry....

Aha, now it works! Super, excellent, I am happy! Yippeeeeee

Cheers, thanx a lot, Jeroen.

Peter C. Lai wrote:

>On Thu, Sep 29, 2005 at 05:06:18PM +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?
>>    
>>
>
>[plai at pulau]:~/speptide % more /usr/local/mpich/share/machines.freebsd 
># Change this file to contain the machines that you want to use
># to run MPI jobs on.  The format is one host name per line, with either
>#    hostname
># or 
>#    hostname:n
># where n is the number of processors in an SMP.  The hostname should
># be the same as the result from the command "hostname"
>pulau:2
>
>I invoke both grompp and mpirun using the -np 2 flag. grompp is also invoked
>using the -sort flag.
>See http://www.gromacs.org/documentation/howtos/mpich_howto.html
>
>In my linked libs, I noticed that both grompp and mdrun were linked to:
>/usr/local/bin/grompp:
>        libmd_mpi.so.3 => /usr/local/lib/libmd_mpi.so.3 (0x280c7000)
>        libgmx_mpi.so.3 => /usr/local/lib/libgmx_mpi.so.3 (0x2810b000)
>        libsrfftw_mpi.so.2 => /usr/local/lib/libsrfftw_mpi.so.2 (0x28225000)
>        libsfftw_mpi.so.2 => /usr/local/lib/libsfftw_mpi.so.2 (0x28228000)
>        libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x2822f000)
>        libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x28254000)
>	libm.so.3 => /lib/libm.so.3 (0x28843000)
>        libpthread.so.1 => /usr/lib/libpthread.so.1 (0x2885e000)
>        libc.so.5 => /lib/libc.so.5 (0x28884000)
>	(X11 libs not shown)
>
>You do not need mpd if you aren't in a clustered env. (it's for cluster
>job control).
>
>  
>
>>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)
>>>--
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>_______________________________________________
>>>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)
>>--
>>
>>    
>>
>
>  
>
>>_______________________________________________
>>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)
--

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051001/87a86ee7/attachment.html>