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

[David]

On Thu, 2005-09-29 at 17:35 +0200, Jeroen Mesters wrote:
> 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?

It's not running under mpi. Try what I suggested in the previous mail.


> 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)
> --
> _______________________________________________
> 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.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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