[gmx-users] mpich/share/machines file for dual processor machine
spoel at xray.bmc.uu.se
Thu Sep 29 17:13:55 CEST 2005
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
you sure that mdrun was compiled for mpi?
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.
> 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
> 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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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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