[gmx-users] MPIRUN problem when switched to 8 np (searched the list)

[liu xin]

Thanks Florian
this is how I tried to invoke the mdrun with mpirun:

mpirun -nolocal -machinefile $PBS_NODESFILE mdrun -np * -v -s ...

the administrator said the three options for mpirun must be added (-nolocal,
-machinefile, $PBS_NODESFILE)
now I'm trying to follow the steps in the webpage you gave to me



On 10/1/07, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
>
> Hi,
>
> On Sunday, 30. September 2007 19:12, liu xin wrote:
> > Thanks Mark
> >
> > But there's no standard error output at all for my problem, it seems
> mdrun
> > stagnated at this point, I dont know if anybody had met this situation
> > before...and now I'm compiling LAMMPI as you suggested, hope this works
> for
> > me.
>
> does your calculation run with PBS or any queuing system?
> You can try to run mpirun or others like mpiexec with a verbose option.
>
> In your previous mail you wrote something about running jobs with mpd, is
> it
> your queuing system
> (http://www-unix.mcs.anl.gov/mpi/mpich1/docs/mpichntman/node39.htm), i
> don`t
> know if its outdated (webpage seems so).
>
>
> Here gromacs run without problems with different mpi implementations also
> with
> intel-mpi, mvapich.
>
> >
> > On 10/1/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > > liu xin wrote:
> > > > Dear GMXers
> > > >
> > > > my mdrun stops when I try to do it with 8 nodes, but there's no
> error
> > > > message, here's the end of the md0.log:
> > >
> > > The log file won't be helpful if the problem is outside of GROMACS,
> and
> > > the fact that it isn't helpful is strongly diagnostic of that. You
> need
> > > the standard error to diagnose what your system problem is.
> > >
> > > > "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M.
> Fraaije
> > > > LINCS: A Linear Constraint Solver for molecular simulations
> > > > J. Comp. Chem. 18 (1997) pp. 1463-1472
> > > > -------- -------- --- Thank You --- -------- --------
> > > >
> > > >
> > > > Initializing LINear Constraint Solver
> > > >   number of constraints is 3632
> > > >   average number of constraints coupled to one constraint is 2.9"
> > > >
> > > >
> > > > I also tried 6 nodes or 10 nodes, but mdrun always stops here,
> there's
> > > > no problem if I ran it by -np 4.
> > > > I searched the list, I found some people said that this probably
> > > > because the MPI version, currently, we used the 1.2.7
> > >
> > > MPICH  for GROMACS is not supported at all. Try LAM if you suspect the
> > > MPI install, and I would suspect it.
> > >
> > > Mark
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
> Greetings,
>
> Florian
>
> --
>
> -------------------------------------------------------------------------------
> Florian Haberl
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Telephone:     +49(0) − 9131 − 85 26581
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> -------------------------------------------------------------------------------
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