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

[Florian Haberl]

Hi,
On Monday, 1. October 2007 13:42, liu xin wrote:
> Thanks Florian
> this is how I tried to invoke the mdrun with mpirun:
>
> mpirun -nolocal -machinefile $PBS_NODESFILE mdrun -np * -v -s ...

mpirun -v 

so its verbose for mpi process.

>
> 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 know if its outdated (webpage seems so).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
> > > > Please search the archive at http://www.gromacs.org/search before
> > > > posting! Please don't post (un)subscribe requests to the list. Use
> > > > the www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > 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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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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