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 <[EMAIL PROTECTED]> 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 know if its outdated (webpage seems so).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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > > > 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 > > ------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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