<div>Thanks Florian</div>
<div>this is how I tried to invoke the mdrun with mpirun:</div>
<div> </div>
<div>mpirun -nolocal -machinefile $PBS_NODESFILE mdrun -np * -v -s ...</div>
<div> </div>
<div>the administrator said the three options for mpirun must be added (-nolocal, -machinefile, $PBS_NODESFILE)</div>
<div>now I'm trying to follow the steps in the webpage you gave to me</div>
<div> <br><br> </div>
<div><span class="gmail_quote">On 10/1/07, <b class="gmail_sendername">Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">Florian.Haberl@chemie.uni-erlangen.de</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>On Sunday, 30. September 2007 19:12, liu xin wrote:<br>> Thanks Mark<br>><br>> But there's no standard error output at all for my problem, it seems mdrun
<br>> stagnated at this point, I dont know if anybody had met this situation<br>> before...and now I'm compiling LAMMPI as you suggested, hope this works for<br>> me.<br><br>does your calculation run with PBS or any queuing system?
<br>You can try to run mpirun or others like mpiexec with a verbose option.<br><br>In your previous mail you wrote something about running jobs with mpd, is it<br>your queuing system<br>(<a href="http://www-unix.mcs.anl.gov/mpi/mpich1/docs/mpichntman/node39.htm">
http://www-unix.mcs.anl.gov/mpi/mpich1/docs/mpichntman/node39.htm</a>), i don`t<br>know if its outdated (webpage seems so).<br><br><br>Here gromacs run without problems with different mpi implementations also with<br>intel-mpi, mvapich.
<br><br>><br>> On 10/1/07, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> > liu xin wrote:<br>> > > Dear GMXers<br>> > ><br>> > > my mdrun stops when I try to do it with 8 nodes, but there's no error
<br>> > > message, here's the end of the md0.log:<br>> ><br>> > The log file won't be helpful if the problem is outside of GROMACS, and<br>> > the fact that it isn't helpful is strongly diagnostic of that. You need
<br>> > the standard error to diagnose what your system problem is.<br>> ><br>> > > "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>> > > LINCS: A Linear Constraint Solver for molecular simulations
<br>> > > J. Comp. Chem. 18 (1997) pp. 1463-1472<br>> > > -------- -------- --- Thank You --- -------- --------<br>> > ><br>> > ><br>> > > Initializing LINear Constraint Solver
<br>> > > number of constraints is 3632<br>> > > average number of constraints coupled to one constraint is 2.9"<br>> > ><br>> > ><br>> > > I also tried 6 nodes or 10 nodes, but mdrun always stops here, there's
<br>> > > no problem if I ran it by -np 4.<br>> > > I searched the list, I found some people said that this probably<br>> > > because the MPI version, currently, we used the 1.2.7<br>> ><br>
> > MPICH for GROMACS is not supported at all. Try LAM if you suspect the<br>> > MPI install, and I would suspect it.<br>> ><br>> > Mark<br>> > _______________________________________________
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<br><br><br>Greetings,<br><br>Florian<br><br>--<br>-------------------------------------------------------------------------------<br>Florian Haberl<br>Computer-Chemie-Centrum<br>Universitaet Erlangen/ Nuernberg<br>Naegelsbachstr 25
<br>D-91052 Erlangen<br>Telephone: +49(0) − 9131 − 85 26581<br>Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">chemie.uni-erlangen.de</a><br>-------------------------------------------------------------------------------
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</a><br>Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
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