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.
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 [email protected] > 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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