Hello, the same happens to me on several computers, but it depends on the system. I'm sorry I cannot dig the examples right now to add more precise information. Could be shake? The system that fails is full of constraints.
Marcelo. mdrun will not leak memory that badly. I would guess your output buffers are not being flushed, so grow without bound. Mark On Oct 25, 2012 12:36 AM, "Pablo Serra" <se...@famaf.unc.edu.ar> wrote: > Dear users, > I'm running a NVT simulation with gromacs 4.5.5,using > the command: > > mdrun -nt $NSLOTS > > and the memory usage grows without bounds until a crash with the message > > /opt/gridengine/default/spool/compute-0-8/job_scripts/1711: line 29: 25200 > Killed /usr/local/bin/mdrun -nt $NSLOTS > > I've got the same result in several machines with 4, 6 and 8 cores, and > ram between 4 to 23 G. Attached is the memory map of one of a typical run. > > I'm running a system of 512 CBrCL_3 molecules (2560 atoms) using the shake > algorithm for the constrains. > The options in the mdp file are: > > constraints = all-bonds > integrator = md > dt = 0.005 > nsteps = 10000000000 > > ns_type = grid > nstxtcout = 1000 > xtc-precision = 1000 > > > nstxout = 0 > nstvout = 0 > nstfout = 0 > > rlist = 1.6 > > coulombtype = Cut-off > rcoulomb = 1.6 > > vdw-type = Cut-off > rvdw = 1.6 > DispCorr = EnerPres > > Tcoupl = Nose-Hoover > tc-grps = System > tau_t = 2.0 > ref_t = 180 > > Pcoupl = no > > gen_vel = no ;yes > gen_temp = 180 > gen_seed = 1993 > > > > ; Type of constraint algorithm > > constraint-algorithm = shake > > shake-tol = 0.0001 > > > Thanks, > Pablo > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
