Thank you. But I did new tests, and the problem does not appear if in the same pc I run the same simulation, but using a single core, here is the top after 73 min, and the memory mantains its initial value.
Cpu(s): 53.2%us, 1.1%sy, 0.0%ni, 44.8%id, 0.0%wa, 0.3%hi, 0.5%si, 0.0%st Mem: 2569180k total, 1598092k used, 971088k free, 85236k buffers Swap: 4094960k total, 141964k used, 3952996k free, 470908k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 31255 serra 20 0 34080 8864 2252 R 99.1 0.3 73:39.51 mdrun ----------------------------------------------------------------------------------- On Wed, Oct 24, 2012 at 11:47 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > > > -- > 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 > -- 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
