[gmx-users] memory usage grows without bounds

[Pablo Serra]

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.abraham at 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" <serra at 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
> >
> > --
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