[gmx-users] memory usage grows without bounds

[Marcelo Carignano]

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" <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
>