[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory

Szilárd Páll szilard.pall at cbr.su.se
Fri Mar 2 14:46:25 CET 2012


First I thought that there might be a memory leak which could have
caused this if you ran for really long time. However, I've just ran
the very same benchmark (dhfr with PME) for one hour, monitored the
memory usage and I couldn't see any change whatsoever (see the plot

I've attached a script I used to monitor the memory usage, feel free
to use if you want check again.


On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod <Efrat.Exlrod at biu.ac.il> wrote:
> Hi,
> I have Gromacs-GPU version 4.5.5 and GTX 580.
> I ran dhfr-solv-PME benchmark test (see below) and my run was killed after
> couple of hours exhausting all the computer memory, including the swap (2G
> + 4G swap).
> Has anyone encountered this problem? What is wrong?
> Thanks, Efrat
>> mdrun-gpu -device
>> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" -deffnm md
>                          :-)  G  R  O  M  A  C  S  (-:
>                    Great Red Oystrich Makes All Chemists Sane
>                             :-)  VERSION 4.5.5  (-:
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>                Berk Hess, David van der Spoel, and Erik Lindahl.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             check out http://www.gromacs.org for more information.
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>                               :-)  mdrun-gpu  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s         md.tpr  Input        Run input file: tpr tpb tpa
>   -o         md.trr  Output       Full precision trajectory: trr trj cpt
>   -x         md.xtc  Output, Opt. Compressed trajectory (portable xdr
> format)
> -cpi         md.cpt  Input, Opt.  Checkpoint file
> -cpo         md.cpt  Output, Opt. Checkpoint file
>   -c         md.gro  Output       Structure file: gro g96 pdb etc.
>   -e         md.edr  Output       Energy file
>   -g         md.log  Output       Log file
> -dhdl        md.xvg  Output, Opt. xvgr/xmgr file
> -field       md.xvg  Output, Opt. xvgr/xmgr file
> -table       md.xvg  Input, Opt.  xvgr/xmgr file
> -tablep      md.xvg  Input, Opt.  xvgr/xmgr file
> -tableb      md.xvg  Input, Opt.  xvgr/xmgr file
> -rerun       md.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi         md.xvg  Output, Opt. xvgr/xmgr file
> -tpid        md.xvg  Output, Opt. xvgr/xmgr file
>  -ei         md.edi  Input, Opt.  ED sampling input
>  -eo         md.edo  Output, Opt. ED sampling output
>   -j         md.gct  Input, Opt.  General coupling stuff
>  -jo         md.gct  Output, Opt. General coupling stuff
> -ffout       md.xvg  Output, Opt. xvgr/xmgr file
> -devout      md.xvg  Output, Opt. xvgr/xmgr file
> -runav       md.xvg  Output, Opt. xvgr/xmgr file
>  -px         md.xvg  Output, Opt. xvgr/xmgr file
>  -pf         md.xvg  Output, Opt. xvgr/xmgr file
> -mtx         md.mtx  Output, Opt. Hessian matrix
>  -dn         md.ndx  Output, Opt. Index file
> -multidir        md  Input, Opt., Mult. Run directory
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -deffnm      string md      Set the default filename for all file options
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -[no]pd      bool   no      Use particle decompostion
> -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
> -npme        int    -1      Number of separate nodes to be used for PME, -1
>                             is guess
> -ddorder     enum   interleave  DD node order: interleave, pp_pme or
> cartesian
> -[no]ddcheck bool   yes     Check for all bonded interactions with DD
> -rdd         real   0       The maximum distance for bonded interactions
> with
>                             DD (nm), 0 is determine from initial coordinates
> -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
> -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or
> yes
> -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
> -gcom        int    -1      Global communication frequency
> -[no]v       bool   no      Be loud and noisy
> -[no]compact bool   yes     Write a compact log file
> -[no]seppot  bool   no      Write separate V and dVdl terms for each
>                             interaction type and node to the log file(s)
> -pforce      real   -1      Print all forces larger than this (kJ/mol nm)
> -[no]reprod  bool   no      Try to avoid optimizations that affect binary
>                             reproducibility
> -cpt         real   15      Checkpoint interval (minutes)
> -[no]cpnum   bool   no      Keep and number checkpoint files
> -[no]append  bool   yes     Append to previous output files when continuing
>                             from checkpoint instead of adding the simulation
>                             part number to all file names
> -maxh        real   -1      Terminate after 0.99 times this time (hours)
> -multi       int    0       Do multiple simulations in parallel
> -replex      int    0       Attempt replica exchange every # steps
> -reseed      int    -1      Seed for replica exchange, -1 is generate a seed
> -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
>                             bombardment on your system
> -device      string
> OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes  Device option
>                             string
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file md.tpr, VERSION 4.5.5 (double precision)
> Back Off! I just backed up md.edr to ./#md.edr.1#
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
> WARNING: Non-supported GPU selected (#0, GeForce GTX 580), forced
> continuing.Note, that the simulation can be slow or it migth even crash.
> Pre-simulation ~15s memtest in progress...done, no errors detected
> starting mdrun 'Protein in water'
> -1 steps, infinite ps.
> Killed
> --
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