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

Efrat Exlrod Efrat.Exlrod at biu.ac.il
Mon Feb 20 10:38:50 CET 2012

Sorry, I forgot to enclose the command line and output

> mdrun-gpu -device "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" -deffnm md
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                            :-)  VERSION 4.5.5  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
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                              :-)  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
-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

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.

From: Efrat Exlrod
Sent: Monday, February 20, 2012 11:33 AM
To: gmx-users at gromacs.org
Subject: Gromacs-GPU benchmark test killed after exhausting the memory


I have Gromacs- GPU version 4.5.5 and GTX 580.
I run dhfr-solv-PME benchmark test (see below) and my run is killed after couple of hours when it exhausts all the computer memory, including the swap (2G + 4G swap).
Has anyone encountered this problem? What do I do wrong?

Thanks, Efrat
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