[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory
Efrat Exlrod
Efrat.Exlrod at biu.ac.il
Wed Feb 29 09:50:35 CET 2012
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120229/3a09b0be/attachment.html>
More information about the gromacs.org_gmx-users
mailing list