Re: [gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory
Hi, 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 attached). I've attached a script I used to monitor the memory usage, feel free to use if you want check again. Cheers, -- Szilárd On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod efrat.exl...@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 -dhdlmd.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 -tpidmd.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 -multidirmd 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 -niceint 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 -npmeint -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 -gcomint -1 Global communication frequency -[no]v bool no
[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory
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 InputRun 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 -dhdlmd.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 -tpidmd.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 -multidirmd 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 -niceint0 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 -npmeint-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 -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-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
[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory
Hi, 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
