As you can see in the attachment (the full output of the testrun), I am using GMX 4.0.2
Are there different versions of 4.0.2 ? On Tue, 2008-11-18 at 16:21 +0100, Berk Hess wrote: > Yes, this is a bug. > And it has been fixed already in 4.0.2. > > Berk > > > Date: Tue, 18 Nov 2008 16:10:51 +0100 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Wrong calculation of runtime > > > > Hi. > > > > I use GMX4.0.2 on a Linux cluster. > > > > When I start my System (242224 atoms on 8CPUs), I can calculate > about 1 > > ns/day. This is also shown at the end of the mdrun output(output is > > marked by "#"): > > # NODE (s) Real (s) (%) > > # Time: 344.000 344.000 100.0 > > # 5:44 > > # (Mnbf/s) (GFlops) (ns/day) (hour/ns) > > #Performance: 52.212 14.794 1.005 23.889 > > #No previous checkpoint file present, assuming this is a new run. > > > > > > But if I abort the run by using -maxh for the same system, the > output > > gets wrong. Here is an example for a test run: -maxh 0.1: > > #starting mdrun 'test' > > #1000000 steps, 2000.0 ps. > > #step 0 > > #NOTE: Turning on dynamic load balancing > > # > > #vol 0.79! imb F 6% step 100, will finish Thu Nov 20 17:03:26 2008 > > #vol 0.79! imb F 4% step 200, will finish Thu Nov 20 15:55:17 2008 > > #vol 0.79! imb F 6% step 300, will finish Thu Nov 20 14:37:03 2008 > > #vol 0.79! imb F 5% step 400, will finish Thu Nov 20 14:39:24 2008 > > #vol 0.79! imb F 5% step 500, will finish Thu Nov 20 14:40:48 2008 > > #vol 0.79! imb F 5% step 600, will finish Thu Nov 20 14:41:45 2008 > > #vol 0.79! imb F 5% step 700, will finish Thu Nov 20 14:42:25 2008 > > #vol 0.79! imb F 9% step 800, will finish Thu Nov 20 14:42:55 2008 > > #vol 0.79! imb F 7% step 900, will finish Thu Nov 20 15:01:49 2008 > > #vol 0.79! imb F 8% step 1000, will finish Thu Nov 20 15:00:17 2008 > > #vol 0.79! imb F 8% step 1100, will finish Thu Nov 20 14:59:02 2008 > > #vol 0.79! imb F 8% step 1200, will finish Thu Nov 20 15:11:51 2008 > > #vol 0.79! imb F 7% step 1300, will finish Thu Nov 20 15:09:54 2008 > > #vol 0.79! imb F 8% step 1400, will finish Thu Nov 20 15:20:08 2008 > > #vol 0.79! imb F 8% step 1500, will finish Thu Nov 20 15:17:53 2008 > > #vol 0.80! imb F 8% step 1600, will finish Thu Nov 20 15:15:55 2008 > > #vol 0.79! imb F 8% step 1700, will finish Thu Nov 20 15:23:59 2008 > > #vol 0.79! imb F 8% step 1800, will finish Thu Nov 20 15:21:54 2008 > > #vol 0.80! imb F 8% step 1900, will finish Thu Nov 20 15:28:48 2008 > > #vol 0.79! imb F 8% step 2000, will finish Thu Nov 20 15:26:41 2008 > > # > > #Step 2070: Run time exceeded 0.099 hours, will terminate the run > > #vol 0.79! imb F 7% > > #Step 2080: Run time exceeded 0.099 hours, will terminate the run > > #step 2080, will finish Thu Nov 20 15:28:21 2008 > > # > > # Average load imbalance: 7.1 % > > # Part of the total run time spent waiting due to load imbalance: > 3.1 % > > # Steps where the load balancing was limited by -rdd, -rcon and/or > -dds: > > #X 9 % > > # > > # > > # Parallel run - timing based on wallclock. > > # > > # NODE (s) Real (s) (%) > > # Time: 359.000 359.000 100.0 > > # 5:59 > > # (Mnbf/s) (GFlops) (ns/day) (hour/ns) > > #Performance: 52.071 14.749 481.337 0.050 > > #No previous checkpoint file present, assuming this is a new run. > > > > The ns/day value is totally wrong! > > The job stopped after 0.1h=6min with 2000 steps. This equates 4000fs > > > > (4000fs / 6min) * 60 (min/h) * 24 (h/day) = 0.96 (ns/day) > > > > Is this a bug? > > > > Greetings, > > Christian. > > > > > > -- > > M. Sc. Christian Seifert > > Department of Biophysics > > University of Bochum > > ND 04/67 > > 44780 Bochum > > Germany > > Tel: +49 (0)234 32 28363 > > Fax: +49 (0)234 32 14626 > > E-Mail: [EMAIL PROTECTED] > > Web: http://www.bph.rub.de > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ______________________________________________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de
NNODES=8, MYRANK=4, HOSTNAME=cln-fg01 NNODES=8, MYRANK=7, HOSTNAME=cln-fg01 NODEID=2 argc=19 NODEID=7 argc=19 :-) G R O M A C S (-: God Rules Over Mankind, Animals, Cosmos and Such :-) VERSION 4.0.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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. :-) /ag-graeter/gromacs/gromacs-4.0.2/bin/mdrun_mpi (-: Option Filename Type Description ------------------------------------------------------------ -s /tmp/cseifert/ATP_md_pr.tpr Input Run input file: tpr tpb tpa -o /tmp/cseifert/ATP_md_pr.trr Output Full precision trajectory: trr trj cpt -x /tmp/cseifert/ATP_md_pr.xtc Output, Opt! Compressed trajectory (portable xdr format) -cpi /ag-graeter/cseifert/ATP/ATP_md_pr.cpt Input, Opt! Checkpoint file -cpo /tmp/cseifert/ATP_md_pr.cpt Output, Opt! Checkpoint file -c /tmp/cseifert/ATP_md_pr.gro Output Structure file: gro g96 pdb -e /tmp/cseifert/ATP_md_pr.edr Output Energy file: edr ene -g md.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi tpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -deffnm string Set the default filename for all file options -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[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 -[no]sum bool yes Sum the energies at every step -[no]v bool yes 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]append bool yes Append to previous output files when restarting from checkpoint -maxh real 0.1 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]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Getting Loaded... Reading file /tmp/cseifert/ATP_md_pr.tpr, VERSION 4.0.2 (single precision) Loaded with Money Making 1D domain decomposition 8 x 1 x 1 WARNING: This run will generate roughly 2011 Mb of data starting mdrun 'test' 1000000 steps, 2000.0 ps. step 0 NOTE: Turning on dynamic load balancing vol 0.79! imb F 6% step 100, will finish Thu Nov 20 17:03:26 2008 vol 0.79! imb F 4% step 200, will finish Thu Nov 20 15:55:17 2008 vol 0.79! imb F 6% step 300, will finish Thu Nov 20 14:37:03 2008 vol 0.79! imb F 5% step 400, will finish Thu Nov 20 14:39:24 2008 vol 0.79! imb F 5% step 500, will finish Thu Nov 20 14:40:48 2008 vol 0.79! imb F 5% step 600, will finish Thu Nov 20 14:41:45 2008 vol 0.79! imb F 5% step 700, will finish Thu Nov 20 14:42:25 2008 vol 0.79! imb F 9% step 800, will finish Thu Nov 20 14:42:55 2008 vol 0.79! imb F 7% step 900, will finish Thu Nov 20 15:01:49 2008 vol 0.79! imb F 8% step 1000, will finish Thu Nov 20 15:00:17 2008 vol 0.79! imb F 8% step 1100, will finish Thu Nov 20 14:59:02 2008 vol 0.79! imb F 8% step 1200, will finish Thu Nov 20 15:11:51 2008 vol 0.79! imb F 7% step 1300, will finish Thu Nov 20 15:09:54 2008 vol 0.79! imb F 8% step 1400, will finish Thu Nov 20 15:20:08 2008 vol 0.79! imb F 8% step 1500, will finish Thu Nov 20 15:17:53 2008 vol 0.80! imb F 8% step 1600, will finish Thu Nov 20 15:15:55 2008 vol 0.79! imb F 8% step 1700, will finish Thu Nov 20 15:23:59 2008 vol 0.79! imb F 8% step 1800, will finish Thu Nov 20 15:21:54 2008 vol 0.80! imb F 8% step 1900, will finish Thu Nov 20 15:28:48 2008 vol 0.79! imb F 8% step 2000, will finish Thu Nov 20 15:26:41 2008 Step 2070: Run time exceeded 0.099 hours, will terminate the run vol 0.79! imb F 7% Step 2080: Run time exceeded 0.099 hours, will terminate the run step 2080, will finish Thu Nov 20 15:28:21 2008 Average load imbalance: 7.1 % Part of the total run time spent waiting due to load imbalance: 3.1 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 359.000 359.000 100.0 5:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 52.071 14.749 481.337 0.050 No previous checkpoint file present, assuming this is a new run. gcq#266: "Why, how now, Claudio ! Whence Comes this Restraint ?" (Lucio in Measure for measure, Act 1, Scene 4, William Shakespeare)
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php