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]
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>
>
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--
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)
_______________________________________________
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Please don't post (un)subscribe requests to the list. Use the
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