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Ah, sorry, I did not read your mail carefully enough.<br>A bug with the -maxh option was fixed in 4.0.2.<br>But you are refering to the ns/day performance.<br>This is indeed incorrect (based on nsteps, not on<br>the actual number of steps performed).<br>I will fix it.<br><br>Berk<br><br>> Date: Tue, 18 Nov 2008 16:30:47 +0100<br>> From: cseifert@bph.ruhr-uni-bochum.de<br>> To: gmx-users@gromacs.org<br>> Subject: RE: [gmx-users] Wrong calculation of runtime<br>> <br>> As you can see in the attachment (the full output of the testrun), I am<br>> using GMX 4.0.2<br>> <br>> Are there different versions of 4.0.2 ?<br>> <br>> <br>> On Tue, 2008-11-18 at 16:21 +0100, Berk Hess wrote:<br>> > Yes, this is a bug.<br>> > And it has been fixed already in 4.0.2.<br>> > <br>> > Berk<br>> > <br>> > > Date: Tue, 18 Nov 2008 16:10:51 +0100<br>> > > From: cseifert@bph.ruhr-uni-bochum.de<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: [gmx-users] Wrong calculation of runtime<br>> > > <br>> > > Hi.<br>> > > <br>> > > I use GMX4.0.2 on a Linux cluster.<br>> > > <br>> > > When I start my System (242224 atoms on 8CPUs), I can calculate<br>> > about 1<br>> > > ns/day. This is also shown at the end of the mdrun output(output is<br>> > > marked by "#"):<br>> > > # NODE (s) Real (s) (%)<br>> > > # Time: 344.000 344.000 100.0<br>> > > # 5:44<br>> > > # (Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>> > > #Performance: 52.212 14.794 1.005 23.889<br>> > > #No previous checkpoint file present, assuming this is a new run.<br>> > > <br>> > > <br>> > > But if I abort the run by using -maxh for the same system, the<br>> > output<br>> > > gets wrong. Here is an example for a test run: -maxh 0.1:<br>> > > #starting mdrun 'test'<br>> > > #1000000 steps, 2000.0 ps.<br>> > > #step 0<br>> > > #NOTE: Turning on dynamic load balancing<br>> > > #<br>> > > #vol 0.79! imb F 6% step 100, will finish Thu Nov 20 17:03:26 2008<br>> > > #vol 0.79! imb F 4% step 200, will finish Thu Nov 20 15:55:17 2008<br>> > > #vol 0.79! imb F 6% step 300, will finish Thu Nov 20 14:37:03 2008<br>> > > #vol 0.79! imb F 5% step 400, will finish Thu Nov 20 14:39:24 2008<br>> > > #vol 0.79! imb F 5% step 500, will finish Thu Nov 20 14:40:48 2008<br>> > > #vol 0.79! imb F 5% step 600, will finish Thu Nov 20 14:41:45 2008<br>> > > #vol 0.79! imb F 5% step 700, will finish Thu Nov 20 14:42:25 2008<br>> > > #vol 0.79! imb F 9% step 800, will finish Thu Nov 20 14:42:55 2008<br>> > > #vol 0.79! imb F 7% step 900, will finish Thu Nov 20 15:01:49 2008<br>> > > #vol 0.79! imb F 8% step 1000, will finish Thu Nov 20 15:00:17 2008<br>> > > #vol 0.79! imb F 8% step 1100, will finish Thu Nov 20 14:59:02 2008<br>> > > #vol 0.79! imb F 8% step 1200, will finish Thu Nov 20 15:11:51 2008<br>> > > #vol 0.79! imb F 7% step 1300, will finish Thu Nov 20 15:09:54 2008<br>> > > #vol 0.79! imb F 8% step 1400, will finish Thu Nov 20 15:20:08 2008<br>> > > #vol 0.79! imb F 8% step 1500, will finish Thu Nov 20 15:17:53 2008<br>> > > #vol 0.80! imb F 8% step 1600, will finish Thu Nov 20 15:15:55 2008<br>> > > #vol 0.79! imb F 8% step 1700, will finish Thu Nov 20 15:23:59 2008<br>> > > #vol 0.79! imb F 8% step 1800, will finish Thu Nov 20 15:21:54 2008<br>> > > #vol 0.80! imb F 8% step 1900, will finish Thu Nov 20 15:28:48 2008<br>> > > #vol 0.79! imb F 8% step 2000, will finish Thu Nov 20 15:26:41 2008<br>> > > #<br>> > > #Step 2070: Run time exceeded 0.099 hours, will terminate the run<br>> > > #vol 0.79! imb F 7%<br>> > > #Step 2080: Run time exceeded 0.099 hours, will terminate the run<br>> > > #step 2080, will finish Thu Nov 20 15:28:21 2008<br>> > > #<br>> > > # Average load imbalance: 7.1 %<br>> > > # Part of the total run time spent waiting due to load imbalance:<br>> > 3.1 %<br>> > > # Steps where the load balancing was limited by -rdd, -rcon and/or<br>> > -dds:<br>> > > #X 9 %<br>> > > #<br>> > > #<br>> > > # Parallel run - timing based on wallclock.<br>> > > #<br>> > > # NODE (s) Real (s) (%)<br>> > > # Time: 359.000 359.000 100.0<br>> > > # 5:59<br>> > > # (Mnbf/s) (GFlops) (ns/day) (hour/ns)<br>> > > #Performance: 52.071 14.749 481.337 0.050<br>> > > #No previous checkpoint file present, assuming this is a new run.<br>> > > <br>> > > The ns/day value is totally wrong!<br>> > > The job stopped after 0.1h=6min with 2000 steps. This equates 4000fs<br>> > > <br>> > > (4000fs / 6min) * 60 (min/h) * 24 (h/day) = 0.96 (ns/day)<br>> > > <br>> > > Is this a bug?<br>> > > <br>> > > Greetings,<br>> > > Christian.<br>> > > <br>> > > <br>> > > -- <br>> > > M. Sc. Christian Seifert<br>> > > Department of Biophysics<br>> > > University of Bochum<br>> > > ND 04/67<br>> > > 44780 Bochum<br>> > > Germany<br>> > > Tel: +49 (0)234 32 28363<br>> > > Fax: +49 (0)234 32 14626<br>> > > E-Mail: cseifert@bph.rub.de<br>> > > Web: http://www.bph.rub.de<br>> > > <br>> > > <br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > ______________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> -- <br>> M. Sc. Christian Seifert<br>> Department of Biophysics<br>> University of Bochum<br>> ND 04/67<br>> 44780 Bochum<br>> Germany<br>> Tel: +49 (0)234 32 28363<br>> Fax: +49 (0)234 32 14626<br>> E-Mail: cseifert@bph.rub.de<br>> Web: http://www.bph.rub.de<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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