[gmx-users] Wrong calculation of runtime

[Berk Hess]

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: cseifert at bph.ruhr-uni-bochum.de
> To: gmx-users at 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: cseifert at bph.rub.de
> Web: http://www.bph.rub.de
> 
> 
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