[gmx-users] Wrong calculation of runtime

[Christian Seifert]

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