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
