if the system sends a termination request to MDRUN, it stops the main cycle and writes down the summary of the run.
Dr. Vitaly V. Chaban On Wed, Feb 26, 2014 at 10:31 AM, delara aghaie <d_agh...@yahoo.com> wrote: > Dear Gromacs users, > we want to simulateHSA protein using8 processors. Usually with our available > system 10ns simulation on 8 processors lasts 2-3 days. > This time we submitted 10 ns simulation, after almost 6 days it has finished > but when we look at md.log file, only 179411 steps has been completed and all > the averages are over this time, although we have submitted the run 5000000 > steps=10ns > 1) First I want to know how the log file shows the end of simulation, > although only 0.35 ns of simulation is done and if we draw RDF the time again > shows completing of 0.35 ns. > you can see the ending part of log file below: > 2) the second point is that the average load imbalance is shown as 110.3% > while for previous runs we had this as 3-4 %. > what can be the reason for this high load imbalance? > and is this responsible for the lower simulation efficiency and higher time? > and the most important that why the log file is written in the way that the > simulation has been completed while only 0.3 ns has passes? > Thanks for your time > ********************************************************** > D O M A I N D E C O M P O S I T I O N S T A T I S T I C S > > av. #atoms communicated per step for force: 2 x 97992.1 > av. #atoms communicated per step for LINCS: 2 x 2373.8 > > Average load imbalance: 110.3 % > Part of the total run time spent waiting due to load imbalance: 1.4 % > > > R E A L C Y C L E A N D T I M E A C C O U N T I N G > > Computing: Nodes Number G-Cycles Seconds % > ----------------------------------------------------------------------- > Domain decomp. 8 35882 556174.638 209101.4 5.1 > DD comm. load 8 359 235.791 88.6 0.0 > Comm. coord. 8 179411 407595.614 153241.1 3.7 > Neighbor search 8 35883 39333.698 14788.0 0.4 > Force 8 179411 205203.393 77149.0 1.9 > Wait + Comm. F 8 179411 471040.171 177093.9 4.3 > PME mesh 8 179411 8699277.459 3270611.0 79.1 > Write traj. 8 752 15563.463 5851.3 0.1 > Update 8 179411 12991.140 4884.2 0.1 > Constraints 8 179411 438837.169 164986.8 4.0 > Comm. energies 8 35884 149298.111 56130.6 1.4 > Rest 8 6090.776 2289.9 0.1 > ----------------------------------------------------------------------- > Total 8 11001641.424 4136215.9 100.0 > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > PME redist. X/F 8 358822 1446552.180 543850.9 13.1 > PME spread/gather 8 358822 820940.059 308643.5 7.5 > PME 3D-FFT 8 358822 6426689.995 2416201.0 58.4 > PME solve 8 179411 5033.523 1892.4 0.0 > ----------------------------------------------------------------------- > > Parallel run - timing based on wallclock. > > NODE (s) Real (s) (%) > Time: 517026.991 517026.991 100.0 > 5d23h37:06 > (Mnbf/s) (MFlops) (ns/day) (hour/ns) > Performance: 9.634 506.361 0.060 400.250 > Finished mdrun on node 0 Tue Feb 25 13:34:48 2014 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
