Thank you Mark for the advice, I will take a look of this.
Stephane Stephane Abel wrote: > Hi gromacs users and experts > > I am doing some simulations using 8 CPU of solvate peptide (8 AA) in > octahedron truncated box (5150) with SPC water with GMX 4.05. To > simulate during a long time i am cutting my simulation in 24 h time > period (25 ns/day) using checkpoints. During my last simulation part, i > have note that the simulation was 2.6 slower (sim_last) than the > preceding run (sim_prev). I have note that message at the end of the log > file of the sim_last > > ---- Log of sim_last ------------- > > 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 35969.0 > av. #atoms communicated per step for LINCS: 2 x 58.1 > > Average load imbalance: 4.6 % > Part of the total run time spent waiting due to load imbalance: 1.5 % > > > 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 1025540 19176.963 6392.1 0.9 > Comm. coord. 8 5127698 12300.804 4100.1 0.6 > Neighbor search 8 1025541 183144.975 61046.2 8.9 > Force 8 5127698 263336.032 87775.6 12.8 > Wait + Comm. F 8 5127698 23995.139 7998.1 1.2 > PME mesh 8 5127698 265259.767 88416.8 12.9 > Write traj. 8 5184 154247.417 51414.0 7.5 > Update 8 5127698 13123.384 4374.3 0.6 > Constraints 8 5127698 16635.925 5545.1 0.8 > Comm. energies 8 5127698 1084187.361 361383.0 52.8 > Rest 8 17552.589 5850.7 0.9 > ----------------------------------------------------------------------- > Total 8 2052960.356 684296.0 100.0 > ----------------------------------------------------------------------- > > NOTE: 53 % of the run time was spent communicating energies, > you might want to use the -nosum option of mdrun > > > Parallel run - timing based on wallclock. > > NODE (s) Real (s) (%) > Time: 85537.000 85537.000 100.0 > 23h45:37 > (Mnbf/s) (GFlops) (ns/day) (hour/ns) > Performance: 144.887 10.126 10.359 2.317 > Finished mdrun on node 0 Fri Sep 25 14:19:07 2009 > > ----------------- Log sim_prev > > 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 35971.8 > av. #atoms communicated per step for LINCS: 2 x 59.7 > > Average load imbalance: 4.6 % > Part of the total run time spent waiting due to load imbalance: 1.5 % > > > 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 2500000 47859.929 15952.7 2.4 > Comm. coord. 8 12500000 38434.207 12810.9 1.9 > Neighbor search 8 2500001 445996.846 148659.9 22.4 > Force 8 12500000 637253.269 212409.6 32.1 > Wait + Comm. F 8 12500000 58421.254 19473.0 2.9 > PME mesh 8 12500000 637267.326 212414.2 32.1 > Write traj. 8 12501 80.674 26.9 0.0 > Update 8 12500000 32011.697 10670.2 1.6 > Constraints 8 12500000 40061.175 13353.2 2.0 > Comm. energies 8 12500000 8407.505 2802.4 0.4 > Rest 8 41890.865 13963.1 2.1 > ----------------------------------------------------------------------- > Total 8 1987684.746 662536.0 100.0 > ----------------------------------------------------------------------- > > Parallel run - timing based on wallclock. > > NODE (s) Real (s) (%) > Time: 82817.000 82817.000 100.0 > 23h00:17 > (Mnbf/s) (GFlops) (ns/day) (hour/ns) > Performance: 364.799 25.495 26.082 0.920 > > My simulation is running on a supercompter that you can see the > characteristic here : http://www.cines.fr/spip.php?article520). I don't > know where is the problem (hardware ?, software ?) Any advice will be > appreciate. sim_last executed many fewer integration steps compared with sim_prev, presumably because of this issue. One theory is that your 8 processors had different relative locality during the two runs, and that this had a severe consequence for network performance (both Write traj. and Comm. energies are high, and these require communication to the master node, and then I/O). Ensuring you get allocated all 8 cores in one node should alleviate any such issue. Mark
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