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.
Stephane
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
