Hi Chris,
thank for the suggestions,
in the previous mail there is a mistake because
couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
Now the problem of the load balance seems reasonable, because
the water box is large ~9.0 nm.
However the problem exist and the performance loss is very high, so I have
redone calculations with this command:
grompp -f
md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n
../index.ndx -o
md.tpr -maxwarn 1
mdrun -s md.tpr -o md
this is part of the md.mdp file:
; Run parameters
; define = -DPOSRES
integrator = md ;
nsteps = 1000 ;
dt = 0.002 ;
[..]
free_energy = yes ; /no
init_lambda = 0.9
delta_lambda = 0.0
couple-moltype = SOL ; solvent water
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol= yes
Result for free energy calculation
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Domain decomp. 8 126 22.050 8.3 0.1
DD comm. load 8 15 0.009 0.0 0.0
DD comm. bounds 8 12 0.031 0.0 0.0
Comm. coord. 8 1001 17.319 6.5 0.0
Neighbor search 8 127 436.569 163.7 1.1
Force 8 1001 34241.576 12840.9 87.8
Wait + Comm. F 8 1001 19.486 7.3 0.0
PME mesh 8 1001 4190.758 1571.6 10.7
Write traj. 8 7 1.827 0.7 0.0
Update 8 1001 12.557 4.7 0.0
Constraints 8 1001 26.496 9.9 0.1
Comm. energies 8 1002 10.710 4.0 0.0
Rest 8 25.142 9.4 0.1
-----------------------------------------------------------------------
Total 8 39004.531 14627.1 100.0
-----------------------------------------------------------------------
-----------------------------------------------------------------------
PME redist. X/F 8 3003 3479.771 1304.9 8.9
PME spread/gather 8 4004 277.574 104.1 0.7
PME 3D-FFT 8 4004 378.090 141.8 1.0
PME solve 8 2002 55.033 20.6 0.1
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 1828.385 1828.385 100.0
30:28
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 3.115 3.223 0.095 253.689
I Switched off only the free_energy keyword and I redone the calculation
I have:
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Domain decomp. 8 77 10.975 4.1 0.6
DD comm. load 8 1 0.001 0.0 0.0
Comm. coord. 8 1001 14.480 5.4 0.8
Neighbor search 8 78 136.479 51.2 7.3
Force 8 1001 1141.115 427.9 61.3
Wait + Comm. F 8 1001 17.845 6.7 1.0
PME mesh 8 1001 484.581 181.7 26.0
Write traj. 8 5 1.221 0.5 0.1
Update 8 1001 9.976 3.7 0.5
Constraints 8 1001 20.275 7.6 1.1
Comm. energies 8 992 5.933 2.2 0.3
Rest 8 19.670 7.4 1.1
-----------------------------------------------------------------------
Total 8 1862.552 698.5 100.0
-----------------------------------------------------------------------
-----------------------------------------------------------------------
PME redist. X/F 8 2002 92.204 34.6 5.0
PME spread/gather 8 2002 192.337 72.1 10.3
PME 3D-FFT 8 2002 177.373 66.5 9.5
PME solve 8 1001 22.512 8.4 1.2
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 87.309 87.309 100.0
1:27
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 439.731 23.995 1.981 12.114
Finished mdrun on node 0 Mon Apr 4 16:52:04 2011
Luca
> If we accept your text at face value, then the simulation slowed down
> by a factor of 1500%, certainly not the 16% of the load balancing.
>
> Please let us know what version of gromacs and cut and paste your
> cammands that you used to run gromacs (so we can verify that you ran
> on the same number of processors) and cut and paste a diff of the .mdp
> files (so that we can verify that you ran for the same number of steps).
>
> You might be correct about the slowdown, but let's rule out some other
> more obvious problems first.
>
> Chris.
>
> -- original message --
>
>
> Dear all,
> when I run a single free energy simulation
> i noticed that there is a loss of performace with respect to
> the normal MD
>
> free_energy = yes
> init_lambda = 0.9
> delta_lambda = 0.0
> couple-moltype = Protein_Chain_P
> couple-lambda0 = vdw-q
> couple-lambda0 = none
> couple-intramol= yes
>
> Average load imbalance: 16.3 %
> Part of the total run time spent waiting due to load imbalance: 12.2 %
> Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> X0 % Time: 1852.712 1852.712 100.0
>
> free_energy = no
> Average load imbalance: 2.7 %
> Part of the total run time spent waiting due to load imbalance: 1.7 %
> Time: 127.394 127.394 100.0
>
> It seems that the loss of performace is due in part to in the load
> imbalance in the domain decomposition, however I tried to change
> these keywords without benefit
> Any comment is welcome.
>
> Thanks
--
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