[gmx-users] FEP and loss of performance

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Apr 4 15:02:03 CEST 2011

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.


-- 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.


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