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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