After mdrun, Performance is reported in log file. How is the performance calculated? I guess it is based on the simulation time and the core time but could not reproduce the number reported in the log file.
Also, in the log file, there is Call Count for Neighbor Search, Force, etc… What is Call count?
Performance is simply the simulation throughput calculated from the elapsed wall-time and amount of nanoseconds simulated. Note that the wall-time only considers the actual MD steps startup or cleanup costs are not counted (as they are assumed to have negligible contribution to a typical production simulation).
Regarding the performance table, you can find a bit more info here:
Briefly, we have an always enabled internal CPU cycle counter-based performance measurement, the result of which is printed in the final table. The entries are the timed regions, call count is a the (approximate) number of times the respective region is invoked during the timed MD steps.
Thank you! That makes sense. Previously I was confused since in the log file, gromacs compares the core time and the wall time to see how much the performance is boosted. It makes sense to not consider the start up cost, etc into considering MD performance.