[obasekia]

Good day all, i am trying to bench mark my simulations using genesis, i am equilibrating using implicit solvent with 22706 atoms using my school’s cluster with 24 MPI processes and 12 OpenMP  thread (288 CPU cores) but a 50 ps equilibration takes more than 6hrs. my question is what is the speed of GENESIS compared to other MD engines?

[jwjung]

I think the performance result is very different from what we observed. Could you first try MPI=8 and OpenMP=3?

For the small system, I think there is no reason to use large number of MPI and OpenMPs.

[obasekia]

Thanks I will try that and give feedback. But I thought increasing number of cores should speed up the simulation?

[jwjung]

Generally, you’re right. Increasing the process number improves performance. However, in this case, it might be better to check what the main reason is.

BTW, could you let me know whether you’re using single or mixed precision? In addition, could you let me know which simulator is used between atdyn and spdyn?

[obasekia]

Reducing the number of cores to 24  as you suggested helped to speed things up but i really don’t understand why(atdyn for implicit solvent). also just an unrelated question. i started GaMD simulation with implicit solvent but i cannot use NPT and the time step of 4fs with hydrogen mass partition hope it wont fact the simulation

[obasekia]

Also you other question i am using double precision. i should also say 24 cores a 500ps takes approximately 7-8hrs though

[jwjung]

Atdyn makes use of atomic decomposition parallelization and it does not have a good parallel performance. According to your tests, I guess there will be no significant performance improvements using atdyn.