[gmx-users] replica exchange simulations performance issues.

[Miro Astore]

Hi everybody. I've been experimenting with REMD for my system running
on 48 cores with 4 gpus (I will need to scale up to 73 replicas
because this is a complicated system with many DOF I'm open to being
told this is all a silly idea).

My run configuration is
mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11
-v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000

the best I can squeeze out of this is 9ns/day. In a non-replica
simulation I can hit 50ns/day with a single GPU and 12 cores.

Looking at my accounting, for a single replica 52% of time is being
spent on the "Force" category with 92% of my Mflops going into NxN
Ewald Elec. + LJ [F]

I'm wondering what I could do to reduce this bottle neck if anything.

Thank you.
-- 
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney