Re: [gmx-users] replica exchange simulations performance issues.

2020-03-31 Thread Szilárd Páll
On Tue, Mar 31, 2020 at 1:45 AM Miro Astore wrote: > I got up to 25-26 ns/day with my 4 replica system (same logic scaled > up to 73 replicas) which I think is reasonable. Could I do better? > Hard to say without complete log file. Please share single run and multi run log files. > > mpirun

Re: [gmx-users] replica exchange simulations performance issues.

2020-03-30 Thread Miro Astore
I got up to 25-26 ns/day with my 4 replica system (same logic scaled up to 73 replicas) which I think is reasonable. Could I do better? mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 I have tried following the manual but I don't think i'm going it

Re: [gmx-users] replica exchange simulations performance issues.

2020-03-30 Thread Szilárd Páll
On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote: > 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). >

Re: [gmx-users] replica exchange simulations performance issues.

2020-03-29 Thread Miro Astore
After much experimentation I managed to run mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 on a single node at 27 ns/day. This scaled up for 73 replicas on my 190 000 atom system ( using the same logic -np num_sims*12) on our gadi cluster in

Re: [gmx-users] replica exchange simulations performance issues.

2020-03-29 Thread Benson Muite
On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > 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).

Re: [gmx-users] replica exchange simulations performance issues.

2020-03-28 Thread Miro Astore
correction: 99.3% is going into NxN Ewald Elec. + LJ [F] On Sun, Mar 29, 2020 at 12:55 PM Miro Astore wrote: > > 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

[gmx-users] replica exchange simulations performance issues.

2020-03-28 Thread 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