[gmx-users] Testing gromacs on IBM POWER8

Fabricio Cannini fcannini at gmail.com
Wed Sep 2 21:25:03 CEST 2015

On 27-08-2015 04:17, Mark Abraham wrote:
> Hi,
> I have no idea what you're trying to show with these graphs. Your vertical
> axis of time makes it looks like a 2.5 year old AMD chip is walking all
> over POWER8?
> Other points
> 1) GROMACS doesn't use configure or fortran, so don't mention that

This is part of a report in which we're testing Quantum Espresso as 
well. So that's why there's configure and fortran there.

> 2) these simulations do not use lapack or blas, so don't mention that

We were not aware of this. Can you please point to benchmarks that use 
blas/lapack, or how can we tell if it does or not ?

> 3) you need to clarify what a "CPU" is... core, hardware thread?

We've edited the graphics to make it more clear.

> 4) when you're using fewer cores than the whole node, then you need to
> report how you are managing thread affinity

We're setting 1 mpi process per core then n openmp threads to its 
hardware threads. OpenMP's BIND_PROC and mpirun's bind-to-core.

> 5) the splines on the graphs are misleading when reporting discrete
> quantities

Would it be clearer using solid bars?

> 6) you need to report times that are measured after auto-tuning completes

Should I discard the time spent before auto-tune completes?

> 7) you need to report whether you are using MPI, thread-MPI or OpenMP to
> distribute work to threads.

We only used MPI and OpenMP.


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