[gmx-users] best performance on GPU

[Szilárd Páll]

Hi,

You can get significantly better performance if you use a more recent
GROMACS version (>=2018) to pick up the improvements to GPU
acceleration (see
https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.26011 Fig 7, top
group of bars), but 300 ns/day on a single machine is unlikely with
your system and settings.

Cheers,
--
Szilárd


On Fri, Aug 2, 2019 at 12:05 AM Maryam <maryam.kowsar at gmail.com> wrote:
>
> Dear all
> I want to run a simulation of approximately 12000 atoms system in gromacs
> 2016.6 on GPU with the following machine structure:
> Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
> support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
> instructions: AVX2_256 FFT library:
> fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
> support: enabled Hwloc support: disabled Tracing support: disabled Built
> on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian at BioServer [CMAKE] Build
> OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
> brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23 Model: 1
> Stepping: 1
> Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
> 7.5, ECC: no, stat: compatible
> i used different commands to get the best performance and i dont know which
> point i am missing. the quickest time possible is got by this command:gmx
> mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
> which is 10 ns/day! and it takes 2 months to end.
>  though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin on
> -resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
> -append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
> with this properties I should be able to run it in  295 ns/day!
> could you help me find out what point i am missing that i can not reach the
> best performance level?
> Thank you
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