[gmx-users] best performance on GPU

[Maryam]

Hi Mark
here is the link to md.log:
https://www.dropbox.com/s/4fuu5g68nwwzys4/MD.log?dl=0
Thank you!


On Thu, Aug 1, 2019 at 6:54 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> We can't tell whether or what the problem is without more information.
> Please upload your .log file to a file sharing service and post a link.
>
> Mark
>
> On Fri, 2 Aug 2019 at 01:05, 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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