[gmx-users] best performance on GPU

[Maryam]

Hi Paul
How can I run it on multiple nodes?
Thanks

On Fri., Aug. 2, 2019, 6:10 p.m. Paul Buscemi, <pbuscemi at q.com> wrote:

> Why run moo on a single node ?
>
> PB
>
> > On Aug 1, 2019, at 5:53 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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