[gmx-users] best performance on GPU

[paul buscemi]

whoops  ---not moo  ( iphone took over ) but mpi….

> On Aug 2, 2019, at 5:09 PM, 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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