[gmx-users] best performance on GPU

[Paul Buscemi]

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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