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.kow...@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@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 > ------------------------------ > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.