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.abra...@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.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. > -- 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.
