Hi Paul How can I run it on multiple nodes? Thanks On Fri., Aug. 2, 2019, 6:10 p.m. Paul Buscemi, <pbusc...@q.com> wrote:
> Why run moo on a single node ? > > PB > > > On Aug 1, 2019, at 5:53 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. > -- 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.