On Tue, Nov 5, 2013 at 12:55 PM, James Starlight <jmsstarli...@gmail.com>wrote:
> Dear Richard, > > > 1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test > gave me performance about 25ns/day for the explicit solved system consisted > of 68k atoms (charmm ff. 1.0 cutoofs) > > gaves slightly worse performation in comparison to the 1) > > Richard suggested mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test, which looks correct to me. -ntomp 6 is probably superfluous Mark > finally > > 3) mdrun -deffnm md_CaM_test > running in the same regime as in the 2) so its also gave me 22ns/day for > the same system. > > How the efficacy of using of dual-GPUs could be increased? > > James > > > 2013/11/5 Richard Broadbent <richard.broadben...@imperial.ac.uk> > > > Dear James, > > > > > > On 05/11/13 11:16, James Starlight wrote: > > > >> My suggestions: > >> > >> 1) During compilstion using -march=corei7-avx-i I have obtained error > that > >> somethng now found ( sorry I didnt save log) so I compile gromacs > without > >> this flag > >> > >> 2) I have twice as better performance using just 1 gpu by means of > >> > >> mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test > >> > >> than using of both gpus > >> > >> mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v -deffnm md_CaM_test > >> > >> in the last case I have obtained warning > >> > >> WARNING: Oversubscribing the available 12 logical CPU cores with 24 > >> threads. > >> This will cause considerable performance loss! > >> > >> here you are requesting 2 thread mpi processes each with 12 openmp > > threads, hence a total of 24 threads however even with hyper threading > > enabled there are only 12 threads on your machine. Therefore, only > allocate > > 12. Try > > > > mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test > > > > or even > > > > mdrun -v -deffnm md_CaM_test > > > > I believe it should autodetect the GPUs and run accordingly for details > of > > how to use gromacs with mpi/thread mpi openmp and GPUs see > > > > http://www.gromacs.org/Documentation/Acceleration_and_parallelization > > > > Which describes how to use these systems > > > > Richard > > > > > > How it could be fixed? > >> All gpu are recognized correctly > >> > >> > >> 2 GPUs detected: > >> #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat: > >> compatible > >> #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat: > >> compatible > >> > >> > >> James > >> > >> > >> 2013/11/4 Szilárd Páll <pall.szil...@gmail.com> > >> > >> You can use the "-march=native" flag with gcc to optimize for the CPU > >>> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge > >>> CPUs. > >>> -- > >>> Szilárd Páll > >>> > >>> > >>> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight < > jmsstarli...@gmail.com > >>> > > >>> wrote: > >>> > >>>> Szilárd, thanks for suggestion! > >>>> > >>>> What kind of CPU optimisation should I take into account assumint that > >>>> > >>> I'm > >>> > >>>> using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as > >>>> 12 > >>>> nodes in Debian). > >>>> > >>>> James > >>>> > >>>> > >>>> 2013/11/4 Szilárd Páll <pall.szil...@gmail.com> > >>>> > >>>> That should be enough. You may want to use the -march (or equivalent) > >>>>> compiler flag for CPU optimization. > >>>>> > >>>>> Cheers, > >>>>> -- > >>>>> Szilárd Páll > >>>>> > >>>>> > >>>>> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight < > >>>>> > >>>> jmsstarli...@gmail.com> > >>> > >>>> wrote: > >>>>> > >>>>>> Dear Gromacs Users! > >>>>>> > >>>>>> I'd like to compile lattest 4.6 Gromacs with native GPU supporting > on > >>>>>> > >>>>> my > >>> > >>>> i7 > >>>>> > >>>>>> cpu with dual GeForces Titans gpu mounted. With this config I'd like > >>>>>> > >>>>> to > >>> > >>>> perform simulations using cpu as well as both gpus simultaneously. > >>>>>> > >>>>>> What flags besides > >>>>>> > >>>>>> cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 > >>>>>> > >>>>>> > >>>>>> should I define to CMAKE for compiling optimized gromacs on such > >>>>>> > >>>>> workstation? > >>>>> > >>>>>> > >>>>>> > >>>>>> Thanks for help > >>>>>> > >>>>>> James > >>>>>> -- > >>>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>>>> * Please search the archive at > >>>>>> > >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>>>> > >>>>>> * Please don't post (un)subscribe requests to the list. Use the > >>>>>> www interface or send it to gmx-users-requ...@gromacs.org. > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>> > >>>>> -- > >>>>> gmx-users mailing list gmx-users@gromacs.org > >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>>> * Please search the archive at > >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>>>> * Please don't post (un)subscribe requests to the list. Use the > >>>>> www interface or send it to gmx-users-requ...@gromacs.org. > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> -- > >>>> gmx-users mailing list gmx-users@gromacs.org > >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>>> * Please search the archive at > >>>> > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> > >>>> * Please don't post (un)subscribe requests to the list. Use the > >>>> www interface or send it to gmx-users-requ...@gromacs.org. > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>> -- > >>> gmx-users mailing list gmx-users@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the > >>> www interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists