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) 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? 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