[gmx-users] Using multiple GPU's

Mark Abraham mark.j.abraham at gmail.com
Sat Aug 11 07:24:07 CEST 2018 

Hi,

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Mark

On Sat, Aug 11, 2018, 05:50 paul buscemi <pbuscemi at q.com> wrote:

> Mark, Kevin,
>
> I’ve uploaded two representative log files to Google Drive.  gms users
> should get the invite.
>
> thanks
> Paul
>
> > On Aug 10, 2018, at 6:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > Kevin means you to upload the file to a file sharing service and share
> the
> > link. Everything you've shown points to using both GPUs, but the relevant
> > output about the decision is not shown.
> >
> > Mark
> >
> > On Sat, Aug 11, 2018, 00:58 paul buscemi <pbuscemi at q.com> wrote:
> >
> >> Thanks Kevin. for the rapid response.
> >>
> >> I am using 2018. I’ll check the 2018 - make sure - I was look at the
> >> proper docs.   I should not note that the  GPUs are not matched.   a gtx
> >> 1080ti  and a gtx 1060
> >>
> >> below is some pertinent information from the log file.  ( not too sure
> how
> >> to post a link on the user group )
> >>
> >> Paul
> >>
> >>> On Aug 10, 2018, at 12:31 PM, Kevin Boyd <kevin.boyd at uconn.edu> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Can you post a link to your log file?
> >>>
> >>> Also, what version of gromacs are you using? Make sure that the
> >>> documentation you are following corresponds to the right version of
> >>> gromacs. If you are using v 5.1 (as the link suggests), strongly
> consider
> >>> upgrading to 2018.
> >>>
> >>> Kevin
> >>>
> >>> On Fri, Aug 10, 2018 at 12:57 PM, paul buscemi <pbuscemi at q.com> wrote:
> >>>
> >>>>
> >>>> Dear Uses,
> >>>>
> >>>> I’ve been following the examples on https://na01.safelinks.
> >>>> protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.
> >>>> org%2Fdocumentation%2F5.1%2Fuser-guide%2Fmdrun-
> >>>> performance.html&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%
> >>>> 7Cb67f423cb92a4abac13508d5fee27522%7C17f1a87e2a254eaab9df9d439034
> >>>> b080%7C0%7C1%7C636695170968044387&amp;sdata=TBSbmbdU%
> >>>> 2F5kxRGsaD1IqLXzEbcJUJ6Kqg7ub%2B%2B9m6xc%3D&amp;reserved=0 for setting
> >> up
> >>>> multiple GP’s but have not succeeded.
> >>>> Using a single GPU gmx runs well.  Nvidia and gmx see the 2 PGUs. and
> >>>> I‘ve  tried   mdrun with   variations of  -gpu_id  01,    and -ntmpi,
> >> but
> >>>> the GPUs are not put to use.
> >>>>
> >>>> Would someone suggest the proper signals to mdrun for  two GPU’s. ?
> >>>>
> >>>> Running on lilnix-min sarah,  I7
> >>>>
> >>>> thanks
> >>>> Paul
> >>>> --
> >>>>
> >>
> >> GROMACS:      gmx mdrun, version 2018
> >> Executable:   /usr/local/gromacs/bin//gmx
> >> Data prefix:  /usr/local/gromacs
> >> Working dir:  /home/rgb/Desktop/PDMS
> >> Command line:
> >>  gmx mdrun -deffnm pdms.sys.nvt -ntmpi 4 -ntomp 2 -gpu_id 01
> >>
> >> GROMACS version:    2018
> >> Precision:          single
> >> Memory model:       64 bit
> >> MPI library:        thread_mpi
> >> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> >> 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:           2018-07-06 18:24:42
> >> Built by:           rgb at RGB [CMAKE]
> >> Build OS/arch:      Linux 4.4.0-21-generic x86_64
> >> Build CPU vendor:   Intel
> >> Build CPU brand:    Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
> >> Build CPU family:   6   Model: 158   Stepping: 9
> >> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle
> htt
> >> intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse
> rdrnd
> >> rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >> C compiler:         /usr/bin/gcc GNU 5.4.0
> >> C compiler flags:    -march=core-avx2     -O3 -DNDEBUG
> -funroll-all-loops
> >> -fexcess-precision=fast
> >> C++ compiler:       /usr/bin/c++ GNU 5.4.0
> >> C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG
> >> -funroll-all-loops -fexcess-precision=fast
> >> CUDA compiler:      /usr/lib/nvidia-cuda-toolkit/bin/nvcc nvcc: NVIDIA
> (R)
> >> Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
> >> Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5,
> V7.5.17
> >> CUDA compiler
> >>
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;-D_FORCE_INLINES;;
> >>
> ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> >> CUDA driver:        9.0
> >> CUDA runtime:       7.50
> >>
> >> ===== latest attempt =======
> >> Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
> >> Hardware detected:
> >>  CPU info:
> >>    Vendor: Intel
> >>    Brand:  Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
> >>    Family: 6   Model: 158   Stepping: 9
> >>    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt
> intel
> >> lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp
> >> rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >>  Hardware topology: Basic
> >>    Sockets, cores, and logical processors:
> >>      Socket  0: [   0   4] [   1   5] [   2   6] [   3   7]
> >>  GPU info:
> >>    Number of GPUs detected: 2
> >>    #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC:  no, stat:
> >> compatible
> >>    #1: NVIDIA GeForce GTX 1060 6GB, compute cap.: 6.1, ECC:  no, stat:
> >> compatible
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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