[gmx-users] Using multiple GPU's

Sat Aug 11 01:34:49 CEST 2018

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
>
> * 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-request at gromacs.org.