[gmx-users] rtx 2080 gpu

Szilárd Páll pall.szilard at gmail.com
Wed Jul 17 17:06:02 CEST 2019 

On Wed, Jul 17, 2019 at 2:13 PM Stefano Guglielmo <
stefano.guglielmo at unito.it> wrote:

> Hi Benson,
> thanks for your answer and sorry for my delay: in the meantime I had to
> restore the OS. I obviously re-installed NVIDIA driver (430.64) and CUDA
> 10.1, I re-compiled Gromacs 2019.2 with the following command:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX2_256 -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DREGRESSIONTEST_DOWNLOAD=ON
>
> I did make test and I got 100% passed. but this is the log file:
>
> GROMACS:      gmx mdrun, version 2019.2
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/stefano/CB2
> Process ID:   117020
> Command line:
>   gmx mdrun -deffnm cb2_trz2c3ohene -ntmpi 1 -pin on
>
> GROMACS version:    2019.2
> 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-3.3.8-sse2-avx-avx2-avx2_128
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> C compiler:         /usr/bin/cc GNU 4.8.5
> C compiler flags:    -mavx2 -mfma     -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> C++ compiler:       /usr/bin/c++ GNU 4.8.5
> C++ compiler flags:  -mavx2 -mfma    -std=c++11   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1,
> V10.1.168
> CUDA compiler
>
> flags:-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_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;;
>
> ;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver:        10.10
> CUDA runtime:       N/A
>
> NOTE: Detection of GPUs failed. The API reported:
>       unknown error
>       GROMACS cannot run tasks on a GPU.
>
> Running on 1 node with total 32 cores, 64 logical cores, 0 compatible GPUs
> Hardware detected:
>   CPU info:
>     Vendor: AMD
>     Brand:  AMD Ryzen Threadripper 2990WX 32-Core Processor
>     Family: 23   Model: 8   Stepping: 2
>     Features: aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf
> misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp
> sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
>   Hardware topology: Basic
>     Sockets, cores, and logical processors:
>       Socket  0: [   0  32] [   1  33] [   2  34] [   3  35] [   4  36] [
> 5  37] [   6  38] [   7  39] [  16  48] [  17  49] [  18  50] [  19  51] [
>  20  52] [  21  53] [  22  54] [  23  55] [   8  40] [   9  41] [  10  42]
> [  11  43] [  12  44] [  13  45] [  14  46] [  15  47] [  24  56] [  25
>  57] [  26  58] [  27  59] [  28  60] [  29  61] [  30  62] [  31  63]
>
> Do you have any suggestions?
>
> PS: I set SIMD option to AVX2_256 with an AMD Ryzen Threadripper 2990WX
> 32-Core Processor: do you think it is a good idea?
>

In general, I suggest you stick to the defaults (which is not AVX2_128),
this will typically be faster, in particular in CPU-only runs. The
difference may not be significant in GPU-accelerated runs and (in some no
too common cases it can even be a little bit faster with AVX2_256).

Cheers,
--
Szilárd


>
> Thanks again
> Stefano
>
> Il giorno mer 10 lug 2019 alle ore 08:13 Benson Muite <
> benson_muite at emailplus.org> ha scritto:
>
> > Hi Stefano,
> >
> > What was your compilation command? (it may be helpful to add SIMD
> > support appropriate to your processor
> >
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support
> > )
> >
> > Did you run make test after compiling?
> >
> > Benson
> >
> > On 7/10/19 1:18 AM, Stefano Guglielmo wrote:
> > > Dear all,
> > > I have a centOS machine equipped with two RTX 2080 cards, with nvidia
> > > drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the
> > log
> > > reported the following message:
> > >
> > > GROMACS version:    2019.2
> > > Precision:          single
> > > Memory model:       64 bit
> > > MPI library:        thread_mpi
> > > OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> > > GPU support:        CUDA
> > > SIMD instructions:  NONE
> > > FFT library:        fftw-3.3.8
> > > RDTSCP usage:       disabled
> > > TNG support:        enabled
> > > Hwloc support:      disabled
> > > Tracing support:    disabled
> > > C compiler:         /usr/bin/cc GNU 4.8.5
> > > C compiler flags:        -O3 -DNDEBUG -funroll-all-loops
> > > -fexcess-precision=fast
> > > C++ compiler:       /usr/bin/c++ GNU 4.8.5
> > > C++ compiler flags:     -std=c++11   -O3 -DNDEBUG -funroll-all-loops
> > > -fexcess-precision=fast
> > > CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
> > compiler
> > > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> > > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1,
> > V10.1.168
> > > CUDA compiler
> > >
> >
> flags:-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_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;;;
> > > ;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> > > CUDA driver:        10.20
> > > CUDA runtime:       N/A
> > >
> > > NOTE: Detection of GPUs failed. The API reported:
> > >        unknown error
> > >        GROMACS cannot run tasks on a GPU.
> > >
> > > Does anyone have any suggestions?
> > > Thanks in advance
> > > Stefano
> > >
> > >
> > >
> > --
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>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
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