On Wed, Jul 17, 2019 at 2:13 PM Stefano Guglielmo < stefano.guglie...@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_mu...@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 > > > > > > > > > > > -- > > 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-requ...@gromacs.org. > > > > > -- > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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