[gmx-users] Problem with cuda toolkit

[Mark Abraham]

Hi,

If that was your cmake command, then CUDA_TOOLKIT_ROOT_DIR would not have
that value, and things should have just worked with nvcc where you report
it is located. But using cmake -DCUDA_TOOLKIT_ROOT_DIR=/usr will let normal
path searching find that nvcc is in the bin directory.

Distributions like Fedora can have other issues, like that the binutils
package from the distribution is not yet installed.

Mark

On Wed, 13 Mar 2019 at 06:48 Shahrokh Nasseri (PhD) <NaseriSH at mums.ac.ir>
wrote:

> Hi Dears Gromacs Developers and users
>
> I want to install gromacs in Fedora core 25.
>
> My Computer Specifications are as follows:
>
> (base) [sn at localhost ~]$ which nvcc
> /usr/bin/nvcc
> (base) [sn at localhost ~]$ nvcc --version
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2016 NVIDIA Corporation
> Built on Tue_Jan_10_13:22:03_CST_2017
> Cuda compilation tools, release 8.0, V8.0.61
> (base) [sn at localhost ~]$ nvidia-smi
> Wed Mar 13 08:09:56 2019
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 378.13                 Driver Version: 378.13
>     |
>
> |-------------------------------+----------------------+----------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute
> M. |
>
> |===============================+======================+======================|
> |   0  GeForce GTX 650 Ti  Off  | 0000:01:00.0     N/A |
> N/A |
> | 20%   32C    P8    N/A /  N/A |    220MiB /   980MiB |     N/A
> Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
> +-----------------------------------------------------------------------------+
> | Processes:                                                       GPU
> Memory |
> |  GPU       PID  Type  Process name                               Usage
>     |
>
> |=============================================================================|
> |    0                  Not Supported
>    |
>
> +-----------------------------------------------------------------------------+
> (base) [sn at localhost ~]$
>
> For installation, I enter the following commands:
> (base) [sn at localhost ~]$ wget
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.1.tar.gz
> ...
> 2019-03-12 18:17:18 (308 KB/s) - ‘gromacs-2019.1.tar.gz’ saved [33435278]
> (base) [sn at localhost ~]$ tar -xzf gromacs-2019.1.tar.gz
> (base) [sn at localhost ~]$ mv gromacs-2019.1.tar.gz gromacs-2019.1
> (base) [sn at localhost ~]$ cd ./gromacs-2019.1/
> (base) [sn at localhost gromacs-2019.1]$ cmake --version
> cmake version 3.6.2
>
> (base) [sn at localhost gromacs-2019.1]$ mkdir build
> (base) [sn at localhost gromacs-2019.1]$ mkdir bin
> (base) [sn at localhost gromacs-2019.1]$ cd build/
> (base) [sn at localhost build]$ ccmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON
> ...
>                                                      Page 1 of 1
>  BUILD_SHARED_LIBS                ON
>  BUILD_TESTING                    ON
>  CMAKE_BUILD_TYPE                 Release
>  CMAKE_INSTALL_PREFIX             /home/sn/gromacs-2019.1/bin
>  CMAKE_PREFIX_PATH
>  CUDA_TOOLKIT_ROOT_DIR            /usr/bin --------------------------->
> Note: I address to location of nvcc
>  GMXAPI                           OFF
>  GMX_BUILD_MDRUN_ONLY             OFF
>  GMX_CLANG_CUDA                   OFF
>  GMX_DEFAULT_SUFFIX               ON
>  GMX_DOUBLE                       OFF
>  GMX_ENABLE_CCACHE                OFF
>  GMX_EXTERNAL_TNG                 OFF
>  GMX_EXTERNAL_ZLIB                OFF
>  GMX_FFT_LIBRARY                  fftw3
>  GMX_GPU                          ON
>  GMX_HWLOC                        AUTO
>  GMX_MIMIC                        OFF
>  GMX_MPI                          OFF
>  GMX_OPENMP                       ON
>  GMX_QMMM_PROGRAM                 None
>  GMX_SIMD                         AUTO
>  GMX_THREAD_MPI                   ON
>  GMX_USE_OPENCL                   OFF
>  GMX_USE_TNG                      ON
>  GMX_X11                          OFF
>  ImageMagick_EXECUTABLE_DIR      /usr/bin
> ...
> Press [c] to configure
> ...
> I get the following error message:
> ...
>  CMake Error at cmake/gmxManageNvccConfig.cmake:194 (message):
>    CUDA compiler does not seem to be functional.
>  Call Stack (most recent call first):
>    cmake/gmxManageGPU.cmake:204 (include)
>    CMakeLists.txt:590 (gmx_gpu_setup)
>
> How should I define "CUDA_TOOLKIT_ROOT_DIR"?
> Please guide me,
> Shahrokh
>
>
>
>
> Shahrokh Nasseri
>
> Assistant Professor of Medical Physics
>
> Department and Research Center of Medical Physics
>
> Mashhad University of Medical Sciences
>
> Mashhad, Iran
>
> Tel: +98 513 8002328
> Fax: +98 513 8002 320
> e-mail: naserish at mums.ac.ir, shahrokh.nasseri at gmail.com
> --
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