[gmx-users] Problem with cuda toolkit

Shahrokh Nasseri (PhD) NaseriSH at mums.ac.ir
Wed Mar 13 06:48:23 CET 2019

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
(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
 CUDA_TOOLKIT_ROOT_DIR            /usr/bin ---------------------------> Note: I address to location of nvcc
 GMXAPI                           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 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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