Installation of gromacs 2018.1

User discussions
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1

GROMACS version:2018.1
GROMACS modification: no
Here post your question:
When I was using this command in installation of gromacs 2018.1
CMAKE_PREFIX_PATH=/opt/fftw:/opt/gsl cmake … -DCMAKE_INSTALL_PREFIX=/opt/gromacs2018 -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DOUBLE=ON -DGMX_GSL=ON -DGMX_X11=ON -DGMX_GPU=OFF

CMake Error at cmake/ThreadMPI.cmake:65 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
CMakeLists.txt:561 (include)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:103 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:104 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:105 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:106 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:107 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxSetBuildInformation.cmake:95 (gmx_run_cpu_detection)
cmake/gmxSetBuildInformation.cmake:108 (gmx_get_build_cpu_string)
CMakeLists.txt:629 (gmx_set_build_information)

CMake Error at cmake/gmxDetectCpu.cmake:88 (try_compile):
Failed to open

/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeTmp/CMakeLists.txt

Permission denied
Call Stack (most recent call first):
cmake/gmxDetectSimd.cmake:70 (gmx_run_cpu_detection)
cmake/gmxDetectSimd.cmake:155 (gmx_suggest_simd)
cmake/gmxManageSimd.cmake:92 (gmx_detect_simd)
CMakeLists.txt:703 (gmx_manage_simd)

CMake Error at cmake/FindFFTW.cmake:101 (message):
Could not find fftw_plan_r2r_1d in /opt/fftw/lib/libfftw3.a, take a look at
the error message in
/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeError.log to find out
what went wrong. If you are using a static lib (.a) make sure you have
specified all dependencies of fftw3 in FFTW_LIBRARY by hand (e.g.
-DFFTW_LIBRARY=‘/path/to/libfftw3.so;/path/to/libm.so’) !
Call Stack (most recent call first):
cmake/gmxManageFFTLibraries.cmake:86 (find_package)
CMakeLists.txt:727 (include)

– Configuring incomplete, errors occurred!
See also “/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeOutput.log”.
See also “/home/test/gromacs-2018.1/build-avx/CMakeFiles/CMakeError.log”.
CMake Error: Unable to open check cache file for write. /home/test/gromacs-2018.1/build-avx/CMakeFiles/cmake.check_cache
I have already downloaded fftw library before and has gsl library and make is also installed
I have already tried by giving path of fftw library in command also still not working but still showing this error, can’t understand ,pls anyone help me out.
i want to built it with GPU

2

Hi Parul!
The issue is quite clearly stated in your error message: “failed to open file”, “permission denied”. When compiling, cmake is trying to open the CMakeLists files, but doesn’t have the permission to do so. You need to check the permissions in your /home/test folder.

1 Like
3

thankx cathrine i will check it.

4

Hi Cathrine

I have same error here but I dont know how to change permission! can you right here what I have to do with that?

5

This depends on the machine where you are trying to install GROMACS and on your root privileges, that is, it depends on the administrator of the machine you are using, it is not a GROMACS related problem. Where are you installing this? Your machine? HPC?

6

Yes it is on my own machine! Can you please help me to figure this out?

7

This means that you are installing somewhere where you have to be superuser. You can work around this by using the sudo command, but this will most likely give rise to some problems in the future. It is better if you change the installation directory to one in which the normal user has writing privileges, for example a directory in your home folder should do the job.