Question 38058 in Ubuntu Question posted in
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Cmake automatically defaults to gcc-5 – Ubuntu

I was trying to compile amber tools using cmake. I am using ubuntu Ubuntu 16.04.7 LTS with the default gcc version gcc-5 and g++5, and amber tool requires at least gcc-6. I have installed gcc-8 and g++8 and specified it using the CMAKE_C_COMPILER and CMAKE_CXX_COMPILER. The cmake command used is the command below:

cmake $AMBER_PREFIX/amber22_src 
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 
-DCOMPILER=GNU 
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE 
-DDOWNLOAD_MINICONDA=TRUE 
-DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DCMAKE_CXX_COMPILER=/usr/bin/g++-8

Even though the gcc g++ is specified I get the following error:

-- Starting configuration of Amber version 22.0.0...
-- CMake Version: 3.14.0
-- For how to use this build system, please read this wiki:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--     http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Setting C compiler to gcc
-- Setting CXX compiler to g++
-- Setting Fortran compiler to gfortran
-- Amber source not found, only building AmberTools
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- The Fortran compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- 
************************************************************
Error: Amber requires at least g++-6.0
See https://ambermd.org/Installation.php for more info
************************************************************
-- 
CMake Error at cmake/VerifyCompilerConfig.cmake:30 (message):
Call Stack (most recent call first):
  cmake/AmberBuildSystem2ndInit.cmake:30 (include)
  CMakeLists.txt:111 (include)


-- Configuring incomplete, errors occurred!
See also "/media/gpu-1/GPU_1_2TB/Ambertools22/amber22_src/build/CMakeFiles/CMakeOutput.log".
You have changed variables that require your cache to be deleted.
Configure will be re-run and you may have to reset some variables.
The following variables have changed:
CMAKE_C_COMPILER= /usr/bin/gcc-8
CMAKE_CXX_COMPILER= /usr/bin/g++-8

-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    DOWNLOAD_MINICONDA
    MPI


-- Build files have been written to: /media/gpu-1/GPU_1_2TB/Ambertools22/amber22_src/build

If the cmake build report looks OK, you should now do the following:

    make install
    source /media/gpu-1/GPU_1_2TB/Ambertools22/amber22/amber.sh

Thank you

Tags:

2

Answers


  1. 0

    I would not call it a problem of CMake, rather on the way Amber performs the control of the compiler through CMake, which most likely is performed by taking the first compiler that appears from the environment variable $PATH.

    If you would like to compile it anyway, I can suggest two cheap ways:

    • using the update-alternatives package, to change the "system
      default" gcc and g++
    • prepend a path in PATH with export PATH=absolute/path/to/a/folder:$PATH, and in this path put two symbolic links called gcc and g++, that points at
      gcc-8 and g++-8
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  2. 0

    According to this, you are still using existing cache files that you’ve generated before you set the new C and CXX compiler.

    You have changed variables that require your cache to be deleted.
Configure will be re-run and you may have to reset some variables.
The following variables have changed:
CMAKE_C_COMPILER= /usr/bin/gcc-8
CMAKE_CXX_COMPILER= /usr/bin/g++-8

    Based on cmake $AMBER_PREFIX/amber22_src you are running this from your build folder. In general I recommend using the syntax cmake -S[source] -B[build]. Your current working directory should be completely deleted. Once you do that, re-run your cmake command and it should be correctly set.

    If it doesn’t work you can do a sanity check by adding

    set(CMAKE_C_COMPILER [path_to_C])
set(CMAKE_CXX_COMPILER [path_to_CXX])

    BE SURE TO PUT IT AT THE START OF THE CMAKELISTS FILE i.e. before any project() line.

    EDIT: Also have you heard about docker? It’s a great tool for creating special contained environments for using legacy tools.

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