From Geos-chem
Revision as of 18:10, 15 October 2019 by Liam (Talk | contribs) (CMake can't find NetCDF. How do I fix this?)

Jump to: navigation, search


What is CMake?

CMake is a program that generates Makefiles. This is an oversimplification, but it describes the essence of CMake.

What versions of GEOS-Chem support CMake?

GEOS-Chem Classic 12.6.0 and later support CMake.

GCHP is expected to support CMake by the end of 2019.


How do I build GEOS-Chem with CMake?

cd <run directory>                       # 1. Go to your run directory
mkdir build                              # 2. Create a build directory
cd build                                 # 3. cd into your build directory
cmake <path to GEOS-Chem's source code>  # 4. Configure GEOS-Chem's build
make -j                                  # 5. Compile GEOS-Chem
make install                             # 6. Install the geos executable in your run directory

See Building GEOS-Chem with CMake more details.

Can I build GEOS-Chem Classic and GCHP in the same environment?

Yes. Because GEOS-Chem Classic's requirements are a subset of GCHP's.

How do I build specific targets?

Pass the target's name as an argument to make. You can build multiple specific targets by passing multiple names.

make <name>

How do I make clean?

You don't need to do this anymore. Now, when you run make, the build system automatically figures out what needs to be recompiled. A "clean" target still exists, but it cleans everything.

If you want to restart the build from scratch, you can do

make clean

How do I continue a build that was terminated before it finished?

Run your make command again. The build system will automatically pick up where it left off.

How do I recompile after I make modifications to the source code?

The build system will automatically figure out what needs to be recompiled when you run make. There is no need to run "cleaning" commands.

How do I clean my build's configuration (i.e. CMake's files)?

Just delete your build directory, and remake it.

rm -rf build
mkdir build
cd build

How do I change GEOS-Chem's build options?

Build options set through CMake variables. You can set CMake variables with -D<name>="<value>" arguments. Note that "ON", "OFF", "TRUE", "FALSE", etc. are valid booleans in CMake.

cmake . -DFOO="BAR"    # set's the variable FOO equal to "BAR"

How do I disable multithreading (i.e. OpenMP)?

cmake . -DOMP=OFF

How do I disable colorized output?


How do I increase the build's verbosity?


How do I build for debugging?

cmake . -DCMAKE_BUILD_TYPE=Debug

I got a CMake error. How do I fix it?

CMake can't find NetCDF. How do I fix this?

If CMake is not finding NetCDF and NetCDF-Fortran on your machine it will print the following error message.

 CMake Error at /usr/share/cmake-3.5/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
       NETCDF_F_LIBRARY: Path to ""
       NETCDF_C_LIBRARY: Path to ""
       NETCDF_C_INCLUDE_DIR: Directory containing "netcdf.h"
       NETCDF_F90_INCLUDE_DIR: Directory containing "netcdf.mod"
       NETCDF_F77_INCLUDE_DIR: Directory containing ""
   Find the directories/files that are listed above.  Specify the directories
   you want CMake to search with the CMAKE_PREFIX_PATH variable (or the
   NetCDF_ROOT environment variable).
 Call Stack (most recent call first):
   /usr/share/cmake-3.5/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
   CMakeScripts/FindNetCDF.cmake:138 (find_package_handle_standard_args)
   CMakeLists.txt:44 (find_package)
 -- Configuring incomplete, errors occurred!
 See also "/stetson-home/bindle/geos-chem/build/CMakeFiles/CMakeOutput.log".

To resolve this, you need to point CMake to your NetCDF or NetCDF-Fortran installation. This can be done by setting the NetCDF_ROOT, NetCDF_C_ROOT, or NetCDF_Fortran environment variables to the directory/directories where NetCDF is installed. The directory/directories where NetCDF is installed should have subdirectories like lib/ and include/.


Can I use Ninja rather than GNU Make?

Yes. You'll need CMake version 3.7 or greater and Kitware's Ninja distribution (for Fortran futures). To use the Ninja generator rather than the Makefile generator, initialize your build directory with cmake -GNinja <path to source code>.

Are the environment variables like FC and ESMF_ROOT necessary?

No, these are just for convenience. You can configure the build with the standard CMAKE_C_COMPILER, CMAKE_CXX_COMPILER, CMAKE_Fortran_COMPILER, and CMAKE_PREFIX_PATH variables, rather than environment variables, if you'd prefer. This means GEOS-Chem doesn't impose environment variable requirements on superprojects.

How do I build GEOS-Chem as a part of an other project?