Compiling GCHP and creating a run directory are independent steps, and their order doesn’t matter. A small exception is the RUNDIR build option, which controls the behaviour of make install; however, this setting can be reconfigured at any time (e.g., after compiling and creating a run directory).
Here in the User Guide, we describe compiling GCHP before we describe creating a run directory. This is so that conceptually the instructions have a linear flow. The Quickstart Guide uses the opposite ordering to minimize the number of commands.
Another resource for GCHP build instructions is our YouTube tutorial.
There are two steps to building GCHP. The first is configuring your build, which is done with cmake; the second step is compiling, which is done with make.
In the first step (build configuration), cmake finds GCHP’s software dependencies on your system, and you can set build options like enabling/disabling components, setting paths to run directories, picking between debug or speed-optimizing compiler flags, etc. The second step (running make) compiles GCHP according your build configuration.
These instructions assume you have loaded a computing environment that satisfies GCHP’s software requirements You can find instructions for building GCHP’s dependencies yourself in the Spack instructions.
Create a build directory¶
A build directory is the working directory for a “build”. Conceptually, a “build” is a case/instance of you compiling GCHP. A build directory stores configuration files and intermediate files related to the build. These files and generated and used by CMake, Make, and compilers. You can think a build directory like the blueprints for a construction project.
Create a new directory and initialize it as a build directory by running CMake. When you initialize a build directory, the path to the source code is a required argument:
gcuser:~$ cd ~/Code.GCHP gcuser:~/Code.GCHP$ mkdir build # create a new directory gcuser:~/Code.GCHP$ cd build gcuser:~/Code.GCHP/build$ cmake ~/Code.GCHP # initialize the current dir as a build dir -- The Fortran compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- The C compiler identification is GNU 9.2.1 -- Check for working Fortran compiler: /usr/bin/f95 -- Check for working Fortran compiler: /usr/bin/f95 -- works ... -- Configuring done -- Generating done -- Build files have been written to: /src/build gcuser:~/Code.GCHP/build$
If your cmake output is similar to the snippet above, and it says configuring & generating done, then your configuration was successful and you can move on to compiling or modifying build settings. If you got an error, don’t worry, that just means the automatic configuration failed. To fix the error you might need to tweak settings with more cmake commands, or you might need to modify your environment and run cmake again to retry the automatic configuration.
If you want to restart configuring your build from scratch, delete your build directory.
Note that the name and location of your build directory doesn’t matter, but a good
build/, and a good place for it is the top-level of your source code.
Resolving initialization errors¶
If your last step was successful, skip this section.
Even if you got a cmake error, your build directory was initialized. This means from now on, you can check if the configuration is fixed by running
gcuser:~/Code.GCHP/build$ cmake . # "." because the cwd is the build dir
To resolve your errors, you might need to modify your environment (e.g., load different software modules), or give CMake a hint about where some software is installed. Once you identify the problem and make the appropriate update, run cmake . to see if the error is fixed.
To start troubleshooting, read the cmake output in full. It is human-readable, and includes important information about how the build was set up on your system, and specifically what error is preventing a successful configuration (e.g., a dependency that wasn’t found, or a compiler that is broken). To begin troubleshooting you should check that:
check that the compilers are what you expect (e.g., GNU 9.2, Intel 19.1, etc.)
check that dependencies like MPI, HDF5, NetCDF, and ESMF were found
check for obvious errors/incompatibilities in the paths to “Found” dependencies
F2PY and ImageMagick are not required. You can safely ignore warnings about them not being found.
Most errors are caused by one or more of the following issues:
The wrong compilers were chosen. Fix this by explicitly setting the compilers.
The compiler’s version is too old. Fix this by using newer compilers.
A software dependency is missing. Fix this by loading the appropriate software. Some hints:
If HDF5 is missing, does h5cc -show or h5pcc -show work?
If NetCDF is missing, do nc-config --all and nf-config --all work?
If MPI is missing, does mpiexec --help work?
A software dependency is loaded but it wasn’t found automatically. Fix this by pointing CMake to the missing software/files with cmake . -DCMAKE_PREFIX_PATH=/path/to/missing/files.
If ESMF is missing, point CMake to your ESMF install with
Software modules that are not compatible. Fix this by loading compatible modules/dependencies/compilers. Some hints:
This often shows as an error message saying a compiler is “broken” or “doesn’t work”
E.g. incompatibility #1: you’re using GNU compilers but HDF5 is built for Intel compilers
E.g. incompatibility #2: ESMF was compiled for a different compiler, MPI, or HDF5
If you are stumped, don’t hesitate to open an issue on GitHub. Your system administrators might
also be able to help. Be sure to include
CMakeCache.txt from your build directory, as it contains
useful information for troubleshooting.
If you get a CMake error saying “Could not find XXXX” (where XXXX is a dependency like
ESMF, NetCDF, HDF5, etc.), the problem is that CMake can’t automatically find where that library
is installed. You can add custom paths to CMake’s default search list by setting the
For example, if you got an error saying “Could not find ESMF”, and ESMF is installed
/software/ESMF, you would do
gcuser:~/Code.GCHP/build$ cmake . -DCMAKE_PREFIX_PATH=/software/ESMF ... -- Found ESMF: /software/ESMF/include (found version "8.1.0") ... -- Configuring done -- Generating done -- Build files have been written to: /src/build gcuser:~/Code.GCHP/build$
See the next section for details on setting variables like
You can explicitly specify compilers by setting the
variables. If the auto-selected compilers are the wrong ones, create a brand new build directory,
and set these variables before you initialize it. E.g.:
gcuser:~/Code.GCHP/build$ cd .. gcuser:~/Code.GCHP$ rm -rf build # build dir initialized with wrong compilers gcuser:~/Code.GCHP$ mkdir build # make a new build directory gcuser:~/Code.GCHP$ cd build gcuser:~/Code.GCHP/build$ export CC=icc # select "icc" as C compiler gcuser:~/Code.GCHP/build$ export CXX=icpc # select "icpc" as C++ compiler gcuser:~/Code.GCHP/build$ export FC=icc # select "ifort" as Fortran compiler gcuser:~/Code.GCHP/build$ cmake ~/Code.GCHP # initialize new build dir -- The Fortran compiler identification is Intel 126.96.36.19991121 -- The CXX compiler identification is Intel 188.8.131.5291121 -- The C compiler identification is Intel 184.108.40.20691121 ...
Configure your build¶
Build settings are controlled by cmake commands like:
$ cmake . -D<NAME>="<VALUE>"
<NAME> is the name of the setting, and
<VALUE> is the
value you are assigning it. These settings are persistent and saved in your build directory.
You can set multiple variables in the same command, and you can run cmake as many times
as needed to configure your desired settings.
. argument is important. It is the path to your build directory which
No build settings are required. You can find the complete list of GCHP’s build settings here.
The most common setting is
RUNDIR, which lets you specify one or more run directories
to install GCHP to. Here, “install” refers to copying the compiled executable, and some supplemental files
with build settings, to your run directory/directories.
You can update build settings after you compile GCHP. Simply rerun make and (optionally) make install, and the build system will automatically figure out what needs to be recompiled.
Since there are no required build settings, so here, we will stick with the default settings.
You should notice that when you run cmake it ends with:
... -- Configuring done -- Generating done -- Build files have been written to: /src/build
This tells you that the configuration was successful, and that you are ready to compile.
You compile GCHP with:
gcuser:~/Code.GCHP/build$ make -j # -j enables compiling in parallel
You can add
VERBOSE=1 to see all the compiler commands.
If you run out of memory while compiling, restrict the number of processes that can
run concurrently (e.g., use
-j20 to restrict to 20 processes)
Compiling GCHP creates
./bin/gchp (the GCHP executable). You can copy
this executable to your run directory manually, or if you set the RUNDIR build option,
you can do
gcuser:~/Code.GCHP/build$ make install # Requires that RUNDIR build option is set
to copy the executable (and supplemental files) to your run directories.
Now you have compiled GCHP! You can move on to creating a run directory!
You need to recompile GCHP if you update a build setting or modify the source code. With CMake, you do not need to clean before recompiling. The build system automatically figures out which files need to be recompiled (it’s usually a small subset). This is known as incremental compiling.
To recompile GCHP, simply do
gcuser:~/Code.GCHP/build$ make -j # -j enables compiling in parallel
and then optionally, make install.
GNU compilers recompile GCHP faster than Intel compilers. This is because of how gfortran
formats Fortran modules files (
*.mod files). Therefore, if you want to be able to recompile quickly, consider
using GNU compilers.
GCHP build options¶
These are persistent build setting that are set with cmake commands like
$ cmake . -D<NAME>="<VALUE>"
<NAME> is the name of the build setting, and
<VALUE> is the value you
are assigning it. Below is the list of build settings for GCHP.
Paths to run directories where make install installs GCHP. Multiple run directories can be specified by a semicolon separated list. A warning is issues if one of these directories does not look like a run directory.
These paths can be relative paths or absolute paths. Relative paths are interpreted as relative to your build directory.
The build type. Valid values are
RelWithDebInfo. Set this to
Debugif you want to build in debug mode.
Extra directories that CMake will search when it’s looking for dependencies. Directories in
CMAKE_PREFIX_PATHhave the highest precedence when CMake is searching for dependencies. Multiple directories can be specified with a semicolon-separated list.
Compiler options for GEOS-Chem for all build types. Valid values for
Additional compiler options for GEOS-Chem for build type
GEOSChem_Fortran_FLAGS_<COMPILER_ID>, but for HEMCO.
GEOSChem_Fortran_FLAGS_<BUILD_TYPE>_<COMPILER_ID>, but for HEMCO.
Switch to enable/disable the RRTMG component.
Switch to enable/disable OpenMP multithreading. As is standard in CMake (see if documentation) valid values are
1(case-insensitive) and valid false values are their opposites.
RUNDIR, except the directories do not need to be run directories.