Terminology

absolute path: The full path to a file, e.g., /example/foo/bar.txt. An absolute path should always start with /. As opposed to a relative path.
build: See compile.
build directory: A directory where build configuration settings are stored, and where intermediate build files like object files, module files, and libraries are stored.
checkpoint file: See restart file.
compile: Generating an executable program from source code (which is in a plain-text format).
dependencies: The software libraries that are needed to compile GCHP. These include HDF5, NetCDF, and ESMF. See Software Requirements for a complete list.
environment: The software packages and software configuration that are active in your current terminal or script. In Linux, the $HOME/.bashrc script performs automatic configuration when your terminal starts. You can manually configure your environment by running commands like source path_to_a_script or with tools like TCL or LMod for modulefiles. Software containers are effectively a prepackaged operating system + software + environment.
gridded component: A formal model component. MAPL organizes model components with a tree structure, and facilitates component interconnections.
HISTORY: The MAPL gridded component that handles model output. All GCHP output diagnostics are facilitated by HISTORY.
relative path: The path to a file relative to the current working directory. For example, the relative path to /example/foo/bar.txt if your current working directory is /example is foo/bar.txt. As opposed to an absolute path.
restart file: A NetCDF file with initial conditions for a simulation. Also called a checkpoint file in GCHP.
run directory: The working directory for a GEOS-Chem simulation. A run directory houses the simulation’s configuration files, the output directory (OutputDir), and input files/links such as restart files or input data directories.
script: A file that scripts a sequence of commands. Typically a bash that is written to execute a sequence of commands.
software environment: See environment.
stretched-grid: A cubed-sphere grid that is “stretched” to enhance the grid resolution in a region.
target face: The face of a stretched-grid that is refined. The target face is centered on the target point.
terminal: A command-line.