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Compilation Database Generation

Goal

To analyze a complete project, you need a compilation database containing all the compiler instructions for its source files. In this guide, we walk you through generating a compile_commands.json file , demonstrated with a Fortran open source project.

Getting ready​

For this demonstration, we will use the Fortran implementation of the Himeno benchmark, a Poisson equation solver. Start by cloning the repository:

git clone https://github.com/codee-com/codee-demos.git

Navigate to the source code directory:

cd codee-demos/Fortran/Himeno

Tools for generating compile_commands.json files​

CMake (meta-build system) and Bear (recommended) are the two most common tools for generating compile_commands.json files.

See all the options: Alternatives to Bear

Warning

Ensure you are using the bear tool distributed with Codee, not other installations of bear, in order to take advantage of its enhanced support for compilers (e.g. GNU, LLVM, Intel, AMD, Nvidia, Cray) and compiler wrappers (e.g. MPI wrappers in supercomputers, Microsoft wrappers).

The recommended way of generating the compilation database is to use bear, which comes bundled with Codee packages. bear is able to intercept the compiler calls made by your build system in order to generate the compile_commands.json file. To use it you only need to prepend bear -- to your typical build command.

To generate it for the Himeno project copy the following command:

bear -- make

Since Himeno is a single-file project, the compilation database will have a single entry:

compile_commands.json
[
  {
    "arguments": [
      "/usr/bin/gfortran",
      "-c",
      "-O3",
      "-I",
      "/usr/include",
      "-I",
      ".",
      "-o",
      "himeno",
      "himeno.f90"
    ],
    "directory": "/home/user/codee-demos/Fortran/Himeno",
    "file": "/home/user/codee-demos/Fortran/Himeno/himeno.f90",
    "output": "/home/user/codee-demos/Fortran/Himeno/himeno"
  }
]
New feature

Running codee commands with the additional --db codee.db flag enables Incremental Static Analysis. This reduces runtime by storing analysis results and reusing them in subsequent analysis, reanalyzing only the source code that has changed.

Now you can use the JSON generated to substitute the compilation command in the Codee invocation. For example:

Codee command
codee checks --check-id PWR069 -p compile_commands.json --db codee.db
Codee output
Date: 2026-03-25  Codee version: 2026.1 License type: Team

Searching Incremental Static Analysis database... Enabled

[1/1] himeno.f90 ... Done

QUALITY CHECKS REPORT

himeno.f90:137:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
himeno.f90:165:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
himeno.f90:224:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
himeno.f90:256:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
himeno.f90:276:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module

OPTIMIZATION CHECKS REPORT

No actionable items were found

SUGGESTIONS

  Use --check-id and --verbose to focus on specific subsets of checkers, e.g.:
        codee checks --check-id PWR069 --verbose -p compile_commands.json --db codee.db

1 built file (0 results taken from cache), 0 dependencies (0 reused from cache)
1 target file, 7 functions, 5 loops, 214 SLOCs successfully analyzed (5 checkers) and 0 non-analyzed files in 351 ms

Using CMake (alternative option)​

Warning

Ensure you are using CMake version 3.5 or higher.

As an alternative, CMake has its own way of obtaining the compile_commands.json file.

Add -DCMAKE_EXPORT_COMPILE_COMMANDS=ON to your usual CMake invocation; for instance:

cmake . -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -G "Ninja" -B build

The compile_commands.json file will be now stored in the build/ directory and it will look like this:

compile_commands.json
[
{
  "directory": "/home/user/codee-demos/Fortran/Himeno/build",
  "command": "/usr/bin/gfortran -c /home/user/codee-demos/Fortran/Himeno/himeno.f90 -o CMakeFiles/himeno.dir/himeno.f90.o",
  "file": "/home/user/codee-demos/Fortran/Himeno/himeno.f90",
  "output": "CMakeFiles/himeno.dir/himeno.f90.o"
}
]

Now you can use the JSON generated to substitute the compilation command in the Codee invocation. For example:

Codee command
codee checks --check-id PWR069 -p build/compile_commands.json --db codee.db
Codee output
Date: 2026-03-25 Codee version: 2026.1 License type: Team

Searching Incremental Static Analysis database... Enabled

[1/1] /home/user/codee-demos/Fortran/Himeno/himeno.f90 ... Done

QUALITY CHECKS REPORT

/home/user/codee-demos/Fortran/Himeno/himeno.f90:137:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
/home/user/codee-demos/Fortran/Himeno/himeno.f90:165:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
/home/user/codee-demos/Fortran/Himeno/himeno.f90:224:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
/home/user/codee-demos/Fortran/Himeno/himeno.f90:256:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module
/home/user/codee-demos/Fortran/Himeno/himeno.f90:276:1 [PWR069] (level: L2): Use the keyword only to explicitly state what to import from a module

OPTIMIZATION CHECKS REPORT

No actionable items were found

SUGGESTIONS

  Use --check-id and --verbose to focus on specific subsets of checkers, e.g.:
        codee checks --check-id PWR069 --verbose -p build/compile_commands.json --db codee.db

1 built file (0 results taken from cache), 0 dependencies (0 reused from cache)
1 target file, 7 functions, 5 loops, 214 SLOCs successfully analyzed (5 checkers) and 0 non-analyzed files in 337 ms
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