I want to debug my c++ code which is a simulation running on remage/Geant4. I need to activate the apptainer container based on the gipert remage-base:latest docker container, which is created by the command apptainer build remage-base_latest.sif docker://gipert/remage-base:latest. My code is compiled by cmake. I create a build folder in my working directory (wd), go inside and use cmake .. and maketo compile my code. Then I start the program with wd/build/Simulation -m run.mac -l.

Now I want to do everything in vscode to use the debugger with breakpoints. For that I wrote a launch.json to run the Simulation in debugging mode using gdb, and a tasks.json to start the apptainer container and compile the code in debugging mode.

launch.json

  "version": "0.2.0",
  "configurations": [
    {
      "type": "cmake",
      "request": "launch",
      "name": "CMake: Configure project",
      "cmakeDebugType": "configure",
      "clean": false,
      "configureAll": false
    },
    {
      "name": "C++ Debugging in Apptainer",
      "type": "cppdbg",
      "request": "launch",
      "program": "${workspaceFolder}/build/MySimulation",
      "args": [
        "-m",
        "${workspaceFolder}/run.mac",
        "-l"
      ],
      "stopAtEntry": false,
      "cwd": "${workspaceFolder}",
      "environment": [],
      "externalConsole": false,
      "MIMode": "gdb",
      "miDebuggerPath": "/usr/bin/gdb",
      "setupCommands": [
        {
          "description": "GDB Pretty Printing",
          "text": "-enable-pretty-printing",
          "ignoreFailures": true
        }
      ],
      "preLaunchTask": "build: cmake & make"
    }
  ]
}

tasks.json

  "version": "2.0.0",
  "tasks": [
    {
      "label": "build: cmake & make",
      "type": "shell",
      "command": "apptainer",
      "args": [
        "exec",
        "../../remage02/remage-base.sif",
        "bash",
        "-c",
        "cmake -DCMAKE_BUILD_TYPE:STRING=Debug -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE -DCMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc -DCMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++ --no-warn-unused-cli -S ${workspaceFolder} -B ${workspaceFolder}/build && make -C ${workspaceFolder}/build"
      ],
      "group": {
        "kind": "build",
        "isDefault": true
      },
      "problemMatcher": [
        "$gcc"
      ],
      "detail": "Run CMake and Make in the Apptainer container"
    }
  ]
}

It doesn't work. The code gets compiled, but afterwards an error appears: error while loading shared libraries: libG4run.so: cannot open shared object file: No such file or directory [1] + Done "/usr/bin/gdb" --interpreter=mi --tty=${DbgTerm} 0<"/tmp/Microsoft-MIEngine-In-a0wh0kw5.tvp" 1>"/tmp/Microsoft-MIEngine-Out-0vw3qdd4.4l5"

My guess is that the debugger should run in the apptainer itself, as the libraries were pulled from the apptainer during compilation. I don't think this works with my launch.json. To run gbd in the container, the container itself must contain gbdserver to communicate with vscode via a port. However, I don't want to have to change the gipert docker image.

What are the possibilities to compile c++ code with cmake in an apptainer container and then debug the code with vscode while the apptainer environment is still needed when running the program?