Let's break down your two distinct debugging problems and walk through actionable solutions for each.

Issue 1: Missing Source Files When Debugging via gdbserver + CLion #

The root cause here is usually either incomplete debug symbols in your Bazel-built binary, or CLion failing to map Bazel's sandboxed source paths to your local filesystem. Here's how to fix it:

• Generate full debug symbols: While -c dbg enables debug mode, you can enforce more granular source-level debug info by adding these flags to your Bazel command:

  bazel run -c dbg --copt=-g3 --copt=-O0 --run_under="gdbserver localhost:9999" //your:target
  

  -g3 includes all debug details, and -O0 disables optimizations—critical for smooth, predictable debugging.

• Map Bazel sandbox paths to local sources: Bazel copies sources into a temporary sandbox during builds, which CLion might not recognize automatically. Fix this:

  1. Open CLion's Settings > Build, Execution, Deployment > Debugger > Source Paths.
  2. Click + to add a new path mapping.
  3. For the Remote path, enter the sandbox path for your Python sources (check Bazel's build logs—this will look like /tmp/bazel-<random-hash>/external/python2_7).
  4. For the Local path, select your actual local Python 2.7 source directory.

• Verify debug symbols exist: Run file /path/to/your/bazel/binary and confirm the output includes "with debug_info". If not, double-check your Bazel build flags and Python compilation setup.

Issue 2: undefined symbol: _Py_RefTotal Error When Debugging via CLion's Bazel Run Debug #

This error occurs because _Py_RefTotal is a debug-only internal Python symbol—it only exists in Python builds compiled with debug mode enabled. Here's how to resolve it:

• Recompile Python 2.7 with debug support: If you originally built Python without debug flags, rebuild it with:

  ./configure --enable-shared --with-pydebug --prefix=/path/to/your/custom/python/install
  make && make install
  

  The --with-pydebug flag enables debug-specific symbols like _Py_RefTotal that your debug build is trying to reference.

• Confirm the symbol is exported: After recompiling, verify _Py_RefTotal exists in your shared library:

  nm -D /path/to/your/custom/python/install/lib/libpython2.7.so | grep _Py_RefTotal
  

  You should see output like 00000000001eXXXX D _Py_RefTotal (the D means it's a defined, exported symbol).

• Force Bazel to link your custom debug Python: Update your Bazel BUILD file to explicitly target your debug Python library and set the correct rpath:

  cc_binary(
      name = "your_target",
      srcs = ["your_source.cc"],
      deps = [...],
      linkopts = [
          "-L/path/to/your/custom/python/install/lib",
          "-lpython2.7",
          "-Wl,-rpath=/path/to/your/custom/python/install/lib",
      ],
      includes = ["/path/to/your/custom/python/install/include/python2.7"],
  )
  

• Fix CLion's debug environment variables: Sometimes CLion overrides LD_LIBRARY_PATH in debug mode. Add your Python library path to your Run/Debug configuration:

  1. Open your debug configuration in CLion.
  2. Under Environment Variables, add LD_LIBRARY_PATH=/path/to/your/custom/python/install/lib:$LD_LIBRARY_PATH.

Final Checks #

After applying these steps:

1. Rebuild your Bazel target with the updated flags.
2. Test both debugging workflows again to confirm the issues are resolved.

内容的提问来源于stack exchange，提问作者Eric Cousineau