onnxruntime: fix cuda by patching protobuf

pkgs/by-name/on/onnxruntime/package.nix

@@ -39,6 +39,29 @@ let
 
   cudaArchitecturesString = cudaPackages.flags.cmakeCudaArchitecturesString;
 
+  # While onnxruntime suggests using (3 year-old) protobuf 21.12
+  # https://github.com/microsoft/onnxruntime/blob/v1.23.2/cmake/deps.txt#L40, using a newer
+  # protobuf version is possible.
+  # We still need to patch the nixpkgs protobuf (32.1) to address the following test failure that
+  # occurs when cudaSupport is enabled:
+  # [libprotobuf ERROR /build/source/src/google/protobuf/descriptor_database.cc:642] File already exists in database: onnx/onnx-ml.proto
+  # [libprotobuf FATAL /build/source/src/google/protobuf/descriptor.cc:1986] CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size):
+  # terminate called after throwing an instance of 'google::protobuf::FatalException'
+  #   what():  CHECK failed: GeneratedDatabase()->Add(encoded_file_descriptor, size):
+  #
+  #
+  # Caused by: https://github.com/protocolbuffers/protobuf/commit/8f7aab29b21afb89ea0d6e2efeafd17ca71486a9
+  # Reported upstream: https://github.com/protocolbuffers/protobuf/issues/21542
+  protobuf' = protobuf.overrideAttrs (old: {
+    patches = (old.patches or [ ]) ++ [
+      (fetchpatch {
+        name = "Workaround nvcc bug in message_lite.h";
+        url = "https://raw.githubusercontent.com/conda-forge/protobuf-feedstock/737a13ea0680484c08e8e0ab0144dab82c10c1b3/recipe/patches/0010-Workaround-nvcc-bug-in-message_lite.h.patch";
+        hash = "sha256-joK50Il4mrwIc6zuNW9gDIfOx9LuA4FlusJuzUf9kqI=";
+      })
+    ];
+  });
+
   # TODO: update the following dependencies according to:
   # https://github.com/microsoft/onnxruntime/blob/v<VERSION>/cmake/deps.txt
 
@@ -134,7 +157,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     cmake
     pkg-config
     python3Packages.python
-    protobuf
+    protobuf'
   ]
   ++ lib.optionals pythonSupport (
     with python3Packages;
@@ -247,7 +270,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
     (lib.cmakeFeature "FETCHCONTENT_SOURCE_DIR_SAFEINT" "${safeint-src}")
     (lib.cmakeFeature "FETCHCONTENT_TRY_FIND_PACKAGE_MODE" "ALWAYS")
     # fails to find protoc on darwin, so specify it
-    (lib.cmakeFeature "ONNX_CUSTOM_PROTOC_EXECUTABLE" (lib.getExe protobuf))
+    (lib.cmakeFeature "ONNX_CUSTOM_PROTOC_EXECUTABLE" (lib.getExe protobuf'))
     (lib.cmakeBool "onnxruntime_BUILD_SHARED_LIB" true)
     (lib.cmakeBool "onnxruntime_BUILD_UNIT_TESTS" finalAttrs.doCheck)
     (lib.cmakeBool "onnxruntime_USE_FULL_PROTOBUF" withFullProtobuf)
@@ -351,7 +374,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
 
   passthru = {
     inherit cudaSupport cudaPackages ncclSupport; # for the python module
-    inherit protobuf;
+    protobuf = protobuf';
     tests = lib.optionalAttrs pythonSupport {
       python = python3Packages.onnxruntime;
     };