upgrade emsdk to 3.1.37 (#15817)

### Description
upgrade emsdk to 3.1.37

WIP branch to debug the mystery memory issue in web assembly
multi-thread build.

Author: fs-eire

Diff for: .gitmodules

@@ -10,7 +10,7 @@
 [submodule "cmake/external/emsdk"]
 	path = cmake/external/emsdk
 	url = https://github.com/emscripten-core/emsdk.git
-	branch = 3.1.32
+	branch = 3.1.37
 [submodule "cmake/external/onnxruntime-extensions"]
 	path = cmake/external/onnxruntime-extensions
 	url = https://github.com/microsoft/onnxruntime-extensions.git

Diff for: cgmanifests/generated/cgmanifest.json

@@ -78,6 +78,56 @@
         "comments": "manylinux dependency LIBXCRYPT"
       }
     },
+    {
+      "component": {
+        "type": "git",
+        "git": {
+          "commitHash": "d10b27fe37736d2944630ecd7557cefa95cf87c9",
+          "repositoryUrl": "https://gitlab.com/libeigen/eigen.git"
+        },
+        "comments": "git submodule at cmake/external/eigen"
+      }
+    },
+    {
+      "component": {
+        "type": "git",
+        "git": {
+          "commitHash": "b113f24842c6e97fe3e352084db09a6e278593ae",
+          "repositoryUrl": "https://github.com/emscripten-core/emsdk.git"
+        },
+        "comments": "git submodule at cmake/external/emsdk"
+      }
+    },
+    {
+      "component": {
+        "type": "git",
+        "git": {
+          "commitHash": "7a2ed51a6b682a83e345ff49fc4cfd7ca47550db",
+          "repositoryUrl": "https://github.com/google/libprotobuf-mutator.git"
+        },
+        "comments": "git submodule at cmake/external/libprotobuf-mutator"
+      }
+    },
+    {
+      "component": {
+        "type": "git",
+        "git": {
+          "commitHash": "9b7bca2a723ff94edcd007d93b5d0cf1838591dc",
+          "repositoryUrl": "https://github.com/onnx/onnx.git"
+        },
+        "comments": "git submodule at cmake/external/onnx"
+      }
+    },
+    {
+      "component": {
+        "type": "git",
+        "git": {
+          "commitHash": "81e7799c69044c745239202085eb0a98f102937b",
+          "repositoryUrl": "https://github.com/microsoft/onnxruntime-extensions.git"
+        },
+        "comments": "git submodule at cmake/external/onnxruntime-extensions"
+      }
+    },
     {
       "component": {
         "type": "git",

Diff for: cmake/adjust_global_compile_flags.cmake

@@ -51,10 +51,8 @@ if (onnxruntime_BUILD_WEBASSEMBLY)
 
   # Build WebAssembly with multi-threads support.
   if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-    string(APPEND CMAKE_C_FLAGS " -pthread")
-    string(APPEND CMAKE_CXX_FLAGS " -pthread")
-    string(APPEND CMAKE_C_FLAGS " -s USE_PTHREADS=1 -Wno-pthreads-mem-growth")
-    string(APPEND CMAKE_CXX_FLAGS " -s USE_PTHREADS=1 -Wno-pthreads-mem-growth")
+    string(APPEND CMAKE_C_FLAGS " -pthread -Wno-pthreads-mem-growth")
+    string(APPEND CMAKE_CXX_FLAGS " -pthread -Wno-pthreads-mem-growth")
   endif()
 endif()
 

Diff for: cmake/external/emsdk

@@ -848,13 +848,20 @@ if (onnxruntime_ENABLE_TRAINING_TORCH_INTEROP)
 endif()
 if (onnxruntime_BUILD_WEBASSEMBLY)
   set_target_properties(onnxruntime_test_all PROPERTIES LINK_DEPENDS ${TEST_SRC_DIR}/wasm/onnxruntime_test_all_adapter.js)
-  set_target_properties(onnxruntime_test_all PROPERTIES LINK_FLAGS "-s ALLOW_MEMORY_GROWTH=1 --pre-js \"${TEST_SRC_DIR}/wasm/onnxruntime_test_all_adapter.js\" -s \"EXPORTED_RUNTIME_METHODS=['FS']\" --preload-file ${CMAKE_CURRENT_BINARY_DIR}/testdata@/testdata -s EXIT_RUNTIME=1")
+  set_target_properties(onnxruntime_test_all PROPERTIES LINK_FLAGS "-s STACK_SIZE=5242880 -s ALLOW_MEMORY_GROWTH=1 --pre-js \"${TEST_SRC_DIR}/wasm/onnxruntime_test_all_adapter.js\" -s \"EXPORTED_RUNTIME_METHODS=['FS']\" --preload-file ${CMAKE_CURRENT_BINARY_DIR}/testdata@/testdata -s EXIT_RUNTIME=1 -s DEMANGLE_SUPPORT=1")
   if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-    set_property(TARGET onnxruntime_test_all APPEND_STRING PROPERTY LINK_FLAGS " -s USE_PTHREADS=1 -s PROXY_TO_PTHREAD=1")
+    set_property(TARGET onnxruntime_test_all APPEND_STRING PROPERTY LINK_FLAGS " -s DEFAULT_PTHREAD_STACK_SIZE=131072 -s PROXY_TO_PTHREAD=1")
   endif()
   if (onnxruntime_USE_JSEP)
     set_property(TARGET onnxruntime_test_all APPEND_STRING PROPERTY LINK_FLAGS " --pre-js \"${ONNXRUNTIME_ROOT}/wasm/js_internal_api.js\"")
   endif()
+
+  ###
+  ### if you want to investigate or debug a test failure in onnxruntime_test_all, replace the following line.
+  ### those flags slow down the CI test significantly, so we don't use them by default.
+  ###
+  #   set_property(TARGET onnxruntime_test_all APPEND_STRING PROPERTY LINK_FLAGS " -s ASSERTIONS=2 -s SAFE_HEAP=1 -s STACK_OVERFLOW_CHECK=2")
+  set_property(TARGET onnxruntime_test_all APPEND_STRING PROPERTY LINK_FLAGS " -s ASSERTIONS=0 -s SAFE_HEAP=0 -s STACK_OVERFLOW_CHECK=1")
 endif()
 
 if (onnxruntime_ENABLE_ATEN)
@@ -1005,7 +1012,7 @@ if(${CMAKE_SYSTEM_NAME} STREQUAL "iOS")
 endif()
 if (onnxruntime_BUILD_WEBASSEMBLY)
   if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-    set_target_properties(onnx_test_runner PROPERTIES LINK_FLAGS "-s NODERAWFS=1 -s ALLOW_MEMORY_GROWTH=1 -s USE_PTHREADS=1 -s PROXY_TO_PTHREAD=1 -s EXIT_RUNTIME=1")
+    set_target_properties(onnx_test_runner PROPERTIES LINK_FLAGS "-s NODERAWFS=1 -s ALLOW_MEMORY_GROWTH=1 -s PROXY_TO_PTHREAD=1 -s EXIT_RUNTIME=1")
   else()
     set_target_properties(onnx_test_runner PROPERTIES LINK_FLAGS "-s NODERAWFS=1 -s ALLOW_MEMORY_GROWTH=1")
   endif()
@@ -1349,7 +1356,7 @@ if (NOT onnxruntime_ENABLE_TRAINING_TORCH_INTEROP)
   set_target_properties(onnxruntime_mlas_test PROPERTIES FOLDER "ONNXRuntimeTest")
   if (onnxruntime_BUILD_WEBASSEMBLY)
     if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-      set_target_properties(onnxruntime_mlas_test PROPERTIES LINK_FLAGS "-s ALLOW_MEMORY_GROWTH=1 -s USE_PTHREADS=1 -s PROXY_TO_PTHREAD=1 -s EXIT_RUNTIME=1")
+      set_target_properties(onnxruntime_mlas_test PROPERTIES LINK_FLAGS "-s ALLOW_MEMORY_GROWTH=1 -s PROXY_TO_PTHREAD=1 -s EXIT_RUNTIME=1")
     else()
       set_target_properties(onnxruntime_mlas_test PROPERTIES LINK_FLAGS "-s ALLOW_MEMORY_GROWTH=1")
     endif()

Diff for: cmake/onnxruntime_unittests.cmake

@@ -242,7 +242,7 @@ else()
     target_link_options(onnxruntime_webassembly PRIVATE
       "SHELL:-s ASSERTIONS=2"
       "SHELL:-s SAFE_HEAP=1"
-      "SHELL:-s STACK_OVERFLOW_CHECK=1"
+      "SHELL:-s STACK_OVERFLOW_CHECK=2"
       "SHELL:-s DEMANGLE_SUPPORT=1"
     )
   else()
@@ -265,7 +265,7 @@ else()
   if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
     target_link_options(onnxruntime_webassembly PRIVATE
       "SHELL:-s EXPORT_NAME=ortWasmThreaded"
-      "SHELL:-s USE_PTHREADS=1"
+      "SHELL:-s DEFAULT_PTHREAD_STACK_SIZE=131072"
     )
     if (onnxruntime_ENABLE_WEBASSEMBLY_SIMD)
       set_target_properties(onnxruntime_webassembly PROPERTIES OUTPUT_NAME "ort-wasm-simd-threaded")

Diff for: cmake/onnxruntime_webassembly.cmake

@@ -191,8 +191,26 @@ class PosixThread : public EnvThread {
         auto [err_no, err_msg] = GetSystemError();
         ORT_THROW("pthread_attr_init failed, error code: ", err_no, " error msg: ", err_msg);
       }
-      if (thread_options.stack_size > 0) {
-        s = pthread_attr_setstacksize(&attr, thread_options.stack_size);
+
+      size_t stack_size = thread_options.stack_size;
+#if defined(__wasm__)
+      // emscripten 3.1.37 has a bug which does not take build flags 'STACK_SIZE' or 'DEFAULT_PTHREAD_STACK_SIZE'.
+      // the pthread stack size will always be 64kB, which is insufficient to run some kernels.
+      // we set the stack_size to a bigger value
+      //
+      // https://github.com/emscripten-core/emscripten/issues/19302
+      //
+      // TODO: once this issue is fixed by emscripten's new release, remove this code.
+      //       future changes to DEFAULT_PTHREAD_STACK_SIZE will be in the following files
+      //       - cmake/onnxruntime_unittests.cmake (target onnxruntime_test_all)
+      //       - cmake/onnxruntime_webassembly.cmake (target onnxruntime_webassembly)
+      //
+      if (stack_size == 0) {
+        stack_size = 131072;
+      }
+#endif
+      if (stack_size > 0) {
+        s = pthread_attr_setstacksize(&attr, stack_size);
         if (s != 0) {
           auto [err_no, err_msg] = GetSystemError();
           ORT_THROW("pthread_attr_setstacksize failed, error code: ", err_no, " error msg: ", err_msg);

Diff for: onnxruntime/core/platform/posix/env.cc

@@ -396,7 +396,7 @@ def convert_arg_line_to_args(self, arg_line):
     # WebAssembly build
     parser.add_argument("--build_wasm", action="store_true", help="Build for WebAssembly")
     parser.add_argument("--build_wasm_static_lib", action="store_true", help="Build for WebAssembly static library")
-    parser.add_argument("--emsdk_version", default="3.1.19", help="Specify version of emsdk")
+    parser.add_argument("--emsdk_version", default="3.1.37", help="Specify version of emsdk")
 
     parser.add_argument("--enable_wasm_simd", action="store_true", help="Enable WebAssembly SIMD")
     parser.add_argument("--enable_wasm_threads", action="store_true", help="Enable WebAssembly multi-threads support")
@@ -1245,6 +1245,9 @@ def generate_build_tree(
             add_default_definition(emscripten_settings, "MALLOC", args.wasm_malloc)
         add_default_definition(emscripten_settings, "MALLOC", "dlmalloc")
 
+        # set -s STACK_SIZE=5242880
+        add_default_definition(emscripten_settings, "STACK_SIZE", "5242880")
+
         if emscripten_settings:
             cmake_args += [f"-Donnxruntime_EMSCRIPTEN_SETTINGS={';'.join(emscripten_settings)}"]
 

Diff for: tools/ci_build/build.py

@@ -81,7 +81,7 @@ stages:
     parameters:
       CommitOverride: true
       BuildConfig: 'Release'
-      ExtraBuildArgs: '--skip_tests --enable_wasm_api_exception_catching --disable_rtti --use_extensions --cmake_extra_defines onnxruntime_WEBASSEMBLY_DEFAULT_EXTENSION_FLAGS=ON ${{ parameters.ExtraBuildArgs }}'
+      ExtraBuildArgs: '--target onnxruntime_webassembly --skip_tests --enable_wasm_api_exception_catching --disable_rtti --use_extensions --cmake_extra_defines onnxruntime_WEBASSEMBLY_DEFAULT_EXTENSION_FLAGS=ON ${{ parameters.ExtraBuildArgs }}'
       PoolName: ${{ parameters.PoolName }}
       BuildJsep: ${{ parameters.BuildJsep }}
 

Diff for: tools/ci_build/github/azure-pipelines/templates/web-ci.yml

@@ -33,7 +33,7 @@ jobs:
   variables:
     EnvSetupScript: setup_env.bat
     buildArch: x64
-    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --cmake_generator "MinGW Makefiles" --build_wasm --use_xnnpack --emsdk_version releases-upstream-4c3772879a04140298c3abde90962d5567b5e2fc-64bit ${{ parameters.ExtraBuildArgs }}'
+    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --cmake_generator "MinGW Makefiles" --build_wasm --use_xnnpack --emsdk_version releases-7c905cfc1ca6699f6ccb288ae174902cfbdcf0a2-64bit ${{ parameters.ExtraBuildArgs }}'
     runCodesignValidationInjection: false
   timeoutInMinutes: ${{ parameters.TimeoutInMinutes }}
   workspace:
@@ -88,10 +88,10 @@ jobs:
       arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)\wasm_threads --enable_wasm_threads'
       workingDirectory: '$(Build.BinariesDirectory)'
   - task: PythonScript@0
-    displayName: 'Build and test (node) (simd + threads)'
+    displayName: 'Build and test (browser) (simd + threads)'
     inputs:
       scriptPath: '$(Build.SourcesDirectory)\tools\ci_build\build.py'
-      arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)\wasm_simd_threads --enable_wasm_simd --enable_wasm_threads'
+      arguments: '$(CommonBuildArgs) --build_dir $(Build.BinariesDirectory)\wasm_simd_threads --enable_wasm_simd --enable_wasm_threads --wasm_run_tests_in_browser'
       workingDirectory: '$(Build.BinariesDirectory)'
   - task: PythonScript@0
     displayName: 'Build and test (node) (simd)'