fix: fix torch's pre_hook

cc/CMakeLists.txt

@@ -1,15 +1,25 @@
-cmake_minimum_required(VERSION 3.17)
+cmake_minimum_required(VERSION 3.17...3.21)
 project(Amanda)
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 14 CACHE STRING "The C++ standard to use")
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+set(default_build_type "Release")
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/../cmake/modules)
 list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)
 
 find_package(Python COMPONENTS Interpreter Development NumPy)
 find_package(TensorFlow REQUIRED)
-# find_package(CUDA 9 REQUIRED)
 
 # set necessary flags
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SSE_FLAGS} -march=native -fopenmp -D_GLIBCXX_USE_CXX11_ABI=${TensorFlow_ABI}")

environment.yml

@@ -4,4 +4,4 @@ dependencies:
     - pip>=19.3
     - cudatoolkit=10.0
     - pip:
-        - poetry==1.1.7
+        - poetry==1.1.10

requirements.txt

@@ -1,4 +1,4 @@
-absl-py==0.13.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.7"
+absl-py==0.14.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.7"
 aiofiles==0.7.0; python_version >= "3.6" and python_version < "4.0"
 aiohttp==3.7.4.post0; python_version >= "3.6"
 alabaster==0.7.12; python_version >= "3.6"
@@ -21,7 +21,7 @@ certifi==2021.5.30; python_version >= "3.6" and python_full_version < "3.0.0" or
 cffi==1.14.6; sys_platform == "linux" and python_version >= "3.6"
 cfgv==3.3.1; python_full_version >= "3.6.1"
 chardet==4.0.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
-charset-normalizer==2.0.5; python_full_version >= "3.6.0" and python_version >= "3.6"
+charset-normalizer==2.0.6; python_full_version >= "3.6.0" and python_version >= "3.6"
 click==8.0.1; python_version >= "3.6"
 colorama==0.4.4; platform_system == "Windows" and python_version >= "3.7" and python_full_version >= "3.6.2" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and python_version >= "3.6" and platform_system == "Windows")
 coverage==5.5; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0" and python_version < "4")
@@ -41,7 +41,7 @@ dephell-specifier==0.2.2; python_version >= "3.6"
 dephell-venvs==0.1.18; python_version >= "3.6"
 dephell-versioning==0.1.2; python_version >= "3.6"
 dephell==0.8.3; python_version >= "3.6"
-distlib==0.3.2; python_full_version >= "3.6.1"
+distlib==0.3.3; python_full_version >= "3.6.1"
 docker==5.0.2; python_version >= "3.6"
 dockerpty==0.4.1; python_version >= "3.6"
 docutils==0.17.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
@@ -56,12 +56,11 @@ google-pasta==0.2.0
 googledrivedownloader==0.4; python_version >= "3.6"
 gprof2dot==2021.2.21
 graphviz==0.17; python_version >= "3.6"
-grpcio-tools==1.40.0; python_version >= "3.6"
-grpcio==1.40.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.6"
+grpcio==1.40.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.2.0"
 guppy3==3.1.1; python_version >= "3.6"
 h5py==2.10.0
 html5lib==1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_version >= "3.6" and python_full_version >= "3.5.0"
-identify==2.2.14; python_full_version >= "3.6.1"
+identify==2.2.15; python_full_version >= "3.6.1"
 idna==3.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 imagesize==1.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 immutables==0.16; python_version >= "3.6"
@@ -90,18 +89,18 @@ matplotlib-inline==0.1.3; python_version >= "3.7"
 mccabe==0.6.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 mistune==0.8.4; python_version >= "3.6"
 mmdnn==0.3.1
-more-itertools==8.9.0; python_version >= "3.5"
+more-itertools==8.10.0; python_version >= "3.5"
 moreorless==0.4.0; python_version >= "3.6"
 multidict==5.1.0; python_version >= "3.6"
 mypy-extensions==0.4.3; python_full_version >= "3.6.2" and python_version >= "3.5"
-mypy-protobuf==2.9; python_version >= "3.6"
+mypy-protobuf==2.10; python_version >= "3.6"
 mypy==0.910; python_version >= "3.5"
 networkx==2.6.3; python_version >= "3.7"
 nodeenv==1.6.0; python_full_version >= "3.6.1"
 numba==0.51.2; python_version >= "3.6"
 numpy==1.18.5; python_version >= "3.5"
 onnx==1.10.1
-onnxruntime==1.8.1
+onnxruntime==1.9.0
 opt-einsum==3.3.0; python_version >= "3.7"
 packaging==21.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 pandas==1.1.5; python_full_version >= "3.6.1" and python_version >= "3.6"
@@ -115,7 +114,7 @@ platformdirs==2.3.0; python_version >= "3.6" and python_full_version >= "3.6.2"
 pluggy==1.0.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 pre-commit==2.15.0; python_full_version >= "3.6.1"
 prompt-toolkit==3.0.20; python_full_version >= "3.6.2" and python_version >= "3.7"
-protobuf==3.17.3
+protobuf==3.18.0
 ptyprocess==0.7.0; sys_platform != "win32" and python_version >= "3.7"
 py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 pybind11==2.7.1; (python_version >= "2.7" and python_version < "3.0") or (python_version > "3.0" and python_version < "3.1") or (python_version > "3.1" and python_version < "3.2") or (python_version > "3.2" and python_version < "3.3") or (python_version > "3.3" and python_version < "3.4") or (python_version > "3.4")
@@ -128,15 +127,15 @@ pyparsing==2.4.7; python_version >= "3.7" and python_full_version < "3.0.0" or p
 pytest-dependency==0.5.1
 pytest-forked==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 pytest-profiling==1.7.0
-pytest-xdist==2.3.0; python_version >= "3.6"
+pytest-xdist==2.4.0; python_version >= "3.6"
 pytest==6.2.5; python_version >= "3.6"
 python-dateutil==2.8.2; python_full_version >= "3.6.1" and python_version >= "3.6"
 python-gnupg==0.4.7; python_version >= "3.6"
 pytz==2021.1; python_full_version >= "3.6.1" and python_version >= "3.6"
 pywin32-ctypes==0.2.0; sys_platform == "win32" and python_version >= "3.6"
 pywin32==227; python_version >= "3.6" and sys_platform == "win32"
 pyyaml==5.4.1; python_full_version >= "3.6.1" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
-rdflib==6.0.0; python_version >= "3.7"
+rdflib==6.0.1; python_version >= "3.7"
 readme-renderer==29.0; python_version >= "3.6"
 regex==2021.8.28; python_full_version >= "3.6.2"
 requests-toolbelt==0.9.1; python_version >= "3.6"
@@ -148,7 +147,7 @@ scikit-learn==0.24.2; python_version >= "3.6"
 scipy==1.6.1; python_version >= "3.7"
 secretstorage==3.3.1; sys_platform == "linux" and python_version >= "3.6"
 shellingham==1.4.0; python_version >= "3.6"
-six==1.16.0; python_full_version >= "3.6.1" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6") and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7")
+six==1.16.0; python_version >= "3.6" and python_full_version >= "3.6.1" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6") and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7")
 snowballstemmer==2.1.0; python_version >= "3.6"
 sphinx==4.2.0; python_version >= "3.6"
 sphinxcontrib-applehelp==1.0.2; python_version >= "3.6"
@@ -166,25 +165,25 @@ threadpoolctl==2.2.0; python_version >= "3.6"
 toml==0.10.2; python_full_version >= "3.6.1" and python_version >= "3.5" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0") and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4")
 tomli==1.2.1; python_version >= "3.6" and python_full_version >= "3.6.2"
 tomlkit==0.7.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
-torch-geometric==2.0.0; python_version >= "3.6"
+torch-geometric==2.0.1; python_version >= "3.6"
 torch-scatter @ https://pytorch-geometric.com/whl/torch-1.8.0+cu102/torch_scatter-2.0.8-cp37-cp37m-linux_x86_64.whl ; python_version >= "3.6"
 torch-sparse @ https://pytorch-geometric.com/whl/torch-1.8.0+cu102/torch_sparse-0.6.11-cp37-cp37m-linux_x86_64.whl ; python_version >= "3.6"
 torch==1.8.1; python_full_version >= "3.6.2"
 torchvision==0.9.1
-tox==3.24.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-tqdm==4.62.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
+tox==3.24.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+tqdm==4.62.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 traitlets==5.1.0; python_version >= "3.7"
 twine==3.4.2; python_version >= "3.6"
 typed-ast==1.4.3; python_version < "3.8" and python_full_version >= "3.6.2" and python_version >= "3.5"
 types-filelock==0.1.5
 types-futures==3.3.0; python_version >= "3.6"
 types-protobuf==3.17.4
-types-setuptools==57.0.2
+types-setuptools==57.4.0
 types-six==1.16.1
-types-toml==0.1.5
+types-toml==0.10.0
 typing-extensions==3.10.0.2
-urllib3==1.26.6; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
-virtualenv==20.7.2; python_full_version >= "3.6.1"
+urllib3==1.26.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
+virtualenv==20.8.0; python_full_version >= "3.6.1"
 volatile==2.1.0; python_version >= "3.6"
 watchdog==2.1.5; python_version >= "3.6"
 wcwidth==0.2.5; python_full_version >= "3.6.2" and python_version >= "3.7"

src/amanda/conversion/listener/CMakeLists.txt

@@ -1,17 +1,46 @@
-cmake_minimum_required(VERSION 3.17)
+cmake_minimum_required(VERSION 3.17...3.21)
 project(amanda_pybind)
 
-set(CMAKE_CXX_STANDARD 14)
+include(CMakePrintHelpers)
+
+set(CMAKE_CXX_STANDARD 14 CACHE STRING "The C++ standard to use")
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+find_program(CCACHE_PROGRAM ccache)
+if(CCACHE_PROGRAM)
+    set(CMAKE_CXX_COMPILER_LAUNCHER "${CCACHE_PROGRAM}")
+    set(CMAKE_CUDA_COMPILER_LAUNCHER "${CCACHE_PROGRAM}") # CMake 3.9+
+    cmake_print_variables(CMAKE_CXX_COMPILER_LAUNCHER)
+endif()
+
+set(default_build_type "Release")
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to '${default_build_type}' as none was specified.")
+  set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
+      STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
 
-find_package(Python COMPONENTS Interpreter Development)
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
 find_package(Torch REQUIRED)
 find_package(pybind11 CONFIG)
 
+find_library(TORCH_PYTHON_LIBRARY torch_python PATHS "${TORCH_INSTALL_PREFIX}/lib")
+cmake_print_variables(TORCH_PYTHON_LIBRARY)
+
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
 
 include_directories(SYSTEM ${Python_INCLUDE_DIRS})
 
 pybind11_add_module(amanda_pybind amanda_pybind.cpp)
 target_link_libraries(amanda_pybind PRIVATE ${PYTHON_LIBRARIES})
 target_link_libraries(amanda_pybind PRIVATE ${TORCH_LIBRARIES})
+target_link_libraries(amanda_pybind PRIVATE ${TORCH_PYTHON_LIBRARY})
+
+add_executable(listener_test listener.cpp)
+target_link_libraries(listener_test PRIVATE ${PYTHON_LIBRARIES})
+target_link_libraries(listener_test PRIVATE ${TORCH_LIBRARIES})
+target_link_libraries(listener_test PRIVATE ${TORCH_PYTHON_LIBRARY})

src/amanda/conversion/listener/README.md

@@ -2,8 +2,6 @@
 - `listener\` contains src for pybind listener.
   - build it first
 ```
-mkdir build
-cd build
-cmake -DCMAKE_PREFIX_PATH=`python -c "import torch;print(torch.utils.cmake_prefix_path)"`\;`python -m pybind11 --cmakedir` ..
-make amanda_pybind
+cmake -DCMAKE_PREFIX_PATH=`python -c "import torch;print(torch.utils.cmake_prefix_path)"`\;`python -m pybind11 --cmakedir` -S src/amanda/conversion/listener -B src/amanda/conversion/listener/build
+cmake --build src/amanda/conversion/listener/build
 ```

src/amanda/conversion/listener/function_pre_hook.cpp

@@ -1,111 +1,39 @@
-#include <torch/csrc/python_headers.h>
-#include <torch/csrc/autograd/function_hook.h>
 #include <torch/csrc/autograd/python_cpp_function.h>
-#include <torch/csrc/autograd/python_hook.h>
-#include <torch/csrc/autograd/python_variable.h>
-#include <torch/csrc/autograd/variable.h>
-#include <torch/csrc/autograd/function.h>
-
-#include <torch/torch.h>
+#include <torch/extension.h>
 #include <iostream>
-
 #include <pybind11/pybind11.h>
 #include <pybind11/functional.h>
 
 using torch::autograd::variable_list;
 
-template<class T>
-class amanda_THPPointer {
-public:
-    amanda_THPPointer(): ptr(nullptr) {};
-    explicit amanda_THPPointer(T *ptr) noexcept : ptr(ptr) {};
-    amanda_THPPointer(amanda_THPPointer &&p) noexcept { free(); ptr = p.ptr; p.ptr = nullptr; };
-
-    ~amanda_THPPointer() { free(); };
-    T * get() { return ptr; }
-    const T * get() const { return ptr; }
-    T * release() { T *tmp = ptr; ptr = nullptr; return tmp; }
-    operator T*() { return ptr; }
-    amanda_THPPointer& operator =(T *new_ptr) noexcept { free(); ptr = new_ptr; return *this; }
-    amanda_THPPointer& operator =(amanda_THPPointer &&p) noexcept { free(); ptr = p.ptr; p.ptr = nullptr; return *this; }
-    T * operator ->() { return ptr; }
-    explicit operator bool() const { return ptr != nullptr; }
-
-private:
-    void free() {if (ptr) Py_DECREF(ptr);}
-    T *ptr = nullptr;
-};
-
-PyObject* THPVariableClass = nullptr;
-bool amanda_pybind_init = false;
-
-// auto tensor_module = amanda_THPPointer<PyObject>(PyImport_ImportModule("torch.tensor"));
-// PyObject* THPVariableClass = PyObject_GetAttrString(tensor_module, "Tensor");
-// bool amanda_pybind_init = true;
-
 void init_THPVariableClass()
 {
-    if (amanda_pybind_init) {
-        return ;
-    }
-    else {
-        auto tensor_module = amanda_THPPointer<PyObject>(PyImport_ImportModule("torch.tensor"));
-        THPVariableClass = PyObject_GetAttrString(tensor_module, "Tensor");
-        amanda_pybind_init = true;
-        return ;
-    }
-}
-
-PyObject* amanda_THPVariable_NewWithVar(PyTypeObject* type, torch::autograd::Variable var)
-{
-    PyObject* obj = type->tp_alloc(type, 0);
-    if (obj) {
-        auto v = (THPVariable*) obj;
-        new (&v->cdata) torch::autograd::Variable(std::move(var));
-        torch::autograd::impl::set_pyobj(v->cdata, obj);
-    }
-    return obj;
+    auto tensor_module = THPObjectPtr(PyImport_ImportModule("torch.tensor"));
+    THPVariableClass = PyObject_GetAttrString(tensor_module, "Tensor");
 }
 
-PyObject * amanda_THPVariable_Wrap(torch::autograd::Variable var)
-{
-    if (!var.defined()) {
-        Py_RETURN_NONE;
-    }
-
-    if (auto obj = torch::autograd::impl::pyobj(var)) {
-        Py_INCREF(obj);
-        return obj;
-    }
-    return amanda_THPVariable_NewWithVar((PyTypeObject *)THPVariableClass, std::move(var));
-}
-
-PyObject* amanda_wrap_variables(const variable_list& c_variables)
+static PyObject* amanda_wrap_variables(const variable_list& c_variables)
 {
     size_t num_vars = c_variables.size();
-    amanda_THPPointer<PyObject> tuple(PyTuple_New(num_vars));
+    THPObjectPtr tuple(PyTuple_New(num_vars));
     if (!tuple) throw python_error();
     for (size_t i = 0; i < num_vars; ++i) {
-        amanda_THPPointer<PyObject> var(amanda_THPVariable_Wrap(c_variables[i]));
+        THPObjectPtr var(THPVariable_Wrap(c_variables[i]));
         if (!var) throw python_error();
         PyTuple_SET_ITEM(tuple.get(), i, var.release());
     }
     return tuple.release();
 
 }
 
-inline bool amanda_THPVariable_Check(PyObject *obj)
+static variable_list amanda_unwrap_variables(PyObject *py_variables)
 {
-    return THPVariableClass && PyObject_IsInstance(obj, THPVariableClass);
-}
-
-variable_list amanda_unwrap_variables(PyObject* py_variables)  {
     variable_list results(PyTuple_GET_SIZE(py_variables));
     for (size_t i = 0; i < results.size(); i++) {
         PyObject* item = PyTuple_GET_ITEM(py_variables, i);
         if (item == Py_None) {
             continue;
-        } else if (amanda_THPVariable_Check(item)) {
+        } else if (THPVariable_Check(item)) {
             results[i] = ((THPVariable*)item)->cdata;
         } else {
             // this should never happen, but just in case...
@@ -120,18 +48,25 @@ variable_list amanda_unwrap_variables(PyObject* py_variables)  {
 class AmandaPreHook : public torch::autograd::FunctionPreHook
 {
 public:
-    AmandaPreHook(PyObject* fn): fn_(fn) {}
+    AmandaPreHook(PyObject* fn): fn_(fn) {
+        Py_INCREF(fn_);
+    }
+
+    ~AmandaPreHook()
+    {
+        pybind11::gil_scoped_acquire gil;
+        Py_DECREF(fn_);
+    }
 
     variable_list operator()(const variable_list& _inputs) override
     {
         pybind11::gil_scoped_acquire gil;
         // wrap cpp vector<torch::autograd::Variable> _inputs -> PyObject inputs
-        amanda_THPPointer<PyObject> inputs(amanda_wrap_variables(_inputs));
+        THPObjectPtr inputs(amanda_wrap_variables(_inputs));
         // call python function from cpp as PyObject
-        amanda_THPPointer<PyObject> res(PyObject_CallFunctionObjArgs(fn_, inputs.get(), nullptr));
+        THPObjectPtr res(PyObject_CallFunctionObjArgs(fn_, inputs.get(), nullptr));
         // unwarp PyObject into vector<torch::autograd::Variable>
-        amanda_THPPointer<PyObject> outputs = std::move(res);
-        return amanda_unwrap_variables(outputs.get());
+        return amanda_unwrap_variables(res.get());
     }
 
 protected:
@@ -140,8 +75,6 @@ class AmandaPreHook : public torch::autograd::FunctionPreHook
 
 int amanda_add_pre_hook(const pybind11::object &grad_fn, const pybind11::object & hook)
 {
-    assert(amanda_pybind_init==true);
-
     PyObject *raw_grad_fn = grad_fn.ptr();
     PyObject *raw_hook = hook.ptr();
     torch::autograd::THPCppFunction *cast_grad_fn = (torch::autograd::THPCppFunction *)raw_grad_fn;