Merge pull request cyclus#1666 from cyclus/fix-python-segfault

Fix Python segmentation fault behavior

.github/workflows/build_test.yml

@@ -70,7 +70,7 @@ jobs:
 
       - name: Cyclus Python Tests
         run: |
-          cd tests && python -m pytest --ignore test_main.py
+          cd tests && python -m pytest
 
       - name: Unit Test Coverage Report
         run: |
@@ -103,4 +103,4 @@ jobs:
     - name: Coveralls Finished
       uses: coverallsapp/github-action@v2
       with:
-        parallel-finished: true
+        parallel-finished: true

CHANGELOG.rst

@@ -46,6 +46,7 @@ Since last release
   quantize, bids that one was not able to fullfill and caused cyclus to crash. (#1552)
 * Resolve deprecation warnings involving <boost/detail/sp_typeinfo.hpp> (#1611)
 * Resolve segmentation faults when calling Cbc (#1614)
+* Resolve segmentation faults when using cyclus via Python (#1666)
 
 
 

cyclus/__init__.py

@@ -1,7 +1,2 @@
-from __future__ import print_function, unicode_literals
-
 __version__ = '1.5.5'
-
-from cyclus.lib import py_import_call_init
-
-py_import_call_init()
+import pymodule, eventhooks, pyinfile

docker/Dockerfile

@@ -134,5 +134,4 @@ RUN cyclus_unit_tests
 
 FROM cyclus-test as cyclus-pytest
 
-RUN cd tests && python -m pytest --ignore test_main.py
-
+RUN cd tests && python -m pytest

src/CMakeLists.txt

@@ -98,6 +98,7 @@ copy_when_diff(
 ###########################################################
 ############# cython configuration ########################
 ###########################################################
+SET(NoCythonLibs ${LIBS})
 if(Cython_FOUND)
     # some setup
     set(cython_include_directories "")
@@ -143,6 +144,28 @@ if(Cython_FOUND)
         IF(NOT "${res_var_c}" STREQUAL "0")
             message(FATAL_ERROR "Cython compilation of ${file} failed!")
         ENDIF()
+
+        ADD_LIBRARY(${name} ${_cc_file})
+        SET(CythonModuleSrc ${CythonModuleSrc} ${_cc_file})
+        SET_TARGET_PROPERTIES(${name} PROPERTIES 
+          OUTPUT_NAME "${name}"
+          PREFIX ""
+          INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib"
+          INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib"
+          )
+        SET(LIBS ${LIBS} ${name})
+
+        TARGET_LINK_LIBRARIES(${name} dl ${NoCythonLibs})
+
+        INSTALL(
+          TARGETS ${name}
+          LIBRARY DESTINATION lib
+          )
+        INSTALL(
+          TARGETS ${name}
+          LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}
+          )
+
         copy_when_diff(${_generated_h} ${_h_file})
         copy_when_diff(${_generated_cc} ${_cc_file})
     endforeach()
@@ -175,6 +198,9 @@ foreach(ccfile ${CYCLUS_COIN_SRC})
 endforeach()
 list(REMOVE_ITEM cc_files ${CMAKE_CURRENT_SOURCE_DIR}/coin_helpers.cc)
 list(REMOVE_ITEM cc_files ${CMAKE_CURRENT_SOURCE_DIR}/prog_translator.cc)
+# The cython modules are built as their own shared libraries
+# We don't want them to be included in libcyclus.so
+list(REMOVE_ITEM cc_files ${CythonModuleSrc})
 
 SET(CYCLUS_CORE_SRC ${CYCLUS_CORE_SRC} ${cc_files})
 

src/pyhooks.cc

@@ -1,10 +1,9 @@
+#include "Python.h"
 #include "pyhooks.h"
 
 #ifdef CYCLUS_WITH_PYTHON
 #include <stdlib.h>
 
-#include "Python.h"
-
 extern "C" {
 #include "eventhooks.h"
 #include "pyinfile.h"
@@ -17,39 +16,58 @@ bool PY_INTERP_INIT = false;
 
 
 void PyAppendInitTab(void) {
-#if PY_MAJOR_VERSION < 3
-  // Not used before Python 3
-#else
-  PyImport_AppendInittab("_cyclus_eventhooks", PyInit_eventhooks);
-  PyImport_AppendInittab("_cyclus_pyinfile", PyInit_pyinfile);
-  PyImport_AppendInittab("_cyclus_pymodule", PyInit_pymodule);
-#endif
+  if (PyImport_AppendInittab("eventhooks", PyInit_eventhooks) == -1) {
+    fprintf(stderr, "Error appending 'eventhooks' to the initialization table\n");
+  }
+
+  if (PyImport_AppendInittab("pyinfile", PyInit_pyinfile) == -1) {
+    fprintf(stderr, "Error appending 'pyinfile' to the initialization table\n");
+  }
+
+  if (PyImport_AppendInittab("pymodule", PyInit_pymodule) == -1) {
+    fprintf(stderr, "Error appending 'pymodule' to the initialization table\n");
+  }
 }
 
 void PyImportInit(void) {
-#if PY_MAJOR_VERSION < 3
-  initeventhooks();
-  initpyinfile();
-  initpymodule();
-#else
-  PyImport_ImportModule("_cyclus_eventhooks");
-  PyImport_ImportModule("_cyclus_pyinfile");
-  PyImport_ImportModule("_cyclus_pymodule");
-#endif
-};
-
+  PyObject* module_eventhooks = PyImport_ImportModule("eventhooks");
+  if (module_eventhooks == NULL) {
+    PyErr_Print(); // Print Python error information
+    fprintf(stderr, "Error importing 'eventhooks' module\n");
+  }
+
+  PyObject* module_pyinfile = PyImport_ImportModule("pyinfile");
+  if (module_pyinfile == NULL) {
+    PyErr_Print();
+    fprintf(stderr, "Error importing 'pyinfile' module\n");
+  }
+
+  PyObject* module_pymodule = PyImport_ImportModule("pymodule");
+  if (module_pymodule == NULL) {
+    PyErr_Print();
+    fprintf(stderr, "Error importing 'pymodule' module\n");
+  }
+}
 
 void PyImportCallInit(void) {
-#if PY_MAJOR_VERSION < 3
-  initeventhooks();
-  initpyinfile();
-  initpymodule();
-#else
-  PyInit_eventhooks();
-  PyInit_pyinfile();
-  PyInit_pymodule();
-#endif
-};
+  PyObject* init_eventhooks = PyInit_eventhooks();
+  if (init_eventhooks == NULL) {
+    PyErr_Print();
+    fprintf(stderr, "Error calling PyInit_eventhooks()\n");
+  }
+
+  PyObject* init_pyinfile = PyInit_pyinfile();
+  if (init_pyinfile == NULL) {
+    PyErr_Print();
+    fprintf(stderr, "Error calling PyInit_pyinfile()\n");
+  }
+
+  PyObject* init_pymodule = PyInit_pymodule();
+  if (init_pymodule == NULL) {
+    PyErr_Print();
+    fprintf(stderr, "Error calling PyInit_pymodule()\n");
+  }
+}
 
 
 void PyStart(void) {