Merge pull request #382 from dilawar/chamcham

Maintenance release 3.1.5

Author: upibhalla

.travis/travis_prepare_linux.sh

@@ -25,7 +25,7 @@ apt-get install -qq libhdf5-serial-dev
 apt-get install -qq make cmake
 apt-get install -qq python-numpy python-matplotlib python-networkx python-pip
 apt-get install -qq python3-numpy python3-matplotlib python3-dev
-apt-get install -qq libboost-all-dev
+apt-get install -qq libboost-all-dev liblapack-dev libblas-dev
 apt-get install -qq libgsl0-dev
 apt-get install -qq python-pip python3-pip
 apt-get install -qq libgraphviz-dev

CMakeLists.txt

@@ -1,17 +1,6 @@
 set(CMAKE_LEGACY_CYGWIN_WIN32 0)
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
-
-
-project(pymoose)
-
-if(COMMAND cmake_policy)
-    cmake_policy(SET CMP0003 NEW)
-    cmake_policy(SET CMP0004 NEW)
-    if(POLICY CMP0050)
-        cmake_policy(SET CMP0050 OLD)
-    endif(POLICY CMP0050)
-endif(COMMAND cmake_policy)
-
+cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
+project(MOOSE)
 
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
 include(CheckCXXCompiler.cmake)
@@ -34,7 +23,7 @@ endif()
 # If from command line, version info is not passed, use the git to generate a
 # version file. If GIT fails, use the previous known version.
 if(NOT VERSION_MOOSE)
-    set(VERSION_MOOSE "3.1.3-${GIT_HEAD}")
+    set(VERSION_MOOSE "3.1.5-${GIT_HEAD}")
 endif()
 
 add_definitions( -DMOOSE_VERSION="${VERSION_MOOSE}")
@@ -91,9 +80,10 @@ endif()
 option(DEBUG "Build with debug support" OFF)
 option(GPROF "Build for profiling using gprof" OFF)
 option(ENABLE_UNIT_TESTS "Enable unit tests (DEBUG should also be ON)" OFF)
+option(WITH_PYTHON "Build native python extension" ON)
 option(WITH_MPI  "Enable Openmpi support" OFF)
 option(WITH_BOOST "Use boost library instead of GSL" OFF)
-option(WITH_GSL  "Use gsl-library. Alternative is WITH_BOOST" ON)
+option(WITH_GSL  "Use gsl library. Alternative is WITH_BOOST" ON)
 option(PARALLELIZED_SOLVERS "Use parallel version of GSOLVE. (alpha)" OFF )
 option(PARALLELIZED_CLOCK "High level parallelization of moose::Clock (alpha)" OFF )
 
@@ -366,7 +356,7 @@ if(MACOSX)
         ${SYSTEM_SHARED_LIBS}
         ${CMAKE_DL_LIBS}
         )
-ELSE(MACOSX)
+else(MACOSX)
     target_link_libraries(libmoose
         "-Wl,--whole-archive"
         ${MOOSE_LIBRARIES}
@@ -384,8 +374,15 @@ endif( WITH_BOOST )
 
 
 ######################### BUILD PYMOOSE ########################################
-# This target is built by pymoose/CMakeLists.txt file.
-add_subdirectory( pymoose )
+# Root of all python module.
+if(WITH_PYTHON)
+    # find_package(Python3 COMPONENTS Interpreter Development)
+    set(Python_ADDITIONAL_VERSIONS 2.7)
+    find_package(PythonInterp 3.4)
+    set(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
+    set(PYTHON_INCLUDE_DIRS ${Python3_INCLUDE_DIRS})
+    add_subdirectory(pymoose)
+endif()
 
 # always override debian default installation directory. It will be installed in
 # site-packages instead of dist-packages.

cmake_modules/FindNumPy.cmake

@@ -2,59 +2,44 @@ add_definitions(-DPYMOOSE)
 include_directories(../basecode ../msg)
 
 set(PYMOOSE_SRCS
-    moosemodule.cpp
-    vec.cpp
-    mfield.cpp
-    pymooseinit.cpp
-    melement.cpp
-    test_moosemodule.cpp
-    PyRun.cpp
-    )
+  moosemodule.cpp
+  vec.cpp
+  mfield.cpp
+  pymooseinit.cpp
+  melement.cpp
+  test_moosemodule.cpp
+  PyRun.cpp)
 
-# current binary directory using cmake.
-add_library( _moose MODULE ${PYMOOSE_SRCS} )
-set(PYMOOSE_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/python/moose")
+# Python development.
+execute_process(COMMAND ${PYTHON_EXECUTABLE}-config --includes
+  OUTPUT_VARIABLE PYTHON_INCLUDE_FLAGS
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+message(STATUS "Python include paths: ${PYTHON_INCLUDE_FLAGS}")
 
-find_package(PythonInterp REQUIRED)
-execute_process( COMMAND
-    ${PYTHON_EXECUTABLE} -c
-        "import importlib.machinery
-print(importlib.machinery.EXTENSION_SUFFIXES[-1])"
-    OUTPUT_VARIABLE PYTHON_SO_EXTENSION
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-if(NOT PYTHON_SO_EXTENSION)
-    set(PYTHON_SO_EXTENSION ".so")
-endif()
-message( STATUS "Python so extension ${PYTHON_SO_EXTENSION}" )
 
-find_package(NumPy REQUIRED)
-include_directories(${NUMPY_INCLUDE_DIRS})
-add_definitions(-DUSE_NUMPY)
+# Numpy
+execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import numpy; print(numpy.get_include())"
+    OUTPUT_VARIABLE Python_NumPy_INCLUDE_DIRS
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+message(STATUS "NumPy include path: ${Python_NumPy_INCLUDE_DIRS}")
 
+add_library( _moose MODULE ${PYMOOSE_SRCS} )
+set(PYMOOSE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/python/moose")
+add_definitions(-DUSE_NUMPY)
 add_definitions(-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
 
-execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --includes
-    OUTPUT_VARIABLE PYTHON_INCLUDE_FLAGS
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --libs
-    OUTPUT_VARIABLE PYTHON_LIBRARIES
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-message( STATUS "Python include flags: ${PYTHON_INCLUDE_FLAGS}" )
-set_target_properties(_moose PROPERTIES
+target_include_directories(_moose 
+  PRIVATE ${PYTHON_INCLUDE_DIRS} ${Python_NumPy_INCLUDE_DIRS})
+
+set(PYTHON_SO_EXTENSION ".so")
+set_target_properties(_moose PROPERTIES 
     COMPILE_DEFINITIONS "PYMOOSE"
-    COMPILE_FLAGS "${PYTHON_INCLUDE_FLAGS}"
+    COMPILE_FLAGS ${PYTHON_INCLUDE_FLAGS}
     LIBRARY_OUTPUT_DIRECTORY ${PYMOOSE_OUTPUT_DIRECTORY}
     PREFIX ""
     SUFFIX ${PYTHON_SO_EXTENSION}
     )
 
-if(NOT(PYTHON_SO_EXTENSION STREQUAL ""))
-    set_target_properties(_moose PROPERTIES
-    SUFFIX ${PYTHON_SO_EXTENSION})
-endif()
 
 # see issue #80
 if(HDF5_LIBRARY_DIRS)
@@ -92,6 +77,4 @@ add_custom_command(TARGET _moose POST_BUILD
         " Run 'sudo make install' to install it. "
         " "
         "NOTE: Run 'pip uninstall moose' to uninstall moose."
-    VERBATIM
-    )
-
+    VERBATIM)

pymoose/CMakeLists.txt

@@ -44,6 +44,7 @@
 #include <cstring>
 #include <map>
 #include <ctime>
+#include <cstring>
 #include <csignal>
 #include <exception>
 
@@ -75,11 +76,11 @@ using namespace std;
 extern void testSync();
 extern void testAsync();
 
-extern void testSyncArray( 
-        unsigned int size,
-        unsigned int numThreads,
-        unsigned int method 
-        );
+extern void testSyncArray(
+    unsigned int size,
+    unsigned int numThreads,
+    unsigned int method
+);
 
 extern void testShell();
 extern void testScheduling();
@@ -103,16 +104,16 @@ extern void test_moosemodule();
 
 
 extern Id init(
-        int argc, char ** argv, bool& doUnitTests
-        , bool& doRegressionTests, unsigned int& benchmark 
-        );
+    int argc, char ** argv, bool& doUnitTests
+    , bool& doRegressionTests, unsigned int& benchmark
+);
 
 extern void initMsgManagers();
 extern void destroyMsgManagers();
 
 extern void speedTestMultiNodeIntFireNetwork(
-        unsigned int size, unsigned int runsteps 
-        );
+    unsigned int size, unsigned int runsteps
+);
 
 extern void mooseBenchmarks( unsigned int option );
 
@@ -2717,14 +2718,25 @@ int defineDestFinfos(const Cinfo * cinfo)
         // if (name.find("get") == 0 || name.find("set") == 0){
         //     continue;
         // }
-        PyGetSetDef destFieldGetSet;
+        PyGetSetDef destFieldGetSet = {.name = (char*) name.c_str()
+	  , .get=nullptr, .set=nullptr
+          , .doc= (char*) "Destination field"
+	  , .closure=nullptr};
         vec.push_back(destFieldGetSet);
 
-        vec[currIndex].name = strdup(name.c_str());
-        vec[currIndex].doc = (char*) "Destination field";
+        // Dilawar:
+        // strncpy can not write to const char* especially with clang++.
+        // Ref: https://docs.python.org/3/c-api/structures.html#c.PyGetSetDef
+        //vec[currIndex].name = (char*)calloc(name.size() + 1, sizeof(char));
+        //strncpy(vec[currIndex].name,
+        //        const_cast<char*>(name.c_str()),
+        //        name.size());
+        // vec[currIndex].doc = (char*) "Destination field";
+
         vec[currIndex].get = (getter)moose_ObjId_get_destField_attr;
         PyObject *args = PyTuple_New(1);
-        if (!args || !vec[currIndex].name) {
+        if (!args || !vec[currIndex].name)
+        {
             cerr << "moosemodule.cpp: defineDestFinfos: allocation failed\n";
             return 0;
         }
@@ -3225,15 +3237,15 @@ PyMODINIT_FUNC MODINIT(_moose)
 
     clock_t defclasses_end = clock();
 
-    LOG( moose::info, "`Time to define moose classes:" 
-            << (defclasses_end - defclasses_start) * 1.0 /CLOCKS_PER_SEC
+    LOG( moose::info, "`Time to define moose classes:"
+         << (defclasses_end - defclasses_start) * 1.0 /CLOCKS_PER_SEC
        );
 
     PyGILState_Release(gstate);
     clock_t modinit_end = clock();
 
-    LOG( moose::info, "`Time to initialize module:" 
-            << (modinit_end - modinit_start) * 1.0 /CLOCKS_PER_SEC 
+    LOG( moose::info, "`Time to initialize module:"
+         << (modinit_end - modinit_start) * 1.0 /CLOCKS_PER_SEC
        );
 
     if (doUnitTests)