Fix builds on Magnum CI + Eigen3 issues + RPATH issues

1. Builds on Magnum CI are finally working again
2. Users can choose their own Eigen3 installation
3. The run_pcm executable has an RPATH that points to both
   the install tree and the build tree. Other executables that
   are not installed (update_reference_files and unit_tests)
   have an RPATH that points to the build tree.

Author: Roberto Di Remigio

.magnum.yml

@@ -2,13 +2,20 @@ language: cpp
 git:
   submodules: false
 before_install:
-    - sudo apt-get update -y
-    - sudo apt-get install gcc g++ gfortran make cmake cmake-data zlib1g-dev python-dateutil python-pyparsing python-numpy python-matplotlib python-pip python-setuptools python-dev -y
-    - cmake --version
-    - gcc --version
-    - g++ --version
-    - gfortran --version
-    - python --version
+  - DEPS_DIR="${HOME}/deps"
+  - mkdir -p ${DEPS_DIR} && cd ${DEPS_DIR}
+  - sudo apt-get update -y
+  - sudo apt-get install -y gcc g++ gfortran make zlib1g-dev python-dev
+  - mkdir ${DEPS_DIR}/cmake
+  - wget --no-check-certificate https://cmake.org/files/v3.4/cmake-3.4.3-Linux-x86_64.tar.gz
+  - tar --strip-components=1 -xzf cmake-3.4.3-Linux-x86_64.tar.gz -C cmake
+  - export PATH=${DEPS_DIR}/cmake/bin:$PATH
+  - cd -
+  - cmake --version
+  - gcc --version
+  - g++ --version
+  - gfortran --version
+  - python --version
 script:
   - python setup.py --cxx=g++ --cc=gcc --fc=gfortran --type=debug --cmake-options='-Hprojects/CMake -DENABLE_FORTRAN_API=ON'
   - cd build

cmake/custom/api.cmake

@@ -5,5 +5,5 @@ install(FILES ${PROJECT_SOURCE_DIR}/api/PCMInput.h DESTINATION include)
 
 if(ENABLE_FORTRAN_API)
     add_definitions(-DENABLE_FORTRAN_API)
-    set_property(GLOBAL APPEND PROPERTY PCMSolver_Fortran_SOURCES ${PROJECT_SOURCE_DIR}/api/pcmsolver.F90)
+    add_library(fortran_bindings OBJECT ${PROJECT_SOURCE_DIR}/api/pcmsolver.F90)
 endif()

cmake/custom/eigen.cmake

@@ -11,7 +11,7 @@
 #   define: '-DEIGEN3_ROOT="{0}"'.format(arguments['--eigen'])
 
 if(EIGEN3_ROOT)
-  set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include/eigen3)
+  set(EIGEN3_INCLUDE_DIR ${EIGEN3_ROOT}/include)
   find_package(Eigen3 3.1.0)
   message(STATUS "Eigen " ${EIGEN3_VERSION} " is located here: " ${EIGEN3_INCLUDE_DIR})
   if(NOT EIGEN3_FOUND)

cmake/custom/pcmsolver.cmake

@@ -23,13 +23,7 @@ set(BOOST_COMPONENTS_REQUIRED "")
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 
-# PCMSolver C++ sources
-set_property(GLOBAL PROPERTY PCMSolver_CXX_SOURCES)
-# PCMSolver C sources
-set_property(GLOBAL PROPERTY PCMSolver_C_SOURCES)
-# PCMSolver Fortran sources
-set_property(GLOBAL PROPERTY PCMSolver_Fortran_SOURCES)
-# PCMSolver headers
+# PCMSolver header directories
 set_property(GLOBAL PROPERTY PCMSolver_HEADER_DIRS)
 
 include_directories(${PROJECT_BINARY_DIR}/include)

cmake/custom/rpath.cmake

@@ -2,6 +2,6 @@ if(APPLE)
     if(NOT DEFINED CMAKE_MACOSX_RPATH)
         set(CMAKE_MACOSX_RPATH ON)
         # Mark as undefined symbols that have to be defined by the host
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,-U,_host_writer")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,-U,_host_writer")
     endif()
 endif()

cmake/custom/test.cmake

@@ -10,7 +10,7 @@ macro(add_Catch_test _name _labels)
   unset(_labels)
 
   # This is the unit tests runner
-  set(RUNNER ${PROJECT_BINARY_DIR}/tests/unit_tests${EXE})
+  set(RUNNER ${PROJECT_BINARY_DIR}/tests/unit_tests)
 
   add_test(NAME ${_name} COMMAND ${RUNNER} [${_name}])
 

doc/programmers/cmake-usage.rst

@@ -6,7 +6,7 @@ This is a brief guide to our CMake infrastructure which is managed
 
 .. warning::
 
-   The minimum required CMake version is 2.8.3
+   The minimum required CMake version is 2.8.8
 
 Adding new source subdirectories and/or files
 ---------------------------------------------
@@ -66,10 +66,9 @@ to generate a template ``CMakeLists.txt.try`` file:
    # List of sources
    list(APPEND sources_list Cavity.cpp Element.cpp GePolCavity.cpp RestartCavity.cpp)
 
+   add_library(cavity OBJECT ${sources_list} ${headers_list})
+   set_target_properties(cavity PROPERTIES POSITION_INDEPENDENT_CODE 1 INTERPROCEDURAL_OPTIMIZATION 1)
    set_property(GLOBAL APPEND PROPERTY PCMSolver_HEADER_DIRS ${CMAKE_CURRENT_LIST_DIR})
-   foreach(_source ${sources_list})
-       set_property(GLOBAL APPEND PROPERTY PCMSolver_CXX_SOURCES ${CMAKE_CURRENT_LIST_DIR}/${_source})
-   endforeach()
    # Sets install directory for all the headers in the list
    foreach(_header ${headers_list})
       install(FILES ${_header} DESTINATION include/cavity)
@@ -83,7 +82,8 @@ hierarchy and it contains set of instructions for:
    hierarchy, possibly excluding some of them
 #. define install targets for the files in this subdirectory.
 
-All the source files are compiled into a unique static library ``libpcm.a``.
+All the source files are compiled into the unique static library ``libpcm.a`` and unique
+dynamic library ``libpcm.so``.
 This library is the one the host QM program need to link.
 
 Searching for libraries

doc/users/building.rst

@@ -28,7 +28,7 @@ the unit test suite.
 Libraries and toolchain programs
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-+ CMake version 2.8.3 and higher;
++ CMake version 2.8.8 and higher;
 + Git version 1.7.1 and higher;
 + Python interpreter 2.4 and higher;
 + Boost libraries version 1.54.0 and higher;
@@ -121,18 +121,40 @@ or with:
 Advanced configuration options
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-As of version 3.1.0 Eigen can fall back to certain BLAS/LAPACK routines as
-implemented in Intel's Math Kernel Library (MKL).  You can enable this feature
-passing the option `-DENABLE_EIGEN_MKL=ON` to the setup script. You need at least
-version 10.3 of Intel MKL.  Be sure to have read
-the relevant `guide <http://eigen.tuxfamily.org/dox/TopicUsingIntelMKL.html>`_
+These options are marked as advanced as it is highly unlikely they will
+be useful when not programming the library:
 
-.. warning::
+* `--exdiag` Enable C++ extended diagnostics flags. Disabled by default.
+* `--ccache` Enable use of ccache for C/C++ compilation caching.
+  Enabled by default, unless ccache is not available.
+* `--build-boost` Deactivate Boost detection and build on-the-fly. Disabled by default.
+* `--eigen` Root directory for Eigen3. Search for Eigen3 in the location provided by the
+  user. If search fails, fall back to the version bundled with the library.
+* `--static` Create only static library. Disabled by default.
 
-   By itself, the module **does not** need to link to any mathematical
-   library. This option makes sense only when linking the module to a QM program
-   that links to Intel MKL. **Use at your own risk!** There is no proof that
-   enabling this option leads to significant speedups!
+Some options can only be tweaked `via` `--cmake-options` to the setup script:
+
+* `ENABLE_CXX11_SUPPORT` Enable C++11 support. Tries to detect which C++11 features
+  are supported by the compiler and enables use of the new standard. Enabled by default.
+
+  .. warning::
+
+     This option is **always** overridden for some compilers that have
+     buggy C++11 support.
+
+* `ENABLE_DOCS` Enable build of documentation. This requires a number of additional dependencies.
+  If any of these are not met, documentation is not built. Enabled by default.
+* `ENABLE_LOGGER` Enable compilation of logger sources. Disabled by default.
+
+  .. warning::
+
+     The logger is not currently in use in any part of the code.
+
+* `ENABLE_TIMER` Enable compilation of timer sources. Enabled by default.
+* `BUILD_STANDALONE` Enable compilation of standalone `run_pcm` executable. Enabled by default.
+* `ENABLE_FORTRAN_API` Enable compilation of the Fortran90 bindings for the API. Disabled by default.
+* `ENABLE_GENERIC` Enable mostly static linking in shared library. Disabled by default.
+* `ENABLE_TESTS` Enable compilation of unit tests suite. Enabled by default.
 
 Build and test
 --------------

src/CMakeLists.txt

@@ -17,26 +17,35 @@ add_subdirectory(pedra)
 add_subdirectory(solver)
 add_subdirectory(utils)
 
-get_property(_pcmsolver_cxx_sources GLOBAL PROPERTY PCMSolver_CXX_SOURCES)
-get_property(_pcmsolver_c_sources GLOBAL PROPERTY PCMSolver_C_SOURCES)
-get_property(_pcmsolver_fortran_sources GLOBAL PROPERTY PCMSolver_Fortran_SOURCES)
-add_library(pcm-base OBJECT ${_pcmsolver_cxx_sources} ${_pcmsolver_c_sources} ${_pcmsolver_fortran_sources})
-if(BUILD_CUSTOM_BOOST)
-  add_dependencies(pcm-base custom_boost)
-endif()
+list(APPEND _objects $<TARGET_OBJECTS:cavity>
+                     $<TARGET_OBJECTS:green>
+                     $<TARGET_OBJECTS:interface>
+                     $<TARGET_OBJECTS:metal>
+                     $<TARGET_OBJECTS:bi_operators>
+                     $<TARGET_OBJECTS:pedra>
+                     $<TARGET_OBJECTS:solver>
+                     $<TARGET_OBJECTS:utils>
+                     $<TARGET_OBJECTS:getkw>
+                     $<TARGET_OBJECTS:fortran_bindings>
+    )
 if(NOT STATIC_LIBRARY_ONLY)
-  set_target_properties(pcm-base PROPERTIES POSITION_INDEPENDENT_CODE 1
-                                            INTERPROCEDURAL_OPTIMIZATION 1)
-  add_library(pcm-shared SHARED $<TARGET_OBJECTS:pcm-base> $<TARGET_OBJECTS:getkw>)
+  add_library(pcm-shared SHARED "${_objects}")
   target_link_libraries(pcm-shared ${ZLIB_LIBRARIES} ${LIBC_INTERJECT})
   set_target_properties(pcm-shared PROPERTIES SOVERSION ${PROJECT_VERSION_MAJOR} CLEAN_DIRECT_OUTPUT 1 OUTPUT_NAME "pcm")
   install(TARGETS pcm-shared DESTINATION lib)
+  if(BUILD_CUSTOM_BOOST)
+    add_dependencies(pcm-shared custom_boost)
+  endif()
 endif()
 
-add_library(pcm-static STATIC $<TARGET_OBJECTS:pcm-base> $<TARGET_OBJECTS:getkw>)
+add_library(pcm-static STATIC "${_objects}")
 set_target_properties(pcm-static PROPERTIES CLEAN_DIRECT_OUTPUT 1 OUTPUT_NAME "pcm")
 install(TARGETS pcm-static ARCHIVE DESTINATION lib)
 
+if(BUILD_CUSTOM_BOOST)
+  add_dependencies(pcm-static custom_boost)
+endif()
+
 # This directory contains source file for executables
 if(BUILD_STANDALONE)
    add_subdirectory(bin)

src/bi_operators/CMakeLists.txt

@@ -4,10 +4,9 @@ list(APPEND headers_list CollocationIntegrator.hpp IntegratorForward.hpp Integra
 # List of sources
 list(APPEND sources_list )
 
+add_library(bi_operators OBJECT ${headers_list} ${sources_list})
+set_target_properties(bi_operators PROPERTIES POSITION_INDEPENDENT_CODE 1 INTERPROCEDURAL_OPTIMIZATION 1)
 set_property(GLOBAL APPEND PROPERTY PCMSolver_HEADER_DIRS ${CMAKE_CURRENT_LIST_DIR})
-foreach(_source ${sources_list})
-    set_property(GLOBAL APPEND PROPERTY PCMSolver_CXX_SOURCES ${CMAKE_CURRENT_LIST_DIR}/${_source})
-endforeach()
 # Sets install directory for all the headers in the list
 foreach(_header ${headers_list})
    install(FILES ${_header} DESTINATION include/bi_operators)