Merge branch 'develop'

cyclus · Sep 7, 2017 · 9956d5c · 9956d5c
2 parents 8d21b3a + e2b0474
commit 9956d5c
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Showing 18 changed files with 279 additions and 169 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -25,7 +25,7 @@ ENDIF()
 # quiets fortify_source warnings when not compiling with optimizations
 # in linux distros where compilers were compiled with fortify_source enabled by
 # default (e.g. Arch linux).
-MESSAGE("${CMAKE_BUILD_TYPE}")
+MESSAGE("-- CMake Build Type: ${CMAKE_BUILD_TYPE}")
 STRING(TOLOWER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
 IF(NOT ${BUILD_TYPE} STREQUAL "release")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=0")
@@ -63,7 +63,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     # (but later on when installing)
     SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 
-    SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+    SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/lib/cyclus")
 
     # add the automatically determined parts of the RPATH
     # which point to directories outside the build tree to the install RPATH
@@ -72,19 +72,41 @@ IF(NOT CYCLUS_DOC_ONLY)
     # the RPATH to be used when installing, but only if it's not a system directory
     LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
     IF("${isSystemDir}" STREQUAL "-1")
-        SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+        SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/lib/cyclus")
+        GET_FILENAME_COMPONENT(cxxCompilerRoot ${CMAKE_CXX_COMPILER} DIRECTORY)
+        GET_FILENAME_COMPONENT(cxxCompilerRoot ${cxxCompilerRoot} DIRECTORY)
+        IF (NOT "${CMAKE_INSTALL_RPATH}" STREQUAL "${cxxCompilerRoot}")
+            SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_RPATH}:${cxxCompilerRoot}/lib:${cxxCompilerRoot}/lib/cyclus")
+        ENDIF (NOT "${CMAKE_INSTALL_RPATH}" STREQUAL "${cxxCompilerRoot}")
+        SET(CMAKE_BUILD_RPATH "${CMAKE_INSTALL_RPATH}")
     ENDIF("${isSystemDir}" STREQUAL "-1")
+    MESSAGE("-- CMAKE_INSTALL_RPATH: ${CMAKE_INSTALL_RPATH}")
 
     # Tell CMake where the modules are
-    SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_DIR}/share/cmake-2.8/Modules")
+    SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_INSTALL_PREFIX}/share/cyclus/cmake")
     SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CYCAMORE_SOURCE_DIR}/cmake)
-    MESSAGE("CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}")
+    MESSAGE("--CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}")
+
+    # get dependency hints
+    if (NOT DEPS_ROOT_DIR)
+        get_filename_component(compdir ${CMAKE_CXX_COMPILER} DIRECTORY)
+        get_filename_component(DEPS_ROOT_DIR ${compdir} DIRECTORY)
+    endif (NOT DEPS_ROOT_DIR)
+    SET(DEPS_HINTS HINTS "${DEPS_ROOT_DIR}")
+    SET(DEPS_BIN_HINTS ${DEPS_HINTS} "${DEPS_ROOT_DIR}/bin")
+    SET(DEPS_LIB_HINTS ${DEPS_HINTS} "${DEPS_ROOT_DIR}/lib")
+    SET(DEPS_INCLUDE_HINTS HINTS "${DEPS_ROOT_DIR}/include")
+    MESSAGE("-- Dependency Root Dir (DEPS_ROOT_DIR): ${DEPS_ROOT_DIR}")
+    MESSAGE("-- Dependency Hints (DEPS_HINTS): ${DEPS_HINTS}")
+    MESSAGE("-- Dependency Binary Hints (DEPS_BIN_HINTS): ${DEPS_BIN_HINTS}")
+    MESSAGE("-- Dependency Library Hints (DEPS_LIB_HINTS): ${DEPS_LIB_HINTS}")
+    MESSAGE("-- Dependency Include Hints (DEPS_INCLUDE_HINTS): ${DEPS_INCLUDE_HINTS}")
 
     # Find cyclus
     FIND_PACKAGE(Cyclus REQUIRED)
     SET(
-      CYCAMORE_INCLUDE_DIRS 
-      ${CYCAMORE_INCLUDE_DIRS} 
+      CYCAMORE_INCLUDE_DIRS
+      ${CYCAMORE_INCLUDE_DIRS}
       ${CYCLUS_CORE_INCLUDE_DIR} # INSTALL_PATH/include/cyclus
       )
     SET(LIBS ${LIBS} ${CYCLUS_CORE_LIBRARIES})
@@ -96,25 +118,32 @@ IF(NOT CYCLUS_DOC_ONLY)
     FIND_PACKAGE(LibXML++ REQUIRED)
     SET(CYCAMORE_INCLUDE_DIRS ${CYCAMORE_INCLUDE_DIRS} ${LibXML++_INCLUDE_DIR} ${Glibmm_INCLUDE_DIRS} ${LibXML++Config_INCLUDE_DIR})
     SET(LIBS ${LIBS} ${LibXML++_LIBRARIES})
-    MESSAGE("--LIBS: ${LIBS}")
-
-    MESSAGE("--LD_LIBRARY_PATH: $ENV{LD_LIBRARY_PATH}")
-
-    # Include the boost header files, system, and filesystem libraries
-    SET(Boost_USE_STATIC_LIBS       OFF)
-    SET(Boost_USE_STATIC_RUNTIME    OFF)
-    #FIND_PACKAGE(Boost COMPONENTS filesystem system REQUIRED)
-    FIND_PACKAGE( Boost 1.46.1 COMPONENTS filesystem system REQUIRED)
+    MESSAGE("-- LIBS: ${LIBS}")
+
+    MESSAGE("-- LD_LIBRARY_PATH: $ENV{LD_LIBRARY_PATH}")
+
+    # Include the boost header files and the program_options library
+    # Please be sure to use Boost rather than BOOST.
+    # Capitalization matters on some platforms
+    SET(Boost_USE_STATIC_LIBS OFF)
+    SET(Boost_USE_STATIC_RUNTIME OFF)
+    # SET(Boost_USE_MULTITHREADED    OFF)
+    if (DEPS_ROOT_DIR)
+      SET(BOOST_ROOT "${DEPS_ROOT_DIR}")
+      SET(BOOST_INCLUDEDIR "${DEPS_INCLUDE_HINTS}")
+    endif (DEPS_ROOT_DIR)
+    FIND_PACKAGE(Boost COMPONENTS program_options filesystem system serialization REQUIRED)
     MESSAGE("--    Boost Root: ${Boost_ROOT}")
     MESSAGE("--    Boost Include directory: ${Boost_INCLUDE_DIR}")
     MESSAGE("--    Boost Library directories: ${Boost_LIBRARY_DIRS}")
+    SET(LIBS ${LIBS} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+    MESSAGE("--    Boost Program Options location: ${Boost_PROGRAM_OPTIONS_LIBRARY}")
     SET(LIBS ${LIBS} ${Boost_SYSTEM_LIBRARY})
     MESSAGE("--    Boost System location: ${Boost_SYSTEM_LIBRARY}")
     SET(LIBS ${LIBS} ${Boost_FILESYSTEM_LIBRARY})
     MESSAGE("--    Boost Filesystem location: ${Boost_FILESYSTEM_LIBRARY}")
-    SET(CYCAMORE_INCLUDE_DIRS ${CYCAMORE_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
-    SET(LIBS ${LIBS} ${Boost_FILESYSTEM_LIBRARY})
-    SET(LIBS ${LIBS} ${Boost_SYSTEM_LIBRARY})
+    SET(LIBS ${LIBS} ${Boost_SERIALIZATION_LIBRARY})
+    MESSAGE("--    Boost Serialization location: ${Boost_SERIALIZATION_LIBRARY}")
 
     # find lapack and link to it
     # note there is no include directory variable:
@@ -124,14 +153,14 @@ IF(NOT CYCLUS_DOC_ONLY)
     MESSAGE("\tFound LAPACK Libraries: ${LAPACK_LIBRARIES}")
 
     # Find HDF5
-    FIND_PACKAGE(HDF5 REQUIRED)
+    FIND_PACKAGE(HDF5 REQUIRED COMPONENTS HL)
     ADD_DEFINITIONS(${HDF5_DEFINITIONS})
-    SET(CYCAMORE_INCLUDE_DIRS ${CYCAMORE_INCLUDE_DIRS} ${HDF5_INCLUDE_DIR})
-    set(LIBS ${LIBS} ${HDF5_LIBRARIES})
+    set(LIBS ${LIBS} ${HDF5_C_LIBRARIES} ${HDF5_C_HL_LIBRARIES})
     MESSAGE("--    HDF5 Root: ${HDF5_ROOT}")
     MESSAGE("--    HDF5 Include directory: ${HDF5_INCLUDE_DIR}")
     MESSAGE("--    HDF5 Library directories: ${HDF5_LIBRARY_DIRS}")
-    MESSAGE("--    HDF5 Libraries: ${HDF5_LIBRARIES}")
+    MESSAGE("--    HDF5 Libraries: ${HDF5_C_LIBRARIES}")
+    MESSAGE("--    HDF5 High Level Libraries: ${HDF5_C_HL_LIBRARIES}")
 
     # find coin and link to it
     FIND_PACKAGE(COIN REQUIRED)
@@ -147,6 +176,74 @@ IF(NOT CYCLUS_DOC_ONLY)
     MESSAGE("--    SQLITE3 Include directories: ${SQLITE3_INCLUDE_DIR}")
     MESSAGE("--    SQLITE3 Libraries: ${SQLITE3_LIBRARIES}")
 
+    #
+    # Some optional libraries to link in, as availble. Required for conda.
+    #
+    # pcre
+    FIND_LIBRARY(PCRE_LIBRARIES pcre ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found PCRE Libraries (optional): ${PCRE_LIBRARIES}")
+    IF(PCRE_LIBRARIES)
+        set(LIBS ${LIBS} ${PCRE_LIBRARIES})
+    ENDIF(PCRE_LIBRARIES)
+
+    # gfortran
+    FIND_LIBRARY(GFORTRAN_LIBRARIES gfortran ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found GFORTRAN Libraries (optional): ${GFORTRAN_LIBRARIES}")
+    IF(GFORTRAN_LIBRARIES)
+        set(LIBS ${LIBS} ${GFORTRAN_LIBRARIES})
+    ENDIF(GFORTRAN_LIBRARIES)
+
+    # openblas
+    FIND_LIBRARY(OPENBLAS_LIBRARIES openblas ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found OPENBLAS Libraries (optional): ${OPENBLAS_LIBRARIES}")
+    IF(OPENBLAS_LIBRARIES)
+        set(LIBS ${LIBS} ${OPENBLAS_LIBRARIES})
+    ENDIF(OPENBLAS_LIBRARIES)
+
+    # ClpSolver
+    FIND_LIBRARY(CLPSOLVER_LIBRARIES ClpSolver ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found CLPSOLVER Libraries (optional): ${CLPSOLVER_LIBRARIES}")
+    IF(CLPSOLVER_LIBRARIES)
+        set(LIBS ${LIBS} ${CLPSOLVER_LIBRARIES})
+    ENDIF(CLPSOLVER_LIBRARIES)
+
+    # iconv
+    FIND_LIBRARY(ICONV_LIBRARIES iconv ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found ICONV Libraries (optional): ${ICONV_LIBRARIES}")
+    IF(ICONV_LIBRARIES)
+        set(LIBS ${LIBS} ${ICONV_LIBRARIES})
+    ENDIF(ICONV_LIBRARIES)
+
+    # icudata
+    FIND_LIBRARY(ICUDATA_LIBRARIES icudata ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found ICUDATA Libraries (optional): ${ICUDATA_LIBRARIES}")
+    IF(ICUDATA_LIBRARIES)
+        set(LIBS ${LIBS} ${ICUDATA_LIBRARIES})
+    ENDIF(ICUDATA_LIBRARIES)
+
+    # icui18n
+    FIND_LIBRARY(ICUI18N_LIBRARIES icui18n ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found ICUI18N Libraries (optional): ${ICUI18N_LIBRARIES}")
+    IF(ICUI18N_LIBRARIES)
+        set(LIBS ${LIBS} ${ICUI18N_LIBRARIES})
+    ENDIF(ICUI18N_LIBRARIES)
+
+    # icuuc
+    FIND_LIBRARY(ICUUC_LIBRARIES icuuc ${DEPS_LIB_HINTS})
+    MESSAGE("-- Found ICUUC Libraries (optional): ${ICUUC_LIBRARIES}")
+    IF(ICUUC_LIBRARIES)
+        set(LIBS ${LIBS} ${ICUUC_LIBRARIES})
+    ENDIF(ICUUC_LIBRARIES)
+
+    # Python
+    find_package(PythonInterp)
+    message("-- PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
+    find_package(PythonLibs)
+    MESSAGE("-- Found Python Libraries (optional): ${PYTHON_LIBRARIES}")
+    IF(PYTHON_LIBRARIES)
+        set(LIBS ${LIBS} ${PYTHON_LIBRARIES})
+    ENDIF(PYTHON_LIBRARIES)
+
     # include all the directories we just found
     INCLUDE_DIRECTORIES(${CYCAMORE_INCLUDE_DIRS})
 
@@ -187,54 +284,20 @@ IF(NOT CYCLUS_DOC_ONLY)
         )
 
     TARGET_LINK_LIBRARIES(cycamore_unit_tests
-        dl ${LIBS} ${CYCLUS_TEST_LIBRARIES})
+        dl
+        ${LIBS}
+        ${CYCLUS_TEST_LIBRARIES}
+        )
 
     INSTALL(TARGETS cycamore_unit_tests
         RUNTIME DESTINATION bin
         COMPONENT testing
         )
 
-    # read tests after building the driver, and add them to ctest
-    set(tgt "cycamore_unit_tests")
-    set(script "${CYCAMORE_SOURCE_DIR}/config/generate_test_macros.py")
-    set(exec "--executable=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${tgt}")
-    set(reg_dir "--reg_dir=${CYCAMORE_SOURCE_DIR}/../${test_dir}")
-    set(out "--output=${CMAKE_BINARY_DIR}/CTestTestfile.cmake")
-    add_custom_command(TARGET ${tgt}
-        POST_BUILD
-        COMMAND python ${script} ${exec} ${reg_dir} ${out}
-        COMMENT "adding tests from ${tgt}"
-        DEPENDS
-        VERBATIM
-        )
-
-    # for post test commands
-    configure_file(
-        "${CMAKE_CURRENT_SOURCE_DIR}/config/CTestCustom.cmake"
-        "${CMAKE_CURRENT_BINARY_DIR}/CTestCustom.cmake"
-        IMMEDIATE @ONLY)
-
-    # for printing regression tests
-    configure_file(
-        "${CMAKE_CURRENT_SOURCE_DIR}/config/print_regs.py"
-        "${CMAKE_CURRENT_BINARY_DIR}/print_regs.py"
-        IMMEDIATE @ONLY)
-
-    # AMS: I don't believe that this is needed anymore.
-    # This just copies the shared dir from cyclus to cycamore.
-    # However, the 'share/' dir should now be the same.  So this
-    # was failing because you can't copy a file to itself.
-    #FILE(GLOB cyclus_shared "${CYCLUS_CORE_SHARE_DIR}/*")
-    #INSTALL(FILES ${cyclus_shared}
-    #  DESTINATION share
-    #  COMPONENT data
-    # )
-
-
     ##############################################################################################
     ################################## begin uninstall target ####################################
     ##############################################################################################
- 
+
     CONFIGURE_FILE(
         "${CMAKE_CURRENT_SOURCE_DIR}/config/cmake_uninstall.cmake.in"
         "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
@@ -247,15 +310,15 @@ IF(NOT CYCLUS_DOC_ONLY)
     ##############################################################################################
     ################################### end uninstall target #####################################
     ##############################################################################################
- 
+
     ##############################################################################################
     ####################################### begin cpack ##########################################
     ##############################################################################################
-    
-    
+
+
     # Here's where we package it with CPack
     SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Cycamore : The Cyclus Additional Module Repository.")
-    
+
     # Here we set some components for installation with cpack
     SET(CPACK_COMPONENTS_ALL cycamore testing libraries data core)
     SET(CPACK_GENERATOR "DEB")
@@ -265,22 +328,22 @@ IF(NOT CYCLUS_DOC_ONLY)
     SET(CPACK_PACKAGE_VENDOR "CNERG, UW-Madison")
     SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.rst")
     SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.rst")
-    
+
     # Version
     SET(CPACK_PACKAGE_VERSION_MAJOR "1")
     SET(CPACK_PACKAGE_VERSION_MINOR "4")
     SET(CPACK_PACKAGE_VERSION_PATCH "0")
-    
+
     # Dependencies
     SET(CPACK_DEBIAN_PACKAGE_DEPENDS "cyclus (>= 1.4.0)")
     MESSAGE("CPACK_DEBIAN_PACKAGE_DEPENDS ${CPACK_DEBIAN_PACKAGE_DEPENDS}")
-    
+
     # Names
     SET(CPACK_PACKAGE_NAME "cycamore")
     SET(CPACK_PACKAGE_INSTALL_DIRECTORY "cycamore_${CPACK_PACKAGE_VERSION_MAJOR}")
     SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_INSTALL_DIRECTORY}.${CPACK_PACKAGE_VERSION_MINOR}")
     SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_INSTALL_DIRECTORY}.${CPACK_PACKAGE_VERSION_PATCH}")
-    
+
     SET(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}")
     SET(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_FILE_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}")
     SET(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_FILE_NAME}.${CPACK_PACKAGE_VERSION_MINOR}")
@@ -303,7 +366,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     SET(ROOT_DIR ${CYCLUS_ROOT_DIR})
     SET(PROJ_DIR ${PROJECT_BINARY_DIR})
     SET(CORE_SHARE_DIR ${CYCLUS_CORE_SHARE_DIR})
-    
+
     ##############################################################################################
     ######################################## end cpack ###########################################
     ##############################################################################################

diff --git a/circle.yml b/circle.yml
@@ -9,15 +9,15 @@ dependencies:
 test:
   override:
     - docker run cyclus/cycamore:latest cycamore_unit_tests
-    - docker run cyclus/cycamore:latest nosetests3 -w /cycamore/tests
+    - docker run cyclus/cycamore:latest nosetests -w /cycamore/tests
 
 deployment:
   develop:
     branch: develop
     commands:
       - docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS
       - docker push cyclus/cycamore:latest
-  
+
   master:
     branch: master
     commands:

diff --git a/docker/develop-ci/Dockerfile b/docker/develop-ci/Dockerfile
@@ -2,8 +2,7 @@ FROM cyclus/cyclus:latest
 
 COPY . /cycamore
 WORKDIR /cycamore
-RUN mkdir Release
-WORKDIR /cycamore/Release
-RUN cmake .. -DCMAKE_BUILD_TYPE=Release
-RUN make -j2 && make install
-
+ENV PATH="/root/.local/bin:${PATH}"
+RUN python install.py -j 2 --build-type=Release \
+    -DBLAS_LIBRARIES="/opt/conda/lib/libblas.so" \
+    -DLAPACK_LIBRARIES="/opt/conda/lib/liblapack.so"
diff --git a/input/enrichment/1_src_enr_rxtr_sink.xml b/input/enrichment/1_src_enr_rxtr_sink.xml
@@ -100,7 +100,7 @@
 
   <recipe>
     <name>natl_u</name>
-    <basis>atom</basis>
+    <basis>mass</basis>
     <nuclide>
       <id>922350000</id>
       <comp>0.7</comp>
@@ -113,7 +113,7 @@
 
   <recipe>
     <name>fuel_recipe</name>
-    <basis>atom</basis>
+    <basis>mass</basis>
     <nuclide>
       <id>922350000</id>
       <comp>4.5</comp>

diff --git a/input/enrichment/linear_src_enr_rxtr_sink.xml b/input/enrichment/linear_src_enr_rxtr_sink.xml
@@ -125,7 +125,7 @@
 
   <recipe>
     <name>natl_u</name>
-    <basis>atom</basis>
+    <basis>mass</basis>
     <nuclide>
       <id>922350000</id>
       <comp>0.7</comp>
@@ -138,7 +138,7 @@
 
   <recipe>
     <name>fuel_recipe</name>
-    <basis>atom</basis>
+    <basis>mass</basis>
     <nuclide>
       <id>922350000</id>
       <comp>4.5</comp>