Merge branch 'release-0.7.0'

openmc-dev · Aug 19, 2015 · 31c1f86 · 31c1f86
2 parents 23279c8 + 3d1af11
commit 31c1f86
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diff --git a/.gitignore b/.gitignore
@@ -8,8 +8,12 @@
 # Compiler python objects
 *.pyc
 
-# OpenMC executable
-src/openmc
+# Python distribution
+dist/
+openmc.egg-info/
+
+# Inputs generated from Python API
+examples/python/**/*.xml
 
 # emacs backups
 *~
@@ -22,22 +26,40 @@ docs/build
 docs/source/_images/*.pdf
 
 # Source build
-src/build
+build
 
 # build from src/utils/setup.py
 src/utils/build
 
 # xml-fortran reader
 src/xml-fortran/xmlreader
 
-# Modules built from XML templates
-src/templates/*.f90
-
 # Test results error file
 results_error.dat
 
+# Test build files
+tests/build/
+tests/ctestscript.run
+
 # HDF5 files
 *.h5
 
+# Build files
+src/CMakeCache.txt
+src/CMakeFiles/
+src/bin/
+src/cmake_install.cmake
+src/install_manifest.txt
+
 # Data downloaded from NNDC
 data/nndc
+
+#Images
+*.ppm
+
+# PyCharm project configuration files
+.idea
+.idea/*
+
+# IPython notebook checkpoints
+.ipynb_checkpoints
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,54 @@
+sudo: false
+language: python
+python:
+  - "2.7"
+  - "3.4"
+addons:
+  apt:
+    packages:
+    - gfortran
+    - g++
+cache:
+  directories:
+  - $HOME/mpich_install
+  - $HOME/hdf5_install
+  - $HOME/phdf5_install
+
+before_install:
+  # ============== Handle Python third-party packages ==============
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy h5py
+  - source activate test-environment
+
+  # Install GCC, MPICH, HDF5, PHDF5
+  - ./tests/travis_install.sh
+  - export FC=gfortran
+  - export MPI_DIR=$HOME/mpich_install
+  - export PHDF5_DIR=$HOME/phdf5_install
+  - export HDF5_DIR=$HOME/hdf5_install
+
+install: true
+
+before_script:
+  - cd data
+  - git clone --branch=master git://github.com/bhermanmit/nndc_xs nndc_xs
+  - cat nndc_xs/nndc.tar.gza* | tar xzvf -
+  - rm -rf nndc_xs
+  - export CROSS_SECTIONS=$PWD/nndc/cross_sections.xml
+  - cd ..
+
+script:
+  - cd tests
+  - export OMP_NUM_THREADS=3
+  - ./travis.sh
+  - cd ..
diff --git a/src/CMakeLists.txt → CMakeLists.txt b/src/CMakeLists.txt → CMakeLists.txt
@@ -21,23 +21,27 @@ endif()
 
 option(openmp   "Enable shared-memory parallelism with OpenMP"   OFF)
 option(profile  "Compile with profiling flags"                   OFF)
-option(petsc    "Enable PETSC for use in CMFD acceleration"      OFF)
 option(debug    "Compile with debug flags"                       OFF)
 option(optimize "Turn on all compiler optimization flags"        OFF)
 option(verbose  "Create verbose Makefiles"                       OFF)
-option(coverage "Compile with flags"                             OFF)
+option(coverage "Compile with coverage analysis flags"           OFF)
+option(mpif08   "Use Fortran 2008 MPI interface"                 OFF)
 
 if (verbose)
   set(CMAKE_VERBOSE_MAKEFILE on)
 endif()
 
+# Maximum number of nested coordinates levels
+set(maxcoord 10 CACHE STRING "Maximum number of nested coordinate levels")
+add_definitions(-DMAX_COORD=${maxcoord})
+
 #===============================================================================
 # MPI for distributed-memory parallelism / HDF5 for binary output
 #===============================================================================
 
 set(MPI_ENABLED FALSE)
 set(HDF5_ENABLED FALSE)
-if($ENV{FC} MATCHES "mpi.*")
+if($ENV{FC} MATCHES "mpi[^/]*$")
   message("-- Detected MPI wrapper: $ENV{FC}")
   add_definitions(-DMPI)
   set(MPI_ENABLED TRUE)
@@ -52,11 +56,24 @@ elseif($ENV{FC} MATCHES "h5pfc$")
   set(HDF5_ENABLED TRUE)
 endif()
 
+# Check for Fortran 2008 MPI interface
+if(MPI_ENABLED AND mpif08)
+  message("-- Using Fortran 2008 MPI bindings")
+  add_definitions(-DMPIF08)
+endif()
+
 #===============================================================================
 # Set compile/link flags based on which compiler is being used
 #===============================================================================
 
 if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+  # Make sure version is sufficient
+  execute_process(COMMAND ${CMAKE_Fortran_COMPILER} -dumpversion
+    OUTPUT_VARIABLE GCC_VERSION)
+  if(GCC_VERSION VERSION_LESS 4.6)
+    message(FATAL_ERROR "gfortran version must be 4.6 or higher")
+  endif()
+
   # GNU Fortran compiler options
   set(f90flags  "-cpp -std=f2008 -fbacktrace")
   if(debug)
@@ -116,7 +133,8 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "PGI")
 
 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "XL")
   # IBM XL compiler options
-  set(f90flags  "-WF,-DNO_F2008 -O2")
+  set(f90flags  "-O2")
+  add_definitions(-DNO_F2008)
   if(debug)
     set(f90flags  "-g -C -qflag=i:i -u")
     set(ldflags   "-g")
@@ -143,78 +161,6 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "Cray")
 
 endif()
 
-#===============================================================================
-# PETSc for CMFD functionality
-#===============================================================================
-
-set (PETSC_ENABLED FALSE)
-if(petsc)
-  set(PETSC_ENABLED TRUE)
-  find_package(PETSc REQUIRED HINTS $ENV{PETSC_DIR}/conf)
-  find_library(libpetsc petsc $ENV{PETSC_DIR}/lib)
-
-  # If libfblas wasn't found, search the PETSc lib directory
-  if(PETSC_FBLAS_LIB STREQUAL "PETSC_FBLAS_LIB-NOTFOUND")
-    find_library(PETSC_FBLAS_LIB fblas $ENV{PETSC_DIR}/lib)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_FBLAS_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_FBLAS_LIB})
-  endif()
-
-  # If libflapack wasn't found, search the PETSc lib directory
-  if(PETSC_FLAPACK_LIB STREQUAL "PETSC_FLAPACK_LIB-NOTFOUND")
-    find_library(PETSC_FLAPACK_LIB flapack $ENV{PETSC_DIR}/lib)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_FLAPACK_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_FLAPACK_LIB})
-  endif()
-
-  # If libdl wasn't found, search /usr/lib64
-  if(PETSC_DL_LIB STREQUAL "PETSC_DL_LIB-NOTFOUND")
-    find_library(PETSC_DL_LIB libdl.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_DL_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_DL_LIB})
-  endif()
-
-  # If libm wasn't found, search /usr/lib64
-  if(PETSC_M_LIB STREQUAL "PETSC_M_LIB-NOTFOUND")
-    find_library(PETSC_M_LIB libm.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_M_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_M_LIB})
-  endif()
-
-  # If libpthread wasn't found, search /usr/lib64
-  if(PETSC_PTHREAD_LIB STREQUAL "PETSC_PTHREAD_LIB-NOTFOUND")
-    find_library(PETSC_PTHREAD_LIB libpthread.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_PTHREAD_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_PTHREAD_LIB})
-  endif()
-
-  # If librt wasn't found, search /usr/lib64
-  if(PETSC_RT_LIB STREQUAL "PETSC_RT_LIB-NOTFOUND")
-    find_library(PETSC_RT_LIB librt.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_RT_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_RT_LIB})
-  endif()
-
-  # If libssl wasn't found, search /usr/lib64
-  if(PETSC_SSL_LIB STREQUAL "PETSC_SSL_LIB-NOTFOUND")
-    find_library(PETSC_SSL_LIB libssl.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_SSL_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_SSL_LIB})
-  endif()
-
-  # If libcrypto wasn't found, search /usr/lib64
-  if(PETSC_CRYPTO_LIB STREQUAL "PETSC_CRYPTO_LIB-NOTFOUND")
-    find_library(PETSC_CRYPTO_LIB libcrypto.so /usr/lib64)
-    list(REMOVE_ITEM PETSC_PACKAGE_LIBS PETSC_CRYPTO_LIB-NOTFOUND)
-    list(INSERT PETSC_PACKAGE_LIBS 0 ${PETSC_CRYPTO_LIB})
-  endif()
-
-  message("-- Using PETSC: ${libpetsc}")
-  add_definitions(-DPETSC)
-  include_directories($ENV{PETSC_DIR}/include)
-  set(libraries "${libpetsc};${PETSC_PACKAGE_LIBS};${libraries}")
-endif()
-
 #===============================================================================
 # git SHA1 hash
 #===============================================================================
@@ -234,21 +180,29 @@ endif()
 
 # Only initialize git submodules if it is not there. User is responsible
 # for future updates of fox xml submodule.
-if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/xml/fox/.git)
-  message("-- Initializing/Updating FoX XML submodule...")
-  execute_process(COMMAND git submodule init
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/..)
-  execute_process(COMMAND git submodule update
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/..)
+if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/xml/fox/.git)
+  if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
+    message("-- Cloning FoX XML git repository...")
+    execute_process(COMMAND git clone https://github.com/mit-crpg/fox.git src/xml/fox
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+    execute_process(COMMAND git checkout bdc852f4f43d969fb1b179cba79295c1e095a455
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/src/xml/fox)
+  else()
+    message("-- Initializing/Updating FoX XML submodule...")
+    execute_process(COMMAND git submodule init
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+    execute_process(COMMAND git submodule update
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  endif()
 endif()
-add_subdirectory(xml/fox)
+add_subdirectory(src/xml/fox)
 
 #===============================================================================
 # Build OpenMC executable
 #===============================================================================
 
 set(program "openmc")
-file(GLOB source *.F90 xml/openmc_fox.F90)
+file(GLOB source src/*.F90 src/xml/openmc_fox.F90)
 add_executable(${program} ${source})
 target_link_libraries(${program} ${libraries} fox_dom)
 set_target_properties(${program} PROPERTIES
@@ -260,24 +214,16 @@ set_target_properties(${program} PROPERTIES
 #===============================================================================
 
 install(TARGETS ${program} RUNTIME DESTINATION bin)
-install(PROGRAMS utils/statepoint_cmp.py
-  DESTINATION bin
-  RENAME statepoint_cmp)
-install(PROGRAMS utils/statepoint_histogram.py
-  DESTINATION bin
-  RENAME statepoint_histogram)
-install(PROGRAMS utils/statepoint_meshplot.py
-  DESTINATION bin
-  RENAME statepoint_meshplot)
-install(FILES ../man/man1/openmc.1 DESTINATION share/man/man1)
-install(FILES ../LICENSE DESTINATION "share/doc/${program}/copyright")
+install(DIRECTORY src/relaxng DESTINATION share/openmc)
+install(FILES man/man1/openmc.1 DESTINATION share/man/man1)
+install(FILES LICENSE DESTINATION "share/doc/${program}/copyright")
 
 find_package(PythonInterp)
 if(PYTHONINTERP_FOUND)
   install(CODE "execute_process(
                   COMMAND ${PYTHON_EXECUTABLE} setup.py install
                   --prefix=${CMAKE_INSTALL_PREFIX}
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/utils)")
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})")
 endif()
 
 #===============================================================================
@@ -288,15 +234,7 @@ endif()
 include(CTest)
 
 # Get a list of all the tests to run
-file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/../tests/test_*.py)
-
-# Check to see if PETSC is compiled for CMFD tests
-if (NOT ${PETSC_ENABLED})
-  file(GLOB_RECURSE CMFD_TESTS ${CMAKE_CURRENT_SOURCE_DIR}/../tests/test_cmfd_jfnk.py)
-  foreach(cmfd_test in ${CMFD_TESTS})
-    list(REMOVE_ITEM TESTS ${cmfd_test})
-  endforeach(cmfd_test)
-endif(NOT ${PETSC_ENABLED})
+file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/tests/test_*.py)
 
 # Check for MEM_CHECK and COVERAGE variables
 if (DEFINED ENV{MEM_CHECK})
@@ -349,6 +287,22 @@ foreach(test ${TESTS})
         WORKING_DIRECTORY ${TEST_PATH}
         COMMAND $<TARGET_FILE:openmc> -p ${TEST_PATH})
 
+    elseif(${test} MATCHES "test_filter_distribcell")
+
+      # Add each case for distribcell tests
+      add_test(NAME ${TEST_NAME}_case-1
+        WORKING_DIRECTORY ${TEST_PATH}/case-1
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH}/case-1)
+      add_test(NAME ${TEST_NAME}_case-2
+        WORKING_DIRECTORY ${TEST_PATH}/case-2
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH}/case-2)
+      add_test(NAME ${TEST_NAME}_case-3
+        WORKING_DIRECTORY ${TEST_PATH}/case-3
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH}/case-3)
+      add_test(NAME ${TEST_NAME}_case-4
+        WORKING_DIRECTORY ${TEST_PATH}/case-4
+        COMMAND $<TARGET_FILE:openmc> ${TEST_PATH}/case-4)
+
     # If a restart test is encounted, need to run with -r and restart file(s)
     elseif(${test} MATCHES "restart")
 

diff --git a/src/CTestConfig.cmake → CTestConfig.cmake b/src/CTestConfig.cmake → CTestConfig.cmake
diff --git a/src/Makefile → Makefile b/src/Makefile → Makefile