Create Pececillo fork for paraboloid fit tests

- Remove flow and hc drivers
- Update to master's cmake build, and remove external libraries

.gitignore

@@ -1,7 +1,7 @@
 build/*
-external/*
 
 *~
 *.ply
 *gmv*
 *TAGS
+*txt

CMakeLists.txt

@@ -1,9 +1,11 @@
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.5)
 
 set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}"
                       "${CMAKE_SOURCE_DIR}/cmake/Modules"
                       "${CMAKE_SOURCE_DIR}/cmake/Utils")
 
+include(NoInSourceBuild)
+
 project(Pececillo Fortran C)
 
 # Override the default installation prefix (/usr/local).
@@ -22,8 +24,6 @@ endif()
 # ---------------------------------------------------------------------------- #
 
 option(ENABLE_TESTS "Build test programs" ON)
-
-# Build the tests
 if (ENABLE_TESTS)
   enable_testing()
 endif()
@@ -38,19 +38,12 @@ endif()
 
 message(STATUS "CMAKE_Fortran_COMPILER_ID=${CMAKE_Fortran_COMPILER_ID}")
 if (CMAKE_Fortran_COMPILER_ID STREQUAL "NAG")
-  set (CMAKE_Fortran_FLAGS_RELEASE "$-u -O3 -w=uda -DNDEBUG")
   # note: need to disable openmp below for traceback support
+  set (CMAKE_Fortran_FLAGS_RELEASE "-u -O3 -w=uda -DNDEBUG")
   set (CMAKE_Fortran_FLAGS_DEBUG   "-g90 -g -gline -O0 -w=uda -C=all")
-  #set (CMAKE_Fortran_FLAGS_DEBUG "-O3 -Oassumed=contig -w=uda -DNDEBUG")
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
   set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -g -DNDEBUG -assume realloc_lhs")
   set (CMAKE_Fortran_FLAGS_DEBUG   "-g -assume realloc_lhs -traceback -fp-stack-check -ftrapuv -check bounds,uninit,noarg-temp-created,pointer")
-  #set (CMAKE_Fortran_FLAGS_DEBUG   "-g -traceback -assume realloc_lhs -fp-stack-check -ftrapuv -check bounds,uninit,noarg-temp-created,pointer -warn all")
-  # set (CMAKE_Fortran_FLAGS_DEBUG   "-g -O0 -traceback -assume realloc_lhs -ftrapuv -fp-stack-check -check all -warn all -WB")
-  set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -g -assume realloc_lhs -traceback")
-  #set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -g -assume realloc_lhs -traceback -fp-stack-check -ftrapuv -check bounds,uninit,noarg-temp-created,pointer")
-  #set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -g -assume realloc_lhs -traceback -fp-stack-check -ftrapuv -check all")
- #message(STATUS "${CMAKE_Fortran_COMPILER_VERSION}")
 endif()
 
 find_package(OpenMP)
@@ -63,39 +56,77 @@ if (OPENMP_FOUND)
 endif (OPENMP_FOUND)
 
 #-------------------------------------------------------------------------------
-# TPLs
+# External dependencies
 #-------------------------------------------------------------------------------
 
-# Find and/or build the required TPLs.
-add_subdirectory(external)
-
-# We need to incorporate netcdf and exodus into the TPL build process, but for
-# now we require them to be prebuilt and installed someplace.  EXODUS_LIB_DIR
-# must be set on the command line to the directory containing the libraries.
-# Source tarballs for the packages are in external/tarballs.
-find_library(EXODUS_LIBRARY exoIIv2c)
-find_library(NETCDF_LIBRARY netcdf)
-if(EXODUS_LIBRARY STREQUAL "EXODUS_LIBRARY-NOTFOUND" OR
-   NETCDF_LIBRARY STREQUAL "NETCDF_LIBRARY-NOTFOUND")
-  message(FATAL_ERROR "ERROR! Could not find the netcdf and/or exoIIv2c "
-          "libraries in EXODUS_LIB_DIR=${EXODUS_LIB_DIR}")
+set(CMAKE_PREFIX_PATH ${PECECILLO_TPL_DIR})
+
+# HYPRE library
+find_package(HYPRE 2.9.0)
+if(HYPRE_FOUND)
+  if(HYPRE_IS_PARALLEL)
+    set(HYPRE_FOUND False)
+    message(STATUS "Require serial HYPRE library but found unsuitable parallel library")
+  endif()
+endif()
+if(NOT HYPRE_FOUND)
+  message(FATAL_ERROR "Could NOT find a suitable Hypre installation")
+endif()
+
+# HDF5 library
+find_package(HDF5 "1.8.8" COMPONENTS C HL)
+if(HDF5_FOUND)
+  if(HDF5_IS_PARALLEL)
+    set(HDF5_FOUND False)
+    message(STATUS "Require serial HDF5 library but found unsuitable parallel library")
+  endif()
+endif()
+if(HDF5_FOUND)
+  add_library(hdf5 INTERFACE)
+  target_link_libraries(hdf5 INTERFACE ${HDF5_LIBRARIES})
+  target_include_directories(hdf5 INTERFACE ${HDF5_INCLUDE_DIRS})
+  target_compile_definitions(hdf5 INTERFACE ${HDF5_DEFINITIONS})
+else()
+  message(FATAL_ERROR "Could NOT find a suitable HDF5 installation")
 endif()
-add_library(exodus STATIC IMPORTED)
-set_target_properties(exodus PROPERTIES
-    IMPORTED_LOCATION ${EXODUS_LIBRARY}
-    IMPORTED_LINK_INTERFACE_LIBRARIES ${NETCDF_LIBRARY})
-message(STATUS "NETCDF_LIBRARY=${NETCDF_LIBRARY}")
 
-find_package(LAPACK)
+# NetCDF library
+find_package(NetCDF "4.1.3")
+if(NETCDF_FOUND)
+  if(NOT NETCDF_HAS_NC4)
+    message(STATUS "Found unsuitable NetCDF without the required netcdf-4 feature")
+    set(NETCDF_FOUND False)
+  endif()
+endif()
+if(NOT NETCDF_FOUND)
+  message(FATAL_ERROR "Could NOT find a suitable NetCDF installation")
+endif()
+
+# ExodusII library
+find_package(Exodus "602" EXACT)
+if(NOT EXODUS_FOUND)
+  message(FATAL_ERROR "Could NOT find a suitable Exodus installation")
+endif()
 
+# YAJL library
+find_package(YAJL)
+if(NOT YAJL_FOUND)
+  message(FATAL_ERROR "Could NOT find a suitable YAJL library")
+endif()
+
+# LAPACK library
+find_package(LAPACK)
+if(NOT LAPACK_FOUND)
+  message(FATAL_ERROR "Could NOT find a suitable LAPACK library")
+endif()
 
 #-------------------------------------------------------------------------------
 # Installation Definitions
 #-------------------------------------------------------------------------------
 
-add_subdirectory(petaca)
-set(Petaca_MODULE_DIR ${Petaca_BINARY_DIR}/mod_files/)
+# RPATH handling for installed shared libraries and dynamically-linked
+# executables.  See http://www.cmake.org/Wiki/CMake_RPATH_handling
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
-set(Pececillo_MODULE_DIR ${Pececillo_BINARY_DIR}/mod_files/)
-set(CMAKE_Fortran_MODULE_DIRECTORY ${Pececillo_MODULE_DIR})
 add_subdirectory(src)

README.md

@@ -0,0 +1,10 @@
+# Paraboloid Curvature
+
+## Building
+
+
+
+    $ mkdir build
+    $ cd build
+    $ cmake -DCMAKE_PREFIX_PATH=/your/pececillo-tpl/install/path ..
+    $ make

cmake/Modules/FindExodus.cmake

@@ -0,0 +1,54 @@
+# This module finds the Exodus library and header file directory.
+# EXODUS_FOUND is set to True if both are found and the following
+# variables are returned.
+#
+#  EXODUS_INCLUDE_DIRS - required include directories
+#  EXODUS_LIBRARIES    - required link libraries
+#  EXODUS_VERSION      - version of exodus found
+#
+# This module also defines the imported library target "exodus".  It is
+# generally enough to include "exodus" as a target link library; cmake
+# will automatically handle adding the appropriate compile include flags
+# and collection of link libraries.
+#
+# Set the variable CMAKE_PREFIX_PATH to provide a hint to the module for
+# where to find the library and header file.  This is searched before the
+# standard system locations.
+#
+# Find_package(NetCDF) should be run before using this module.
+
+#if(Exodus_FIND_QUIETLY)
+#  set(_find_netcdf_arg QUIET)
+#endif()
+#find_package(NetCDF ${_find_netcdf_arg})
+#unset(_find_netcdf_arg)
+
+find_path(EXODUS_INCLUDE_DIR exodusII.h)
+find_library(EXODUS_LIBRARY exoIIv2c)
+
+# Identify the ExodusII API version (not exactly the library version)
+if(EXODUS_INCLUDE_DIR)
+  set(exodusii_h ${EXODUS_INCLUDE_DIR}/exodusII.h)
+  include(SearchHeaderFile)
+  search_header_file(${exodusii_h} "EX_API_VERS_NODOT" EXODUS_VERSION)
+endif()
+
+# Set EXODUS_FOUND to TRUE of the REQUIRED variables have been set.
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Exodus
+                                  REQUIRED_VARS EXODUS_LIBRARY EXODUS_INCLUDE_DIR
+                                  VERSION_VAR EXODUS_VERSION)
+
+if(EXODUS_FOUND)
+  set(EXODUS_INCLUDE_DIRS ${EXODUS_INCLUDE_DIR} ${NETCDF_C_INCLUDE_DIRS})
+  set(EXODUS_LIBRARIES ${EXODUS_LIBRARY} ${NETCDF_C_LIBRARIES})
+  list(REMOVE_DUPLICATES EXODUS_INCLUDE_DIRS)
+  mark_as_advanced(EXODUS_INCLUDE_DIR EXODUS_LIBRARY)
+  if(NOT TARGET exodus)
+    add_library(exodus UNKNOWN IMPORTED)
+    set_target_properties(exodus PROPERTIES
+        IMPORTED_LOCATION "${EXODUS_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${EXODUS_INCLUDE_DIRS}"
+        INTERFACE_LINK_LIBRARIES "${NETCDF_C_LIBRARIES}")
+  endif()
+endif()

cmake/Modules/FindHYPRE.cmake

@@ -6,107 +6,68 @@
 # === Variables ===
 #
 # HYPRE_FOUND             Flag indicating if HYPRE is found
-# HYPRE_VERSION           HYPRE version 
-# HYPRE_INCLUDE_DIRS      List of paths required to compile 
+# HYPRE_VERSION           HYPRE version
+# HYPRE_INCLUDE_DIRS      List of paths required to compile
 #                         with HYPRE
 # HYPRE_LIBRARIES         List libraries (targets?) required
 #                         to link against HYPRE.
-# HYPRE_IS_PARALLEL       HYPRE was found 
+# HYPRE_IS_PARALLEL       HYPRE was found
 #
 # HYPRE_INSTALL_PREFIX    Hypre installation prefix. Used in the
 #                         library and include file search.
 # === Usage ===
-# 
+#
 # Call this module with FIND_PACKAGE(HYPRE) in any CMakeLists.txt
 # that requires HYPRE include directories or libraries. The search
 # can be bypassed by explicitly setting HYPRE_INCLUDE_DIRS and
-# HYPRE_LIBRARIES variables. 
+# HYPRE_LIBRARIES variables.
 #
 # The variables HYPRE_INSTALL_PREFIX or ENV HYPRE_ROOT control
 # search locations for include and libraries.
 #
-include(FindPackageHandleStandardArgs)
-include(PrintVariable)
-
-# --- MACROS/FUNCTIONS
-FUNCTION(_search_hypre_config_file config_h defmacro outvar)
-  if ( EXISTS "${config_h}" )
-    set(_regexp ".define[ \\t]+${defmacro}")
-    set(_quote "\"")
-    FILE(STRINGS "${config_h}" _tmp_string REGEX "${_regexp}")
-    STRING(REGEX REPLACE ".define ${defmacro}[ \\t]+(.*)$" "\\1" _result "${_tmp_string}")
-    STRING(REPLACE "${_quote}" " " _result "${_result}")
-    STRING(REGEX REPLACE "[ \t\n]+" "" _result "${_result}")
-  else()
-    set(_result ${outvar}-NOTFOUND)
-  endif()
-  set(${outvar} ${_result} PARENT_SCOPE)
-
-ENDFUNCTION()
 
-# --- Begin main
+set(hypre_search_paths ${HYPRE_DIR} ENV HYPRE_ROOT)
+find_library(HYPRE_LIBRARY HYPRE HINTS ${hypre_search_paths} PATH_SUFFIXES lib)
+find_path(HYPRE_INCLUDE_DIR HYPRE.h HINTS ${hypre_search_paths} PATH_SUFFIXES include)
 
-# Search for HYPRE.h
-find_path(HYPRE_INCLUDE_DIR
-          NAMES HYPRE.h
-          HINTS ENV HYPRE_ROOT ${HYPRE_INSTALL_PREFIX}
-	  PATH_SUFFIXES include)
-
-# Search for HYPRE library
-find_library(HYPRE_LIBRARY
-             NAMES HYPRE
-             HINTS ENV HYPRE_ROOT ${HYPRE_INSTALL_PREFIX}
-	     PATH_SUFFIXES lib)
-
-# Define the cofig header file, will mine this to determine version
-# and build type (MPI, non-MPI)
-if ( HYPRE_INCLUDE_DIR )
+if(HYPRE_INCLUDE_DIR)
   set(HYPRE_CONFIG_FILE ${HYPRE_INCLUDE_DIR}/HYPRE_config.h)
-endif()
-
-# Define the version
-if ( NOT HYPRE_VERSION  AND HYPRE_CONFIG_FILE )
-  _search_hypre_config_file(${HYPRE_CONFIG_FILE} HYPRE_RELEASE_VERSION HYPRE_VERSION)
-endif()
-
-# Define the build (MPI or non-MPI)
-if (HYPRE_CONFIG_FILE)
-  _search_hypre_config_file(${HYPRE_CONFIG_FILE} HYPRE_HAVE_MPI HYPRE_IS_PARALLEL)
+  include(SearchHeaderFile)
+  search_header_file(${HYPRE_CONFIG_FILE} "HYPRE_HAVE_MPI" HYPRE_IS_PARALLEL)
   if(HYPRE_IS_PARALLEL)
     set(HYPRE_IS_PARALLEL True)
   else()
     set(HYPRE_IS_PARALLEL False)
   endif()
-  if (HYPRE_IS_PARALLEL)
-    find_package(MPI)
-  endif()  
+  if(NOT HYPRE_VERSION)
+    search_header_file(${HYPRE_CONFIG_FILE} HYPRE_RELEASE_VERSION HYPRE_VERSION STRIP_QUOTES)
+  endif()
+  unset(HYPRE_CONFIG_FILE)
 endif()
 
-# Define the include directories, append MPI if needed
-if ( NOT HYPRE_INCLUDE_DIRS)
-  set(HYPRE_INCLUDE_DIRS ${HYPRE_INCLUDE_DIR})
-  if (HYPRE_IS_PARALLEL)
-    if (MPI_C_FOUND)
-      list(APPEND HYPRE_INCLUDE_DIRS ${MPI_C_INCLUDE_PATH})
-    endif()
-  endif()
+if(HYPRE_IS_PARALLEL)
+  find_package(MPI)
 endif()
 
-# Define the  libraries
-if ( NOT HYPRE_LIBRARIES )
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(HYPRE
+				  REQUIRED_VARS HYPRE_LIBRARY HYPRE_INCLUDE_DIR
+                                  VERSION_VAR HYPRE_VERSION)
+
+if(HYPRE_FOUND)
+  set(HYPRE_INCLUDE_DIRS ${HYPRE_INCLUDE_DIR})
   set(HYPRE_LIBRARIES ${HYPRE_LIBRARY})
-  if (HYPRE_IS_PARALLEL)
+  if(HYPRE_IS_PARALLEL AND MPI_C_FOUND)
     list(APPEND HYPRE_LIBRARIES ${MPI_C_LIBRARIES})
+    list(APPEND HYPRE_INCLUDE_DIRS ${MPI_C_INCLUDE_PATH})
   endif()
-endif()  
-
-# Send a useful message if everything is found
-find_package_handle_standard_args(HYPRE 
-                                  VERSION_VAR HYPRE_VERSION
-				  REQUIRED_VARS HYPRE_LIBRARY HYPRE_INCLUDE_DIRS HYPRE_LIBRARIES)
-
-mark_as_advanced(
-                 HYPRE_INCLUDE_DIR
-                 HYPRE_CONFIG_FILE
-                 HYPRE_LIBRARY)
-
+  if(NOT TARGET hypre)
+    add_library(hypre UNKNOWN IMPORTED)
+    set_target_properties(hypre PROPERTIES
+        IMPORTED_LOCATION "${HYPRE_LIBRARY}"
+        #IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+        INTERFACE_INCLUDE_DIRECTORIES "${HYPRE_INCLUDE_DIRS}"
+        INTERFACE_LINK_LIBRARIES "${HYPRE_LIBRARIES}")
+        #INTERFACE_COMPILE_DEFINITIONS "${MPI_C_COMPILE_FLAGS}")
+  endif()
+endif()