Merge remote-tracking branch 'upstream/release/2013.03' into combined

CMakeLists.txt

@@ -36,7 +36,7 @@ set (${project}_DEPS
 	# Tim Davis' SuiteSparse archive
 	"SuiteSparse COMPONENTS umfpack"
 	# solver
-	"SUPERLU"
+	"SuperLU"
 	# xml processing (for config parsing)
 	"TinyXML"
 	# Ensembles-based Reservoir Tools (ERT)
@@ -97,8 +97,13 @@ include (UseOptimization)
 # dependencies, in case they alter the list of warnings
 include (UseWarnings)
 
+# parallel computing must be explicitly enabled
+option (USE_MPI "Use Message Passing Interface for parallel computing" OFF)
+if (NOT USE_MPI)
+	set (CMAKE_DISABLE_FIND_PACKAGE_MPI TRUE)
+endif (NOT USE_MPI)
+
 ### --- begin opm-core specific --- ###
-# parallel programming
 include (UseOpenMP)
 find_openmp (${project})
 ### --- end opm-core specific --- ###

cmake/Modules/Duplicates.cmake

@@ -22,23 +22,17 @@ endmacro (remove_duplicate_libraries module)
 
 # headers can be trimmed from the end, since adding a directory to
 # the list is an idempotent action
-macro (remove_duplicate_headers module)
+macro (remove_duplicate_var module suffix)
-  if (DEFINED ${module}_INCLUDE_DIRS)
+  if (DEFINED ${module}_${suffix})
-	list (REMOVE_DUPLICATES ${module}_INCLUDE_DIRS)
+	list (REMOVE_DUPLICATES ${module}_${suffix})
-  endif (DEFINED ${module}_INCLUDE_DIRS)
+  endif (DEFINED ${module}_${suffix})
-endmacro (remove_duplicate_headers module)
+endmacro (remove_duplicate_var module suffix)
-
-# linker flags may not be specified at all
-macro (remove_duplicate_flags module)
-  if (DEFINED ${module}_LINKER_FLAGS)
-	list (REMOVE_DUPLICATES ${module}_LINKER_FLAGS)
-  endif (DEFINED ${module}_LINKER_FLAGS)
-endmacro (remove_duplicate_flags module)
 
 # fix up both headers and libraries, in case two dependencies have
 # included the same second-level library independently
 macro (remove_dup_deps module)
-  remove_duplicate_headers (${module})
+  remove_duplicate_var (${module} INCLUDE_DIRS)
+  remove_duplicate_var (${module} LINKER_FLAGS)
+  remove_duplicate_var (${module} CONFIG_VARS)
   remove_duplicate_libraries (${module})
-  remove_duplicate_flags (${module})
 endmacro (remove_dup_deps module)

cmake/Modules/Finddune-common.cmake

@@ -18,7 +18,8 @@ find_opm_package (
   # dependencies
   "CXX11Features REQUIRED;
   BLAS REQUIRED;
-  LAPACK REQUIRED
+  LAPACK REQUIRED;
+  MPI
   "
   # header to search for
   "dune/common/fvector.hh"

cmake/Modules/Finddune-istl.cmake

@@ -24,7 +24,7 @@ find_opm_package (
 
   # required dependencies
   "dune-common ${_require_dune_common};
-  SUPERLU
+  SuperLU
   "
   # header to search for
   "dune/istl/bcrsmatrix.hh"

cmake/Modules/Findopm-core.cmake

@@ -24,7 +24,7 @@ find_opm_package (
   BLAS REQUIRED;
   LAPACK REQUIRED;
   SuiteSparse COMPONENTS umfpack;
-  SUPERLU;
+  SuperLU;
   TinyXML;
   ERT;
   dune-istl

cmake/Modules/OpmFind.cmake

@@ -51,6 +51,14 @@ foreach (name IN LISTS _opm_proj_vars)
   endif (NOT DEFINED ${CMAKE_PROJECT_NAME}_${name})
 endforeach (name)
 
+# these dependencies must always be handled by the find module
+set (_opm_proj_exemptions
+  dune-common
+  dune-istl
+  dune-grid
+  dune-geometry
+  )
+
 # insert this boilerplate whenever we are going to find a new package
 macro (find_and_append_package_to prefix name)
   # if we have specified a directory, don't revert to searching the
@@ -71,6 +79,28 @@ macro (find_and_append_package_to prefix name)
 	  set (${name}_DIR "${${NAME}_ROOT}")
 	endif (EXISTS ${${NAME}_ROOT}/${name}-config.cmake OR EXISTS ${${NAME}_ROOT}/${name}Config.cmake)
   endif (NOT DEFINED ${name}_DIR AND (DEFINED ${name}_ROOT OR DEFINED ${NAME}_ROOT))
+
+  # these libraries need special handling which is not provided in
+  # the -config.cmake file, but which must be provided by this project,
+  # something which is done in our find module
+  list (FIND _opm_proj_exemptions "${name}" _${name}_exempted)
+  if ((NOT (_${name}_exempted EQUAL -1)) AND (DEFINED ${name}_DIR))
+	# most often we are given the name to the build directory and this
+	# is a sub-directory of the source tree
+	if (${name}_DIR MATCHES "build")
+	  get_filename_component (${name}_ROOT "${${name}_DIR}" PATH)
+	else (${name}_DIR MATCHES "build")
+	  set (${name}_ROOT "${${name}_DIR}")
+	endif (${name}_DIR MATCHES "build")
+	# store this for later, in case we reconfigure
+	set (${name}_ROOT "${${name}_ROOT}" CACHE LOCATION "Path to ${name}")
+	# clear this to not use config mode
+	unset (${name}_DIR)
+	# variables that are given on the command-line is also put in the cache
+	# removing the local copy only "unshadows" this one
+	unset (${name}_DIR CACHE)
+  endif ((NOT (_${name}_exempted EQUAL -1)) AND (DEFINED ${name}_DIR))
+
   # using config mode is better than using module (aka. find) mode
   # because then the package has already done all its probes and
   # stored them in the config file for us
@@ -81,23 +111,40 @@ macro (find_and_append_package_to prefix name)
 	message (STATUS "Finding package ${name} using module mode")
 	find_package (${name} ${ARGN})
   endif (${name}_DIR)
-  if (${name}_FOUND)
+
+  # the variable "NAME" may be replaced during find_package (as this is
+  # now a macro, and not a function anymore), so we must reinitialize
+  string (TOUPPER "${name}" NAME)
+  string (REPLACE "-" "_" NAME "${NAME}")
+
+  if (${name}_FOUND OR ${NAME}_FOUND)
 	foreach (var IN LISTS _opm_proj_vars)
 	  if (DEFINED ${name}_${var})
 		list (APPEND ${prefix}_${var} ${${name}_${var}})
-		# cleanup lists
+	  # some packages define an uppercase version of their own name
-		if ("${var}" STREQUAL "LIBRARIES")
+	  elseif (DEFINED ${NAME}_${var})
-		  remove_duplicate_libraries (${prefix})
+		list (APPEND ${prefix}_${var} ${${NAME}_${var}})
-		else ("${var}" STREQUAL "LIBRARIES")
-		  list (REMOVE_DUPLICATES ${prefix}_${var})
-		endif ("${var}" STREQUAL "LIBRARIES")
 	  endif (DEFINED ${name}_${var})
+	  # some packages define _PATH instead of _DIRS (Hi, MPI!)
+	  if ("${var}" STREQUAL "INCLUDE_DIRS")
+		if (DEFINED ${name}_INCLUDE_PATH)
+		  list (APPEND ${prefix}_INCLUDE_DIRS ${${name}_INCLUDE_PATH})
+		elseif (DEFINED ${NAME}_INCLUDE_PATH)
+		  list (APPEND ${prefix}_INCLUDE_DIRS ${${NAME}_INCLUDE_PATH})
+		endif (DEFINED ${name}_INCLUDE_PATH)
+	  endif ("${var}" STREQUAL "INCLUDE_DIRS")
+	  # cleanup lists
+	  if ("${var}" STREQUAL "LIBRARIES")
+		remove_duplicate_libraries (${prefix})
+	  else ("${var}" STREQUAL "LIBRARIES")
+		remove_duplicate_var (${prefix} ${var})
+	  endif ("${var}" STREQUAL "LIBRARIES")
 	endforeach (var)
 	# some libraries only define xxx_FOUND and not a corresponding HAVE_xxx
 	if (NOT DEFINED HAVE_${NAME})
 	  set (HAVE_${NAME} 1)
 	endif (NOT DEFINED HAVE_${NAME})
-  endif (${name}_FOUND)
+  endif (${name}_FOUND OR ${NAME}_FOUND)
 endmacro (find_and_append_package_to prefix name)
 
 # append to the list of variables associated with the project

cmake/Modules/OpmPackage.cmake

@@ -37,7 +37,8 @@
 
 # <http://www.vtk.org/Wiki/CMake:How_To_Find_Libraries>
 
-include (Duplicates)
+include (OpmFind)
+
 # append all items from src into dst; both must be *names* of lists
 macro (append_found src dst)
   foreach (_item IN LISTS ${src})
@@ -47,7 +48,7 @@ macro (append_found src dst)
   endforeach (_item)
 endmacro (append_found src dst)
 
-function (find_opm_package module deps header lib defs prog conf)
+macro (find_opm_package module deps header lib defs prog conf)
   # variables to pass on to other packages
   if (FIND_QUIETLY)
 	set (${module}_QUIET "QUIET")
@@ -60,16 +61,6 @@ function (find_opm_package module deps header lib defs prog conf)
 	return ()
   endif (${${module}_FOUND})
 
-  # dependencies on other packages; underscore version only contains the
-  # name of the other package
-  set (_deps)
-  foreach (_dep IN LISTS deps)
-	separate_arguments (_args UNIX_COMMAND ${_dep})
-	find_package (${_args} QUIET)
-	list (GET _args 0 _name_only)
-	list (APPEND _deps ${_name_only})
-  endforeach (_dep)
-
   # see if there is a pkg-config entry for this package, and use those
   # settings as a starting point
   find_package (PkgConfig)
@@ -88,17 +79,22 @@ function (find_opm_package module deps header lib defs prog conf)
   # in standard system locations either, then start to wander
   # about and look for it in proximity to ourself. Qt Creator likes
   # to put the build-directories as siblings to the source trees,
-  # but with a -build suffix
+  # but with a -build suffix, DUNE likes to have the the build tree
+  # in a "build-cmake" sub-directory of each module
   if (NOT (${module}_DIR OR ${module}_ROOT OR ${MODULE}_ROOT))
 	string (TOLOWER "${module}" _module_lower)
 	set (_guess
 	  "../${module}"
-	  "../${module}-build"
 	  "../${_module_lower}"
+	  )
+	set (_guess_bin_only
+	  "../${module}-build"
 	  "../${_module_lower}-build"
+	  "../../${module}/build-cmake"
+	  "../../${_module_lower}/build-cmake"
 	  )
 	set (_guess_bin)
-	foreach (_item IN ITEMS ${_guess})
+	foreach (_item IN ITEMS ${_guess} ${_guess_bin_only})
 	  list (APPEND _guess_bin "${PROJECT_BINARY_DIR}/${_item}")
 	endforeach (_item)
   endif (NOT (${module}_DIR OR ${module}_ROOT OR ${MODULE}_ROOT))
@@ -122,7 +118,7 @@ function (find_opm_package module deps header lib defs prog conf)
 	  NAMES "${lib}"
 	  PATHS ${_guess_bin}
 	  HINTS ${${module}_DIR} ${${module}_ROOT} ${${MODULE}_ROOT} ${PkgConf_${module}_LIBRARY_DIRS}
-	  PATH_SUFFIXES "lib" "lib/.libs" ".libs" "lib${_BITS}" "lib/${CMAKE_LIBRARY_ARCHITECTURE}"
+	  PATH_SUFFIXES "lib" "lib/.libs" ".libs" "lib${_BITS}" "lib/${CMAKE_LIBRARY_ARCHITECTURE}" "build-cmake/lib"
 	  )
   else (NOT "${lib}" STREQUAL "")
 	set (${module}_LIBRARY "")
@@ -132,45 +128,31 @@ function (find_opm_package module deps header lib defs prog conf)
   # list of necessities to build with the software
   set (${module}_INCLUDE_DIRS "${${module}_INCLUDE_DIR}")
   set (${module}_LIBRARIES "${${module}_LIBRARY}")
-  foreach (_dep IN LISTS _deps)
+  set (_deps)
-	# only add those packages we actually found (find_package will show
+  foreach (_dep IN ITEMS ${deps})
-	# an error if it was marked as REQUIRED)
+	separate_arguments (_args UNIX_COMMAND ${_dep})
-	if (${_dep}_FOUND)
+	find_and_append_package_to (${module} ${_args} ${${module}_QUIET})
-	  list (APPEND ${module}_INCLUDE_DIRS ${${_dep}_INCLUDE_DIRS})
+	list (GET _args 0 _name_only)
-	  list (APPEND ${module}_LIBRARIES ${${_dep}_LIBRARIES})
+	list (APPEND _deps ${_name_only})
-	  list (APPEND ${module}_DEFINITIONS ${${_dep}_DEFINITIONS})
-	  list (APPEND ${module}_CONFIG_VARS ${${_dep}_CONFIG_VARS})
-	  list (APPEND ${module}_LINKER_FLAGS ${${_dep}_LINKER_FLAGS})
-	endif (${_dep}_FOUND)
   endforeach (_dep)
 
   # compile with this option to avoid avalanche of warnings
   set (${module}_DEFINITIONS "${${module}_DEFINITIONS}")
-  foreach (_def IN LISTS defs)
+  foreach (_def IN ITEMS ${defs})
 	list (APPEND ${module}_DEFINITIONS "-D${_def}")
   endforeach (_def)
 
   # tidy the lists before returning them
-  list (REMOVE_DUPLICATES ${module}_INCLUDE_DIRS)
+  remove_dup_deps (${module})
-  remove_duplicate_libraries (${module})
-  list (REMOVE_DUPLICATES ${module}_DEFINITIONS)
 
   # these defines are used in dune/${module} headers, and should be put
   # in config.h when we include those
-  foreach (_var IN LISTS conf)
+  foreach (_var IN ITEMS ${conf})
 	# massage the name to remove source code formatting
 	string (REGEX REPLACE "^[\n\t\ ]+" "" _var "${_var}")
 	string (REGEX REPLACE "[\n\t\ ]+$" "" _var "${_var}")
 	list (APPEND ${module}_CONFIG_VARS ${_var})
   endforeach (_var)
-  foreach (_dep in _deps)
-	if (DEFINED ${_dep}_CONFIG_VARS)
-	  list (APPEND ${module}_CONFIG_VARS ${_dep}_CONFIG_VARS)
-	endif (DEFINED ${_dep}_CONFIG_VARS)
-  endforeach (_dep)
-  if (${module}_CONFIG_VARS)
-	list (REMOVE_DUPLICATES ${module}_CONFIG_VARS)
-  endif (${module}_CONFIG_VARS)
 
   # these are the defines that should be set when compiling
   # without config.h
@@ -209,17 +191,13 @@ function (find_opm_package module deps header lib defs prog conf)
 
   # some genius that coded the FindPackageHandleStandardArgs figured out
   # that the module name should be in uppercase (?!)
-  set (${module}_FOUND "${${MODULE_UPPER}_FOUND}" PARENT_SCOPE)
+  set (${module}_FOUND "${${MODULE_UPPER}_FOUND}")
 
-  # return these variables to the caller
+  # print everything out if we're asked to
-  set (${module}_INCLUDE_DIRS "${${module}_INCLUDE_DIRS}" PARENT_SCOPE)
+  if (${module}_DEBUG)
-  set (${module}_LIBRARIES "${${module}_LIBRARIES}" PARENT_SCOPE)
+	debug_find_vars (${module})
-  set (${module}_DEFINITIONS "${${module}_DEFINITIONS}" PARENT_SCOPE)
+  endif (${module}_DEBUG)
-  set (${module}_CONFIG_VARS "${${module}_CONFIG_VARS}" PARENT_SCOPE)
+endmacro (find_opm_package module deps header lib defs prog conf)
-  set (${module}_LINKER_FLAGS "${${module}_LINKER_FLAGS}" PARENT_SCOPE)
-  set (${module}_QUIET "${${module}_QUIET}" PARENT_SCOPE)
-  set (HAVE_${MODULE} "${HAVE_${MODULE}}" PARENT_SCOPE)
-endfunction (find_opm_package module deps header lib defs prog conf)
 
 # print all variables defined by the above macro
 function (debug_find_vars module)

configure

@@ -22,6 +22,7 @@ Optional Features:
   --disable-silent-rules  print every compilation statement as executed
   --enable-system-debug   put .debug files in global GDB debug dir
                           [default=yes if prefix=/usr, no otherwise]
+  --enable-parallel       process in parallel using MPI [default=no]
   --enable-openmp         activate experimental support for OpenMP
   --disable-option-checking  ignore unrecognized --enable/--with options
 
@@ -93,6 +94,7 @@ buildtype=Debug
 pch_use=
 #use_openmp=" -DUSE_OPENMP=OFF"
 use_openmp=
+use_mpi=
 #silent_rules=" -DCMAKE_VERBOSE_MAKEFILE=OFF"
 silent_rules=
 #debug_loc=" -DSYSTEM_DEBUG=OFF"
@@ -226,6 +228,10 @@ for OPT in "$@"; do
               use_openmp=" -DUSE_OPENMP=OFF"
               pkgname=""
               ;;
+            parallel)
+              use_mpi=" -DUSE_MPI=OFF"
+              pkgname=""
+              ;;
             agmg |\
             ert  |\
             superlu)
@@ -260,6 +266,15 @@ for OPT in "$@"; do
               # special flag; don't set shared/static
               shared=""
               ;;
+            parallel)
+              use_openmp=" -DUSE_MPI=ON"
+              # special flag; don't set shared/static
+              shared=""
+              ;;
+            pch)
+              pch_use=" -DPRECOMPILE_HEADERS:BOOL=ON"
+              shared=""
+              ;;
             # this flag is just for compatibility with the deprecation
             # flag in DUNE, so we can build without warnings
             fieldvector-size-is-method)
@@ -308,7 +323,7 @@ for a in "${VARS[@]}"; do
 done
 
 # pass everything on to CMake
-CMDLINE="env ${ENVVARS} ${CMAKE_COMMAND} \"${srcdir}\" \"-DCMAKE_INSTALL_PREFIX=$prefix\" -DCMAKE_BUILD_TYPE=${buildtype}${pch_use}${silent_rules}${debug_loc}${use_openmp} ${FEATURES}"
+CMDLINE="env ${ENVVARS} ${CMAKE_COMMAND} \"${srcdir}\" \"-DCMAKE_INSTALL_PREFIX=$prefix\" -DCMAKE_BUILD_TYPE=${buildtype}${pch_use}${silent_rules}${debug_loc}${use_openmp}${use_mpi} ${FEATURES}"
 echo --- calling CMake ---
 echo ${CMDLINE}
 eval exec ${CMDLINE}

opm/core/io/eclipse/EclipseGridParser.cpp

@@ -1090,7 +1090,7 @@ void EclipseGridParser::getNumericErtFields(const string& filename)
 {
 #ifdef HAVE_ERT
     // Read file
-    ecl_file_type * ecl_file = ecl_file_open(filename.c_str());
+  ecl_file_type * ecl_file = ecl_file_open(filename.c_str() , 0);
     if (ecl_file == NULL) {
         THROW("Could not open IMPORTed file " << filename);
     }