Adapt examples to cmake build system.

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/100k/CMakeLists.txt

@@ -0,0 +1,35 @@
+# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification)
+# is a mathematical modelling environment that enables the application of finite element
+# analysis techniques to a variety of complex bioengineering problems.
+# 
+# The OpenCMISS project website can be found at http://www.opencmiss.org
+# For more information see http://www.opencmiss.org/documentation
+
+# Include the OpenCMISS initalisation & macro definition file.
+include(./OpenCMISS.cmake)
+
+# Project setup
+# -------------
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+project(OpenCMISS-Example VERSION 1.0 LANGUAGES C)
+enable_language(Fortran OPTIONAL)
+enable_testing()
+
+# Find OpenCMISS
+# --------------
+#
+# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. 
+# Currently available OpenCMISS package components: Iron Zinc
+# Requiring Iron will also include the iron_c bindings target if available.
+#
+# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components.
+# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include
+# paths needed!               
+find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG)
+
+# CMake application code
+# ----------------------
+#add_subdirectory(C)
+if (CMAKE_Fortran_COMPILER)
+    add_subdirectory(Fortran)
+endif()

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/100k/Fortran/CMakeLists.txt

@@ -0,0 +1,60 @@
+
+# Add example executable
+add_executable(100k  src/100kExample.f90)
+
+# Turn on Fortran preprocessing (#include directives)
+if (MSVC)
+    set(PROC_OPT "/fpp")
+else()
+    set(PROC_OPT "-cpp")
+endif()
+
+# in debug mode, add flag that make Floating point exceptions fatal
+set(OPT "")
+if (FALSE)
+    if(CMAKE_BUILD_TYPE MATCHES DEBUG)
+        set(OPT "-ffpe-trap=invalid,zero,underflow,overflow,denormal")		# GCC: make floating point exceptions fatal
+    endif()
+endif()
+
+target_compile_options(100k PRIVATE ${PROC_OPT} ${OPT} "-fbacktrace")
+
+# Link to opencmiss
+# -----------------
+#
+# This simply uses the opencmiss target created by OC_INIT() above.
+#
+# Alternatively, you can also directly invoke 'find_package(Iron <IRON_VERSION>)' to explicitly
+# require that version. But then you have to deal with setting up the correct MPI include directives and library paths.
+#
+# If required, add any other required link libraries (cellml, petsc ..) here, too.
+# For example, if you needed PetSC functionality, issue
+#
+#     find_package(PETSC <PETSC_VERSION> REQUIRED)
+#     target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc)
+#
+# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name.
+target_link_libraries(100k PRIVATE opencmiss)
+
+# Add a simple test that runs the executable
+add_test(NAME test_100k COMMAND 100k)
+add_opencmiss_environment(test_100k)
+
+###################
+# Developer notice!
+#
+# If you write Fortran code and use MPI, you need to use the following MPI directives:
+#
+# #ifndef NOMPIMOD
+#   USE MPI
+# #endif
+# [...]
+#   IMPLICIT NONE
+# [...]
+# #ifdef NOMPIMOD
+#     #include "mpif.h"
+# #endif
+#
+# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make
+# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly.
+#

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/100k/OpenCMISS.cmake

@@ -0,0 +1,95 @@
+###########################
+# *DO NOT CHANGE THIS FILE*
+###########################
+#
+# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations.
+#
+# Search order:
+#     - OPENCMISS_INSTALL_DIR variable
+#     - OPENCMISS_INSTALL_DIR environment variable
+#     - OPENCMISS_SDK_DIR variable
+#     - OPENCMISS_SDK_DIR environment variable
+#     - [Windows only] The Registry is searched additionally for installed SDKs.
+#
+# If found
+#     - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows)
+
+# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places
+if (DEFINED OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.")
+    endif()
+endif()    
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_SDK_DIR)
+    endif()
+endif()
+# On windows: check the registry for installed OpenCMISS SDKs
+if(NOT OPENCMISS_INSTALL_DIR AND WIN32)
+    foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE)
+        foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK)
+            set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]")
+            get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE)
+            #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+            if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+                message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+                break()
+            else()
+                unset(OPENCMISS_INSTALL_DIR)
+            endif()         
+        endforeach()
+        if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+            break()
+        endif()
+    endforeach()
+endif()
+
+if(OPENCMISS_INSTALL_DIR)
+    message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}")
+    # Use the OpenCMISS scripts to also allow choosing a separate toolchain
+    # This file is located at the opencmiss installation rather than the local example
+    # as it avoids file replication and makes maintenance much easier
+    if (TOOLCHAIN)
+        set(_OCTC ${OPENCMISS_INSTALL_DIR}/cmake/OCToolchainCompilers.cmake)
+        if (EXISTS "${_OCTC}")
+            include(${_OCTC})
+        else()
+            message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.")
+        endif()
+        unset(_OCTC)
+    endif()
+    set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation")    
+else()
+    message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.")
+endif()
+

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/100k/build_debug/build.sh

@@ -0,0 +1,2 @@
+#ccc && cmake -DOPENCMISS_BUILD_TYPE=DEBUG -DCMAKE_BUILD_TYPE=DEBUG  .. && make all
+cmake -DOPENCMISS_BUILD_TYPE=DEBUG -DCMAKE_BUILD_TYPE=DEBUG  .. && make all

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/10k/CMakeLists.txt

@@ -0,0 +1,35 @@
+# OpenCMISS (Open Continuum Mechanics, Imaging, Signal processing and System identification)
+# is a mathematical modelling environment that enables the application of finite element
+# analysis techniques to a variety of complex bioengineering problems.
+# 
+# The OpenCMISS project website can be found at http://www.opencmiss.org
+# For more information see http://www.opencmiss.org/documentation
+
+# Include the OpenCMISS initalisation & macro definition file.
+include(./OpenCMISS.cmake)
+
+# Project setup
+# -------------
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+project(OpenCMISS-Example VERSION 1.0 LANGUAGES C)
+enable_language(Fortran OPTIONAL)
+enable_testing()
+
+# Find OpenCMISS
+# --------------
+#
+# This call tries to find a matching OpenCMISS (SDK) installation for your (default) Toolchain and MPI choice. 
+# Currently available OpenCMISS package components: Iron Zinc
+# Requiring Iron will also include the iron_c bindings target if available.
+#
+# This function creates a link target 'opencmiss' that contains references to the requested OpenCMISS components.
+# For Iron, it also adds the necessary MPI information - no further find_package(MPI ..) and setting of extra include
+# paths needed!               
+find_package(OpenCMISS 1.1 REQUIRED COMPONENTS Iron CONFIG)
+
+# CMake application code
+# ----------------------
+#add_subdirectory(C)
+if (CMAKE_Fortran_COMPILER)
+    add_subdirectory(Fortran)
+endif()

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/10k/Fortran/CMakeLists.txt

@@ -0,0 +1,60 @@
+
+# Add example executable
+add_executable(10k  src/10kExample.f90)
+
+# Turn on Fortran preprocessing (#include directives)
+if (MSVC)
+    set(PROC_OPT "/fpp")
+else()
+    set(PROC_OPT "-cpp")
+endif()
+
+# in debug mode, add flag that make Floating point exceptions fatal
+set(OPT "")
+if (FALSE)
+    if(CMAKE_BUILD_TYPE MATCHES DEBUG)
+        set(OPT "-ffpe-trap=invalid,zero,underflow,overflow,denormal")		# GCC: make floating point exceptions fatal
+    endif()
+endif()
+
+target_compile_options(10k PRIVATE ${PROC_OPT} ${OPT} "-fbacktrace")
+
+# Link to opencmiss
+# -----------------
+#
+# This simply uses the opencmiss target created by OC_INIT() above.
+#
+# Alternatively, you can also directly invoke 'find_package(Iron <IRON_VERSION>)' to explicitly
+# require that version. But then you have to deal with setting up the correct MPI include directives and library paths.
+#
+# If required, add any other required link libraries (cellml, petsc ..) here, too.
+# For example, if you needed PetSC functionality, issue
+#
+#     find_package(PETSC <PETSC_VERSION> REQUIRED)
+#     target_link_libraries(${EXAMPLE_BINARY} PRIVATE petsc)
+#
+# All the OpenCMISS dependencies provide a target you can link against corresponding to the (lowercase) component name.
+target_link_libraries(10k PRIVATE opencmiss)
+
+# Add a simple test that runs the executable
+add_test(NAME test_10k COMMAND 10k)
+add_opencmiss_environment(test_10k)
+
+###################
+# Developer notice!
+#
+# If you write Fortran code and use MPI, you need to use the following MPI directives:
+#
+# #ifndef NOMPIMOD
+#   USE MPI
+# #endif
+# [...]
+#   IMPLICIT NONE
+# [...]
+# #ifdef NOMPIMOD
+#     #include "mpif.h"
+# #endif
+#
+# Reasoning: In some cases like Windows/MPICH2 there sometimes is no mpi.mod file. In order to yet make
+# the example work the build system adds the definition 'NOMPIMOD', which can be checked and acted to accordingly.
+#

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/10k/OpenCMISS.cmake

@@ -0,0 +1,95 @@
+###########################
+# *DO NOT CHANGE THIS FILE*
+###########################
+#
+# Prepares the use of OpenCMISS by scanning at various path locations for OpenCMISS (SDK) installations.
+#
+# Search order:
+#     - OPENCMISS_INSTALL_DIR variable
+#     - OPENCMISS_INSTALL_DIR environment variable
+#     - OPENCMISS_SDK_DIR variable
+#     - OPENCMISS_SDK_DIR environment variable
+#     - [Windows only] The Registry is searched additionally for installed SDKs.
+#
+# If found
+#     - Includes the toolchain config script of the found opencmiss installation to enable toolchain selection logic (non-windows)
+
+# Convenience: The OPENCMISS_INSTALL_DIR may also be defined in the environment and various other places
+if (DEFINED OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using specified installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The specified OPENCMISS_INSTALL_DIR '${OPENCMISS_INSTALL_DIR}' does not exist. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_INSTALL_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_INSTALL_DIR}" OPENCMISS_INSTALL_DIR)
+    get_filename_component(OPENCMISS_INSTALL_DIR "${OPENCMISS_INSTALL_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+        message(STATUS "Using environment installation directory '${OPENCMISS_INSTALL_DIR}'")
+    else()
+        message(WARNING "The environment variable OPENCMISS_INSTALL_DIR='${OPENCMISS_INSTALL_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_INSTALL_DIR)
+    endif()
+endif()
+if (NOT OPENCMISS_INSTALL_DIR AND DEFINED OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The specified OPENCMISS_SDK_DIR '${OPENCMISS_SDK_DIR}' does not exist. Skipping.")
+    endif()
+endif()    
+if(NOT OPENCMISS_INSTALL_DIR AND NOT "$ENV{OPENCMISS_SDK_DIR}" STREQUAL "")
+    file(TO_CMAKE_PATH "$ENV{OPENCMISS_SDK_DIR}" OPENCMISS_SDK_DIR)
+    get_filename_component(OPENCMISS_SDK_DIR "${OPENCMISS_SDK_DIR}" ABSOLUTE)
+    if (EXISTS "${OPENCMISS_SDK_DIR}")
+        message(STATUS "Using environment SDK installation directory: ${OPENCMISS_SDK_DIR}")
+        set(OPENCMISS_INSTALL_DIR "${OPENCMISS_SDK_DIR}")
+    else()
+        message(WARNING "The environment variable OPENCMISS_SDK_DIR='${OPENCMISS_SDK_DIR}' contains an invalid path. Skipping.")
+        unset(OPENCMISS_SDK_DIR)
+    endif()
+endif()
+# On windows: check the registry for installed OpenCMISS SDKs
+if(NOT OPENCMISS_INSTALL_DIR AND WIN32)
+    foreach(ROOT HKEY_CURRENT_USER HKEY_LOCAL_MACHINE)
+        foreach(PACKAGE OpenCMISSUserSDK OpenCMISSDeveloperSDK)
+            set(_REG_KEY "[${ROOT}\\Software\\Auckland Bioengineering Institute\\${PACKAGE}]")
+            get_filename_component(OPENCMISS_INSTALL_DIR "${_REG_KEY}" ABSOLUTE)
+            #message(STATUS "Trying registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+            if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+                message(STATUS "Found ${PACKAGE} in Windows registry key ${_REG_KEY}: ${OPENCMISS_INSTALL_DIR}")
+                break()
+            else()
+                unset(OPENCMISS_INSTALL_DIR)
+            endif()         
+        endforeach()
+        if (EXISTS "${OPENCMISS_INSTALL_DIR}")
+            break()
+        endif()
+    endforeach()
+endif()
+
+if(OPENCMISS_INSTALL_DIR)
+    message(STATUS "OPENCMISS_INSTALL_DIR=${OPENCMISS_INSTALL_DIR}")
+    # Use the OpenCMISS scripts to also allow choosing a separate toolchain
+    # This file is located at the opencmiss installation rather than the local example
+    # as it avoids file replication and makes maintenance much easier
+    if (TOOLCHAIN)
+        set(_OCTC ${OPENCMISS_INSTALL_DIR}/cmake/OCToolchainCompilers.cmake)
+        if (EXISTS "${_OCTC}")
+            include(${_OCTC})
+        else()
+            message(WARNING "TOOLCHAIN specified but OpenCMISS config script could not be found at ${_OCTC}. Trying CMake defaults.")
+        endif()
+        unset(_OCTC)
+    endif()
+    set(OpenCMISS_DIR "${OPENCMISS_INSTALL_DIR}" CACHE PATH "Path to the found OpenCMISS (SDK) installation")    
+else()
+    message(WARNING "No OpenCMISS (SDK) installation directory detected. Using default system environment.")
+endif()
+

42TestingPoints/SinglePhysics/LinearProblems/StaticProblems/Stokes/3D/HEX/QuadraticVelocityLinearPressure/LEVEL_3/10k/build_debug/build.sh

@@ -0,0 +1,2 @@
+#ccc && cmake -DOPENCMISS_BUILD_TYPE=DEBUG -DCMAKE_BUILD_TYPE=DEBUG  .. && make all
+cmake -DOPENCMISS_BUILD_TYPE=DEBUG -DCMAKE_BUILD_TYPE=DEBUG  .. && make all