Add meshkit as an optional package

CMakeLists.txt

@@ -113,7 +113,8 @@ function (superbuild_find_projects var)
     list(APPEND projects
       fontconfig
       gperf
-      libxml2)
+      libxml2
+      meshkit)
   endif ()
 
   if (WIN32)

meshkit/CMakeLists.txt

+cmake_minimum_required(VERSION 3.6.1)
+
+project(meshkit-superbuild)
+
+function (superbuild_find_projects var)
+  set(projects
+    cgm
+    cxx11
+    eigen
+    hdf5
+    meshkit
+    moab
+    netcdf
+    szip
+    zlib)
+
+  set("${var}"
+    ${projects}
+    PARENT_SCOPE)
+endfunction ()
+
+function (superbuild_sanity_check)
+  if (NOT meshkit_enabled)
+    message(FATAL_ERROR "Meshkit is disabled...")
+  endif ()
+endfunction ()
+
+list(APPEND superbuild_version_files
+  "${CMAKE_CURRENT_LIST_DIR}/versions.cmake"
+  "${CMAKE_CURRENT_LIST_DIR}/../versions.cmake")
+list(APPEND superbuild_project_roots
+  "${CMAKE_CURRENT_LIST_DIR}/projects"
+  "${CMAKE_CURRENT_LIST_DIR}/../projects")
+
+# set the default arguments used for "git clone"
+set(_git_clone_arguments_default --progress)
+
+# set the default for meshkit to be enabled for this project
+set(_superbuild_default_meshkit ON)
+
+if (NOT EXISTS "${CMAKE_CURRENT_LIST_DIR}/../superbuild/CMakeLists.txt")
+  message(FATAL_ERROR "It appears as though the superbuild infrastructure "
+                      "is missing; did you forget to do `git submodule init` "
+                      "and `git submodule update`?")
+endif ()
+
+add_subdirectory("${CMAKE_CURRENT_LIST_DIR}/../superbuild" "${CMAKE_CURRENT_BINARY_DIR}/superbuild")

meshkit/projects/cgm.cmake

+superbuild_add_project(cgm
+  DEPENDS_OPTIONAL cxx11
+  CMAKE_ARGS
+    # Set link path on linux
+    -DCMAKE_INSTALL_RPATH:PATH=$ORIGIN/../lib
+    # Set link path on OSX
+    -DCMAKE_INSTALL_NAME_DIR:PATH=<INSTALL_DIR>/lib
+    -DCGM_OCC:BOOL=OFF
+    -DUSE_MPI:BOOL=OFF)
+
+superbuild_add_extra_cmake_args(
+  -DCGM_DIR:PATH=<INSTALL_DIR>/lib/cmake/CGM)

meshkit/projects/meshkit.cmake

+superbuild_add_project(meshkit
+  DEPENDS moab cgm
+  CMAKE_ARGS
+    # Set link path on linux
+    -DCMAKE_INSTALL_RPATH:PATH=$ORIGIN/../lib
+    -DCGM_DIR:PATH=<INSTALL_DIR>/lib/cmake/CGM
+    -DBUILD_ALGS:BOOL=ON
+    -DBUILD_SRC:BOOL=ON
+    -DBUILD_UTILS:BOOL=ON
+    -DBUILD_RGG:BOOL=ON
+    -DWITH_MPI:BOOL=OFF
+    -DENABLE_TESTING:BOOL=OFF)
+
+# MOAB has public headers which include Eigen, but it doesn't add the include
+# flags properly.
+superbuild_append_flags(cxx_flags "-I<INSTALL_DIR>/include/eigen3" PROJECT_ONLY)

meshkit/projects/moab.cmake

+superbuild_add_project(moab
+  DEPENDS cgm eigen netcdf zlib
+  CMAKE_ARGS
+    # Set link path on OSX
+    -DCMAKE_INSTALL_NAME_DIR:PATH=<INSTALL_DIR>/lib
+    -DCMAKE_INSTALL_LIBDIR:STRING=lib
+    -DENABLE_IMESH:BOOL=ON
+    -DENABLE_CGM:BOOL=ON
+    -DENABLE_NETCDF:BOOL=ON
+    -DENABLE_IREL:BOOL=ON
+    -DENABLE_HDF5:BOOL=OFF
+    -DENABLE_PNETCDF:BOOL=OFF
+    -DENABLE_MPI:BOOL=OFF
+    -DENABLE_TESTING:BOOL=OFF
+    -DNETCDF_ROOT:PATH=<INSTALL_DIR>)
+
+superbuild_apply_patch(moab disable-fortran
+"Disable use of fortran")
+
+# By default, linux and os x cmake looks in <INSTALL_DIR>/lib/cmake for
+# things. On windows, it does not. So, we set MOAB_DIR to point to the
+# location of MOABConfig.cmake for everyone.
+superbuild_add_extra_cmake_args(
+  -DMOAB_DIR:PATH=<INSTALL_DIR>/lib/cmake/MOAB)

meshkit/projects/patches/moab-disable-fortran.patch

+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index bc5b0cef..a5b75198 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -2,24 +2,24 @@ cmake_minimum_required( VERSION 3.0 )
+ SET(PACKAGE_NAME "MOAB")
+ SET(PACKAGE_VERSION "5.1.1")
+
+-if (NOT WIN32)
+-  #This all breaks on windows.
+-  SET(CMAKE_Fortran_COMPILER_INIT ${CMAKE_GENERATOR_FC})
+-  SET(CMAKE_CXX_FLAGS_INIT "-fPIC -DPIC")
+-  SET(CMAKE_CXX_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_CXX_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
+-  SET(CMAKE_C_FLAGS_INIT "-fPIC -DPIC")
+-  SET(CMAKE_C_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_C_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_C_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
+-  SET(CMAKE_Fortran_FLAGS_INIT "-fPIC")
+-  SET(CMAKE_Fortran_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2")
+-  SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_INIT "")
+-  SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS_INIT "")
+-endif()
++#if (NOT WIN32)
++#  #This all breaks on windows.
++#  SET(CMAKE_Fortran_COMPILER_INIT ${CMAKE_GENERATOR_FC})
++#  SET(CMAKE_CXX_FLAGS_INIT "-fPIC -DPIC")
++#  SET(CMAKE_CXX_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_CXX_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
++#  SET(CMAKE_C_FLAGS_INIT "-fPIC -DPIC")
++#  SET(CMAKE_C_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_C_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_C_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
++#  SET(CMAKE_Fortran_FLAGS_INIT "-fPIC")
++#  SET(CMAKE_Fortran_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2")
++#  SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_INIT "")
++#  SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS_INIT "")
++#endif()
+
+ project( MOAB )
+
+@@ -395,29 +395,29 @@ CONFIGURE_FILE(
+     IMMEDIATE @ONLY
+     )
+
+-if (ENABLE_FORTRAN)
+-  enable_language(Fortran)
+-
+-  # Include CMake's Fortran mangling evaluation macros
+-  include(FortranCInterface)
+-
+-  if ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-    set(FC_CASE "NAME")
+-  else ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-    set(FC_CASE "name")
+-  endif ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-  if (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
+-    set(FortranCInterface_GLOBAL_SUFFIX "## ${FortranCInterface_GLOBAL_SUFFIX}")
+-  endif (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
+-  if (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
+-    set(FortranCInterface_GLOBAL__SUFFIX "## ${FortranCInterface_GLOBAL__SUFFIX}")
+-  endif (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
+-
+-  set(MOAB_F77_FUNC  "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
+-  set(MOAB_F77_FUNC_ "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
+-  set(MOAB_FC_FUNC   "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
+-  set(MOAB_FC_FUNC_  "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
+-endif (ENABLE_FORTRAN)
++  #if (ENABLE_FORTRAN)
++  #  enable_language(Fortran)
++  #
++  #  # Include CMake's Fortran mangling evaluation macros
++  #  include(FortranCInterface)
++  #
++  #  if ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #    set(FC_CASE "NAME")
++  #  else ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #    set(FC_CASE "name")
++  #  endif ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #  if (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
++  #    set(FortranCInterface_GLOBAL_SUFFIX "## ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  endif (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
++  #  if (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
++  #    set(FortranCInterface_GLOBAL__SUFFIX "## ${FortranCInterface_GLOBAL__SUFFIX}")
++  #  endif (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
++  #
++  #  set(MOAB_F77_FUNC  "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  set(MOAB_F77_FUNC_ "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
++  #  set(MOAB_FC_FUNC   "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  set(MOAB_FC_FUNC_  "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
++  #endif (ENABLE_FORTRAN)
+
+ # Generate the CMake input header file and then pass it through configuration
+ ## execute_process( COMMAND cat MOABConfig.h.in COMMAND sed -e "s/#undef /#cmakedefine MOAB_/g"

meshkit/projects/unix/moab.cmake

+superbuild_add_project(moab
+  DEPENDS cgm eigen netcdf zlib
+  CMAKE_ARGS
+    # Set link path properly on linux
+    -DCMAKE_INSTALL_RPATH:PATH=$ORIGIN/../lib
+    -DCMAKE_INSTALL_LIBDIR:STRING=lib
+    -DENABLE_BLASLAPACK:BOOL=OFF
+    -DENABLE_IMESH:BOOL=ON
+    -DENABLE_CGM:BOOL=ON
+    -DENABLE_NETCDF:BOOL=ON
+    -DENABLE_IREL:BOOL=ON
+    -DENABLE_HDF5:BOOL=OFF
+    -DENABLE_PNETCDF:BOOL=OFF
+    -DENABLE_MPI:BOOL=OFF
+    -DENABLE_TESTING:BOOL=OFF
+    -DNETCDF_ROOT:PATH=<INSTALL_DIR>)
+
+superbuild_apply_patch(moab disable-fortran
+"Disable use of fortran")
+
+# By default, linux and os x cmake looks in <INSTALL_DIR>/lib/cmake for
+# things. On windows, it does not. So, we set MOAB_DIR to point to the
+# location of MOABConfig.cmake for everyone.
+superbuild_add_extra_cmake_args(
+  -DMOAB_DIR:PATH=<INSTALL_DIR>/lib/cmake/MOAB)

meshkit/projects/unix/patches/moab-disable-fortran.patch

+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index bc5b0cef..a5b75198 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -2,24 +2,24 @@ cmake_minimum_required( VERSION 3.0 )
+ SET(PACKAGE_NAME "MOAB")
+ SET(PACKAGE_VERSION "5.1.1")
+
+-if (NOT WIN32)
+-  #This all breaks on windows.
+-  SET(CMAKE_Fortran_COMPILER_INIT ${CMAKE_GENERATOR_FC})
+-  SET(CMAKE_CXX_FLAGS_INIT "-fPIC -DPIC")
+-  SET(CMAKE_CXX_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_CXX_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
+-  SET(CMAKE_C_FLAGS_INIT "-fPIC -DPIC")
+-  SET(CMAKE_C_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_C_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_C_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
+-  SET(CMAKE_Fortran_FLAGS_INIT "-fPIC")
+-  SET(CMAKE_Fortran_FLAGS_DEBUG_INIT "-O0 -g")
+-  SET(CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
+-  SET(CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2")
+-  SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_INIT "")
+-  SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS_INIT "")
+-endif()
++#if (NOT WIN32)
++#  #This all breaks on windows.
++#  SET(CMAKE_Fortran_COMPILER_INIT ${CMAKE_GENERATOR_FC})
++#  SET(CMAKE_CXX_FLAGS_INIT "-fPIC -DPIC")
++#  SET(CMAKE_CXX_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_CXX_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
++#  SET(CMAKE_C_FLAGS_INIT "-fPIC -DPIC")
++#  SET(CMAKE_C_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_C_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_C_FLAGS_RELEASE_INIT "-O2 -DNDEBUG")
++#  SET(CMAKE_Fortran_FLAGS_INIT "-fPIC")
++#  SET(CMAKE_Fortran_FLAGS_DEBUG_INIT "-O0 -g")
++#  SET(CMAKE_Fortran_FLAGS_RELWITHDEBINFO_INIT "-O2 -g")
++#  SET(CMAKE_Fortran_FLAGS_RELEASE_INIT "-O2")
++#  SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_INIT "")
++#  SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS_INIT "")
++#endif()
+
+ project( MOAB )
+
+@@ -395,29 +395,29 @@ CONFIGURE_FILE(
+     IMMEDIATE @ONLY
+     )
+
+-if (ENABLE_FORTRAN)
+-  enable_language(Fortran)
+-
+-  # Include CMake's Fortran mangling evaluation macros
+-  include(FortranCInterface)
+-
+-  if ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-    set(FC_CASE "NAME")
+-  else ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-    set(FC_CASE "name")
+-  endif ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
+-  if (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
+-    set(FortranCInterface_GLOBAL_SUFFIX "## ${FortranCInterface_GLOBAL_SUFFIX}")
+-  endif (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
+-  if (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
+-    set(FortranCInterface_GLOBAL__SUFFIX "## ${FortranCInterface_GLOBAL__SUFFIX}")
+-  endif (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
+-
+-  set(MOAB_F77_FUNC  "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
+-  set(MOAB_F77_FUNC_ "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
+-  set(MOAB_FC_FUNC   "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
+-  set(MOAB_FC_FUNC_  "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
+-endif (ENABLE_FORTRAN)
++  #if (ENABLE_FORTRAN)
++  #  enable_language(Fortran)
++  #
++  #  # Include CMake's Fortran mangling evaluation macros
++  #  include(FortranCInterface)
++  #
++  #  if ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #    set(FC_CASE "NAME")
++  #  else ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #    set(FC_CASE "name")
++  #  endif ("${FortranCInterface_GLOBAL_CASE}" MATCHES "UPPER")
++  #  if (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
++  #    set(FortranCInterface_GLOBAL_SUFFIX "## ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  endif (NOT "${FortranCInterface_GLOBAL_SUFFIX}" STREQUAL "")
++  #  if (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
++  #    set(FortranCInterface_GLOBAL__SUFFIX "## ${FortranCInterface_GLOBAL__SUFFIX}")
++  #  endif (NOT "${FortranCInterface_GLOBAL__SUFFIX}" STREQUAL "")
++  #
++  #  set(MOAB_F77_FUNC  "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  set(MOAB_F77_FUNC_ "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
++  #  set(MOAB_FC_FUNC   "${FortranCInterface_GLOBAL_PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL_SUFFIX}")
++  #  set(MOAB_FC_FUNC_  "${FortranCInterface_GLOBAL__PREFIX} ${FC_CASE} ${FortranCInterface_GLOBAL__SUFFIX}")
++  #endif (ENABLE_FORTRAN)
+
+ # Generate the CMake input header file and then pass it through configuration
+ ## execute_process( COMMAND cat MOABConfig.h.in COMMAND sed -e "s/#undef /#cmakedefine MOAB_/g"

meshkit/projects/win32/moab.cmake

+include("${CMAKE_CURRENT_LIST_DIR}/../moab.cmake")
+
+superbuild_apply_patch(moab quote-compiler-path
+  "Add quotations around compiler path to avoid whitespace warnings.")
+
+superbuild_apply_patch(moab remove-flags-from-link-list
+  "Remove CMake error where linker flags are a part of the link library list")
+
+superbuild_apply_patch(moab msvc-fixes
+  "Many windows-specific fixes for moab (not developed on windows).")

meshkit/projects/win32/patches/moab-msvc-fixes.patch

+diff -Nr -U5 moab/src/GeomQueryTool.cpp moab_patched/src/GeomQueryTool.cpp
+--- moab/src/GeomQueryTool.cpp	Fri Jan 19 16:55:39 2018
++++ moab_patched/src/GeomQueryTool.cpp	Fri Jan 19 16:53:37 2018
+@@ -7,10 +7,12 @@
+ #include <limits>
+ #include <algorithm>
+ #include <set>
+ 
+ #include <ctype.h>
++#define _USE_MATH_DEFINES
++#include <math.h>
+ #include <string.h>
+ #include <stdlib.h>
+ #include <stdio.h>
+ 
+ #include "moab/OrientedBoxTreeTool.hpp"
+diff -Nr -U5 moab/src/IntxMesh/Intx2MeshOnSphere.cpp moab_patched/src/IntxMesh/Intx2MeshOnSphere.cpp
+--- moab/src/IntxMesh/Intx2MeshOnSphere.cpp	Fri Jan 19 16:55:39 2018
++++ moab_patched/src/IntxMesh/Intx2MeshOnSphere.cpp	Fri Jan 19 16:53:37 2018
+@@ -2,10 +2,13 @@
+  * Intx2MeshOnSphere.cpp
+  *
+  *  Created on: Oct 3, 2012
+  */
+ 
++#define _USE_MATH_DEFINES
++#include <cmath>
++
+ #include "moab/IntxMesh/Intx2MeshOnSphere.hpp"
+ #include "moab/IntxMesh/IntxUtils.hpp"
+ #include "moab/GeomUtil.hpp"
+ #ifdef MOAB_HAVE_MPI
+ #include "moab/ParallelComm.hpp"
+diff -Nr -U5 moab/src/IntxMesh/IntxUtils.cpp moab_patched/src/IntxMesh/IntxUtils.cpp
+--- moab/src/IntxMesh/IntxUtils.cpp	Fri Jan 19 16:55:39 2018
++++ moab_patched/src/IntxMesh/IntxUtils.cpp	Fri Jan 19 16:53:37 2018
+@@ -2,10 +2,11 @@
+  * IntxUtils.cpp
+  *
+  *  Created on: Oct 3, 2012
+  */
+ 
++#define _USE_MATH_DEFINES
+ #include <math.h>
+ #include "moab/IntxMesh/IntxUtils.hpp"
+ // this is from mbcoupler; maybe it should be moved somewhere in moab src
+ // right now, add a dependency to mbcoupler
+ // #include "ElemUtil.hpp"
+diff -Nr -U5 moab/src/MeshGeneration.cpp moab_patched/src/MeshGeneration.cpp
+--- moab/src/MeshGeneration.cpp	Fri Jan 19 16:55:39 2018
++++ moab_patched/src/MeshGeneration.cpp	Fri Jan 19 16:53:37 2018
+@@ -6,10 +6,12 @@
+ #include "moab/MeshGeneration.hpp"
+ #include "moab/MergeMesh.hpp"
+ #include <iostream>
+ #include <vector>
+ 
++#include <time.h>
++
+ #ifdef MOAB_HAVE_MPI
+ #include "moab_mpi.h"
+ #include "moab/ParallelComm.hpp"
+ #include "MBParallelConventions.h"
+ #include "moab/ParallelMergeMesh.hpp"
+diff -Nr -U5 moab/src/moab/Util.hpp moab_patched/src/moab/Util.hpp
+--- moab/src/moab/Util.hpp	Fri Jan 19 16:55:40 2018
++++ moab_patched/src/moab/Util.hpp	Fri Jan 19 16:53:38 2018
+@@ -18,20 +18,23 @@
+ 
+ #include "moab/MOABConfig.h"
+ #include "moab/Forward.hpp"
+ #include "moab/CartVect.hpp"
+ 
+-#include <math.h>
+-#if defined MOAB_HAVE_ISFINITE
+-#define moab_isfinite(f) isfinite(f)
+-#elif defined MOAB_HAVE_STDISFINITE
+ #include <cmath>
+-#define moab_isfinite(f) std::isfinite(f)
++#if defined MOAB_HAVE_ISFINITE
++# define moab_isfinite(f) isfinite(f)
++//If we have c++11 support, we will have std::isfinite
++#elif (defined(__cplusplus) && __cplusplus >= 201103L)
++# define moab_isfinite(f) std::isfinite(f)
++#elif (defined(_WIN32) && defined(_MSC_VER)) || defined(__MINGW32__)
++# include <float.h>
++# define moab_isfinite(A) _finite(A)
+ #elif defined MOAB_HAVE_FINITE
+-#define moab_isfinite(f) finite(f)
++# define moab_isfinite(f) finite(f)
+ #else
+-#define moab_isfinite(f) (!isinf(f) && !isnan(f))
++# define moab_isfinite(f) (!isinf(f) && !isnan(f))
+ #endif
+ 
+ namespace moab {
+ 
+ /** \class Util
+diff -Nr -U5 moab/src/ProgOptions.cpp moab_patched/src/ProgOptions.cpp
+--- moab/src/ProgOptions.cpp	Fri Jan 19 16:55:40 2018
++++ moab_patched/src/ProgOptions.cpp	Fri Jan 19 16:53:38 2018
+@@ -1,5 +1,7 @@
++#define NOMINMAX
++#include <algorithm>
+ #include <iostream>
+ #include <sstream>
+ #include <iomanip>
+ #include <cstdlib>
+ #include <list>
+diff -Nr -U5 moab/test/perf/CMakeLists.txt moab_patched/test/perf/CMakeLists.txt
+--- moab/test/perf/CMakeLists.txt	Fri Jan 19 16:55:40 2018
++++ moab_patched/test/perf/CMakeLists.txt	Fri Jan 19 16:53:38 2018
+@@ -11,12 +11,12 @@
+            perf.cpp
+            perftool.cpp
+            umr_perf.cpp )
+ 
+ if ( MOAB_HAVE_IMESH )
+-  set(TESTS ${TESTS} tstt_perf_binding.cpp)
+-  set(tstt_perf_binding_CMDARGS 4;B)
++#  set(TESTS ${TESTS} tstt_perf_binding.cpp)
++#  set(tstt_perf_binding_CMDARGS 4;B)
+   set(LIBS ${LIBS} iMesh )
+ endif()
+ if ( MOAB_HAVE_CGM )
+   set(LIBS ${LIBS} ${CGM_LIBRARIES})
+ endif()
+diff -Nr -U5 moab/test/spherical_area_test.cpp moab_patched/test/spherical_area_test.cpp
+--- moab/test/spherical_area_test.cpp	Fri Jan 19 16:55:40 2018
++++ moab_patched/test/spherical_area_test.cpp	Fri Jan 19 16:53:38 2018
+@@ -1,10 +1,13 @@
+ /*
+  * spherical_area_test.cpp
+  *
+  *  Created on: Feb 1, 2013
+  */
++#define _USE_MATH_DEFINES
++#include <math.h>
++
+ #include <iostream>
+ #include "moab/Core.hpp"
+ #include "moab/Interface.hpp"
+ #include "moab/IntxMesh/IntxUtils.hpp"
+ #include "TestUtil.hpp"
+diff -Nr -U5 moab/test/urefine_mesh_test.cpp moab_patched/test/urefine_mesh_test.cpp
+--- moab/test/urefine_mesh_test.cpp	Fri Jan 19 16:55:40 2018
++++ moab_patched/test/urefine_mesh_test.cpp	Fri Jan 19 16:53:38 2018
+@@ -1,10 +1,9 @@
+ /*This unit test is for the uniform refinement capability based on AHF datastructures*/
+ #include <iostream>
+ #include <string>
+ #include <sstream>
+-#include <sys/time.h>
+ #include <vector>
+ #include <algorithm>
+ #include "moab/Core.hpp"
+ #include "moab/Range.hpp"
+ #include "moab/MeshTopoUtil.hpp"
+diff -Nr -U5 moab/tools/umr.cpp moab_patched/tools/umr.cpp
+--- moab/tools/umr.cpp	Fri Jan 19 16:55:41 2018
++++ moab_patched/tools/umr.cpp	Fri Jan 19 16:53:39 2018
+@@ -3,11 +3,10 @@
+ #include <vector>
+ #include <string>
+ #include <stdio.h>
+ #include <iomanip>
+ #include <fstream>
+-#include <sys/time.h>
+ #include <time.h>
+ #include <math.h>
+ #include <assert.h>
+ #include <float.h>
+ 

meshkit/projects/win32/patches/moab-quote-compiler-path.patch

+diff -Nr -U5 src/config/MOABConfig.cmake.in src.new/config/MOABConfig.cmake.in
+--- src/config/MOABConfig.cmake.in	2017-11-29 11:03:38.000000000 -0500
++++ src.new/config/MOABConfig.cmake.in	2018-01-24 10:26:22.000000000 -0500
+@@ -8,14 +8,14 @@
+ # MOAB_CXX, MOAB_CC, MOAB_F77, MOAB_FC - compilers used to compile MOAB
+ # MOAB_CXXFLAGS, MOAB_CCFLAGS, MOAB_FFLAGS, MOAB_FCFLAGS - compiler flags used to compile MOAB; possibly need to use these in add_definitions or CMAKE_<LANG>_FLAGS_<MODE> 
+ 
+ set(MOAB_FOUND 1)
+ 
+-set(MOAB_CC @CC@)
+-set(MOAB_CXX @CXX@)
+-set(MOAB_FC @FC@)
+-set(MOAB_F77 @F77@)
++set(MOAB_CC "@CC@")
++set(MOAB_CXX "@CXX@")
++set(MOAB_FC "@FC@")
++set(MOAB_F77 "@F77@")
+ # Compiler flags used by MOAB
+ set(MOAB_CFLAGS "@CFLAGS@")
+ set(MOAB_CXXFLAGS "@CXXFLAGS@")
+ set(MOAB_FCFLAGS "@FCFLAGS@")
+ set(MOAB_FFLAGS "@FFLAGS@")
+diff -Nr -U5 src/config/MOABConfig.cmake.cmake src_patched/config/MOABConfig.cmake.cmake
+--- src/config/MOABConfig.cmake.cmake	2017-11-29 11:03:38.000000000 -0500
++++ src_patched/config/MOABConfig.cmake.cmake	2018-02-14 16:08:31.000000000 -0500
+@@ -8,14 +8,14 @@
+ # MOAB_CXX, MOAB_CC, MOAB_F77, MOAB_FC - compilers used to compile MOAB
+ # MOAB_CXXFLAGS, MOAB_CCFLAGS, MOAB_FFLAGS, MOAB_FCFLAGS - compiler flags used to compile MOAB; possibly need to use these in add_definitions or CMAKE_<LANG>_FLAGS_<MODE> 
+ 
+ set(MOAB_FOUND 1)
+ 
+-set(MOAB_CC @CMAKE_C_COMPILER@)
+-set(MOAB_CXX @CMAKE_CXX_COMPILER@)
+-set(MOAB_FC @CMAKE_Fortran_COMPILER@)
+-set(MOAB_F77 @CMAKE_Fortran_COMPILER@)
++set(MOAB_CC "@CMAKE_C_COMPILER@")
++set(MOAB_CXX "@CMAKE_CXX_COMPILER@")
++set(MOAB_FC "@CMAKE_Fortran_COMPILER@")
++set(MOAB_F77 "@CMAKE_Fortran_COMPILER@")
+ # Compiler flags used by MOAB
+ set(MOAB_CFLAGS "@CFLAGS@")
+ set(MOAB_CXXFLAGS "@CXXFLAGS@")
+ set(MOAB_FCFLAGS "@FFLAGS@")
+ set(MOAB_FFLAGS "@FFLAGS@")

meshkit/projects/win32/patches/moab-remove-flags-from-link-list.patch

+diff -Nr -U5 src/src/CMakeLists.txt src.new/src/CMakeLists.txt
+--- src/src/CMakeLists.txt	2017-11-29 11:03:38.000000000 -0500
++++ src.new/src/CMakeLists.txt	2018-01-19 15:58:49.000000000 -0500
+@@ -279,11 +279,11 @@
+   SOVERSION ${MOAB_VERSION_MAJOR}
+   )
+ 
+ target_link_libraries(
+   MOAB
+-  ${CMAKE_EXE_LINKER_FLAGS} ${MOAB_DEP_LIBRARIES} ${MOAB_LIBS} ${MOAB_CGM_LIBS} ${MPI_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES}
++  ${MOAB_DEP_LIBRARIES} ${MOAB_LIBS} ${MOAB_CGM_LIBS} ${MPI_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES}
+   )
+ 
+ install(
+   TARGETS MOAB
+   EXPORT MOABTargets

meshkit/versions.cmake

+superbuild_set_revision(cgm
+  GIT_REPOSITORY "https://bitbucket.org/fathomteam/cgm.git"
+  GIT_TAG 18403e5b100fe8d49a8ac0d6a2e849a0bbeae3bd)
+
+superbuild_set_revision(meshkit
+  GIT_REPOSITORY  "https://haocheng_liu@bitbucket.org/haocheng_liu/meshkit.git"
+  GIT_TAG         osx-10-dot-13-patch)
+
+superbuild_set_revision(moab
+  GIT_REPOSITORY "https://bitbucket.org/fathomteam/moab.git"
+  GIT_TAG 78d0b938fcf80fcdfb34fa39583fbce544b56953)

projects/apple/cmb.bundle.apple.cmake

@@ -135,3 +135,15 @@ install(
   DIRECTORY   "${superbuild_install_location}/share/cmb/workflows/"
   DESTINATION "Workflows"
   COMPONENT   superbuild)
+
+if (meshkit_enabled)
+  foreach (meshkit_exe IN ITEMS coregen assygen)
+    superbuild_apple_install_utility(
+      "\${CMAKE_INSTALL_PREFIX}/${cmb_package}"
+      "modelbuilder.app"
+      "${superbuild_install_location}/bin/${meshkit_exe}"
+      SEARCH_DIRECTORIES  "${library_paths}"
+      FRAMEWORK_DEST      "Frameworks/meshkit"
+      LIBRARY_DEST        "Libraries/meshkit")
+  endforeach ()
+endif ()

projects/hdf5.cmake

+# The common superbuild's hdf5 configuration does not set CMAKE_INSTALL_RPATH,
+# so we override it with our own hdf5 configuration.
+
+superbuild_add_project(hdf5
+  CAN_USE_SYSTEM
+  DEPENDS zlib szip
+
+  CMAKE_ARGS
+    -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+    -DCMAKE_INSTALL_RPATH:PATH=$ORIGIN/../lib
+    -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=TRUE
+    -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=TRUE
+    -DHDF5_ENABLE_SZIP_ENCODING:BOOL=TRUE
+    -DHDF5_BUILD_HL_LIB:BOOL=TRUE
+    -DHDF5_BUILD_WITH_INSTALL_NAME:BOOL=ON)
+
+superbuild_add_extra_cmake_args(
+  -DHDF5_ROOT:PATH=<INSTALL_DIR>
+  -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE:BOOL=ON)
+
+superbuild_apply_patch(hdf5 fix-ext-pkg-find