new ENABLE_SYSTEM_CONTRIB to enable/disable looking for system versions of contrib/ libraries

motivated by crash in system Metis 5

CMakeLists.txt

@@ -85,6 +85,7 @@ opt(PRIVATE_API "Enable private API" OFF)
 opt(REVOROPT "Enable Revoropt (used for CVT remeshing)" OFF)
 opt(SLEPC "Enable SLEPc eigensolvers (required for conformal compounds)" ${DEFAULT})
 opt(SOLVER "Enable built-in finite element solvers (required for compounds)" ${DEFAULT})
+opt(SYSTEM_CONTRIB "Use system versions of contrib libraries, when possible" ${DEFAULT})
 opt(TCMALLOC "Enable libtcmalloc, a fast malloc implementation but that does not release memory" OFF)
 opt(VISUDEV "Enable additional visualization capabilities for development purpose" OFF)
 opt(VOROPP "Enable voro++ (for hex meshing, experimental)" ${DEFAULT})
@@ -657,14 +658,14 @@ if(HAVE_MESH OR HAVE_PLUGINS)
   if(ENABLE_ANN)
     find_library(ANN_LIB ann PATH_SUFFIXES lib)
     find_path(ANN_INC "ANN.h" PATH_SUFFIXES src include ANN)
-    if(ANN_LIB AND ANN_INC)
+    if(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC)
+      message(STATUS "Using system version of ANN")
       list(APPEND EXTERNAL_LIBRARIES ${ANN_LIB})
       list(APPEND EXTERNAL_INCLUDES ${ANN_INC})
-    else(ANN_LIB AND ANN_INC)
-      message(STATUS "System ANN not found: using contrib/ANN instead")
+    else(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC)
       add_subdirectory(contrib/ANN)
       include_directories(contrib/ANN/include)
-    endif(ANN_LIB AND ANN_INC)
+    endif(ENABLE_SYSTEM_CONTRIB AND ANN_LIB AND ANN_INC)
     set_config_option(HAVE_ANN "Ann")
   endif(ENABLE_ANN)
 endif(HAVE_MESH OR HAVE_PLUGINS)
@@ -753,16 +754,16 @@ if(HAVE_MESH OR HAVE_SOLVER)
   if(ENABLE_METIS)
     find_library(METIS_LIB metis PATH_SUFFIXES lib)
     find_path(METIS_INC "metis.h" PATH_SUFFIXES include)
-    if(METIS_LIB AND METIS_INC)
+    if(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC)
+       message(STATUS "Using system version of METIS")
        list(APPEND EXTERNAL_LIBRARIES ${METIS_LIB})
        list(APPEND EXTERNAL_INCLUDES ${METIS_INC})
-    else(METIS_LIB AND METIS_INC)
-       message(STATUS "System METIS not found: using contrib/metis instead")
+    else(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC)
        add_definitions(-DUSE_GKREGEX)
        add_subdirectory(contrib/metis)
        include_directories(contrib/metis/include contrib/metis/libmetis
                            contrib/metis/GKlib)
-    endif(METIS_LIB AND METIS_INC)
+    endif(ENABLE_SYSTEM_CONTRIB AND METIS_LIB AND METIS_INC)
     set_config_option(HAVE_METIS "Metis")
   endif(ENABLE_METIS)
 endif(HAVE_MESH OR HAVE_SOLVER)
@@ -775,14 +776,14 @@ if(HAVE_MESH)
   if(ENABLE_VOROPP)
     find_library(VOROPP_LIB voro++ PATH_SUFFIXES lib)
     find_path(VOROPP_INC "voro++.hh" PATH_SUFFIXES include)
-    if(VOROPP_LIB AND VOROPP_INC)
+    if(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC)
+      message(STATUS "Using system version of voro++")
       list(APPEND EXTERNAL_LIBRARIES ${VOROPP_LIB})
       list(APPEND EXTERNAL_INCLUDES ${VOROPP_INC})
-    else(VOROPP_LIB AND VOROPP_INC)
-      message(STATUS "System voro++ not found: using contrib/voro++ instead")
+    else(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC)
       add_subdirectory(contrib/voro++)
       include_directories(contrib/voro++/src)
-    endif(VOROPP_LIB AND VOROPP_INC)
+    endif(ENABLE_SYSTEM_CONTRIB AND VOROPP_LIB AND VOROPP_INC)
     set_config_option(HAVE_VOROPP "Voro++")
   endif(ENABLE_VOROPP)
 
@@ -810,14 +811,14 @@ if(HAVE_MESH)
   if(ENABLE_MMG3D)
     find_library(MMG3D_LIB mmg3dlib4.0 PATH_SUFFIXES lib)
     find_path(MMG3D_INC "libmmg3d.h" PATH_SUFFIXES src include)
-    if(MMG3D_LIB AND MMG3D_INC)
+    if(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC)
+       message(STATUS "Using system version of MMG3D")
        list(APPEND EXTERNAL_LIBRARIES ${MMG3D_LIB})
        list(APPEND EXTERNAL_INCLUDES ${MMG3D_INC})
-    else(MMG3D_LIB AND MMG3D_INC)
-       message(STATUS "System MMG3D not found: using contrib/mmg3d instead")
+    else(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC)
        add_subdirectory(contrib/mmg3d)
        include_directories(contrib/mmg3d/build/sources)
-    endif(MMG3D_LIB AND MMG3D_INC)
+    endif(ENABLE_SYSTEM_CONTRIB AND MMG3D_LIB AND MMG3D_INC)
     set_config_option(HAVE_MMG3D "Mmg3d")
   endif(ENABLE_MMG3D)
 endif(HAVE_MESH)
@@ -874,12 +875,12 @@ endif(ENABLE_MED OR ENABLE_CGNS)
 if(HAVE_SOLVER)
   if(ENABLE_GMM)
     find_path(GMM_INC "gmm.h" PATH_SUFFIXES src include include/gmm)
-    if(GMM_INC)
+    if(ENABLE_SYSTEM_CONTRIB AND GMM_INC)
+      message(STATUS "Using system version of GMM")
       list(APPEND EXTERNAL_INCLUDES ${GMM_INC})
-    else(GMM_INC)
-      message(STATUS "System GMM not found: using contrib/gmm instead")
+    else(ENABLE_SYSTEM_CONTRIB AND GMM_INC)
       include_directories(contrib/gmm)
-    endif(GMM_INC)
+    endif(ENABLE_SYSTEM_CONTRIB AND GMM_INC)
     set_config_option(HAVE_GMM "Gmm")
   endif(ENABLE_GMM)
 

doc/texinfo/cmake_options.texi

@@ -25,13 +25,15 @@ Enable Android NDK library target (experimental) (default: OFF)
 @item ENABLE_BUILD_IOS
 Enable iOS library target (experimental) (default: OFF)
 @item ENABLE_CGNS
-Enable CGNS mesh export (experimental) (default: OFF)
+Enable CGNS mesh import (default: ON)
 @item ENABLE_CAIRO
 Enable Cairo to render fonts (experimental) (default: ON)
 @item ENABLE_CXX11
 Enable C++11 (default: ON)
 @item ENABLE_C99
 Enable C99 (default: ON)
+@item ENABLE_PROFILE
+Enable profiling compiler flags (default: OFF)
 @item ENABLE_DINTEGRATION
 Enable discrete integration (needed for levelsets) (default: ON)
 @item ENABLE_FLTK
@@ -110,6 +112,8 @@ Enable Revoropt (used for CVT remeshing) (default: OFF)
 Enable SLEPc eigensolvers (required for conformal compounds) (default: ON)
 @item ENABLE_SOLVER
 Enable built-in finite element solvers (required for compounds) (default: ON)
+@item ENABLE_SYSTEM_CONTRIB
+Use system versions of contrib libraries, when possible (default: ON)
 @item ENABLE_TCMALLOC
 Enable libtcmalloc, a fast malloc implementation but that does not release memory (default: OFF)
 @item ENABLE_VISUDEV

doc/texinfo/opt_general.texi

@@ -158,7 +158,7 @@ Saved in: @code{General.SessionFileName}
 
 @item General.Version
 Gmsh version (read-only)@*
-Default value: @code{"3.0.7"}@*
+Default value: @code{"3.0.7-git-4294b937e"}@*
 Saved in: @code{-}
 
 @item General.WatchFilePattern

doc/texinfo/opt_mesh.texi

@@ -16,6 +16,11 @@ Threshold angle below which normals are not smoothed@*
 Default value: @code{30}@*
 Saved in: @code{General.OptionsFileName}
 
+@item Mesh.AngleToleranceFacetOverlap
+Consider connected facets as overlapping when the dihedral angle between the facets is smaller than the user's defined tolerance@*
+Default value: @code{0.1}@*
+Saved in: @code{General.OptionsFileName}
+
 @item Mesh.AnisoMax
 Maximum anisotropy of the mesh@*
 Default value: @code{1e+33}@*
@@ -302,8 +307,8 @@ Default value: @code{1}@*
 Saved in: @code{General.OptionsFileName}
 
 @item Mesh.PartitionCreatePhysicals
-Create physical groups for partitions@*
-Default value: @code{0}@*
+Create physical groups for partitions, based on existing physical groups@*
+Default value: @code{1}@*
 Saved in: @code{General.OptionsFileName}
 
 @item Mesh.PartitionCreateGhostCells

doc/texinfo/opt_plugin.texi

@@ -11,35 +11,35 @@ The ICN measure is related to the condition number of the stiffness matrix.@*
 @*
 Parameters:@*
 @*
-- Jacobian determinant = @{0, 1@}@*
+- JacobianDeterminant = @{0, 1@}@*
 @*
-- IGE measure = @{0, 1@}@*
+- IGEMeasure = @{0, 1@}@*
 @*
-- ICN measure = @{0, 1@}@*
+- ICNMeasure = @{0, 1@}@*
 @*
-- Hiding threshold = [0, 1]: Hides all element for which min(mu) is strictly greater than the threshold, where mu is the ICN if ICN measure == 1, otherwise mu is the IGE it IGE measure == 1, otherwise mu is the Jacobian determinant.@*
+- HidingThreshold = [0, 1]: Hides all element for which min(mu) is strictly greater than the threshold, where mu is the ICN if ICN measure == 1, otherwise mu is the IGE it IGE measure == 1, otherwise mu is the Jacobian determinant.@*
 If threshold == 0, hides all elements except invalid.@*
 @*
 - DrawPView = @{0, 1@}: Creates a PView of min(J)/max(J), min(IGE) and/or min(ICN) according to what is asked. If 'Recompute' = 1, new PViews are created.@*
 @*
 - Recompute = @{0,1@}: Should be 1 if the mesh has changed.@*
 @*
-- Dimension = @{-1, 1, 2, 3, 4@}: If == -1, analyse element of the greater dimension. If == 4, analyse 2D and 3D elements.
+- DimensionOfElements = @{-1, 1, 2, 3, 4@}: If == -1, analyse element of the greater dimension. If == 4, analyse 2D and 3D elements.
 Numeric options:
 @table @code
-@item Jacobian determinant
-Default value: @code{1}
-@item IGE measure
-Default value: @code{1}
-@item ICN measure
-Default value: @code{1}
-@item Hiding threshold
+@item JacobianDeterminant
+Default value: @code{0}
+@item IGEMeasure
+Default value: @code{0}
+@item ICNMeasure
+Default value: @code{0}
+@item HidingThreshold
 Default value: @code{9}
 @item DrawPView
 Default value: @code{0}
 @item Recompute
 Default value: @code{0}
-@item Dimension of elements
+@item DimensionOfElements
 Default value: @code{-1}
 @end table
 

doc/texinfo/opt_print.texi

@@ -166,7 +166,7 @@ Save SICN (signed inverse condition number) quality measure in mesh statistics e
 Default value: @code{0}@*
 Saved in: @code{General.OptionsFileName}
 
-@item Print.PostSICN
+@item Print.PostSIGE
 Save SIGE (signed inverse gradient error) quality measure in mesh statistics exported as post-processing views@*
 Default value: @code{0}@*
 Saved in: @code{General.OptionsFileName}