COMP: adjustments to makeCGAL for compilation with alternative mpfr/gmp

- document special steps for using ThirdParty mpfr/gmp with clang etc

BUILD.md

@@ -83,9 +83,9 @@ automatically as part of the top-level OpenFOAM `Allwmake`.
 Nonetheless it may be necessary or useful to build various
 ThirdParty components prior to building OpenFOAM itself.
 
+### Bootstrapping *(optional)*
 
-### Build Sequence
-1. `makeGcc` _or_ `makeLLVM` <a name="makeGcc"></a> *(optional)*
+* `makeGcc` _or_ `makeLLVM` <a name="makeGcc"></a>
    - Makes a third-party [gcc](#gcc-compiler) or [clang](#clang-compiler) installation,
      which is needed if the system gcc is [too old](#gcc-compiler).
      If your system compiler is recent enough, you can skip this step.
@@ -93,30 +93,75 @@ ThirdParty components prior to building OpenFOAM itself.
      OpenFOAM `etc/bashrc` or your equivalent `prefs.sh` file:
      - `WM_COMPILER_TYPE=ThirdParty`
      - `WM_COMPILER=Gcc48` (for example)
-     - or `WM_COMPILER=Clang` and adjust the `clang_version` entry in the OpenFOAM
+     - `WM_COMPILER=Clang40` (for example)
+     - or `WM_COMPILER=Clang` and adjust `clang_version` in the OpenFOAM
      `etc/config.sh/compiler` or equivalent.
    - More description is contained in the header comments of the
      `makeGcc` and `makeLLVM` files.
    - *Attention*: If you are building a newer version of clang, you may need to
      update your CMake beforehand.
-2. `makeCmake`  *(optional)*
+* `makeCmake`
    - Makes a third-party [CMake](#general-packages) installation, which is
      needed if a system CMake does not exist or is [too old](#min-cmake),
    - Note that CMake is being used by an number of third-party packages
      (CGAL, LLVM, ParaView, VTK, ...)
      so this may become an increasingly important aspect of the build.
-3. `Allwmake`
+
+Note that the order of the bootstrapping process may need to be
+reversed, or even require a few loops. For example, if you may need a
+newer version of CMake before being able to build LLVM/Clang and
+subsequently use the newly build clang to create a newer version of
+CMake in the desired location.
+
+Additionally, if you are using clang but with ThirdParty locations for
+gmp/mpfr you will need some extra work. Here is an example:
+
+* Compile a new ThirdParty clang version:
+
+      ./makeLLVM llvm-4.0.1
+
+* Now adjust the OpenFOAM `prefs.sh` to use the new compiler settings,
+  and update the OpenFOAM environment (eg, `wmRefresh`)
+
+* Next use (abuse) the `makeGcc` script to compile gmp/mpfr libraries.
+  It is best to pass the desired versions explicitly, and necessary
+  to set the CC/CXX variables so that the correct compiler is used:
+
+      CC=clang CXX=clang++  ./makeGcc gmp-6.1.2 mpfr-4.0.0 gcc-system
+
+  specifying `gcc-system` effectively disables building of gcc,
+  but will build the gmp/mpfr components.
+
+* As a final step, it will be necessary to add the ThirdParty
+  gmp/mpfr locations in the OpenFOAM config files since they are
+  normally only used in combination with a ThirdParty gcc.
+  The location to make these changes is in the `etc/config.sh/CGAL`,
+  since this is the component that uses the mpfr library.
+  For example,
+
+      gmp_version=gmp-6.1.2
+      mpfr_version=mpfr-4.0.0
+
+      export GMP_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$gmp_version
+      export GMP_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH/$mpfr_version
+
+* Update update the OpenFOAM environment (eg, `wmRefresh`) again.
+
+
+### Build Sequence
+
+1. `Allwmake`
    - This will be automatically invoked by the top-level OpenFOAM `Allwmake`, but
      can also be invoked directly to find possible build errors.
    - Builds an mpi library (openmpi or mpich), scotch decomposition, boost, CGAL, FFTW.
    - If the optional kahip or metis  directories are found, they will also be compiled.
-4. `makeParaView`  *(optional but highly recommended)*
+2. `makeParaView`  *(optional but highly recommended)*
    - This is optional, but extremely useful for visualization and for
      run-time post-processing function objects.
      You can build this at a later point in time, but then you should
      remember to rebuild the post-processing function objects and the
      reader module as well.
-5. Make any additional optional components
+3. Make any additional optional components
 
 
 #### Optional Components
@@ -180,6 +225,9 @@ and save some disk space.
 
 ## Build Notes
 
+### CGAL
+- The zlib library and zlib development headers are required.
+
 ### Scotch
 - The zlib library and zlib development headers are required.
 
@@ -480,4 +528,4 @@ that clang compiler for building the newer llvm/clang version.
 
 ---
 
-Copyright 2016-2017 OpenCFD Ltd
+Copyright 2016-2018 OpenCFD Ltd

makeCGAL

@@ -60,11 +60,10 @@ cd ${0%/*} && wmakeCheckPwd "$WM_THIRD_PARTY_DIR" 2>/dev/null || {
 }
 . etc/tools/ThirdPartyFunctions
 #------------------------------------------------------------------------------
-
-unset BOOST_ARCH_PATH CGAL_ARCH_PATH                     # Purge current values
+unset BOOST_ARCH_PATH CGAL_ARCH_PATH GMP_ARCH_PATH MPFR_ARCH_PATH   # Purge old
 
 # CGAL, boost and gmp/mpfr versions from OpenFOAM etc/config.sh files.
-# Get compiler first and let CGAL config override GMP (eg, when there is no GMP)
+# Get compiler first and let CGAL config override GMP and MPFR
 _foamEtc config.sh/compiler
 _foamEtc config.sh/CGAL
 
@@ -124,24 +123,26 @@ do
         gmpPACKAGE="gmp-system"
         mpfrPACKAGE="mpfr-system"
         boostPACKAGE="boost-system"
-        unset BOOST_ARCH_PATH           # avoid inconsistency
+        unset BOOST_ARCH_PATH GMP_ARCH_PATH MPFR_ARCH_PATH
         ;;
     -no-lib)
         optHeadersOnly=true
         ;;
     gmp-[4-9]* | gmp-system | gmp-none)
         gmpPACKAGE="${1%%/}"
+        unset GMP_ARCH_PATH
         ;;
     mpfr-[2-9]* | mpfr-system | mpfr-none)
         mpfrPACKAGE="${1%%/}"
-        ;;
-    CGAL-[0-9]*)
-        cgalPACKAGE="${1%%/}"
-        unset CGAL_ARCH_PATH            # avoid inconsistency
+        unset MPFR_ARCH_PATH
         ;;
     boost-[0-9]* | boost_[0-9]* | boost-system )
         boostPACKAGE="${1%%/}"
-        unset BOOST_ARCH_PATH           # avoid inconsistency
+        unset BOOST_ARCH_PATH
+        ;;
+    CGAL-[0-9]*)
+        cgalPACKAGE="${1%%/}"
+        unset CGAL_ARCH_PATH
         ;;
     *)
         die "unknown option/argument: '$1'"
@@ -186,14 +187,37 @@ then
     echo "Using boost-system (skip ThirdParty build of BOOST)"
 
     # Tagged as 'system' but could actually point to a central location
-    [ -d "$BOOST_ARCH_PATH/include" ] || {
+
+    if [ -d "$boostInc" ]
+    then
+        if BOOST_ARCH_PATH=$(cd $BOOST_ARCH_PATH 2>/dev/null && pwd -P)
+        then
+            boostPACKAGE=${BOOST_ARCH_PATH##*/}
+        else
+            echo "ERROR: bad path for BOOST_ARCH_PATH"
+            echo "stopping build"
+            exit 1
+        fi
+
+        libdir="$BOOST_ARCH_PATH/lib"
+    else
         boostInc="/usr/include"
         boostLib="/usr/lib$WM_COMPILER_LIB_ARCH"
-    }
+        libdir="/usr/lib"
+    fi
+
+    # Use lib/ when lib64/ does not exist
+    [ ! -d "$boostLib" -a -d "$libdir" ] && boostLib="$libdir"
 
 elif [ -f "$boostInc/boost/version.hpp" ]
 then
     echo "Using $boostPACKAGE"
+
+    libdir="$BOOST_ARCH_PATH/lib"
+
+    # Use lib when lib64 does not exist
+    [ ! -d "$boostLib" -a -d "$libdir" ] && boostLib="$libdir"
+
 else
     echo "Starting build: $boostPACKAGE"
     echo
@@ -218,7 +242,7 @@ else
     }
 fi
 
-# nothing left to build
+# Nothing left to build
 if _foamIsSystem $cgalPACKAGE
 then
     echo "Using cgal-system (skip ThirdParty build of CGAL)"
@@ -239,18 +263,6 @@ else
     exit 1
 fi
 
-#------------------------------------------------------------------------------
-
-cat<<SUMMARY
-CGAL configuration
-------------------
-    CGAL    = $cgalPACKAGE
-    BOOST   = $boostPACKAGE
-    GMP     = $gmpPACKAGE
-    MPFR    = $mpfrPACKAGE
-------------------
-SUMMARY
-
 #------------------------------------------------------------------------------
 #
 # Build CGAL
@@ -268,22 +280,61 @@ CGAL_BUILD_DIR=$buildBASE/$cgalPACKAGE
 : ${CGAL_ARCH_PATH:=$installBASE/$cgalPACKAGE}      # Fallback
 
 # gmp/mpfr are installed without compiler name
-installBASE=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH
-
-GMP_ARCH_PATH=$installBASE/$gmpPACKAGE
-MPFR_ARCH_PATH=$installBASE/$mpfrPACKAGE
+mpfrBASE=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER_ARCH
 
 # Enable/disable gmp/mpfr together
 if _foamIsNone $gmpPACKAGE || _foamIsNone $mpfrPACKAGE
 then
     GMP_ARCH_PATH=none
     MPFR_ARCH_PATH=none
-elif _foamIsSystem $GMP_ARCH_PATH || _foamIsSystem $MPFR_ARCH_PATH
+elif _foamIsSystem $gmpPACKAGE || _foamIsSystem $mpfrPACKAGE
 then
-    GMP_ARCH_PATH=system    # for an accurate record
+    # May really be system, but could also by a central installation
+    # Ensure everything is accurately recorded. Resolve paths etc.
+
+    if [ -d "$GMP_ARCH_PATH" ]
+    then
+        if GMP_ARCH_PATH=$(cd $GMP_ARCH_PATH 2>/dev/null && pwd -P)
+        then
+            gmpPACKAGE=${GMP_ARCH_PATH##*/}
+        else
+            echo "ERROR: bad path for GMP_ARCH_PATH"
+            echo "stopping build"
+            exit 1
+        fi
+    else
+        GMP_ARCH_PATH=system
+    fi
+
+    if [ -d "$MPFR_ARCH_PATH" ]
+    then
+        if MPFR_ARCH_PATH=$(cd $MPFR_ARCH_PATH 2>/dev/null && pwd -P)
+        then
+            mpfrPACKAGE=${MPFR_ARCH_PATH##*/}
+        else
+            echo "ERROR: bad path for MPFR_ARCH_PATH"
+            echo "stopping build"
+            exit 1
+        fi
+    else
         MPFR_ARCH_PATH=system
+    fi
+else
+    GMP_ARCH_PATH=$mpfrBASE/$gmpPACKAGE
+    MPFR_ARCH_PATH=$mpfrBASE/$mpfrPACKAGE
 fi
 
+#------------------------------------------------------------------------------
+
+cat<<SUMMARY
+CGAL configuration
+------------------
+    CGAL    = $cgalPACKAGE
+    BOOST   = $boostPACKAGE
+    GMP     = $gmpPACKAGE
+    MPFR    = $mpfrPACKAGE
+------------------
+SUMMARY
 
 #
 # build information recorded for later use
@@ -311,7 +362,7 @@ BUILD_INFO
 }
 
 
-# compare expected vs what is extracted as KEY=... in text
+# Compare expected vs what is extracted as KEY=... in text
 # $1 = key
 # $2 = expected
 # $3 = text to extract from
@@ -327,10 +378,11 @@ infoValueEq()
     fi
 }
 
-# needs build
+# Needs build
 cgalIsCurrent()
 {
-    local info=$(cat $buildInfoFile 2>/dev/null)
+    # Only need VAR=... (also avoids embedded '#' that bothers some shells)
+    local info=$(sed -n -e '/^[A-Z]/p' $buildInfoFile 2>/dev/null)
     [ -n "$info" ] || return 1
 
     local libDirName="lib$WM_COMPILER_LIB_ARCH"
@@ -381,17 +433,20 @@ fi
     # See http://doc.cgal.org/latest/Manual/installation.html
     if _foamIsSystem $boostPACKAGE
     then
-        echo "    system         : boost"
         # Tagged as 'system' but could actually point to a central location
         if [ -d "$BOOST_ARCH_PATH/include" ]
         then
+            echo "    boost          : ${BOOST_ARCH_PATH##*/}"
             configBoost="-DBOOST_ROOT=$BOOST_ARCH_PATH"
+        else
+            echo "    boost          : system"
         fi
+
         ## For system - possible that /usr/lib64 not being found?
         ## configBoost="-DBoost_LIBRARY_DIRS=$boostLib"
     elif [ -d "$BOOST_ARCH_PATH" ]
     then
-        echo "    ThirdParty     : boost"
+        echo "    boost          : $boostPACKAGE"
         configBoost=$(cat <<CMAKE_OPTIONS
  -DBoost_INCLUDE_DIR=$boostInc
  -DBoost_LIBRARY_DIRS=$boostLib
@@ -406,44 +461,64 @@ CMAKE_OPTIONS
 
     if _foamIsSystem $GMP_ARCH_PATH
     then
-        echo "    system         : gmp"
+        echo "    gmp            : system"
     elif _foamIsNone $GMP_ARCH_PATH
     then
-        echo "    disabled       : gmp"
+        echo "    gmp            : disabled"
         configGmp="-DCGAL_DISABLE_GMP=TRUE"  # Also used for mpfr
     elif [ -d "$GMP_ARCH_PATH" ]
     then
-        echo "    ThirdParty     : gmp"
+        echo "    gmp            : $gmpPACKAGE"
+
+        for libdir in \
+            $GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
+            $GMP_ARCH_PATH/lib \
+        ;
+        do
+            if [ -f "$libdir/libgmp.so" ]
+            then
                 configGmp=$(cat <<CMAKE_OPTIONS
  -DGMP_INCLUDE_DIR=$GMP_ARCH_PATH/include
- -DGMP_LIBRARIES_DIR=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH
- -DGMP_LIBRARIES=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libgmp.so
- -DGMPXX_INCLUDE_DIR=$GMP_ARCH_PATH/include
- -DGMPXX_LIBRARIES=$GMP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libgmpxx.so
+ -DGMP_LIBRARIES_DIR=$libdir
+ -DGMP_LIBRARIES=$libdir/libgmp.so
 CMAKE_OPTIONS
 )
+                break
+            fi
+        done
     else
         echo "    system         : gmp (did not find $GMP_ARCH_PATH)"
     fi
 
     if _foamIsSystem $MPFR_ARCH_PATH
     then
-        echo "    system         : mpfr"
+        echo "    mpfr           : system"
     elif _foamIsNone $MPFR_ARCH_PATH
     then
-        echo "    disabled       : mpfr"
+        echo "    mpfr           : disabled"
         configGmp="-DCGAL_DISABLE_GMP=TRUE"  # Also used for mpfr
     elif [ -d "$MPFR_ARCH_PATH" ]
     then
-        echo "    ThirdParty     : mpfr"
+        echo "    mpfr           : $mpfrPACKAGE"
+
+        for libdir in \
+            $MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH \
+            $MPFR_ARCH_PATH/lib \
+        ;
+        do
+            if [ -f "$libdir/libmpfr.so" ]
+            then
                 configMpfr=$(cat <<CMAKE_OPTIONS
  -DMPFR_INCLUDE_DIR=$MPFR_ARCH_PATH/include
- -DMPFR_LIBRARIES_DIR=$MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH
- -DMPFR_LIBRARIES=$MPFR_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmpfr.so
+ -DMPFR_LIBRARIES_DIR=$libdir
+ -DMPFR_LIBRARIES=$libdir/libmpfr.so
 CMAKE_OPTIONS
 )
+                break
+            fi
+        done
     else
-        echo "    system         : mpfr (did not find $MPFR_ARCH_PATH)"
+        echo "    mpfr           : system (did not find $MPFR_ARCH_PATH)"
     fi
 
     cmake=$(findCMake)
@@ -481,7 +556,7 @@ CMAKE_OPTIONS
         fi
     done
 
-    # record our build-status
+    # Record our build-status
     recordCGALinfo
 
     echo "Done CGAL"

makeGcc

@@ -39,6 +39,7 @@ cd ${0%/*} && wmakeCheckPwd "$WM_THIRD_PARTY_DIR" 2>/dev/null || {
 }
 . etc/tools/ThirdPartyFunctions
 #------------------------------------------------------------------------------
+unset GMP_ARCH_PATH MPFR_ARCH_PATH                                  # Purge old
 
 [ "${WM_COMPILER#Gcc}" = "$WM_COMPILER" ] && WM_COMPILER=Gcc        # Force gcc
 WM_COMPILER_TYPE=ThirdParty                # Ensure we get the correct settings
@@ -99,12 +100,15 @@ do
         gmpPACKAGE="gmp-system"
         mpfrPACKAGE="mpfr-system"
         mpcPACKAGE="mpc-system"
+        unset GMP_ARCH_PATH MPFR_ARCH_PATH
         ;;
     gmp-[4-9]* | gmp-system)
         gmpPACKAGE="${1%%/}"
+        unset GMP_ARCH_PATH
         ;;
     mpfr-[2-9]* | mpfr-system)
         mpfrPACKAGE="${1%%/}"
+        unset MPFR_ARCH_PATH
         ;;
     mpc-[0-9]* | mpc-system)
         mpcPACKAGE="${1%%/}"
@@ -169,7 +173,7 @@ addLib()
 # Build GMP
 # ================
 echo "---------------"
-if [ -d $GMP_ARCH_PATH ]
+if [ -d "$GMP_ARCH_PATH" ]
 then
     echo "Already built: $gmpPACKAGE"
 elif _foamIsSystem $GMP_ARCH_PATH