Merge branch 'develop' into 'master'

Update master to match develop

See merge request !2

legacyCompile/README.md

@@ -34,6 +34,7 @@ and package versions, it may not work for all users and environments.
      * MesaLib-x.y.z files (replace by mesa-x.y.z)
      * llvm-x.y.z.src TarFile (remove .src part in filename and in subdir)
      * cfe-x.y.z.src TarFile must be moved to llvm-x.y.z/tools/clang
+     * openmp-x.y.z.src TarFile must be moved to llvm-x.y.z/tools/openmp
      * ParaView-v* TarFile (remove -source part in filename and in subdir)
         Note: when unpacking ParaView, it may create a subdir with suffix
         -source. Please remove this suffix as well and tar the package
@@ -52,18 +53,17 @@ and package versions, it may not work for all users and environments.
 
 ---
 
-## Script Configuration
+## Configuration
 
 Users need to define the desired packages and versions to use for the
 OpenFOAM compilation. The packages and versions need to be input under the
-paragraph `USER INPUT (2)`, stating whether the default version is to be
+section `[software]`, stating whether the default version is to be
 used, or the user needs to use a different version. If both entries have
 information, the user-preference will prevail. In any case, a suitable
 tar/zip file with packageName-versionNumber needs to be placed under subdir
 `packages/`.  The value `ompiType` refers to the openmpi type (system|third).
 
-    # USER INPUT (2)
-    # ~~~~~~~~~~~~~~
+    [software]
     # Preferred software versions etc. Use 'third' for ThirdParty.
     #---------------------+-------------------+-------------------+
     #   package           | default           | user-preference   |
@@ -95,23 +95,21 @@ tar/zip file with packageName-versionNumber needs to be placed under subdir
 
 ## Usage
 
-    ./legacyCompile [OPTION] OPERATION [...OPERATION]
+    ./legacyCompile [OPTIONS] OPERATION [...OPERATION] configFile
+    options:
+      -purge                Purge old directories before unpacking (CAUTION)
+      -int32  | -int64      Label width
+      -SP     | -DP         Precision
+      -sigfpe | -no-sigfpe  Activate/deactivate FOAM_SIGFPE handling
+      -help
+
     operations:
       -unpack           Unpack sources, configure
       -third            Compile ThirdParty
       -foam             Compile OpenFOAM
       -list             List configured versions only
-      -all              Alias for  -unpack -third -foam
-      -rebuild          Alias for  -third -foam
-
-    options:
-      -purge            Purge old directories before unpacking (CAUTION)
-      -help
-
-    Config options:
-      -int32  | -int64      Label width (default: 32)
-      -SP     | -DP         Precision (default: DP)
-      -sigfpe |-no-sigfpe   Activate/deactivate FOAM_SIGFPE handling
+      -all              Alias for -unpack -third -foam
+      -rebuild          Alias for -third -foam
 
 
 The script contains the three essential operations:
@@ -127,43 +125,43 @@ unpack stage).
 
 * To compile first time (from scratch) with default label size and precision:
 
-    ./legacyCompile -all
+    ./legacyCompile -all configFile
 
 * To repeat the same, **overwriting** any existing installation:
 
-    ./legacyCompile -all -purge
+    ./legacyCompile -all -purge configFile
 
 
 * To unpack all packages and configure some OpenFOAM settings without
   compiling:
 
-    ./legacyCompile -unpack
-    ./legacyCompile -unpack -purge   # caution: removes existing installation
+    ./legacyCompile -unpack  configFile
+    ./legacyCompile -unpack -purge configFile # Caution: removes existing installation
 
 
 To compile with 64 bit label size in single precission:
 
-    ./legacyCompile -all -int64 -SP
+    ./legacyCompile -all -int64 -SP configFile
 
 
 If you change your third-party package selections or the preferred
 configuration (SP, DP etc), you will need the `-unpack` operation,
 which also includes some configuration operations.
 
-    ./legacyCompile -unpack
+    ./legacyCompile -unpack configFile
 
 
 To (re)compile ThirdParty and OpenFOAM individually:
 
-    ./legacyCompile -unpack -third -purge
+    ./legacyCompile -unpack -third -purge configFile
     (to compile ThirdParty from scratch)
 
-    ./legacyCompile -foam
+    ./legacyCompile -foam configFile
     (to compile OpenFOAM from existing ThirdParty)
 
 To compile with 32 bit label size in single precission:
 
-    ./legacyCompile -all -int64 -SP
+    ./legacyCompile -all -int64 -SP configFile
 
 ---
 
@@ -183,4 +181,4 @@ building Clang), you should remove the corrsponding logfile(s) before
 recompiling with the '-unpack -third` options.
 
 ---
-2016-12-21
+2017-06-29

legacyCompile/v1612.cfg

+#------------------------------------------------------------------------------
+# File
+#     v1612.cfg
+#
+# Description
+#     Configuration file for legacyCompile
+#------------------------------------------------------------------------------
+
+# Top-level package information
+[package]
+
+FoamVersion=v1612+
+OFdirName=OpenFOAM-v1612+
+TPdirName=ThirdParty-v1612+
+
+# If source packages differ from the directory names, uncomment and adjust
+
+# OFsource=OpenFOAM-plus
+# TPsource=ThirdParty-plus
+
+# Architecture
+[arch]
+label=32
+scalar=64
+sigfpe=false
+
+
+[software]
+# Preferred software versions etc. Use 'third' for ThirdParty.
+#---------------------+-------------------+-------------------+
+#   package           | default           | user-preference   |
+#---------------------+-------------------+-------------------+
+    boost               boost_1_62_0
+    cgal                CGAL-4.9
+    fftw                fftw-3.3.5
+    openmpi             openmpi-1.10.4
+    scotch              scotch_6.0.3
+    paraview            ParaView-5.0.1
+    cmake               cmake-system        cmake-3.5.2
+    vtk                 none                VTK-7.1.0
+    mesa                none                mesa-13.0.1
+    qt                  qt-system           qt-4.8.7
+    llvm                llvm-3.7.0
+    gcc                 system              gcc-4.8.5
+    gmp                 system              gmp-6.1.1
+    mpfr                system              mpfr-3.1.5
+    mpc                 system              mpc-1.0.3
+
+    ompiType            system              third
+    compilerType        system              third
+    compiler            Gcc                 Clang
+
+# -----------------------------------------------------------------------------

legacyCompile/v1706.cfg

+#------------------------------------------------------------------------------
+# File
+#     v1706.cfg
+#
+# Description
+#     Configuration file for legacyCompile
+#------------------------------------------------------------------------------
+
+# Top-level package information
+[package]
+
+FoamVersion=v1706
+OFdirName=OpenFOAM-v1706
+TPdirName=ThirdParty-v1706
+
+# If source packages differ from the directory names, uncomment and adjust
+
+# OFsource=OpenFOAM-plus
+# TPsource=ThirdParty-plus
+
+# Architecture
+[arch]
+label=32
+scalar=32
+sigfpe=false
+
+
+[software]
+# Preferred software versions etc. Use 'third' for ThirdParty.
+#---------------------+-------------------+-------------------+
+#   package           | default           | user-preference   |
+#---------------------+-------------------+-------------------+
+    boost               boost_1_64_0
+    cgal                CGAL-4.9.1
+    fftw                fftw-3.3.6-pl1
+    openmpi             openmpi-1.10.4
+    scotch              scotch_6.0.3
+    paraview            ParaView-5.4.0
+    cmake               cmake-system        cmake-3.5.2
+    vtk                 none                VTK-8.1.0
+    mesa                none                mesa-17.1.1
+    qt                  qt-system           qt-4.8.7
+    llvm                llvm-3.7.0
+    gcc                 system              gcc-4.8.5
+    gmp                 system              gmp-6.1.1
+    mpfr                system              mpfr-3.1.5
+    mpc                 system              mpc-1.0.3
+
+    ompiType            system              third
+    compilerType        system              third
+    compiler            Gcc                 Clang
+
+# -----------------------------------------------------------------------------

legacyCompile/v1712.cfg

+#------------------------------------------------------------------------------
+# File
+#     v1712.cfg
+#
+# Description
+#     Configuration file for legacyCompile
+#------------------------------------------------------------------------------
+
+# Top-level package information
+[package]
+
+FoamVersion=v1712
+OFdirName=OpenFOAM-v1712
+TPdirName=ThirdParty-v1712
+
+# If source packages differ from the directory names, uncomment and adjust
+
+# OFsource=OpenFOAM-plus
+# TPsource=ThirdParty-plus
+
+# Architecture
+[arch]
+label=32
+scalar=32
+
+
+[software]
+# Preferred software versions etc. Use 'third' for ThirdParty.
+#---------------------+-------------------+-------------------+
+#   package           | default           | user-preference   |
+#---------------------+-------------------+-------------------+
+    boost               boost_1_64_0
+    cgal                CGAL-4.9.1
+    fftw                fftw-3.3.7
+    openmpi             openmpi-1.10.4
+    scotch              scotch_6.0.3
+    kahip               kahip-2.00
+    paraview            ParaView-5.4.1
+    cmake               cmake-system        cmake-3.6.0
+    vtk                 none                VTK-8.1.0
+    mesa                none                mesa-17.1.1
+    qt                  qt-system           qt-5.9.3
+    llvm                llvm-3.7.1
+    gcc                 system              gcc-4.8.5
+    gmp                 system              gmp-6.1.1
+    mpfr                system              mpfr-3.1.5
+    mpc                 system              mpc-1.0.3
+
+    ompiType            system              third
+    compilerType        system              third
+    compiler            Gcc                 Clang
+
+# -----------------------------------------------------------------------------

modules/foamCreateModuleInclude

@@ -73,7 +73,7 @@ do
     '')
         # Ignore empty args
         ;;
-    -h | -help)
+    -h | -help*)
         usage
         ;;
     -debug)
@@ -178,11 +178,38 @@ else
 fi
 
 
+# Snapshot of aliases - sorted
+printAlias()
+{
+    alias | sort -f
+}
+
+
+# Snapshot of environment - without functions
+# Sorted as non-OpenFOAM, WM_*, FOAM_*
+printEnv()
+{
+    # Non FOAM_*, WM_* settings
+    echo "# non-OpenFOAM"
+    env | sed -n -e '\@^FOAM_@d' -e '\@^WM_@d' -e '\@^[^ {}]@p' \
+        | sort -f
+
+    # WM_* settings
+    echo "# OpenFOAM"
+    env | sed -n -e '\@^WM_@p' \
+        | sort -f
+
+    # FOAM_* settings
+    echo "# OpenFOAM"
+    env | sed -n -e '\@^FOAM_@p' \
+        | sort -f
+}
+
 #
-# Initial snapshot of the environment, without any functions
+# Initial snapshot of the environment (without functions)
 #
-env   | sed -n -e '/^[^ {}]/p' | sort -f > $tmpFiles.env.pre.log
-alias | sort -f > $tmpFiles.alias.pre.log
+printEnv   > $tmpFiles.env.pre.log
+printAlias > $tmpFiles.alias.pre.log
 
 # OpenFOAM settings
 . $projectDir/etc/bashrc ''
@@ -195,6 +222,9 @@ unset FOAM_JOB_DIR FOAM_RUN FOAM_SETTINGS FOAM_INST_DIR
 unset WM_PROJECT_USER_DIR WM_THIRD_PARTY_DIR
 unset SCOTCH_VERSION
 
+
+# Also remove user directories as being unreliable
+
 foamOldDirs="$CEI_HOME $BOOST_ARCH_PATH $CGAL_ARCH_PATH $FFTW_ARCH_PATH $MPI_ARCH_PATH $SCOTCH_ARCH_PATH \
 $FOAM_SITE_APPBIN $FOAM_SITE_LIBBIN $WM_PROJECT_SITE \
 $FOAM_USER_APPBIN $FOAM_USER_LIBBIN"
@@ -222,11 +252,6 @@ unset ENSIGHT10_INPUT ENSIGHT10_READER
 # Always consider site to be bogus. If needed, should be done elsewhere.
 unset FOAM_SITE_APPBIN FOAM_SITE_LIBBIN WM_PROJECT_SITE
 
-# Make user directories more generic.
-export FOAM_USER_APPBIN='$env(HOME)/OpenFOAM/$env(USER)-'"$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/bin"
-export FOAM_USER_LIBBIN='$env(HOME)/OpenFOAM/$env(USER)-'"$WM_PROJECT_VERSION/platforms/$WM_OPTIONS/lib"
-
-
 # Remove non-essential aliases
 unalias wmDP        2>/dev/null
 unalias wmInt32     2>/dev/null
@@ -247,11 +272,22 @@ unalias util        2>/dev/null
 
 #------------------------------------------------
 
+# Generalize environment.
+# This needs rethinking since it largely duplicates logic from the etc/config.sh/settings
+rewriteEnv()
+{
+    sed \
+    -e 's@^\(FOAM_USER_APPBIN=\).*@\1$env(HOME)/OpenFOAM/$env(USER)-$env(WM_PROJECT_VERSION)/platforms/$env(WM_OPTIONS)/bin@' \
+    -e 's@^\(FOAM_USER_LIBBIN=\).*@\1$env(HOME)/OpenFOAM/$env(USER)-$env(WM_PROJECT_VERSION)/platforms/$env(WM_OPTIONS)/lib@' \
+    ;
+}
+
 #
-# Updated snapshot of the environment, without any functions
+# Updated snapshot of the environment (without functions)
 #
-env   | sed -n -e '/^[^ {}]/p' | sort -f > $tmpFiles.env.post.log
-alias | sort -f > $tmpFiles.alias.post.log
+printEnv   | rewriteEnv > $tmpFiles.env.post.log
+printAlias > $tmpFiles.alias.post.log
+
 
 # Create a diff of the environment and aliases
 diff $tmpFiles.env.pre.log    $tmpFiles.env.post.log   > $tmpFiles.env.diff.log
@@ -259,7 +295,7 @@ diff $tmpFiles.alias.pre.log  $tmpFiles.alias.post.log > $tmpFiles.alias.diff.lo
 
 echo "# -------------------"  > $moduleOutput
 
-# -------------------
+# --------------------------------------------------
 # Environment other than PATH, LD_LIBRARY_PATH
 echo "# Environment"  >> $moduleOutput
 grep '> ' $tmpFiles.env.diff.log | \
@@ -270,7 +306,7 @@ sed \
     -e 's/=/ "/' -e 's/$/\"/' >> $moduleOutput
 
 
-# -------------------
+# --------------------------------------------------
 # Changes in PATH - without junk and system directories
 echo "# PATH"  >> $moduleOutput
 
@@ -290,9 +326,9 @@ sed \
     -e 's/^/append-path PATH "/' \
     -e 's/$/\"/' \
     $tmpFiles.path.diff.log  >> $moduleOutput
-# -------------------
+# --------------------------------------------------
 
-# -------------------
+# --------------------------------------------------
 # Changes in LD_LIBRARY_PATH - without junk and system directories
 echo "# LD_LIBRARY_PATH"  >> $moduleOutput