FEATURE: Porting fixes and GGI bug fix. Author: Hrvoje Jasak. Merge: Hrvoje Jasak.

ThirdParty/AllMake.stage2

@@ -102,7 +102,7 @@ then
     [ ! -z "$WM_THIRD_PARTY_USE_OPENMPI_188" ] && {
 	echo "Building openmpi 1.8.8"
 	( rpm_make -p openmpi-1.8.8 -s openmpi-1.8.8.spec  -u http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.gz \
-          -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_165_ConfigureAdditionalArgs"')
+          -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs"')
     }
 else
     echo "Using system installed OpenMPI"

applications/utilities/parallelProcessing/decomposeSets/decomposeSets.C

@@ -45,6 +45,7 @@ int main(int argc, char *argv[])
 
     // Add option to write empty sets
     argList::validOptions.insert("writeEmptySets", "");
+    argList::validOptions.insert("liveObjectsOnly", "");
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -52,6 +53,7 @@ int main(int argc, char *argv[])
     Info<< "Time = " << runTime.timeName() << endl;
 
     bool writeEmptySets = args.optionFound("writeEmptySets");
+    bool liveObjectsOnly = args.optionFound("liveObjectsOnly");
 
     // Determine the processor count directly
     label nProcs = 0;
@@ -128,10 +130,18 @@ int main(int argc, char *argv[])
         {
             const labelList& addr = procMeshes.pointProcAddressing()[procI];
 
+            const label nProcPoints = procMeshes.meshes()[procI].nPoints();
+
             labelHashSet procSet;
 
             forAll (addr, pointI)
             {
+                // Skip list when nPoints is reached
+                if (liveObjectsOnly && pointI >= nProcPoints)
+                {
+                    break;
+                }
+
                 if (set.found(addr[pointI]))
                 {
                     procSet.insert(pointI);
@@ -143,14 +153,14 @@ int main(int argc, char *argv[])
                 // Set created, write it
                 Info<< "Writing point set " << set.name()
                     << " on processor " << procI << endl;
-                pointSet cs
+                pointSet ps
                 (
                     procMeshes.meshes()[procI],
                     set.name(),
                     procSet,
                     IOobject::NO_WRITE
                 );
-                cs.write();
+                ps.write();
             }
         }
     }
@@ -172,10 +182,18 @@ int main(int argc, char *argv[])
         {
             const labelList& addr = procMeshes.faceProcAddressing()[procI];
 
+            const label nProcFaces = procMeshes.meshes()[procI].nFaces();
+
             labelHashSet procSet;
 
             forAll (addr, faceI)
             {
+                // Skip list when nPoints is reached
+                if (liveObjectsOnly && faceI >= nProcFaces)
+                {
+                    break;
+                }
+
                 // Note faceProcAddressing peculiarity:
                 // change of sign and offset.  HJ, 7/Mar/2011
                 if (set.found(mag(addr[faceI]) - 1))
@@ -189,14 +207,14 @@ int main(int argc, char *argv[])
                 // Set created, write it
                 Info<< "Writing face set " << set.name()
                     << " on processor " << procI << endl;
-                faceSet cs
+                faceSet fs
                 (
                     procMeshes.meshes()[procI],
                     set.name(),
                     procSet,
                     IOobject::NO_WRITE
                 );
-                cs.write();
+                fs.write();
             }
         }
     }
@@ -218,6 +236,8 @@ int main(int argc, char *argv[])
         {
             const labelList& addr = procMeshes.cellProcAddressing()[procI];
 
+            // There are no retired cells: no special handling required
+
             labelHashSet procSet;
 
             forAll (addr, cellI)

doc/buildInstructions/Windows/README.txt

@@ -157,7 +157,7 @@ Version: 1.11.4-1 (or above)
 URL    : http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-bin.zip, http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-dep.zip, http://downloads.sourceforge.net/gnuwin32/wget-1.11.4-1-doc.zip
 For    : Automatically downloading files from internet (eg. for use in automated build scripts)
 
-git clone --branch nameClashesForWinPort   git://git.code.sf.net/u/dominikchrist/foam-extend-3.1-dc foam-extend-3.1-win
+git clone --branch nextRelease git://git.code.sf.net/p/openfoam-extend/foam-extend-3.1
 
 
 4. EXAMPLE OUTPUT FROM SOUCING etc/bashrc.mingw
@@ -199,14 +199,14 @@ Checking versions of installed system tools (based on PATH) ...
 Bison:       /bin/bison.exe [bison (GNU Bison) 2.4.2]
 CMake:       /c/Programs/cmake-3.2.3-win32-x86/bin/cmake.exe [cmake version 3.2.3]
 Flex:        /bin/flex.exe [flex 2.5.35]
-G++:         /c/Programs/x86_64-4.8.2-release-win32-seh-rt_v3-rev3/mingw64/bin/g++.exe [g++.exe (x86_64-win32-seh-rev3, Built by MinGW-W64 project) 4.8.2]
+G++:         /c/Programs/mingw64/bin/g++.exe [g++.exe (x86_64-win32-seh-rev3, Built by MinGW-W64 project) 4.8.2]
-GCC:         /c/Programs/x86_64-4.8.2-release-win32-seh-rt_v3-rev3/mingw64/bin/gcc.exe [gcc.exe (x86_64-win32-seh-rev3, Built by MinGW-W64 project) 4.8.2]
+GCC:         /c/Programs/mingw64/bin/gcc.exe [gcc.exe (x86_64-win32-seh-rev3, Built by MinGW-W64 project) 4.8.2]
 GMake:       /c/Programs/strawberry-perl-5.20.2.1-64bit/c/bin/gmake.exe [GNU Make 4.0.90]
 Git:         /c/Programs/Git/cmd/git.exe [git version 1.9.5.msysgit.1]
 Java:        /c/ProgramData/Oracle/Java/javapath/java.exe [java version "1.8.0_45"]
 M4:          /bin/m4.exe [m4 (GNU M4) 1.4.16]
 Make:        /bin/make.exe [GNU Make 3.81]
-MinGW-w64:   /c/Programs/x86_64-4.8.2-release-win32-seh-rt_v3-rev3/mingw64
+MinGW-w64:   /c/Programs/mingw64
 OpenMPI:     /c/Programs/OpenMPI_v1.6.1-x64/bin/mpirun.exe [mpirun.exe (OpenRTE) 1.6.1]
 PEexports:   /c/Programs/strawberry-perl-5.20.2.1-64bit/c/bin/pexports.exe [PExports 0.44 Copyright 1998, Anders Norlander]
 ParaView:    /c/Programs/ParaView-4.3.1

etc/cshrc

@@ -153,7 +153,7 @@ if ( ! $?WM_PRECISION_OPTION ) setenv WM_PRECISION_OPTION DP
 
 # WM_COMPILE_OPTION = Opt | Debug | Prof
 if ( ! $?WM_COMPILE_OPTION ) setenv WM_COMPILE_OPTION Opt
-setenv WM_COMPILE_OPTION Opt
+#setenv WM_COMPILE_OPTION Opt
 #setenv WM_COMPILE_OPTION Debug
 
 # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI | MVAPICH2

etc/prefs.csh-EXAMPLE

@@ -203,7 +203,7 @@ setenv WM_THIRD_PARTY_USE_CMAKE_322 1
 #
 # For AllMake.stage2
 setenv WM_THIRD_PARTY_USE_OPENMPI_188 1
-setenv WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs '--enable-mpi-cxx --with-verbs=/usr --with-verbs-libdir=/usr/lib64'
+#setenv WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs '--enable-mpi-cxx --with-verbs=/usr --with-verbs-libdir=/usr/lib64'
 #setenv WM_THIRD_PARTY_USE_OPENMPI_165 1
 #setenv WM_THIRD_PARTY_USE_OPENMPI_165_ConfigureAdditionalArgs '--enable-mpi-cxx --with-openib=/usr --with-openib-libdir=/usr/lib64'
 #setenv WM_THIRD_PARTY_USE_OPENMPI_15 1

etc/prefs.sh-EXAMPLE

@@ -213,7 +213,7 @@ export WM_THIRD_PARTY_USE_CMAKE_322=1
 #
 # For AllMake.stage2
 export WM_THIRD_PARTY_USE_OPENMPI_188=1
-export WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs='--enable-mpi-cxx --with-openib=/usr --with-openib-libdir=/usr/lib64'
+#export WM_THIRD_PARTY_USE_OPENMPI_188_ConfigureAdditionalArgs='--enable-mpi-cxx --with-openib=/usr --with-openib-libdir=/usr/lib64'
 #export WM_THIRD_PARTY_USE_OPENMPI_165=1
 #export WM_THIRD_PARTY_USE_OPENMPI_165_ConfigureAdditionalArgs='--enable-mpi-cxx --with-openib=/usr --with-openib-libdir=/usr/lib64'
 #export WM_THIRD_PARTY_USE_OPENMPI_15=1

src/foam/interpolations/GGIInterpolation/GGIInterpolate.C

@@ -145,8 +145,11 @@ void GGIInterpolation<MasterPatch, SlavePatch>::maskedBridge
             {
                 // Gone beyond my index: my face is not present in the mask
                 // Go one back and check for next uncovered face
-
+                if (maskAddrI > 0)
+                {
                     maskAddrI--;
+                }
+
                 break;
             }
         }

src/meshTools/sets/topoSets/cellSet.C

@@ -61,7 +61,7 @@ cellSet::cellSet
 :
     topoSet(mesh, typeName, name, r, w)
 {
-    // Make sure set within valid range
+    // Make sure set within valid range: there are no retired cells
     check(mesh.nCells());
 }
 

src/meshTools/sets/topoSets/faceSet.C

@@ -63,7 +63,8 @@ faceSet::faceSet
 :
     topoSet(mesh, typeName, name, r, w)
 {
-    check(mesh.nFaces());
+    // Sets can also contain retired faces.  HJ, 17/Aug/2015
+    check(mesh.allFaces().size());
 }
 
 
@@ -228,7 +229,7 @@ void faceSet::sync(const polyMesh& mesh)
 
 label faceSet::maxSize(const polyMesh& mesh) const
 {
-    return mesh.nFaces();
+    return mesh.allFaces().size();
 }
 
 

src/meshTools/sets/topoSets/pointSet.C

@@ -62,7 +62,8 @@ pointSet::pointSet
 :
     topoSet(mesh, typeName, name, r, w)
 {
-    check(mesh.nPoints());
+    // Sets can contain retired points.  HJ, 17/Aug/2015
+    check(mesh.allPoints().size());
 }
 
 
@@ -147,7 +148,7 @@ void pointSet::sync(const polyMesh& mesh)
 
 label pointSet::maxSize(const polyMesh& mesh) const
 {
-    return mesh.nPoints();
+    return mesh.allPoints().size();
 }