Merge branch 'master' into feature/gzip

CMakeLists.txt

@@ -8,9 +8,13 @@ PROJECT(Nektar++)
 # Helps organize projects in IDEs.
 SET_PROPERTY(GLOBAL PROPERTY USE_FOLDERS ON)
 
-SET(NEKTAR_VERSION_MAJOR 3)
-SET(NEKTAR_VERSION_MINOR 2)
-SET(NEKTAR_VERSION_PATCH 0)
+# Extract the version number from the VERSION file and set in CMake
+# The format of this file must be X.X.X
+FILE(STRINGS "VERSION" NEKVER)
+STRING(REPLACE "." ";" NEKVERLIST ${NEKVER})
+LIST(GET NEKVERLIST 0 NEKTAR_VERSION_MAJOR)
+LIST(GET NEKVERLIST 1 NEKTAR_VERSION_MINOR)
+LIST(GET NEKVERLIST 2 NEKTAR_VERSION_PATCH)
 SET(NEKTAR_VERSION ${NEKTAR_VERSION_MAJOR}.${NEKTAR_VERSION_MINOR}.${NEKTAR_VERSION_PATCH})
 
 INCLUDE(CMakeExportBuildSettings)

cmake/FindFFTW.cmake

@@ -18,7 +18,7 @@ ENDIF (FFTW_LIB)
 
 IF (FFTW_FOUND)
   IF (NOT FFTW_LIB_FIND_QUIETLY)
-     MESSAGE(STATUS "Found FFTW")
+     MESSAGE(STATUS "Found FFTW: ${FFTW_LIB}")
      GET_FILENAME_COMPONENT(FFTW_PATH ${FFTW_LIB} PATH CACHE)
      SET(FFTW_INCLUDE_DIR ${FFTW_PATH}/../include CACHE FILEPATH "FFTW include directory.")
      MARK_AS_ADVANCED(FFTW_PATH)

cmake/NektarCommon.cmake

@@ -167,10 +167,10 @@ MACRO(ADD_NEKTAR_EXECUTABLE name component sources)
         ${Boost_FILESYSTEM_LIBRARY} 
         ${Boost_SYSTEM_LIBRARY}
         ${Boost_PROGRAM_OPTIONS_LIBRARY} 
-        ${Boost_ZLIB_LIBRARY} 
+        ${ZLIB_LIBRARY} 
         optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
 	)
-    ADD_DEPENDENCIES(${name} boost tinyxml zlib)
+    ADD_DEPENDENCIES(${name} boost tinyxml zlib-1.2.7)
 
     IF( NEKTAR_USE_MPI )
         TARGET_LINK_LIBRARIES(${name} ${MPI_LIBRARY} ${MPI_EXTRA_LIBRARY})
@@ -221,7 +221,8 @@ MACRO(ADD_NEKTAR_LIBRARY name component type)
 
     # NIST Sparse BLAS only static, so link into Nektar libraries directly.
     TARGET_LINK_LIBRARIES( ${name} ${NIST_SPARSE_BLAS} ${METIS_LIB})
-    ADD_DEPENDENCIES(${name} spblastk0.9b modmetis-5.0.2 boost tinyxml zlib)
+    ADD_DEPENDENCIES(${name} spblastk0.9b modmetis-5.0.2 boost tinyxml
+        zlib-1.2.7)
     SET_PROPERTY(TARGET ${name} PROPERTY FOLDER ${component})
     IF (NEKTAR_USE_MPI)
         TARGET_LINK_LIBRARIES( ${name} ${GSMPI_LIBRARY} ${XXT_LIBRARY})

cmake/ThirdPartyBoost.cmake

@@ -40,10 +40,10 @@ IF (THIRDPARTY_BUILD_BOOST)
             INSTALL_COMMAND ""
             BUILD_IN_SOURCE 1
         )
-
+    
         # If building ThirdParty zlib, force zlib build before boost
         IF (THIRDPARTY_BUILD_ZLIB)
-            ADD_DEPENDENCIES(boost zlib)
+             ADD_DEPENDENCIES(boost zlib-1.2.7)
         ENDIF(THIRDPARTY_BUILD_ZLIB)
 
         # Set up CMake variables
@@ -86,8 +86,7 @@ IF (THIRDPARTY_BUILD_BOOST)
         )
     ENDIF ()
 ELSE (THIRDPARTY_BUILD_BOOST)
-    SET(Boost_DEBUG 1)
-    SET(Boost_ADDITIONAL_VERSIONS "1.51" "1.51.0" "1.50" "1.50.0" "1.49" "1.49.0" "1.48" "1.48.0" "1.47.0" "1.47" "1.46" "1.46. 1" "1.40" "1.40.0" "1.35.0" "1.35")
+    SET(Boost_DEBUG 0)
     SET(Boost_NO_BOOST_CMAKE ON)
 
     #If the user has not set BOOST_ROOT, look in a couple common places first.
@@ -96,19 +95,40 @@ ELSE (THIRDPARTY_BUILD_BOOST)
         IF (DEFINED TEST_ENV)
             SET(Boost_NO_SYSTEM_PATHS ON)
             SET(BOOST_ROOT $ENV{BOOST_HOME})
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time
                 filesystem system program_options regex )
         ELSE ()
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/ThirdParty/boost)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/../ThirdParty/boost)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
             SET(BOOST_ROOT ${CMAKE_SOURCE_DIR}/ThirdParty/dist)
-            FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
+            FIND_PACKAGE( Boost QUIET COMPONENTS thread iostreams date_time filesystem system program_options regex)
         ENDIF()
     ELSE()
         FIND_PACKAGE( Boost COMPONENTS thread iostreams zlib date_time filesystem system program_options regex)
     ENDIF()
+    IF (Boost_IOSTREAMS_FOUND)
+        MESSAGE(STATUS "Found Boost iostreams library: ${Boost_IOSTREAMS_LIBRARY}")
+    ENDIF ()
+    IF (Boost_THREAD_FOUND)
+        MESSAGE(STATUS "Found Boost thread library: ${Boost_THREAD_LIBRARY}")
+    ENDIF ()
+    IF (Boost_DATE_TIME_FOUND)
+        MESSAGE(STATUS "Found Boost date_time library: ${Boost_DATE_TIME_LIBRARY}")
+    ENDIF ()
+    IF (Boost_FILESYSTEM_FOUND)
+        MESSAGE(STATUS "Found Boost filesystem library: ${Boost_FILESYSTEM_LIBRARY}")
+    ENDIF ()
+    IF (Boost_SYSTEM_FOUND)
+        MESSAGE(STATUS "Found Boost system library: ${Boost_SYSTEM_LIBRARY}")
+    ENDIF ()
+    IF (Boost_PROGRAM_OPTIONS_FOUND)
+        MESSAGE(STATUS "Found Boost program_options library: ${Boost_PROGRAM_OPTIONS_LIBRARY}")
+    ENDIF ()
+    IF (Boost_REGEX_FOUND)
+        MESSAGE(STATUS "Found Boost regex library: ${Boost_REGEX_LIBRARY}")
+    ENDIF ()
 ENDIF (THIRDPARTY_BUILD_BOOST)
 
 INCLUDE_DIRECTORIES(SYSTEM ${Boost_INCLUDE_DIRS})

cmake/ThirdPartyFFTW.cmake

@@ -21,6 +21,7 @@ IF( NEKTAR_USE_FFTW )
         SET(FFTW_LIB fftw3)
         MARK_AS_ADVANCED(FFTW_LIB)
         INCLUDE_DIRECTORIES(${TPSRC}/dist/include)
+        MESSAGE(STATUS "Build FFTW: ${TPSRC}/dist/lib/lib${FFTW_LIB}.so")
     ELSE ()
         INCLUDE (FindFFTW)
         INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIR})

cmake/ThirdPartyMPI.cmake

@@ -31,6 +31,8 @@ IF( NEKTAR_USE_MPI )
         SET(XXT_LIBRARY xxt CACHE FILEPATH
             "XXT path" FORCE)
         MARK_AS_ADVANCED(XXT_LIBRARY)
+        MESSAGE(STATUS "Build GSMPI: ${TPSRC}/dist/lib/lib${GSMPI_LIBRARY}.a")
+        MESSAGE(STATUS "Build XXT: ${TPSRC}/dist/lib/lib${XXT_LIBRARY}.a")
     ELSE (THIRDPARTY_BUILD_GSMPI)
         INCLUDE (FindGSMPI)
         INCLUDE (FindXXT)

cmake/ThirdPartyMetis.cmake

@@ -16,6 +16,7 @@ IF (THIRDPARTY_BUILD_METIS)
     MARK_AS_ADVANCED(METIS_LIB)
     LINK_DIRECTORIES(${TPSRC}/dist/lib)
     INCLUDE_DIRECTORIES(${TPSRC}/dist/include)
+    MESSAGE(STATUS "Build Metis: ${TPSRC}/dist/lib/lib${METIS_LIB}.a")
 ELSE (THIRDPARTY_BUILD_METIS)
     INCLUDE (FindMetis)
 ENDIF (THIRDPARTY_BUILD_METIS)

cmake/ThirdPartyQT4.cmake

@@ -6,4 +6,7 @@ IF( NEKTAR_USE_QT4 )
     FIND_PACKAGE(Qt4 COMPONENTS QtCore QtGui REQUIRED)
     INCLUDE(${QT_USE_FILE})
     ADD_DEFINITIONS(${QT_DEFINITIONS})
+    IF (QT4_FOUND)
+        MESSAGE(STATUS "Found QT4: ${QT_INCLUDE_DIR}")
+    ENDIF(QT4_FOUND)
 ENDIF( NEKTAR_USE_QT4 )

cmake/ThirdPartySpblastk.cmake

@@ -15,6 +15,7 @@ IF (THIRDPARTY_BUILD_NIST_SPBLASTK)
         "Path to NIST Sparse BLAS." FORCE)
     MARK_AS_ADVANCED(NIST_SPARSE_BLAS)
     LINK_DIRECTORIES(${TPSRC}/dist/lib)
+    MESSAGE(STATUS "Build NIST Sparse BLAS: ${TPSRC}/dist/lib/lib${NIST_SPARSE_BLAS}.a")
 ELSE (THIRDPARTY_BUILD_NIST_SPBLASTK)
     INCLUDE(FindNistSparseBlas)
 ENDIF (THIRDPARTY_BUILD_NIST_SPBLASTK)

cmake/ThirdPartyVTK.cmake

@@ -25,9 +25,11 @@ IF( NEKTAR_USE_VTK )
         INCLUDE (${VTK_DIR}/VTKConfig.cmake)
     ELSE()
         INCLUDE (FindVTK)
-        IF (NOT VTK_FOUND)
+        IF (VTK_FOUND)
+            MESSAGE(STATUS "Found VTK: ${VTK_USE_FILE}")
+        ELSE (VTK_FOUND)
             MESSAGE(FATAL_ERROR "VTK not found")
-        ENDIF (NOT VTK_FOUND)
+        ENDIF (VTK_FOUND)
     ENDIF()
     
     INCLUDE (${VTK_USE_FILE})

cmake/ThirdPartyZlib.cmake

-OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" OFF)
+########################################################################
+#
+# ThirdParty configuration for Nektar++
+#
+# ZLib
+#
+########################################################################
 
+# Attempt to identify Macports libraries, if they exist. This prevents
+# cmake warnings later on.
+SET(ZLIB_ROOT /opt/local/)
+
+
+# Find a system ZLIB library
+# If not found enable the THIRDPARTY_BUILD_ZLIB option
+FIND_PACKAGE( ZLIB )
+IF (ZLIB_FOUND AND NOT ZLIB_VERSION_PATCH LESS 7 )
+    SET(ZLIB_LIBRARY ${ZLIB_LIBRARIES})
+    SET(ZLIB_LIBRARY_DEBUG ${ZLIB_LIBRARIES})
+    SET(ZLIB_LIBRARY_RELEASE ${ZLIB_LIBRARIES})
+    MESSAGE(STATUS "Found Zlib library: ${ZLIB_LIBRARY}")
+    OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" OFF)
+ELSE ()
+    OPTION(THIRDPARTY_BUILD_ZLIB "Build ZLib library" ON)
+ENDIF()
+
+
+# If we or the user
 IF (THIRDPARTY_BUILD_ZLIB)
+    MESSAGE(STATUS "Will build Zlib 1.2.7")
     # Build the Zlib library separately
     EXTERNALPROJECT_ADD(
-        zlib
+        zlib-1.2.7
         PREFIX ${TPSRC}
-        URL ${TPURL}/zlib-1.2.3.tar.bz2
-        URL_MD5 "dee233bf288ee795ac96a98cc2e369b6"
+        URL ${TPURL}/zlib-1.2.7.tar.gz
+        URL_MD5 "4a162e0f643232e7e278d59a0603ceb0"
         DOWNLOAD_DIR ${TPSRC}
-        CONFIGURE_COMMAND ./configure --shared --prefix=${TPSRC}/dist
-        BUILD_IN_SOURCE 1
+        CONFIGURE_COMMAND ${CMAKE_COMMAND} -DCMAKE_INSTALL_PREFIX:PATH=${TPSRC}/dist -DCMAKE_C_FLAGS:STRING=-fPIC ${TPSRC}/src/zlib-1.2.7
     )
-    SET(Boost_ZLIB_LIBRARY z)
-    SET(Boost_ZLIB_LIBRARY_DEBUG z)
-    SET(Boost_ZLIB_LIBRARY_RELEASE z)
-ELSE (THIRDPARTY_BUILD_ZLIB)
-  # Attempt to identify Macports libraries, if they exist. This prevents
-  # cmake warnings later on.
-  IF (APPLE)
-    FIND_LIBRARY(ZLIB_LIBRARY z PATHS /opt/local/lib NO_DEFAULT_PATH)
-  ENDIF()
-  
-  # Find a system ZLIB library and use that instead
-  IF (ZLIB_LIBRARY-NOTFOUND OR NOT APPLE) 
-    FIND_PACKAGE( ZLIB )
-    IF (ZLIB_FOUND)
-      SET(ZLIB_LIBRARY ${ZLIB_LIBRARIES})
-    ENDIF()
-  ENDIF()
-  
-  IF (ZLIB_LIBRARY)
-    SET(Boost_ZLIB_LIBRARY ${ZLIB_LIBRARY})
-    SET(Boost_ZLIB_LIBRARY_RELEASE ${ZLIB_LIBRARY})
-    SET(Boost_ZLIB_LIBRARY_DEBUG ${ZLIB_LIBRARY})
-  ENDIF()
+    IF (WIN32)
+        SET(ZLIB_LIBRARY zlib)
+        SET(ZLIB_LIBRARY_DEBUG zlib)
+        SET(ZLIB_LIBRARY_RELEASE zlib)
+    ELSE (WIN32)
+        SET(ZLIB_LIBRARY z)
+        SET(ZLIB_LIBRARY_DEBUG z)
+        SET(ZLIB_LIBRARY_RELEASE z)
+    ENDIF (WIN32)
 ENDIF (THIRDPARTY_BUILD_ZLIB)
 
-

library/Demos/LocalRegions/CMakeLists.txt

@@ -5,7 +5,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
 )
 

library/Demos/MultiRegions/CMakeLists.txt

@@ -6,7 +6,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
     optimized sbtk    debug sbtk
 )

library/Demos/MultiRegions/ExtraDemos/CMakeLists.txt

@@ -6,7 +6,7 @@ SET(LinkLibraries
     optimized LibUtilities debug LibUtilities-g
     optimized ${Boost_THREAD_LIBRARY_RELEASE} debug ${Boost_THREAD_LIBRARY_DEBUG}
     optimized ${Boost_IOSTREAMS_LIBRARY_RELEASE} debug ${Boost_IOSTREAMS_LIBRARY_DEBUG}
-    optimized ${Boost_ZLIB_LIBRARY_RELEASE} debug ${Boost_ZLIB_LIBRARY_DEBUG}
+    optimized ${ZLIB_LIBRARY_RELEASE} debug ${ZLIB_LIBRARY_DEBUG}
     optimized ${TINYXML_LIB} debug ${TINYXML_LIB}
     optimized sbtk    debug sbtk
 )

library/LibUtilities/BasicUtils/MeshPartition.cpp

@@ -62,7 +62,7 @@ namespace Nektar
     namespace LibUtilities
     {
         MeshPartition::MeshPartition(const LibUtilities::SessionReaderSharedPtr& pSession) :
-                m_comm(pSession->GetComm()->GetRowComm())
+                m_comm(pSession->GetComm())
         {
             ReadMesh(pSession);
         }
@@ -74,9 +74,9 @@ namespace Nektar
 
         void MeshPartition::PartitionMesh()
         {
-            ASSERTL0(m_comm->GetSize() > 1,
+            ASSERTL0(m_comm->GetRowComm()->GetSize() > 1,
                      "Partitioning only necessary in parallel case.");
-            ASSERTL0(m_meshElements.size() >= m_comm->GetSize(),
+            ASSERTL0(m_meshElements.size() >= m_comm->GetRowComm()->GetSize(),
                      "Too few elements for this many processes.");
 
             CreateGraph(m_mesh);
@@ -96,7 +96,7 @@ namespace Nektar
 
             vNew.LinkEndChild(vElmtNektar);
 
-            std::string vFilename = pSession->GetSessionName() + "_P" + boost::lexical_cast<std::string>(m_comm->GetRank()) + ".xml";
+            std::string vFilename = pSession->GetSessionName() + "_P" + boost::lexical_cast<std::string>(m_comm->GetRowComm()->GetRank()) + ".xml";
             vNew.SaveFile(vFilename.c_str());
         }
 
@@ -325,7 +325,7 @@ namespace Nektar
             BoostVertexIterator    vertit, vertit_end;
             Array<OneD, int> part(nGraphVerts,0);
 
-            if (m_comm->GetRank() == 0)
+            if (m_comm->GetRowComm()->GetRank() == 0)
             {
                 int acnt = 0;
                 int vcnt = 0;
@@ -349,21 +349,36 @@ namespace Nektar
                 }
 
                 // Call Metis and partition graph
-                int npart = m_comm->GetSize();
+                int npart = m_comm->GetRowComm()->GetSize();
                 int vol = 0;
 
                 try
                 {
-                    // Attempt partitioning using METIS.
-                    Metis::PartGraphVKway(nGraphVerts, xadj, adjncy, vwgt, vsize, npart, vol, part);
-
-                    // Check METIS produced a valid partition and fix if not.
-                    CheckPartitions(part);
-
-                    // Distribute partitioning to all processes.
-                    for (i = 1; i < m_comm->GetSize(); ++i)
+					//////////////////////////////////////////////////////
+					// On a cartesian communicator do mesh partiotion just on the first column
+					// so there is no doubt the partitions are all the same in all the columns
+					if(m_comm->GetColumnComm()->GetRank() == 0)
+					{
+						// Attempt partitioning using METIS.
+						Metis::PartGraphVKway(nGraphVerts, xadj, adjncy, vwgt, vsize, npart, vol, part);
+						// Check METIS produced a valid partition and fix if not.
+						CheckPartitions(part);
+						// distribute among columns
+						for (i = 1; i < m_comm->GetColumnComm()->GetSize(); ++i)
+						{
+							m_comm->GetColumnComm()->Send(i, part);
+						}
+					}
+					else 
+					{
+						m_comm->GetColumnComm()->Recv(0, part);
+					}
+					m_comm->GetColumnComm()->Block();
+					//////////////////////////////////
+					// distribute among rows
+                    for (i = 1; i < m_comm->GetRowComm()->GetSize(); ++i)
                     {
-                        m_comm->Send(i, part);
+                        m_comm->GetRowComm()->Send(i, part);
                     }
                 }
                 catch (...)
@@ -374,7 +389,7 @@ namespace Nektar
             }
             else
             {
-                m_comm->Recv(0, part);
+                m_comm->GetRowComm()->Recv(0, part);
             }
 
             // Create boost subgraph for this process's partitions
@@ -386,7 +401,7 @@ namespace Nektar
                   vertit != vertit_end;
                   ++vertit, ++i)
             {
-                if (part[i] == m_comm->GetRank())
+                if (part[i] == m_comm->GetRowComm()->GetRank())
                 {
                     pGraph[*vertit].partition = part[i];
                     pGraph[*vertit].partid = boost::num_vertices(pLocalPartition);
@@ -400,7 +415,7 @@ namespace Nektar
         {
             unsigned int       i     = 0;
             unsigned int       cnt   = 0;
-            const unsigned int npart = m_comm->GetSize();
+            const unsigned int npart = m_comm->GetRowComm()->GetSize();
             bool               valid = true;
 
             // Check that every process has at least one element assigned

library/LibUtilities/BasicUtils/SessionReader.cpp

@@ -814,10 +814,13 @@ namespace Nektar
             FunctionVariableMap::const_iterator it2;
             std::string vName = boost::to_upper_copy(pName);
 
-            if ((it1 = m_functions.find(vName))     != m_functions.end() &&
-                (it2 = it1->second.find(pVariable)) != it1->second.end())
+            // Check function exists
+            if ((it1 = m_functions.find(vName))     != m_functions.end())
             {
-                return true;
+                bool varExists =
+                    (it2 = it1->second.find(pVariable)) != it1->second.end() ||
+                    (it2 = it1->second.find("*")) != it1->second.end();
+                return varExists;
             }
             return false;
         }
@@ -831,18 +834,33 @@ namespace Nektar
             const std::string &pVariable) const
         {
             FunctionMap::const_iterator it1;
-            FunctionVariableMap::const_iterator it2;
+            FunctionVariableMap::const_iterator it2, it3;
             std::string vName = boost::to_upper_copy(pName);
 
             ASSERTL0((it1 = m_functions.find(vName)) != m_functions.end(),
                      std::string("No such function '") + pName
                      + std::string("' has been defined in the session file."));
-            ASSERTL0((it2 = it1->second.find(pVariable)) != it1->second.end(),
+
+            // Check for specific and wildcard definitions
+            bool specific = (it2 = it1->second.find(pVariable)) !=
+                            it1->second.end();
+            bool wildcard = (it3 = it1->second.find("*")) !=
+                            it1->second.end();
+
+            // Check function is defined somewhere
+            ASSERTL0(specific || wildcard,
                      std::string("No such variable '") + pVariable
                      + std::string("' defined for function '") + pName
                      + std::string("' in session file."));
+
+            // If not specific, must be wildcard
+            if (!specific)
+            {
+                it2 = it3;
+            }
+
             ASSERTL0((it2->second.m_type == eFunctionTypeExpression),
-                     std::string("Function is defined by a file."));
+                    std::string("Function is defined by a file."));
             return it2->second.m_expression;
         }
 
@@ -867,17 +885,32 @@ namespace Nektar
             const std::string &pVariable) const
         {
             FunctionMap::const_iterator it1;
-            FunctionVariableMap::const_iterator it2;
+            FunctionVariableMap::const_iterator it2, it3;
             std::string vName = boost::to_upper_copy(pName);
 
             it1 = m_functions.find(vName);
             ASSERTL0 (it1 != m_functions.end(),
                       std::string("Function '") + pName
                       + std::string("' not found."));
-            ASSERTL0 ((it2 = it1->second.find(pVariable)) != it1->second.end(),
-                    std::string("No such variable '") + pVariable
-                    + std::string("' defined for function '") + pName
-                    + std::string("' in session file."));
+
+            // Check for specific and wildcard definitions
+            bool specific = (it2 = it1->second.find(pVariable)) !=
+                            it1->second.end();
+            bool wildcard = (it3 = it1->second.find("*")) !=
+                            it1->second.end();
+
+            // Check function is defined somewhere
+            ASSERTL0(specific || wildcard,
+                     std::string("No such variable '") + pVariable
+                     + std::string("' defined for function '") + pName
+                     + std::string("' in session file."));
+
+            // If not specific, must be wildcard
+            if (!specific)
+            {
+                it2 = it3;
+            }
+
             return it2->second.m_type;
         }
 
@@ -902,17 +935,32 @@ namespace Nektar
             const std::string &pVariable) const
         {
             FunctionMap::const_iterator it1;
-            FunctionVariableMap::const_iterator it2;
+            FunctionVariableMap::const_iterator it2, it3;
             std::string vName = boost::to_upper_copy(pName);
 
             it1 = m_functions.find(vName);
             ASSERTL0 (it1 != m_functions.end(),
                       std::string("Function '") + pName
                       + std::string("' not found."));
-            ASSERTL0 ((it2 = it1->second.find(pVariable)) != it1->second.end(),
-                    std::string("No such variable '") + pVariable
-                    + std::string("' defined for function '") + pName
-                    + std::string("' in session file."));
+
+            // Check for specific and wildcard definitions
+            bool specific = (it2 = it1->second.find(pVariable)) !=
+                            it1->second.end();
+            bool wildcard = (it3 = it1->second.find("*")) !=
+                            it1->second.end();
+
+            // Check function is defined somewhere
+            ASSERTL0(specific || wildcard,
+                     std::string("No such variable '") + pVariable
+                     + std::string("' defined for function '") + pName
+                     + std::string("' in session file."));
+
+            // If not specific, must be wildcard
+            if (!specific)
+            {
+                it2 = it3;
+            }
+
             return it2->second.m_filename;
         }
 
@@ -1202,7 +1250,7 @@ namespace Nektar
                 vPartitioner->PartitionMesh();
                 vPartitioner->WriteLocalPartition(vSession);
                 
-                vCommMesh->Block();
+                m_comm->Block();
 
                 m_filename = GetSessionNameRank() + ".xml";
 
@@ -1715,11 +1763,16 @@ namespace Nektar
                     FunctionVariableDefinition funcDef;
                     std::string conditionType = variable->Value();
 
-                    // All function variables must specify VAR
-                    ASSERTL0(variable->Attribute("VAR"),
-                             "Attribute VAR expected for function '"
-                             + functionStr + "'.");
-                    std::string variableStr = variable->Attribute("VAR");
+                    // If no var is specified, assume wildcard
+                    std::string variableStr;
+                    if (!variable->Attribute("VAR"))
+                    {
+                        variableStr = "*";
+                    }
+                    else
+                    {
+                        variableStr = variable->Attribute("VAR");
+                    }
 
                     // Parse list of variables
                     std::vector<std::string> variableList;

library/LocalRegions/QuadExp.cpp

@@ -139,9 +139,16 @@ namespace Nektar
 
                 if(out_d2.num_elements())
                 {
-                    Vmath::Vmul  (nqtot,gmat[4],1,diff0,1, out_d2, 1);
-                    Vmath::Vvtvp (nqtot,gmat[5],1,diff1,1, out_d2, 1,
-                                  out_d2,1);
+                    if (m_geom->GetCoordim() == 3)
+                    {
+                        Vmath::Vmul  (nqtot,gmat[4],1,diff0,1, out_d2, 1);
+                        Vmath::Vvtvp (nqtot,gmat[5],1,diff1,1, out_d2, 1,
+                                        out_d2,1);
+                    }
+                    else
+                    {
+                        Vmath::Zero  (nqtot, out_d2, 1);
+                    }
                 }
             }
             else // regular geometry
@@ -160,8 +167,15 @@ namespace Nektar
 
                 if(out_d2.num_elements())
                 {
-                    Vmath::Smul (nqtot, gmat[4][0], diff0,1, out_d2, 1);
-                    Blas::Daxpy (nqtot, gmat[5][0], diff1,1, out_d2, 1);
+                    if (m_geom->GetCoordim() == 3)
+                    {
+                        Vmath::Smul (nqtot, gmat[4][0], diff0,1, out_d2, 1);
+                        Blas::Daxpy (nqtot, gmat[5][0], diff1,1, out_d2, 1);
+                    }
+                    else
+                    {