Merge branch 'master' into feature/SpongeBC

# Conflicts: # CHANGELOG.md # library/SolverUtils/Forcing/ForcingAbsorption.cpp # solvers/APESolver/EquationSystems/APE.cpp

Merge branch 'master' into feature/SpongeBC
# Conflicts: # CHANGELOG.md # library/SolverUtils/Forcing/ForcingAbsorption.cpp # solvers/APESolver/EquationSystems/APE.cpp
79fc5473 · Kilian Lackhove · ed40906e · 56f554e3 · 79fc5473 · 79fc5473
Commit 79fc5473 authored Oct 04, 2017 by Kilian Lackhove
--- a/.clang-format
+++ b/.clang-format
@@ -11,6 +11,6 @@ AllowShortCaseLabelsOnASingleLine: false
 AllowShortIfStatementsOnASingleLine: false
 AllowShortLoopsOnASingleLine: false
 IndentCaseLabels: true
-Standard: Cpp03
+Standard: Cpp11
 AccessModifierOffset: -4
 BinPackParameters: true
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
 Changelog
 =========

-v4.5.0
+v5.0.0
 ------
-**NekMesh**:
- Add periodic boundary condition meshing in 2D (!733)
- Adjust boundary layer thickness in corners in 2D (!739)
-
 **Library**
 - Added in sum factorisation version for pyramid expansions and orthogonal
  expansion in pyramids (!750)
+- Significant overhaul of CMake infrastructure (!770, !804)
+- Fix ThridpartyCCM options (!802)
+- Fix Windows CRLF tokens in GEO reader and improve comment handling (!805)
+- Use chrono in Timer (!807)
+- Fix caching of FUNCTION tags that read from file and provide the same
+  functionality in FUNCTIONs defined for forcings (!759)
+- Add ARPACK thirdparty build capabilities (!828)
+- Added native support for csv files in addititon to pts (!760 !835)
+- Utilize LAPACK_DIR env variable to find the native blas/lapack install (!827)
+- Simplify RawType typedefs (!840)
+- Remove unused files from BasicUtils (!841)
+- Remove checks for old boost versions which are no longer supported (!841)
+- Refactor ParseUtils to be more consistent (!843)
 - Added support for using the distance to a specific region (e.g. outlet) in the
  function definitions for the Absorption Forcing (!769)

+**NekMesh**:
+- Add feature to read basic 2D geo files as CAD (!731)
+- Add periodic boundary condition meshing in 2D (!733)
+- Adjust boundary layer thickness in corners in 2D (!739)
+- Add non-O BL meshing in 2D (!757)
+- Add ability to compile CCIO library but tar file is not yet openly
+  available whist we seek permission from Simens (!799)
+- Fix issue with reading CCM files due to definition of default arrays
+  rather than a vector (!797)
+- Fix inverted triangles and small memory issue in surface meshing (!798)
+- Additional curve types in GEO reader: BSpline, Circle, Ellipse (!800)
+
+**FieldConvert**:
+- Add input module for Semtex field files (!777)
+- Fixed interppoints module (!760)
+- Move StreamFunction utility to a FieldConvert module (!809)
+- Enable output to multiple files (!844)
+
 **Documentation**:
 - Added the developer-guide repository as a submodule (!751)

+<<<<<<< CHANGELOG.md
+v4.4.2
+------
+**NekMesh**:
+- Fix uninitialised memory bug in Nek5000 input module (!801)
+
+**Library**
+- Fix ability to set default implementation in Collections and added an option
+  to set eNoCollections in FieldConvert as default (!789)
+- Fix performance issue in ProcessIsoContour in relation to memory consumption
+  (!821)
+- Fix performance issue with ExtractPhysToBndElmt (!796)
+
+**Utilities**
+- Fix vtkToFld missing dependency which prevented compiling with VTK 7.1 (!808)
+
+=======
+>>>>>>> CHANGELOG.md
 v4.4.1
 ------
 **Library**
+- Remove m_offset_elmt_id and GetOffsetElmtId which fixed problems in 2D when
+  quad elements are listed before tri elements (!758)
 - Remove the duplicate output of errorutil (!756)
+- Fix BLAS CMake dependencies (!763)
+- Fix interpolation issue with Lagrange basis functions (!768)
+- Fix issue with average fields not working with different polynomial order
+  fields (!776)
+- Fix rounding of integer parameters (!774)
+- Fix Hdf5 output in FilterFieldConvert (!781)
+- Fixed extreme memory consumption of Interpolator when interpolating from pts
+  to fld or between different meshes (!783)
+- Fix deadlock with HDF5 input (!786)
+- Fix missing entriess in LibUtilities::kPointsTypeStr (!792)
+- Fix compiler warnings with CommDataType (!793)
+- Fix ability to set default implementation in Collections and added an option 
+  to set eNoCollections in FieldConvert as default (!789)
+- Fix performance issue in ProcessIsoContour in relation to memory consumption
+  (!821)
+- Fix performance issue with ExtractPhysToBndElmt (!796)
+- Fix available classes being listed multiple times (!817)

-**FieldConvert**:
+**FieldConvert:**
+- Fix issue with field ordering in the interppointdatatofld module (!754)
 - Fix issue with FieldConvert when range flag used (!761)
+- Fix issue when using output-points combined with noequispaced (!775)
+- Fix equispacedoutput for 3DH1D with triangles (!787)

 **NekMesh**:
 - Fix memory consumption issue with Gmsh output (!747, !762)
 - Rework meshing control so that if possible viewable meshes will be dumped
  when some part of the system fails (!756)
 - Add manifold meshing option (!756)
+- Fix issue with older rea input files (!765)
+- Fix memory leak in variational optimiser, add small optimisations (!785)
+- Check the dimensionality of the CAD system before running the 2D generator (!780)
+- Fix uninitialised memory bug in Nek5000 input module (!801)

-**FieldConvert:**
- Fix issue with field ordering in the interppointdatatofld module (!754)
+**IncNavierStokesSolver**
+- Fix an initialisation issue when using an additional advective field (!779)
+
+**Utilities**
+- Fix vtkToFld missing dependency which prevented compiling with VTK 7.1 (!808)
+
+**Packaging**
+- Added missing package for FieldUtils library (!755)

 v4.4.0
 ------
@@ -128,6 +205,7 @@ v4.4.0
  (!712)
 - 2D to 3D mesh extrusion module (!715)
 - Add new two-dimensional mesher from NACA code or step file (!720)
+- Add basic gmsh cad (.geo) reader to the meshing system (!731)
 - Fix inverted boundary layer in 2D (!736)
 - More sensible element sizing with boundary layers in 2D (!736)
 - Change variable names in mcf file to make more sense (!736)

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,14 +5,34 @@ RelWithDebInfo MinSizeRel.")

 PROJECT(Nektar++ C CXX)

+# Nektar++ requires C++11. Try to infer this for older CMake versions (less than
+# 3.1.0)
+IF ("${CMAKE_VERSION}" VERSION_LESS "3.1")
+    IF (NOT MSVC)
+        INCLUDE(CheckCXXCompilerFlag)
+        CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+
+        IF (COMPILER_SUPPORTS_CXX11)
+            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+        ELSE()
+            MESSAGE(FATAL_ERROR "Nektar++ requires a compiler with C++11 support.")
+        ENDIF()
+    ELSEIF(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 18.0)
+        MESSAGE(FATAL_ERROR "Nektar++ requires full C++11 support: please upgrade to Visual Studio 2013 or later")
+    ENDIF()
+ELSE()
+    SET(CMAKE_CXX_STANDARD 11)
+    SET(CMAKE_CXX_STANDARD_REQUIRED ON)
+    SET(CMAKE_CXX_EXTENSIONS OFF)
+ENDIF()

 INCLUDE(CheckLanguage)

 CHECK_LANGUAGE(Fortran)
 IF(CMAKE_Fortran_COMPILER)
-  ENABLE_LANGUAGE(Fortran)
+    ENABLE_LANGUAGE(Fortran)
 ELSE()
-  MESSAGE(STATUS "No Fortran support")
+    MESSAGE(STATUS "No Fortran support")
 ENDIF()

 # Helps organize projects in IDEs.
@@ -29,6 +49,7 @@ SET(NEKTAR_VERSION ${NEKTAR_VERSION_MAJOR}.${NEKTAR_VERSION_MINOR}.${NEKTAR_VERS

 # Add support for CMAKE_DEPENDENT_OPTION
 INCLUDE(CMakeDependentOption)
+INCLUDE(CMakeParseArguments)

 # Enable CTest.
 ENABLE_TESTING()
@@ -156,33 +177,25 @@ IF (${CMAKE_COMPILER_IS_GNUCXX})
    MARK_AS_ADVANCED(NEKTAR_ENABLE_PROFILE)
 ENDIF (${CMAKE_COMPILER_IS_GNUCXX})

-OPTION(NEKTAR_USE_EXPRESSION_TEMPLATES
-    "Use Expression templates." OFF)
-MARK_AS_ADVANCED(NEKTAR_USE_EXPRESSION_TEMPLATES)
-
 # BLAS Support
-OPTION(NEKTAR_USE_BLAS_LAPACK "Use Blas and lapack routines." ON)
+CMAKE_DEPENDENT_OPTION(NEKTAR_USE_SYSTEM_BLAS_LAPACK
+    "Use the system provided blas and lapack libraries" ON
+    "UNIX; NOT APPLE; NOT NEKTAR_USE_OPENBLAS; NOT NEKTAR_USE_MKL; NOT NEKTAR_USE_ACML; NOT NEKTAR_USE_ACCELERATE_FRAMEWORK" OFF)
 CMAKE_DEPENDENT_OPTION(NEKTAR_USE_OPENBLAS
    "Use OpenBLAS library as a substitute to native BLAS." OFF
-    "NEKTAR_USE_BLAS_LAPACK" OFF)
-CMAKE_DEPENDENT_OPTION(NEKTAR_USE_SMV
-    "Use LibSMV library for faster small matrix-vector multiplies." OFF
-    "NEKTAR_USE_BLAS_LAPACK" OFF)
+    "NOT NEKTAR_USE_SYSTEM_BLAS_LAPACK" OFF)
 CMAKE_DEPENDENT_OPTION(NEKTAR_USE_ACML
    "Use the AMD Core Math Library (ACML) for BLAS and Lapack support." OFF
-    "NEKTAR_USE_BLAS_LAPACK" OFF)
+    "NOT NEKTAR_USE_SYSTEM_BLAS_LAPACK" OFF)
 CMAKE_DEPENDENT_OPTION(NEKTAR_USE_MKL
    "Use the Intel Math Kernel Library (MKL) for BLAS and Lapack support." OFF
-    "NEKTAR_USE_BLAS_LAPACK" OFF)
-CMAKE_DEPENDENT_OPTION(NEKTAR_USE_SYSTEM_BLAS_LAPACK
-    "Use the system provided blas and lapack libraries" ON
-    "NEKTAR_USE_BLAS_LAPACK; UNIX; NOT APPLE; NOT NEKTAR_USE_OPENBLAS; NOT NEKTAR_USE_MKL; NOT NEKTAR_USE_ACML; NOT NEKTAR_USE_ACCELERATE_FRAMEWORK" OFF)
+    "NOT NEKTAR_USE_SYSTEM_BLAS_LAPACK" OFF)
 CMAKE_DEPENDENT_OPTION(NEKTAR_USE_ACCELERATE_FRAMEWORK
    "Use the Mac Accelerate Framework for BLAS and Lapack support." ON
-    "NEKTAR_USE_BLAS_LAPACK; APPLE" OFF)
+    "NOT NEKTAR_USE_SYSTEM_BLAS_LAPACK; APPLE" OFF)
 CMAKE_DEPENDENT_OPTION(NEKTAR_USE_WIN32_LAPACK
    "Use Win32 Lapack provided with the Third Party Distribution."
-    ON "NEKTAR_USE_BLAS_LAPACK; WIN32" OFF)
+    ON "NOT NEKTAR_USE_SYSTEM_BLAS_LAPACK; WIN32" OFF)

 # Memory pools
 OPTION(NEKTAR_USE_MEMORY_POOLS
@@ -222,7 +235,6 @@ ENDIF ()

 # Find ThirdParty libraries and headers.
 INCLUDE (ThirdPartyTinyxml)
-INCLUDE (ThirdPartyLoki)
 INCLUDE (ThirdPartyMetis)
 INCLUDE (ThirdPartyHDF5)
 INCLUDE (ThirdPartyScotch)
@@ -232,7 +244,6 @@ INCLUDE (ThirdPartyFFTW)
 INCLUDE (ThirdPartyArpack)
 INCLUDE (ThirdPartyMPI)
 INCLUDE (ThirdPartyVTK)
-INCLUDE (ThirdPartySMV)
 INCLUDE (ThirdPartyOCE)
 INCLUDE (ThirdPartyTetGen)
 INCLUDE (ThirdPartyCCM)
@@ -241,32 +252,18 @@ INCLUDE (Doxygen)

 IF( NEKTAR_USE_MKL )
    INCLUDE (FindMKL)
-    SET(NEKTAR_USING_BLAS TRUE)
-    SET(NEKTAR_USING_LAPACK TRUE)
-    SET(NEKTAR_USING_MKL TRUE)
 ENDIF( NEKTAR_USE_MKL )

 IF( NEKTAR_USE_OPENBLAS )
    INCLUDE (FindOpenBlas)
-    SET(NEKTAR_USING_OPENBLAS TRUE)
 ENDIF( NEKTAR_USE_OPENBLAS )

-IF( NEKTAR_USE_SMV )
-    INCLUDE (FindSMV)
-    SET(NEKTAR_USING_SMV TRUE)
-    ADD_DEFINITIONS(-DNEKTAR_USING_SMV)
-ENDIF( NEKTAR_USE_SMV )
-
 IF( NEKTAR_USE_ACCELERATE_FRAMEWORK )
    INCLUDE (FindAccelerateFramework)
 ENDIF( NEKTAR_USE_ACCELERATE_FRAMEWORK )

 IF( NEKTAR_USE_ACML )
    INCLUDE (FindACML)
-    SET(NEKTAR_USING_BLAS TRUE)
-    SET(NEKTAR_USING_LAPACK TRUE)
-    SET(NEKTAR_USING_ACML TRUE)
-    ADD_DEFINITIONS(-DUSE_ACML)
 ENDIF( NEKTAR_USE_ACML )

 IF( NEKTAR_USE_WIN32_LAPACK )
@@ -275,28 +272,12 @@ ENDIF( NEKTAR_USE_WIN32_LAPACK )

 IF( NEKTAR_USE_SYSTEM_BLAS_LAPACK )
    INCLUDE(ThirdPartyBlasLapack)
-    SET(NEKTAR_USING_BLAS TRUE)
-    SET(NEKTAR_USING_LAPACK TRUE)
 ENDIF( NEKTAR_USE_SYSTEM_BLAS_LAPACK )

-IF( NEKTAR_USE_BLAS_LAPACK )
-    SET(NEKTAR_USING_BLAS TRUE)
-    SET(NEKTAR_USING_LAPACK TRUE)
-    ADD_DEFINITIONS( -DNEKTAR_USING_LAPACK -DNEKTAR_USING_BLAS )
-ENDIF( NEKTAR_USE_BLAS_LAPACK )
-
 IF( NEKTAR_USE_TINYXML_STL )
    ADD_DEFINITIONS( -DTIXML_USE_STL)
 ENDIF( NEKTAR_USE_TINYXML_STL )

-IF( NEKTAR_USE_DIRECT_BLAS_CALLS )
-    ADD_DEFINITIONS(-DNEKTAR_USING_DIRECT_BLAS_CALLS)
-ENDIF( NEKTAR_USE_DIRECT_BLAS_CALLS )
-
-IF( NEKTAR_USE_EXPRESSION_TEMPLATES )
-    ADD_DEFINITIONS(-DNEKTAR_USE_EXPRESSION_TEMPLATES -DNEKTAR_USING_CMAKE)
-ENDIF( NEKTAR_USE_EXPRESSION_TEMPLATES )
-
 IF( NEKTAR_USE_MEMORY_POOLS )
    ADD_DEFINITIONS(-DNEKTAR_MEMORY_POOL_ENABLED)
 ELSE( NEKTAR_USE_MEMORY_POOLS )
@@ -324,25 +305,26 @@ ENDIF (APPLE)

 INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR})

-# Build active components
+# Build active components. Add utilities and solvers directories first, because
+# that allows us to detect library dependencies automatically.
 IF (NEKTAR_BUILD_LIBRARY)
-    SET(NEKTAR++_LIBRARIES SolverUtils LibUtilities StdRegions SpatialDomains LocalRegions
-        MultiRegions Collections GlobalMapping FieldUtils NekMeshUtils)
    INCLUDE_DIRECTORIES(library)
+ENDIF()
+
+INCLUDE_DIRECTORIES(utilities)
+ADD_SUBDIRECTORY(utilities)
+
+INCLUDE_DIRECTORIES(solvers)
+ADD_SUBDIRECTORY(solvers)
+
+IF (NEKTAR_BUILD_LIBRARY)
+    # List of Nektar++ libraries will be rebuilt every configuration.
+    SET(NEKTAR++_LIBRARIES "" CACHE INTERNAL "")
+
    ADD_SUBDIRECTORY(library)
    INSTALL(EXPORT Nektar++Libraries DESTINATION ${LIB_DIR}/cmake COMPONENT dev)
 ENDIF (NEKTAR_BUILD_LIBRARY)

-IF (NEKTAR_BUILD_SOLVERS)
-    INCLUDE_DIRECTORIES(solvers)
-    ADD_SUBDIRECTORY(solvers)
-ENDIF(NEKTAR_BUILD_SOLVERS)
-
-IF (NEKTAR_BUILD_UTILITIES)
-    INCLUDE_DIRECTORIES(utilities)
-    ADD_SUBDIRECTORY(utilities)
-ENDIF (NEKTAR_BUILD_UTILITIES)
-
 IF (NEKTAR_BUILD_TESTS)
    INCLUDE_DIRECTORIES(tests)
    ADD_SUBDIRECTORY(tests)
@@ -374,17 +356,18 @@ INSTALL(FILES ${CMAKE_BINARY_DIR}/Nektar++Config.cmake
 # Install ThirdParty headers to subdirectory of ${NEKTAR_INCLUDE_DIR}
 INSTALL(DIRECTORY ${TPDIST}/include/
    DESTINATION ${NEKTAR_INCLUDE_DIR}/ThirdParty
-    COMPONENT ThirdParty
+    COMPONENT dev
 )

-# Install ThirdParty libraries into ${NEKTAR_LIB_DIR}
+# Install ThirdParty libraries into ${NEKTAR_LIB_DIR}. These are shipped with
+# the LibUtilities library.
 INSTALL(DIRECTORY ${TPDIST}/lib/
    DESTINATION ${NEKTAR_LIB_DIR}
-    COMPONENT ThirdParty
+    COMPONENT libutilities
 )

+ADD_SUBDIRECTORY(docs)
+
 IF(NEKTAR_BUILD_PACKAGES)
-    add_subdirectory(pkg)
+    ADD_SUBDIRECTORY(pkg)
 ENDIF(NEKTAR_BUILD_PACKAGES)
-
-ADD_SUBDIRECTORY(docs)
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -44,7 +44,9 @@ project. It's a pretty simple process:
   diff and are not quite ready to merge, use the `[WIP]` tag in the title to
   prevent your code from being accidentally merged.
 5. Put a comment in the MR saying that it's ready to be merged.
-6. Respond to any comments in the code review.
+6. If your branch is a minor fix that could appear in the next patch release,
+   then add the `Proposed patch` label to the merge request.
+7. Respond to any comments in the code review.

 ## Submission checklist
 - Did you add regression tests (for fixes) or unit tests and/or normal tests for
@@ -155,6 +157,78 @@ stick to the following process:
 - Once feedback received from the branch author (if necessary) and reviewers are
  happy, the branch will be merged.

+## Release branches
+Nektar++ releases are versioned in the standard form `x.y.z` where `x` is a
+major release, `y` a minor release and `z` a patch release:
+
+- major releases are extremely infrequent (on the order of every 2-3 years) and
+  denote major changes in functionality and the API;
+- minor releases occur around twice per year and contain new features with minor
+  API changes;
+- patch releases are targeted on roughly a monthly basis and are intended to
+  fix minor issues in the code.
+
+The repository contains a number of _release branches_ named `release/x.y` for
+each minor release, which are intended to contain **fixes and very minor
+changes** from `master` and which form the next patch release. This allows us to
+use `master` for the next minor release, whilst still having key fixes in patch
+releases.
+
+### Cherry-picking process
+
+Any branches that are marked with the `Proposed patch` label should follow the
+following additional steps to cherry pick commits into the `release/x.y` branch.
+
+1. If the branch is on a remote other than `nektar/nektar`, make sure that's
+   added to your local repository.
+2. On a local terminal, run `git fetch --all` to pull the latest changes. It's
+   important for the commands below that you do this _before_ you merge the
+   branch into `master`.
+3. Merge the branch into master as usual using GitLab.
+4. Switch to the appropriate branch with `git checkout release/x.y` and update
+   with `git pull`.
+5. Now check the list of commits to cherry-pick.
+
+   ```bash
+   git log --oneline --no-merges --reverse origin/master..REMOTE/fix/BRANCHNAME
+   ```
+
+   where `REMOTE` is the remote on which the branch lives and `BRANCHNAME` is
+   the fix branch. If the list is empty, you probably did a `git fetch` after
+   you merged the branch into `master`; in this case use `origin/master^`.
+6. If you're happy with the list (compare to the MR list on the GitLab MR if
+   necessary), cherry-pick the commits with the command:
+
+   ```bash
+   git cherry-pick -x $(git rev-list --no-merges --reverse origin/master..REMOTE/fix/BRANCHNAME)
+   ```
+
+7. It's likely you'll encounter some conflicts, particularly with the
+   `CHANGELOG`. To fix these:
+   - `git status` to see what's broken
+   - Fix appropriately
+   - `git commit -a` to commit your fix
+   - `git cherry-pick --continue`
+8. If everything becomes horribly broken, `git cherry-pick --abort`.
+9. Once you're happy, `git push` to send your changes back to GitLab.
+
+Steps 5 and 6 can be simplified by creating a script
+```bash
+#!/bin/bash
+src=$1
+
+logopts="--oneline --no-merges --reverse"
+commits=`git log $logopts master..$1 | cut -f 1 -d " " | xargs`
+
+echo "Will cherry-pick the following commits: $commits"
+echo "Press ENTER to continue..."
+read
+
+cherryopts="-x --allow-empty --allow-empty-message"
+git cherry-pick $cherryopts $commits
+```
+which accepts the name of the source branch as the sole argument.
+
 ## Formatting guidelines
 Nektar++ uses C++, a language notorious for being easy to make obtuse and
 difficult to follow code. To hopefully alleviate this problem, there are a

--- a/cmake/FindGSMPI.cmake
+++ b/cmake/FindGSMPI.cmake
-
-SET(GSMPI_SEARCH_PATHS 
-	${CMAKE_SOURCE_DIR}/ThirdParty/gsmpi-1.2/
-	${CMAKE_SOURCE_DIR}/ThirdParty/gsmpi-1.2/build/
-	${CMAKE_SOURCE_DIR}/../ThirdParty/gsmpi-1.2/
-	${CMAKE_SOURCE_DIR}/../ThirdParty/gsmpi-1.2/build 
-    ${CMAKE_SOURCE_DIR}/ThirdParty/dist/lib 
-    ${CMAKE_SOURCE_DIR}/../ThirdParty/dist/lib)
-
-FIND_LIBRARY(GSMPI_LIBRARY NAMES gsmpi PATHS ${GSMPI_SEARCH_PATHS})
-
-SET(GSMPI_FOUND FALSE)
-IF (GSMPI_LIBRARY)
-  SET(GSMPI_FOUND TRUE)
-  MARK_AS_ADVANCED(GSMPI_LIBRARY)
-ENDIF (GSMPI_LIBRARY)
-
-IF (GSMPI_FOUND)
-  IF (NOT GSMPI_FIND_QUIETLY)
-     MESSAGE(STATUS "Found GSMPI")
-  ENDIF (NOT GSMPI_FIND_QUIETLY)
-ELSE(GSMPI_FOUND)
-  IF (GSMPI_FIND_REQUIRED)
-     MESSAGE(FATAL_ERROR "Could not find GSLib")
-  ENDIF (GSMPI_FIND_REQUIRED)
-ENDIF (GSMPI_FOUND)
--- a/cmake/FindNativeBlasLapack.cmake
+++ b/cmake/FindNativeBlasLapack.cmake

-
-SET(NATIVE_BLAS_LAPACK_SEARCH_PATHS /usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64 )
+SET(TEST_ENV $ENV{LAPACK_DIR})
+IF(NOT DEFINED LAPACK_DIR AND DEFINED TEST_ENV)
+	SET(LAPACK_DIR $ENV{LAPACK_DIR})
+ENDIF()
+
+SET( NATIVE_BLAS_LAPACK_SEARCH_PATHS /usr/lib
+									 /usr/lib64
+									 /usr/local/lib
+									 /usr/local/lib64
+									 ${LAPACK_DIR}/lib64
+									 ${LAPACK_DIR}/lib)

 FIND_LIBRARY(NATIVE_BLAS NAMES blas PATHS ${NATIVE_BLAS_LAPACK_SEARCH_PATHS})
 FIND_LIBRARY(NATIVE_LAPACK NAMES lapack PATHS ${NATIVE_BLAS_LAPACK_SEARCH_PATHS})

--- a/cmake/FindPETSc.cmake
+++ b/cmake/FindPETSc.cmake
@@ -198,7 +198,7 @@ show :
    else (WIN32)
      set (libname ${name})
    endif (WIN32)
-    find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
+    find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} ${libname}_real HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
    set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
    mark_as_advanced (PETSC_LIBRARY_${suffix})
  endmacro (PETSC_FIND_LIBRARY suffix name)

--- a/cmake/FindPackageMultipass.cmake
+++ b/cmake/FindPackageMultipass.cmake
@@ -25,7 +25,7 @@
 #  Always runs the given test, use this when you need to re-run tests
 #  because parent variables have made old cache entries stale. The LANGUAGE
 #  variable is either C or CXX indicating which compiler the test should
-#  use. 
+#  use.
 # MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
 #  DEPRECATED! This is only included for backwards compatability. Use
 #  the more general MULTIPASS_SOURCE_RUNS instead.
@@ -46,7 +46,7 @@ macro (FIND_PACKAGE_MULTIPASS _name _current)
      # The name of the stored value for the given state
      set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
      if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
-	set (_states_current "NO")
+        set (_states_current "NO")
      endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
      set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
      list (REMOVE_AT _args 0)
@@ -68,7 +68,7 @@ macro (FIND_PACKAGE_MULTIPASS _name _current)
    if (_cmd STREQUAL "DEPENDENTS")
      list (REMOVE_AT _args 0)
      foreach (dep ${_args})
-	set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+        set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
      endforeach (dep)
    endif (_cmd STREQUAL "DEPENDENTS")
    set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)

--- a/cmake/FindSMV.cmake
+++ b/cmake/FindSMV.cmake
-
-SET(SMV_SEARCH_PATHS 
-	${CMAKE_SOURCE_DIR}/ThirdParty/libsmv/build/lib
-	${CMAKE_SOURCE_DIR}/../ThirdParty/libsmv/build/lib
-    ${CMAKE_SOURCE_DIR}/ThirdParty/dist/build/lib
-    ${CMAKE_SOURCE_DIR}/../ThirdParty/dist/build/lib)
-
-FIND_PATH(SMV_INCLUDE_DIR NAMES smv.h PATHS ${SMV_SEARCH_PATHS})
-FIND_LIBRARY(SMV_LIBRARY NAMES smv PATHS ${SMV_SEARCH_PATHS})
-
-
-SET(SMV_FOUND FALSE)
-IF (SMV_LIBRARY)
-  SET(SMV_FOUND TRUE)
-  INCLUDE_DIRECTORIES(${SMV_INCLUDE_DIR})
-  MARK_AS_ADVANCED(SMV_LIBRARY)
-  MARK_AS_ADVANCED(SMV_INCLUDE_DIR)
-ENDIF (SMV_LIBRARY)
-
-IF (SMV_FOUND)
-  IF (NOT SMV_FIND_QUIETLY)
-     MESSAGE(STATUS "Found SMV: ${SMV_INCLUDE_DIR}")
-  ENDIF (NOT SMV_FIND_QUIETLY)
-ELSE(SMV_FOUND)
-  IF (SMV_FIND_REQUIRED)
-     MESSAGE(FATAL_ERROR "Could not find SMV")
-  ENDIF (SMV_FIND_REQUIRED)
-ENDIF (SMV_FOUND)
--- a/cmake/FindXXT.cmake
+++ b/cmake/FindXXT.cmake
-
-SET(XXT_SEARCH_PATHS 
-	${CMAKE_SOURCE_DIR}/ThirdParty/gsmpi-1.2/
-	${CMAKE_SOURCE_DIR}/ThirdParty/gsmpi-1.2/build/
-	${CMAKE_SOURCE_DIR}/../ThirdParty/gsmpi-1.2/
-	${CMAKE_SOURCE_DIR}/../ThirdParty/gsmpi-1.2/build 
-    ${CMAKE_SOURCE_DIR}/ThirdParty/dist/lib 
-    ${CMAKE_SOURCE_DIR}/../ThirdParty/dist/lib)
-
-FIND_LIBRARY(XXT_LIBRARY NAMES xxt PATHS ${XXT_SEARCH_PATHS})
-
-SET(XXT_FOUND FALSE)
-IF (XXT_LIBRARY)
-  SET(XXT_FOUND TRUE)
-  MARK_AS_ADVANCED(XXT_LIBRARY)
-ENDIF (XXT_LIBRARY)
-
-IF (XXT_FOUND)
-  IF (NOT XXT_FIND_QUIETLY)
-     MESSAGE(STATUS "Found XXT")
-  ENDIF (NOT XXT_FIND_QUIETLY)
-ELSE(XXT_FOUND)
-  IF (XXT_FIND_REQUIRED)
-     MESSAGE(FATAL_ERROR "Could not find XXT")
-  ENDIF (XXT_FIND_REQUIRED)
-ENDIF (XXT_FOUND)
--- a/cmake/Nektar++Config.cmake.in
+++ b/cmake/Nektar++Config.cmake.in
@@ -50,10 +50,6 @@ SET(Boost_LIBRARY_DIRS "@Boost_CONFIG_LIBRARY_DIR@")
 SET(NEKTAR++_TP_LIBRARIES
    ${NEKTAR++_TP_LIBRARIES} ${Boost_LIBRARIES})

-SET(LOKI_INCLUDE_DIRS "@LOKI_CONFIG_INCLUDE_DIR@")
-SET(NEKTAR++_TP_INCLUDE_DIRS
-    ${NEKTAR++_TP_INCLUDE_DIRS} ${LOKI_INCLUDE_DIRS})
-
 SET(TINYXML_INCLUDE_DIRS "@TINYXML_CONFIG_INCLUDE_DIR@")
 SET(NEKTAR++_TP_INCLUDE_DIRS
    ${NEKTAR++_TP_INCLUDE_DIRS} ${TINYXML_INCLUDE_DIRS})

--- a/cmake/NektarCommon.cmake
+++ b/cmake/NektarCommon.cmake
-MACRO(CHANGE_EXTENSION output var new_ext)
-    GET_FILENAME_COMPONENT(FileName ${var} NAME_WE)
-    GET_FILENAME_COMPONENT(Path ${var} PATH)
-    SET(${output} ${Path}/${FileName}.${new_ext})
+##
+## NektarCommon.cmake
+##
+## Frequently used Nektar++ CMake configuration macros and functions
+##
+
+#
+# THIRDPARTY_LIBRARY(varname DESCRIPTION <description> [STATIC|SHARED] lib1 [lib2]...)
+#
+# Updates a variable containing the name of a third-party shared or static
+# library to point to an absolute path defining its location instead of adding
+# `-llibname` to the linker flags. This avoids the issue of e.g. linking against
+# an outdated system zlib installation.
+#
+# Arguments:
+#   - `varname`: variable name containing the third-party library name. On
+#     output will be altered to update the correct path.
+#   - `DESCRIPTION`: a brief description of the variable (used in the SET
+#     command).
+#   - `SHARED`: if the library will be built as a shared library
+#   - `STATIC`: if the library will be built as a static library
+#
+MACRO(THIRDPARTY_LIBRARY varname)
+    CMAKE_PARSE_ARGUMENTS(TPLIB "" "DESCRIPTION" "STATIC;SHARED" ${ARGN})
+
+    IF(TPLIB_SHARED)
+        SET(LIBTYPE "SHARED")
+        SET(TPLIBS ${TPLIB_SHARED})