bump to 3.3.4

(grafted from 9fbdf02059
)

CMakeLists.txt

@@ -541,7 +541,8 @@ if (NOT CMAKE_VERSION VERSION_LESS 3.0)
   set (_Eigen3_CMAKE_SIZEOF_VOID_P ${CMAKE_SIZEOF_VOID_P})
   unset (CMAKE_SIZEOF_VOID_P)
   write_basic_package_version_file (Eigen3ConfigVersion.cmake
-    VERSION ${EIGEN_VERSION_NUMBER} COMPATIBILITY SameMajorVersion)
+                                    VERSION ${EIGEN_VERSION_NUMBER}
+                                    COMPATIBILITY SameMajorVersion)
   set (CMAKE_SIZEOF_VOID_P ${_Eigen3_CMAKE_SIZEOF_VOID_P})
 
   # The Eigen target will be located in the Eigen3 namespace. Other CMake
@@ -551,13 +552,8 @@ if (NOT CMAKE_VERSION VERSION_LESS 3.0)
   # CMake even if it has not been installed to a standard directory.
   export (PACKAGE Eigen3)
 
-  install (EXPORT Eigen3Targets NAMESPACE Eigen3:: DESTINATION
-    ${CMAKEPACKAGE_INSTALL_DIR})
-  install (FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
-    ${CMAKE_CURRENT_BINARY_DIR}/Eigen3ConfigVersion.cmake
-    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/UseEigen3.cmake
-    DESTINATION ${CMAKEPACKAGE_INSTALL_DIR})
+  install (EXPORT Eigen3Targets NAMESPACE Eigen3:: DESTINATION ${CMAKEPACKAGE_INSTALL_DIR})
+
 else (NOT CMAKE_VERSION VERSION_LESS 3.0)
   # Fallback to legacy Eigen3Config.cmake without the imported target
   
@@ -581,16 +577,20 @@ else (NOT CMAKE_VERSION VERSION_LESS 3.0)
     set(PACKAGE_EIGEN_ROOT_DIR ${EIGEN_ROOT_DIR})
     configure_file ( ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Eigen3ConfigLegacy.cmake.in
                      ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
-                     @ONLY ESCAPE_QUOTES
-                   )
+                     @ONLY ESCAPE_QUOTES )
   endif()
 
-  install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/UseEigen3.cmake
-                  ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
-            DESTINATION ${CMAKEPACKAGE_INSTALL_DIR}
-          )
+  write_basic_package_version_file( Eigen3ConfigVersion.cmake
+                                    VERSION ${EIGEN_VERSION_NUMBER}
+                                    COMPATIBILITY SameMajorVersion )
+
 endif (NOT CMAKE_VERSION VERSION_LESS 3.0)
 
+install ( FILES ${CMAKE_CURRENT_SOURCE_DIR}/cmake/UseEigen3.cmake
+                ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
+                ${CMAKE_CURRENT_BINARY_DIR}/Eigen3ConfigVersion.cmake
+          DESTINATION ${CMAKEPACKAGE_INSTALL_DIR} )
+
 # Add uninstall target
 add_custom_target ( uninstall
     COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake/EigenUninstall.cmake)

Eigen/Core

@@ -321,12 +321,16 @@ inline static const char *SimdInstructionSetsInUse(void) {
 #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
 #endif
 
+namespace Eigen {
+
 // we use size_t frequently and we'll never remember to prepend it with std:: everytime just to
 // ensure QNX/QCC support
 using std::size_t;
 // gcc 4.6.0 wants std:: for ptrdiff_t
 using std::ptrdiff_t;
 
+}
+
 /** \defgroup Core_Module Core module
   * This is the main module of Eigen providing dense matrix and vector support
   * (both fixed and dynamic size) with all the features corresponding to a BLAS library
@@ -405,6 +409,7 @@ using std::ptrdiff_t;
 // on CUDA devices
 #include "src/Core/arch/CUDA/Complex.h"
 
+#include "src/Core/IO.h"
 #include "src/Core/DenseCoeffsBase.h"
 #include "src/Core/DenseBase.h"
 #include "src/Core/MatrixBase.h"
@@ -452,7 +457,6 @@ using std::ptrdiff_t;
 #include "src/Core/Redux.h"
 #include "src/Core/Visitor.h"
 #include "src/Core/Fuzzy.h"
-#include "src/Core/IO.h"
 #include "src/Core/Swap.h"
 #include "src/Core/CommaInitializer.h"
 #include "src/Core/GeneralProduct.h"

Eigen/QtAlignedMalloc

@@ -14,7 +14,7 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-void *qMalloc(size_t size)
+void *qMalloc(std::size_t size)
 {
   return Eigen::internal::aligned_malloc(size);
 }
@@ -24,7 +24,7 @@ void qFree(void *ptr)
   Eigen::internal::aligned_free(ptr);
 }
 
-void *qRealloc(void *ptr, size_t size)
+void *qRealloc(void *ptr, std::size_t size)
 {
   void* newPtr = Eigen::internal::aligned_malloc(size);
   memcpy(newPtr, ptr, size);

Eigen/Sparse

@@ -25,7 +25,9 @@
 
 #include "SparseCore"
 #include "OrderingMethods"
+#ifndef EIGEN_MPL2_ONLY
 #include "SparseCholesky"
+#endif
 #include "SparseLU"
 #include "SparseQR"
 #include "IterativeLinearSolvers"

Eigen/StdDeque

@@ -14,7 +14,7 @@
 #include "Core"
 #include <deque>
 
-#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 /* MSVC auto aligns in 64 bit builds */
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_DEQUE_SPECIALIZATION(...)
 

Eigen/StdList

@@ -13,7 +13,7 @@
 #include "Core"
 #include <list>
 
-#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 /* MSVC auto aligns in 64 bit builds */    
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_LIST_SPECIALIZATION(...)
 

Eigen/StdVector

@@ -14,7 +14,7 @@
 #include "Core"
 #include <vector>
 
-#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 /* MSVC auto aligns in 64 bit builds */
+#if EIGEN_COMP_MSVC && EIGEN_OS_WIN64 && (EIGEN_MAX_STATIC_ALIGN_BYTES<=16) /* MSVC auto aligns up to 16 bytes in 64 bit builds */
 
 #define EIGEN_DEFINE_STL_VECTOR_SPECIALIZATION(...)
 

Eigen/src/Core/Array.h

@@ -231,10 +231,16 @@ class Array
             : Base(other)
     { }
 
+  private:
+    struct PrivateType {};
+  public:
+
     /** \sa MatrixBase::operator=(const EigenBase<OtherDerived>&) */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC
-    EIGEN_STRONG_INLINE Array(const EigenBase<OtherDerived> &other)
+    EIGEN_STRONG_INLINE Array(const EigenBase<OtherDerived> &other,
+                              typename internal::enable_if<internal::is_convertible<typename OtherDerived::Scalar,Scalar>::value,
+                                                           PrivateType>::type = PrivateType())
       : Base(other.derived())
     { }
 

Eigen/src/Core/ArrayBase.h

@@ -175,7 +175,7 @@ template<typename Derived> class ArrayBase
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator-=(const ArrayBase<OtherDerived> &other)
 {
   call_assignment(derived(), other.derived(), internal::sub_assign_op<Scalar,typename OtherDerived::Scalar>());
@@ -188,7 +188,7 @@ ArrayBase<Derived>::operator-=(const ArrayBase<OtherDerived> &other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator+=(const ArrayBase<OtherDerived>& other)
 {
   call_assignment(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
@@ -201,7 +201,7 @@ ArrayBase<Derived>::operator+=(const ArrayBase<OtherDerived>& other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator*=(const ArrayBase<OtherDerived>& other)
 {
   call_assignment(derived(), other.derived(), internal::mul_assign_op<Scalar,typename OtherDerived::Scalar>());
@@ -214,7 +214,7 @@ ArrayBase<Derived>::operator*=(const ArrayBase<OtherDerived>& other)
   */
 template<typename Derived>
 template<typename OtherDerived>
-EIGEN_STRONG_INLINE Derived &
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived &
 ArrayBase<Derived>::operator/=(const ArrayBase<OtherDerived>& other)
 {
   call_assignment(derived(), other.derived(), internal::div_assign_op<Scalar,typename OtherDerived::Scalar>());

Eigen/src/Core/ArrayWrapper.h

@@ -32,7 +32,8 @@ struct traits<ArrayWrapper<ExpressionType> >
   // Let's remove NestByRefBit
   enum {
     Flags0 = traits<typename remove_all<typename ExpressionType::Nested>::type >::Flags,
-    Flags = Flags0 & ~NestByRefBit
+    LvalueBitFlag = is_lvalue<ExpressionType>::value ? LvalueBit : 0,
+    Flags = (Flags0 & ~(NestByRefBit | LvalueBit)) | LvalueBitFlag
   };
 };
 }
@@ -129,7 +130,8 @@ struct traits<MatrixWrapper<ExpressionType> >
   // Let's remove NestByRefBit
   enum {
     Flags0 = traits<typename remove_all<typename ExpressionType::Nested>::type >::Flags,
-    Flags = Flags0 & ~NestByRefBit
+    LvalueBitFlag = is_lvalue<ExpressionType>::value ? LvalueBit : 0,
+    Flags = (Flags0 & ~(NestByRefBit | LvalueBit)) | LvalueBitFlag
   };
 };
 }

Eigen/src/Core/AssignEvaluator.h

@@ -515,7 +515,7 @@ struct dense_assignment_loop<Kernel, LinearTraversal, CompleteUnrolling>
 template<typename Kernel>
 struct dense_assignment_loop<Kernel, SliceVectorizedTraversal, NoUnrolling>
 {
-  EIGEN_DEVICE_FUNC static inline void run(Kernel &kernel)
+  EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE void run(Kernel &kernel)
   {
     typedef typename Kernel::Scalar Scalar;
     typedef typename Kernel::PacketType PacketType;
@@ -563,7 +563,7 @@ struct dense_assignment_loop<Kernel, SliceVectorizedTraversal, NoUnrolling>
 template<typename Kernel>
 struct dense_assignment_loop<Kernel, SliceVectorizedTraversal, InnerUnrolling>
 {
-  EIGEN_DEVICE_FUNC static inline void run(Kernel &kernel)
+  EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE void run(Kernel &kernel)
   {
     typedef typename Kernel::DstEvaluatorType::XprType DstXprType;
     typedef typename Kernel::PacketType PacketType;
@@ -701,6 +701,26 @@ protected:
 * Part 5 : Entry point for dense rectangular assignment
 ***************************************************************************/
 
+template<typename DstXprType,typename SrcXprType, typename Functor>
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
+void resize_if_allowed(DstXprType &dst, const SrcXprType& src, const Functor &/*func*/)
+{
+  EIGEN_ONLY_USED_FOR_DEBUG(dst);
+  EIGEN_ONLY_USED_FOR_DEBUG(src);
+  eigen_assert(dst.rows() == src.rows() && dst.cols() == src.cols());
+}
+
+template<typename DstXprType,typename SrcXprType, typename T1, typename T2>
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
+void resize_if_allowed(DstXprType &dst, const SrcXprType& src, const internal::assign_op<T1,T2> &/*func*/)
+{
+  Index dstRows = src.rows();
+  Index dstCols = src.cols();
+  if(((dst.rows()!=dstRows) || (dst.cols()!=dstCols)))
+    dst.resize(dstRows, dstCols);
+  eigen_assert(dst.rows() == dstRows && dst.cols() == dstCols);
+}
+
 template<typename DstXprType, typename SrcXprType, typename Functor>
 EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void call_dense_assignment_loop(DstXprType& dst, const SrcXprType& src, const Functor &func)
 {
@@ -711,10 +731,7 @@ EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void call_dense_assignment_loop(DstXprType
 
   // NOTE To properly handle A = (A*A.transpose())/s with A rectangular,
   // we need to resize the destination after the source evaluator has been created.
-  Index dstRows = src.rows();
-  Index dstCols = src.cols();
-  if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
-    dst.resize(dstRows, dstCols);
+  resize_if_allowed(dst, src, func);
 
   DstEvaluatorType dstEvaluator(dst);
     

Eigen/src/Core/CoreEvaluators.h

@@ -1556,9 +1556,7 @@ struct evaluator<Diagonal<ArgType, DiagIndex> >
   { }
  
   typedef typename XprType::Scalar Scalar;
-  // FIXME having to check whether ArgType is sparse here i not very nice.
-  typedef typename internal::conditional<!internal::is_same<typename ArgType::StorageKind,Sparse>::value,
-                                         typename XprType::CoeffReturnType,Scalar>::type CoeffReturnType;
+  typedef typename XprType::CoeffReturnType CoeffReturnType;
 
   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
   CoeffReturnType coeff(Index row, Index) const

Eigen/src/Core/CwiseBinaryOp.h

@@ -46,7 +46,7 @@ struct traits<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
   typedef typename remove_reference<LhsNested>::type _LhsNested;
   typedef typename remove_reference<RhsNested>::type _RhsNested;
   enum {
-    Flags = _LhsNested::Flags & RowMajorBit
+    Flags = cwise_promote_storage_order<typename traits<Lhs>::StorageKind,typename traits<Rhs>::StorageKind,_LhsNested::Flags & RowMajorBit,_RhsNested::Flags & RowMajorBit>::value
   };
 };
 } // end namespace internal

Eigen/src/Core/CwiseNullaryOp.h

@@ -105,7 +105,7 @@ class CwiseNullaryOp : public internal::dense_xpr_base< CwiseNullaryOp<NullaryOp
   */
 template<typename Derived>
 template<typename CustomNullaryOp>
-EIGEN_STRONG_INLINE const CwiseNullaryOp<CustomNullaryOp, typename DenseBase<Derived>::PlainObject>
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const CwiseNullaryOp<CustomNullaryOp, typename DenseBase<Derived>::PlainObject>
 DenseBase<Derived>::NullaryExpr(Index rows, Index cols, const CustomNullaryOp& func)
 {
   return CwiseNullaryOp<CustomNullaryOp, PlainObject>(rows, cols, func);
@@ -150,7 +150,7 @@ DenseBase<Derived>::NullaryExpr(Index size, const CustomNullaryOp& func)
   */
 template<typename Derived>
 template<typename CustomNullaryOp>
-EIGEN_STRONG_INLINE const CwiseNullaryOp<CustomNullaryOp, typename DenseBase<Derived>::PlainObject>
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const CwiseNullaryOp<CustomNullaryOp, typename DenseBase<Derived>::PlainObject>
 DenseBase<Derived>::NullaryExpr(const CustomNullaryOp& func)
 {
   return CwiseNullaryOp<CustomNullaryOp, PlainObject>(RowsAtCompileTime, ColsAtCompileTime, func);
@@ -192,7 +192,7 @@ DenseBase<Derived>::Constant(Index rows, Index cols, const Scalar& value)
   * \sa class CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Constant(Index size, const Scalar& value)
 {
   return DenseBase<Derived>::NullaryExpr(size, internal::scalar_constant_op<Scalar>(value));
@@ -208,7 +208,7 @@ DenseBase<Derived>::Constant(Index size, const Scalar& value)
   * \sa class CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Constant(const Scalar& value)
 {
   EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived)
@@ -220,7 +220,7 @@ DenseBase<Derived>::Constant(const Scalar& value)
   * \sa LinSpaced(Index,Scalar,Scalar), setLinSpaced(Index,const Scalar&,const Scalar&)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
 DenseBase<Derived>::LinSpaced(Sequential_t, Index size, const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
@@ -232,7 +232,7 @@ DenseBase<Derived>::LinSpaced(Sequential_t, Index size, const Scalar& low, const
   * \sa LinSpaced(Scalar,Scalar)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
 DenseBase<Derived>::LinSpaced(Sequential_t, const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
@@ -264,7 +264,7 @@ DenseBase<Derived>::LinSpaced(Sequential_t, const Scalar& low, const Scalar& hig
   * \sa setLinSpaced(Index,const Scalar&,const Scalar&), CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
 DenseBase<Derived>::LinSpaced(Index size, const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
@@ -276,7 +276,7 @@ DenseBase<Derived>::LinSpaced(Index size, const Scalar& low, const Scalar& high)
   * Special version for fixed size types which does not require the size parameter.
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::RandomAccessLinSpacedReturnType
 DenseBase<Derived>::LinSpaced(const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
@@ -286,7 +286,7 @@ DenseBase<Derived>::LinSpaced(const Scalar& low, const Scalar& high)
 
 /** \returns true if all coefficients in this matrix are approximately equal to \a val, to within precision \a prec */
 template<typename Derived>
-bool DenseBase<Derived>::isApproxToConstant
+EIGEN_DEVICE_FUNC bool DenseBase<Derived>::isApproxToConstant
 (const Scalar& val, const RealScalar& prec) const
 {
   typename internal::nested_eval<Derived,1>::type self(derived());
@@ -301,7 +301,7 @@ bool DenseBase<Derived>::isApproxToConstant
   *
   * \returns true if all coefficients in this matrix are approximately equal to \a value, to within precision \a prec */
 template<typename Derived>
-bool DenseBase<Derived>::isConstant
+EIGEN_DEVICE_FUNC bool DenseBase<Derived>::isConstant
 (const Scalar& val, const RealScalar& prec) const
 {
   return isApproxToConstant(val, prec);
@@ -312,7 +312,7 @@ bool DenseBase<Derived>::isConstant
   * \sa setConstant(), Constant(), class CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE void DenseBase<Derived>::fill(const Scalar& val)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void DenseBase<Derived>::fill(const Scalar& val)
 {
   setConstant(val);
 }
@@ -322,7 +322,7 @@ EIGEN_STRONG_INLINE void DenseBase<Derived>::fill(const Scalar& val)
   * \sa fill(), setConstant(Index,const Scalar&), setConstant(Index,Index,const Scalar&), setZero(), setOnes(), Constant(), class CwiseNullaryOp, setZero(), setOnes()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setConstant(const Scalar& val)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setConstant(const Scalar& val)
 {
   return derived() = Constant(rows(), cols(), val);
 }
@@ -337,7 +337,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setConstant(const Scalar& val)
   * \sa MatrixBase::setConstant(const Scalar&), setConstant(Index,Index,const Scalar&), class CwiseNullaryOp, MatrixBase::Constant(const Scalar&)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setConstant(Index size, const Scalar& val)
 {
   resize(size);
@@ -356,7 +356,7 @@ PlainObjectBase<Derived>::setConstant(Index size, const Scalar& val)
   * \sa MatrixBase::setConstant(const Scalar&), setConstant(Index,const Scalar&), class CwiseNullaryOp, MatrixBase::Constant(const Scalar&)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setConstant(Index rows, Index cols, const Scalar& val)
 {
   resize(rows, cols);
@@ -380,7 +380,7 @@ PlainObjectBase<Derived>::setConstant(Index rows, Index cols, const Scalar& val)
   * \sa LinSpaced(Index,const Scalar&,const Scalar&), CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(Index newSize, const Scalar& low, const Scalar& high)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(Index newSize, const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
   return derived() = Derived::NullaryExpr(newSize, internal::linspaced_op<Scalar,PacketScalar>(low,high,newSize));
@@ -400,7 +400,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(Index newSize, con
   * \sa LinSpaced(Index,const Scalar&,const Scalar&), setLinSpaced(Index, const Scalar&, const Scalar&), CwiseNullaryOp
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(const Scalar& low, const Scalar& high)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(const Scalar& low, const Scalar& high)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
   return setLinSpaced(size(), low, high);
@@ -423,7 +423,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setLinSpaced(const Scalar& low,
   * \sa Zero(), Zero(Index)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Zero(Index rows, Index cols)
 {
   return Constant(rows, cols, Scalar(0));
@@ -446,7 +446,7 @@ DenseBase<Derived>::Zero(Index rows, Index cols)
   * \sa Zero(), Zero(Index,Index)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Zero(Index size)
 {
   return Constant(size, Scalar(0));
@@ -463,7 +463,7 @@ DenseBase<Derived>::Zero(Index size)
   * \sa Zero(Index), Zero(Index,Index)
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Zero()
 {
   return Constant(Scalar(0));
@@ -478,7 +478,7 @@ DenseBase<Derived>::Zero()
   * \sa class CwiseNullaryOp, Zero()
   */
 template<typename Derived>
-bool DenseBase<Derived>::isZero(const RealScalar& prec) const
+EIGEN_DEVICE_FUNC bool DenseBase<Derived>::isZero(const RealScalar& prec) const
 {
   typename internal::nested_eval<Derived,1>::type self(derived());
   for(Index j = 0; j < cols(); ++j)
@@ -496,7 +496,7 @@ bool DenseBase<Derived>::isZero(const RealScalar& prec) const
   * \sa class CwiseNullaryOp, Zero()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setZero()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setZero()
 {
   return setConstant(Scalar(0));
 }
@@ -511,7 +511,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setZero()
   * \sa DenseBase::setZero(), setZero(Index,Index), class CwiseNullaryOp, DenseBase::Zero()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setZero(Index newSize)
 {
   resize(newSize);
@@ -529,7 +529,7 @@ PlainObjectBase<Derived>::setZero(Index newSize)
   * \sa DenseBase::setZero(), setZero(Index), class CwiseNullaryOp, DenseBase::Zero()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setZero(Index rows, Index cols)
 {
   resize(rows, cols);
@@ -553,7 +553,7 @@ PlainObjectBase<Derived>::setZero(Index rows, Index cols)
   * \sa Ones(), Ones(Index), isOnes(), class Ones
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Ones(Index rows, Index cols)
 {
   return Constant(rows, cols, Scalar(1));
@@ -576,7 +576,7 @@ DenseBase<Derived>::Ones(Index rows, Index cols)
   * \sa Ones(), Ones(Index,Index), isOnes(), class Ones
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Ones(Index newSize)
 {
   return Constant(newSize, Scalar(1));
@@ -593,7 +593,7 @@ DenseBase<Derived>::Ones(Index newSize)
   * \sa Ones(Index), Ones(Index,Index), isOnes(), class Ones
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename DenseBase<Derived>::ConstantReturnType
 DenseBase<Derived>::Ones()
 {
   return Constant(Scalar(1));
@@ -608,7 +608,7 @@ DenseBase<Derived>::Ones()
   * \sa class CwiseNullaryOp, Ones()
   */
 template<typename Derived>
-bool DenseBase<Derived>::isOnes
+EIGEN_DEVICE_FUNC bool DenseBase<Derived>::isOnes
 (const RealScalar& prec) const
 {
   return isApproxToConstant(Scalar(1), prec);
@@ -622,7 +622,7 @@ bool DenseBase<Derived>::isOnes
   * \sa class CwiseNullaryOp, Ones()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setOnes()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setOnes()
 {
   return setConstant(Scalar(1));
 }
@@ -637,7 +637,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::setOnes()
   * \sa MatrixBase::setOnes(), setOnes(Index,Index), class CwiseNullaryOp, MatrixBase::Ones()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setOnes(Index newSize)
 {
   resize(newSize);
@@ -655,7 +655,7 @@ PlainObjectBase<Derived>::setOnes(Index newSize)
   * \sa MatrixBase::setOnes(), setOnes(Index), class CwiseNullaryOp, MatrixBase::Ones()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived&
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived&
 PlainObjectBase<Derived>::setOnes(Index rows, Index cols)
 {
   resize(rows, cols);
@@ -679,7 +679,7 @@ PlainObjectBase<Derived>::setOnes(Index rows, Index cols)
   * \sa Identity(), setIdentity(), isIdentity()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::IdentityReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::IdentityReturnType
 MatrixBase<Derived>::Identity(Index rows, Index cols)
 {
   return DenseBase<Derived>::NullaryExpr(rows, cols, internal::scalar_identity_op<Scalar>());
@@ -696,7 +696,7 @@ MatrixBase<Derived>::Identity(Index rows, Index cols)
   * \sa Identity(Index,Index), setIdentity(), isIdentity()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::IdentityReturnType
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::IdentityReturnType
 MatrixBase<Derived>::Identity()
 {
   EIGEN_STATIC_ASSERT_FIXED_SIZE(Derived)
@@ -771,7 +771,7 @@ struct setIdentity_impl<Derived, true>
   * \sa class CwiseNullaryOp, Identity(), Identity(Index,Index), isIdentity()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity()
 {
   return internal::setIdentity_impl<Derived>::run(derived());
 }
@@ -787,7 +787,7 @@ EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity()
   * \sa MatrixBase::setIdentity(), class CwiseNullaryOp, MatrixBase::Identity()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity(Index rows, Index cols)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity(Index rows, Index cols)
 {
   derived().resize(rows, cols);
   return setIdentity();
@@ -800,7 +800,7 @@ EIGEN_STRONG_INLINE Derived& MatrixBase<Derived>::setIdentity(Index rows, Index
   * \sa MatrixBase::Unit(Index), MatrixBase::UnitX(), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::Unit(Index newSize, Index i)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::Unit(Index newSize, Index i)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
   return BasisReturnType(SquareMatrixType::Identity(newSize,newSize), i);
@@ -815,7 +815,7 @@ EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBa
   * \sa MatrixBase::Unit(Index,Index), MatrixBase::UnitX(), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::Unit(Index i)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::Unit(Index i)
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
   return BasisReturnType(SquareMatrixType::Identity(),i);
@@ -828,7 +828,7 @@ EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBa
   * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitX()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitX()
 { return Derived::Unit(0); }
 
 /** \returns an expression of the Y axis unit vector (0,1{,0}^*)
@@ -838,7 +838,7 @@ EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBa
   * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitY()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitY()
 { return Derived::Unit(1); }
 
 /** \returns an expression of the Z axis unit vector (0,0,1{,0}^*)
@@ -848,7 +848,7 @@ EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBa
   * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitZ()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitZ()
 { return Derived::Unit(2); }
 
 /** \returns an expression of the W axis unit vector (0,0,0,1)
@@ -858,7 +858,7 @@ EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBa
   * \sa MatrixBase::Unit(Index,Index), MatrixBase::Unit(Index), MatrixBase::UnitY(), MatrixBase::UnitZ(), MatrixBase::UnitW()
   */
 template<typename Derived>
-EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitW()
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const typename MatrixBase<Derived>::BasisReturnType MatrixBase<Derived>::UnitW()
 { return Derived::Unit(3); }
 
 } // end namespace Eigen

Eigen/src/Core/DenseBase.h

@@ -296,7 +296,7 @@ template<typename Derived> class DenseBase
     EIGEN_DEVICE_FUNC
     Derived& operator=(const ReturnByValue<OtherDerived>& func);
 
-    /** \ínternal
+    /** \internal
       * Copies \a other into *this without evaluating other. \returns a reference to *this.
       * \deprecated */
     template<typename OtherDerived>
@@ -463,7 +463,17 @@ template<typename Derived> class DenseBase
     EIGEN_DEVICE_FUNC
     void visit(Visitor& func) const;
 
-    inline const WithFormat<Derived> format(const IOFormat& fmt) const;
+    /** \returns a WithFormat proxy object allowing to print a matrix the with given
+      * format \a fmt.
+      *
+      * See class IOFormat for some examples.
+      *
+      * \sa class IOFormat, class WithFormat
+      */
+    inline const WithFormat<Derived> format(const IOFormat& fmt) const
+    {
+      return WithFormat<Derived>(derived(), fmt);
+    }
 
     /** \returns the unique coefficient of a 1x1 expression */
     EIGEN_DEVICE_FUNC
@@ -474,9 +484,9 @@ template<typename Derived> class DenseBase
       return derived().coeff(0,0);
     }
 
-    bool all() const;
-    bool any() const;
-    Index count() const;
+    EIGEN_DEVICE_FUNC bool all() const;
+    EIGEN_DEVICE_FUNC bool any() const;
+    EIGEN_DEVICE_FUNC Index count() const;
 
     typedef VectorwiseOp<Derived, Horizontal> RowwiseReturnType;
     typedef const VectorwiseOp<const Derived, Horizontal> ConstRowwiseReturnType;

Eigen/src/Core/DenseStorage.h

@@ -13,9 +13,9 @@
 #define EIGEN_MATRIXSTORAGE_H
 
 #ifdef EIGEN_DENSE_STORAGE_CTOR_PLUGIN
-  #define EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN EIGEN_DENSE_STORAGE_CTOR_PLUGIN;
+  #define EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(X) X; EIGEN_DENSE_STORAGE_CTOR_PLUGIN;
 #else
-  #define EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+  #define EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(X)
 #endif
 
 namespace Eigen {
@@ -184,12 +184,16 @@ template<typename T, int Size, int _Rows, int _Cols, int _Options> class DenseSt
 {
     internal::plain_array<T,Size,_Options> m_data;
   public:
-    EIGEN_DEVICE_FUNC DenseStorage() {}
+    EIGEN_DEVICE_FUNC DenseStorage() {
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(Index size = Size)
+    }
     EIGEN_DEVICE_FUNC
     explicit DenseStorage(internal::constructor_without_unaligned_array_assert)
       : m_data(internal::constructor_without_unaligned_array_assert()) {}
     EIGEN_DEVICE_FUNC 
-    DenseStorage(const DenseStorage& other) : m_data(other.m_data) {}
+    DenseStorage(const DenseStorage& other) : m_data(other.m_data) {
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(Index size = Size)
+    }
     EIGEN_DEVICE_FUNC 
     DenseStorage& operator=(const DenseStorage& other)
     { 
@@ -197,7 +201,7 @@ template<typename T, int Size, int _Rows, int _Cols, int _Options> class DenseSt
       return *this; 
     }
     EIGEN_DEVICE_FUNC DenseStorage(Index size, Index rows, Index cols) {
-      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       eigen_internal_assert(size==rows*cols && rows==_Rows && cols==_Cols);
       EIGEN_UNUSED_VARIABLE(size);
       EIGEN_UNUSED_VARIABLE(rows);
@@ -343,7 +347,7 @@ template<typename T, int _Options> class DenseStorage<T, Dynamic, Dynamic, Dynam
     EIGEN_DEVICE_FUNC DenseStorage(Index size, Index rows, Index cols)
       : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_rows(rows), m_cols(cols)
     {
-      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       eigen_internal_assert(size==rows*cols && rows>=0 && cols >=0);
     }
     EIGEN_DEVICE_FUNC DenseStorage(const DenseStorage& other)
@@ -351,6 +355,7 @@ template<typename T, int _Options> class DenseStorage<T, Dynamic, Dynamic, Dynam
       , m_rows(other.m_rows)
       , m_cols(other.m_cols)
     {
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(Index size = m_rows*m_cols)
       internal::smart_copy(other.m_data, other.m_data+other.m_rows*other.m_cols, m_data);
     }
     EIGEN_DEVICE_FUNC DenseStorage& operator=(const DenseStorage& other)
@@ -403,7 +408,7 @@ template<typename T, int _Options> class DenseStorage<T, Dynamic, Dynamic, Dynam
           m_data = internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size);
         else
           m_data = 0;
-        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       }
       m_rows = rows;
       m_cols = cols;
@@ -422,7 +427,7 @@ template<typename T, int _Rows, int _Options> class DenseStorage<T, Dynamic, _Ro
     explicit DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_cols(0) {}
     EIGEN_DEVICE_FUNC DenseStorage(Index size, Index rows, Index cols) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_cols(cols)
     {
-      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       eigen_internal_assert(size==rows*cols && rows==_Rows && cols >=0);
       EIGEN_UNUSED_VARIABLE(rows);
     }
@@ -430,6 +435,7 @@ template<typename T, int _Rows, int _Options> class DenseStorage<T, Dynamic, _Ro
       : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(_Rows*other.m_cols))
       , m_cols(other.m_cols)
     {
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(Index size = m_cols*_Rows)
       internal::smart_copy(other.m_data, other.m_data+_Rows*m_cols, m_data);
     }
     EIGEN_DEVICE_FUNC DenseStorage& operator=(const DenseStorage& other)
@@ -477,7 +483,7 @@ template<typename T, int _Rows, int _Options> class DenseStorage<T, Dynamic, _Ro
           m_data = internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size);
         else
           m_data = 0;
-        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       }
       m_cols = cols;
     }
@@ -495,7 +501,7 @@ template<typename T, int _Cols, int _Options> class DenseStorage<T, Dynamic, Dyn
     explicit DenseStorage(internal::constructor_without_unaligned_array_assert) : m_data(0), m_rows(0) {}
     EIGEN_DEVICE_FUNC DenseStorage(Index size, Index rows, Index cols) : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size)), m_rows(rows)
     {
-      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       eigen_internal_assert(size==rows*cols && rows>=0 && cols == _Cols);
       EIGEN_UNUSED_VARIABLE(cols);
     }
@@ -503,6 +509,7 @@ template<typename T, int _Cols, int _Options> class DenseStorage<T, Dynamic, Dyn
       : m_data(internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(other.m_rows*_Cols))
       , m_rows(other.m_rows)
     {
+      EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN(Index size = m_rows*_Cols)
       internal::smart_copy(other.m_data, other.m_data+other.m_rows*_Cols, m_data);
     }
     EIGEN_DEVICE_FUNC DenseStorage& operator=(const DenseStorage& other)
@@ -550,7 +557,7 @@ template<typename T, int _Cols, int _Options> class DenseStorage<T, Dynamic, Dyn
           m_data = internal::conditional_aligned_new_auto<T,(_Options&DontAlign)==0>(size);
         else
           m_data = 0;
-        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN
+        EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
       }
       m_rows = rows;
     }

Eigen/src/Core/Diagonal.h

@@ -21,7 +21,7 @@ namespace Eigen {
   * \param MatrixType the type of the object in which we are taking a sub/main/super diagonal
   * \param DiagIndex the index of the sub/super diagonal. The default is 0 and it means the main diagonal.
   *              A positive value means a superdiagonal, a negative value means a subdiagonal.
-  *              You can also use Dynamic so the index can be set at runtime.
+  *              You can also use DynamicIndex so the index can be set at runtime.
   *
   * The matrix is not required to be square.
   *

Eigen/src/Core/Dot.h

@@ -51,7 +51,8 @@ struct dot_nocheck<T, U, true>
 
 } // end namespace internal
 
-/** \returns the dot product of *this with other.
+/** \fn MatrixBase::dot
+  * \returns the dot product of *this with other.
   *
   * \only_for_vectors
   *

Eigen/src/Core/EigenBase.h

@@ -14,6 +14,7 @@
 namespace Eigen {
 
 /** \class EigenBase
+  * \ingroup Core_Module
   * 
   * Common base class for all classes T such that MatrixBase has an operator=(T) and a constructor MatrixBase(T).
   *
@@ -128,6 +129,7 @@ template<typename Derived> struct EigenBase
   */
 template<typename Derived>
 template<typename OtherDerived>
+EIGEN_DEVICE_FUNC
 Derived& DenseBase<Derived>::operator=(const EigenBase<OtherDerived> &other)
 {
   call_assignment(derived(), other.derived());
@@ -136,6 +138,7 @@ Derived& DenseBase<Derived>::operator=(const EigenBase<OtherDerived> &other)
 
 template<typename Derived>
 template<typename OtherDerived>
+EIGEN_DEVICE_FUNC
 Derived& DenseBase<Derived>::operator+=(const EigenBase<OtherDerived> &other)
 {
   call_assignment(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
@@ -144,6 +147,7 @@ Derived& DenseBase<Derived>::operator+=(const EigenBase<OtherDerived> &other)
 
 template<typename Derived>
 template<typename OtherDerived>
+EIGEN_DEVICE_FUNC
 Derived& DenseBase<Derived>::operator-=(const EigenBase<OtherDerived> &other)
 {
   call_assignment(derived(), other.derived(), internal::sub_assign_op<Scalar,typename OtherDerived::Scalar>());

Eigen/src/Core/GeneralProduct.h

@@ -224,50 +224,65 @@ template<> struct gemv_dense_selector<OnTheRight,ColMajor,true>
       // on, the other hand it is good for the cache to pack the vector anyways...
       EvalToDestAtCompileTime = (ActualDest::InnerStrideAtCompileTime==1),
       ComplexByReal = (NumTraits<LhsScalar>::IsComplex) && (!NumTraits<RhsScalar>::IsComplex),
-      MightCannotUseDest = (ActualDest::InnerStrideAtCompileTime!=1) || ComplexByReal
+      MightCannotUseDest = (!EvalToDestAtCompileTime) || ComplexByReal
     };
 
-    gemv_static_vector_if<ResScalar,ActualDest::SizeAtCompileTime,ActualDest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
-
-    const bool alphaIsCompatible = (!ComplexByReal) || (numext::imag(actualAlpha)==RealScalar(0));
-    const bool evalToDest = EvalToDestAtCompileTime && alphaIsCompatible;
-
-    RhsScalar compatibleAlpha = get_factor<ResScalar,RhsScalar>::run(actualAlpha);
-
-    ei_declare_aligned_stack_constructed_variable(ResScalar,actualDestPtr,dest.size(),
-                                                  evalToDest ? dest.data() : static_dest.data());
-
-    if(!evalToDest)
-    {
-      #ifdef EIGEN_DENSE_STORAGE_CTOR_PLUGIN
-      Index size = dest.size();
-      EIGEN_DENSE_STORAGE_CTOR_PLUGIN
-      #endif
-      if(!alphaIsCompatible)
-      {
-        MappedDest(actualDestPtr, dest.size()).setZero();
-        compatibleAlpha = RhsScalar(1);
-      }
-      else
-        MappedDest(actualDestPtr, dest.size()) = dest;
-    }
-
     typedef const_blas_data_mapper<LhsScalar,Index,ColMajor> LhsMapper;
     typedef const_blas_data_mapper<RhsScalar,Index,RowMajor> RhsMapper;
-    general_matrix_vector_product
-        <Index,LhsScalar,LhsMapper,ColMajor,LhsBlasTraits::NeedToConjugate,RhsScalar,RhsMapper,RhsBlasTraits::NeedToConjugate>::run(
-        actualLhs.rows(), actualLhs.cols(),
-        LhsMapper(actualLhs.data(), actualLhs.outerStride()),
-        RhsMapper(actualRhs.data(), actualRhs.innerStride()),
-        actualDestPtr, 1,
-        compatibleAlpha);
+    RhsScalar compatibleAlpha = get_factor<ResScalar,RhsScalar>::run(actualAlpha);
 
-    if (!evalToDest)
+    if(!MightCannotUseDest)
     {
-      if(!alphaIsCompatible)
-        dest.matrix() += actualAlpha * MappedDest(actualDestPtr, dest.size());
-      else
-        dest = MappedDest(actualDestPtr, dest.size());
+      // shortcut if we are sure to be able to use dest directly,
+      // this ease the compiler to generate cleaner and more optimzized code for most common cases
+      general_matrix_vector_product
+          <Index,LhsScalar,LhsMapper,ColMajor,LhsBlasTraits::NeedToConjugate,RhsScalar,RhsMapper,RhsBlasTraits::NeedToConjugate>::run(
+          actualLhs.rows(), actualLhs.cols(),
+          LhsMapper(actualLhs.data(), actualLhs.outerStride()),
+          RhsMapper(actualRhs.data(), actualRhs.innerStride()),
+          dest.data(), 1,
+          compatibleAlpha);
+    }
+    else
+    {
+      gemv_static_vector_if<ResScalar,ActualDest::SizeAtCompileTime,ActualDest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
+
+      const bool alphaIsCompatible = (!ComplexByReal) || (numext::imag(actualAlpha)==RealScalar(0));
+      const bool evalToDest = EvalToDestAtCompileTime && alphaIsCompatible;
+
+      ei_declare_aligned_stack_constructed_variable(ResScalar,actualDestPtr,dest.size(),
+                                                    evalToDest ? dest.data() : static_dest.data());
+
+      if(!evalToDest)
+      {
+        #ifdef EIGEN_DENSE_STORAGE_CTOR_PLUGIN
+        Index size = dest.size();
+        EIGEN_DENSE_STORAGE_CTOR_PLUGIN
+        #endif
+        if(!alphaIsCompatible)
+        {
+          MappedDest(actualDestPtr, dest.size()).setZero();
+          compatibleAlpha = RhsScalar(1);
+        }
+        else
+          MappedDest(actualDestPtr, dest.size()) = dest;
+      }
+
+      general_matrix_vector_product
+          <Index,LhsScalar,LhsMapper,ColMajor,LhsBlasTraits::NeedToConjugate,RhsScalar,RhsMapper,RhsBlasTraits::NeedToConjugate>::run(
+          actualLhs.rows(), actualLhs.cols(),
+          LhsMapper(actualLhs.data(), actualLhs.outerStride()),
+          RhsMapper(actualRhs.data(), actualRhs.innerStride()),
+          actualDestPtr, 1,
+          compatibleAlpha);
+
+      if (!evalToDest)
+      {
+        if(!alphaIsCompatible)
+          dest.matrix() += actualAlpha * MappedDest(actualDestPtr, dest.size());
+        else
+          dest = MappedDest(actualDestPtr, dest.size());
+      }
     }
   }
 };

Eigen/src/Core/GenericPacketMath.h

@@ -230,7 +230,7 @@ pload1(const typename unpacket_traits<Packet>::type  *a) { return pset1<Packet>(
   * duplicated to form: {from[0],from[0],from[1],from[1],from[2],from[2],from[3],from[3]}
   * Currently, this function is only used for scalar * complex products.
   */
-template<typename Packet> EIGEN_DEVICE_FUNC inline Packet
+template<typename Packet> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet
 ploaddup(const typename unpacket_traits<Packet>::type* from) { return *from; }
 
 /** \internal \returns a packet with elements of \a *from quadrupled.
@@ -278,7 +278,7 @@ inline void pbroadcast2(const typename unpacket_traits<Packet>::type *a,
 }
 
 /** \internal \brief Returns a packet with coefficients (a,a+1,...,a+packet_size-1). */
-template<typename Packet> inline Packet
+template<typename Packet> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet
 plset(const typename unpacket_traits<Packet>::type& a) { return a; }
 
 /** \internal copy the packet \a from to \a *to, \a to must be 16 bytes aligned */
@@ -482,7 +482,7 @@ EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void pstoret(Scalar* to, const Packet& fro
   * by the current computation.
   */
 template<typename Packet, int LoadMode>
-inline Packet ploadt_ro(const typename unpacket_traits<Packet>::type* from)
+EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Packet ploadt_ro(const typename unpacket_traits<Packet>::type* from)
 {
   return ploadt<Packet, LoadMode>(from);
 }

Eigen/src/Core/IO.h

@@ -105,24 +105,10 @@ class WithFormat
     }
 
   protected:
-    const typename ExpressionType::Nested m_matrix;
+    typename ExpressionType::Nested m_matrix;
     IOFormat m_format;
 };
 
-/** \returns a WithFormat proxy object allowing to print a matrix the with given
-  * format \a fmt.
-  *
-  * See class IOFormat for some examples.
-  *
-  * \sa class IOFormat, class WithFormat
-  */
-template<typename Derived>
-inline const WithFormat<Derived>
-DenseBase<Derived>::format(const IOFormat& fmt) const
-{
-  return WithFormat<Derived>(derived(), fmt);
-}
-
 namespace internal {
 
 // NOTE: This helper is kept for backward compatibility with previous code specializing

Eigen/src/Core/Inverse.h

@@ -45,6 +45,7 @@ class Inverse : public InverseImpl<XprType,typename internal::traits<XprType>::S
 public:
   typedef typename XprType::StorageIndex StorageIndex;
   typedef typename XprType::PlainObject                       PlainObject;
+  typedef typename XprType::Scalar                            Scalar;
   typedef typename internal::ref_selector<XprType>::type      XprTypeNested;
   typedef typename internal::remove_all<XprTypeNested>::type  XprTypeNestedCleaned;
   typedef typename internal::ref_selector<Inverse>::type Nested;

Eigen/src/Core/MathFunctions.h

@@ -1061,11 +1061,24 @@ double log(const double &x) { return ::log(x); }
 
 template<typename T>
 EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
-typename NumTraits<T>::Real abs(const T &x) {
+typename internal::enable_if<NumTraits<T>::IsSigned || NumTraits<T>::IsComplex,typename NumTraits<T>::Real>::type
+abs(const T &x) {
   EIGEN_USING_STD_MATH(abs);
   return abs(x);
 }
 
+template<typename T>
+EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
+typename internal::enable_if<!(NumTraits<T>::IsSigned || NumTraits<T>::IsComplex),typename NumTraits<T>::Real>::type
+abs(const T &x) {
+  return x;
+}
+
+#if defined(__SYCL_DEVICE_ONLY__)
+EIGEN_ALWAYS_INLINE float   abs(float x) { return cl::sycl::fabs(x); }
+EIGEN_ALWAYS_INLINE double  abs(double x) { return cl::sycl::fabs(x); }
+#endif // defined(__SYCL_DEVICE_ONLY__)
+
 #ifdef __CUDACC__
 template<> EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
 float abs(const float &x) { return ::fabsf(x); }

Eigen/src/Core/MatrixBase.h

@@ -294,7 +294,7 @@ template<typename Derived> class MatrixBase
       *          fuzzy comparison such as isApprox()
       * \sa isApprox(), operator!= */
     template<typename OtherDerived>
-    inline bool operator==(const MatrixBase<OtherDerived>& other) const
+    EIGEN_DEVICE_FUNC inline bool operator==(const MatrixBase<OtherDerived>& other) const
     { return cwiseEqual(other).all(); }
 
     /** \returns true if at least one pair of coefficients of \c *this and \a other are not exactly equal to each other.
@@ -302,7 +302,7 @@ template<typename Derived> class MatrixBase
       *          fuzzy comparison such as isApprox()
       * \sa isApprox(), operator== */
     template<typename OtherDerived>
-    inline bool operator!=(const MatrixBase<OtherDerived>& other) const
+    EIGEN_DEVICE_FUNC inline bool operator!=(const MatrixBase<OtherDerived>& other) const
     { return cwiseNotEqual(other).any(); }
 
     NoAlias<Derived,Eigen::MatrixBase > noalias();

Eigen/src/Core/NumTraits.h

@@ -215,6 +215,8 @@ struct NumTraits<Array<Scalar, Rows, Cols, Options, MaxRows, MaxCols> >
   static inline RealScalar epsilon() { return NumTraits<RealScalar>::epsilon(); }
   EIGEN_DEVICE_FUNC
   static inline RealScalar dummy_precision() { return NumTraits<RealScalar>::dummy_precision(); }
+
+  static inline int digits10() { return NumTraits<Scalar>::digits10(); }
 };
 
 template<> struct NumTraits<std::string>

Eigen/src/Core/PlainObjectBase.h

@@ -41,7 +41,7 @@ template<> struct check_rows_cols_for_overflow<Dynamic> {
   {
     // http://hg.mozilla.org/mozilla-central/file/6c8a909977d3/xpcom/ds/CheckedInt.h#l242
     // we assume Index is signed
-    Index max_index = (size_t(1) << (8 * sizeof(Index) - 1)) - 1; // assume Index is signed
+    Index max_index = (std::size_t(1) << (8 * sizeof(Index) - 1)) - 1; // assume Index is signed
     bool error = (rows == 0 || cols == 0) ? false
                : (rows > max_index / cols);
     if (error)
@@ -58,6 +58,28 @@ template<typename MatrixTypeA, typename MatrixTypeB, bool SwapPointers> struct m
 
 } // end namespace internal
 
+#ifdef EIGEN_PARSED_BY_DOXYGEN
+namespace doxygen {
+
+// This is a workaround to doxygen not being able to understand the inheritance logic
+// when it is hidden by the dense_xpr_base helper struct.
+// Moreover, doxygen fails to include members that are not documented in the declaration body of
+// MatrixBase if we inherits MatrixBase<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >,
+// this is why we simply inherits MatrixBase, though this does not make sense.
+
+/** This class is just a workaround for Doxygen and it does not not actually exist. */
+template<typename Derived> struct dense_xpr_base_dispatcher;
+/** This class is just a workaround for Doxygen and it does not not actually exist. */
+template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
+struct dense_xpr_base_dispatcher<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
+    : public MatrixBase {};
+/** This class is just a workaround for Doxygen and it does not not actually exist. */
+template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
+struct dense_xpr_base_dispatcher<Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
+    : public ArrayBase {};
+
+} // namespace doxygen
+
 /** \class PlainObjectBase
   * \ingroup Core_Module
   * \brief %Dense storage base class for matrices and arrays.
@@ -65,26 +87,10 @@ template<typename MatrixTypeA, typename MatrixTypeB, bool SwapPointers> struct m
   * This class can be extended with the help of the plugin mechanism described on the page
   * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_PLAINOBJECTBASE_PLUGIN.
   *
+  * \tparam Derived is the derived type, e.g., a Matrix or Array
+  *
   * \sa \ref TopicClassHierarchy
   */
-#ifdef EIGEN_PARSED_BY_DOXYGEN
-namespace doxygen {
-
-// this is a workaround to doxygen not being able to understand the inheritance logic
-// when it is hidden by the dense_xpr_base helper struct.
-/** This class is just a workaround for Doxygen and it does not not actually exist. */
-template<typename Derived> struct dense_xpr_base_dispatcher;
-/** This class is just a workaround for Doxygen and it does not not actually exist. */
-template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
-struct dense_xpr_base_dispatcher<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
-    : public MatrixBase<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> > {};
-/** This class is just a workaround for Doxygen and it does not not actually exist. */
-template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
-struct dense_xpr_base_dispatcher<Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
-    : public ArrayBase<Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> > {};
-
-} // namespace doxygen
-
 template<typename Derived>
 class PlainObjectBase : public doxygen::dense_xpr_base_dispatcher<Derived>
 #else
@@ -554,7 +560,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
 
   public:
 
-    /** \copydoc DenseBase::operator=(const EigenBase<OtherDerived>&)
+    /** \brief Copies the generic expression \a other into *this.
+      * \copydetails DenseBase::operator=(const EigenBase<OtherDerived> &other)
       */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC 
@@ -805,6 +812,13 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
       this->_set_noalias(other);
     }
 
+    // Initialize an arbitrary matrix from an object convertible to the Derived type.
+    template<typename T>
+    EIGEN_DEVICE_FUNC
+    EIGEN_STRONG_INLINE void _init1(const Derived& other){
+      this->_set_noalias(other);
+    }
+
     // Initialize an arbitrary matrix from a generic Eigen expression
     template<typename T, typename OtherDerived>
     EIGEN_DEVICE_FUNC
@@ -827,7 +841,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
       this->derived() = r;
     }
     
-    // For fixed -size arrays:
+    // For fixed-size Array<Scalar,...>
     template<typename T>
     EIGEN_DEVICE_FUNC
     EIGEN_STRONG_INLINE void _init1(const Scalar& val0,
@@ -839,6 +853,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
       Base::setConstant(val0);
     }
     
+    // For fixed-size Array<Index,...>
     template<typename T>
     EIGEN_DEVICE_FUNC
     EIGEN_STRONG_INLINE void _init1(const Index& val0,

Eigen/src/Core/ProductEvaluators.h

@@ -158,10 +158,7 @@ struct Assignment<DstXprType, Product<Lhs,Rhs,Options>, internal::add_assign_op<
   static EIGEN_STRONG_INLINE
   void run(DstXprType &dst, const SrcXprType &src, const internal::add_assign_op<Scalar,Scalar> &)
   {
-    Index dstRows = src.rows();
-    Index dstCols = src.cols();
-    if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
-      dst.resize(dstRows, dstCols);
+    eigen_assert(dst.rows() == src.rows() && dst.cols() == src.cols());
     // FIXME shall we handle nested_eval here?
     generic_product_impl<Lhs, Rhs>::addTo(dst, src.lhs(), src.rhs());
   }
@@ -176,10 +173,7 @@ struct Assignment<DstXprType, Product<Lhs,Rhs,Options>, internal::sub_assign_op<
   static EIGEN_STRONG_INLINE
   void run(DstXprType &dst, const SrcXprType &src, const internal::sub_assign_op<Scalar,Scalar> &)
   {
-    Index dstRows = src.rows();
-    Index dstCols = src.cols();
-    if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
-      dst.resize(dstRows, dstCols);
+    eigen_assert(dst.rows() == src.rows() && dst.cols() == src.cols());
     // FIXME shall we handle nested_eval here?
     generic_product_impl<Lhs, Rhs>::subTo(dst, src.lhs(), src.rhs());
   }
@@ -213,6 +207,12 @@ struct evaluator_assume_aliasing<CwiseBinaryOp<internal::scalar_sum_op<typename
   static const bool value = true;
 };
 
+template<typename OtherXpr, typename Lhs, typename Rhs>
+struct evaluator_assume_aliasing<CwiseBinaryOp<internal::scalar_difference_op<typename OtherXpr::Scalar,typename Product<Lhs,Rhs,DefaultProduct>::Scalar>, const OtherXpr,
+                                               const Product<Lhs,Rhs,DefaultProduct> >, DenseShape > {
+  static const bool value = true;
+};
+
 template<typename DstXprType, typename OtherXpr, typename ProductType, typename Func1, typename Func2>
 struct assignment_from_xpr_op_product
 {
@@ -377,7 +377,6 @@ struct generic_product_impl<Lhs,Rhs,DenseShape,DenseShape,GemvProduct>
   {
     LhsNested actual_lhs(lhs);
     RhsNested actual_rhs(rhs);
-
     internal::gemv_dense_selector<Side,
                             (int(MatrixType::Flags)&RowMajorBit) ? RowMajor : ColMajor,
                             bool(internal::blas_traits<MatrixType>::HasUsableDirectAccess)

Eigen/src/Core/SelfAdjointView.h

@@ -45,7 +45,7 @@ struct traits<SelfAdjointView<MatrixType, UpLo> > : traits<MatrixType>
 };
 }
 
-// FIXME could also be called SelfAdjointWrapper to be consistent with DiagonalWrapper ??
+
 template<typename _MatrixType, unsigned int UpLo> class SelfAdjointView
   : public TriangularBase<SelfAdjointView<_MatrixType, UpLo> >
 {
@@ -60,10 +60,12 @@ template<typename _MatrixType, unsigned int UpLo> class SelfAdjointView
     /** \brief The type of coefficients in this matrix */
     typedef typename internal::traits<SelfAdjointView>::Scalar Scalar; 
     typedef typename MatrixType::StorageIndex StorageIndex;
+    typedef typename internal::remove_all<typename MatrixType::ConjugateReturnType>::type MatrixConjugateReturnType;
 
     enum {
       Mode = internal::traits<SelfAdjointView>::Mode,
-      Flags = internal::traits<SelfAdjointView>::Flags
+      Flags = internal::traits<SelfAdjointView>::Flags,
+      TransposeMode = ((Mode & Upper) ? Lower : 0) | ((Mode & Lower) ? Upper : 0)
     };
     typedef typename MatrixType::PlainObject PlainObject;
 
@@ -187,6 +189,36 @@ template<typename _MatrixType, unsigned int UpLo> class SelfAdjointView
                                    TriangularView<typename MatrixType::AdjointReturnType,TriMode> >::type(tmp2);
     }
 
+    typedef SelfAdjointView<const MatrixConjugateReturnType,Mode> ConjugateReturnType;
+    /** \sa MatrixBase::conjugate() const */
+    EIGEN_DEVICE_FUNC
+    inline const ConjugateReturnType conjugate() const
+    { return ConjugateReturnType(m_matrix.conjugate()); }
+
+    typedef SelfAdjointView<const typename MatrixType::AdjointReturnType,TransposeMode> AdjointReturnType;
+    /** \sa MatrixBase::adjoint() const */
+    EIGEN_DEVICE_FUNC
+    inline const AdjointReturnType adjoint() const
+    { return AdjointReturnType(m_matrix.adjoint()); }
+
+    typedef SelfAdjointView<typename MatrixType::TransposeReturnType,TransposeMode> TransposeReturnType;
+     /** \sa MatrixBase::transpose() */
+    EIGEN_DEVICE_FUNC
+    inline TransposeReturnType transpose()
+    {
+      EIGEN_STATIC_ASSERT_LVALUE(MatrixType)
+      typename MatrixType::TransposeReturnType tmp(m_matrix);
+      return TransposeReturnType(tmp);
+    }
+
+    typedef SelfAdjointView<const typename MatrixType::ConstTransposeReturnType,TransposeMode> ConstTransposeReturnType;
+    /** \sa MatrixBase::transpose() const */
+    EIGEN_DEVICE_FUNC
+    inline const ConstTransposeReturnType transpose() const
+    {
+      return ConstTransposeReturnType(m_matrix.transpose());
+    }
+
     /** \returns a const expression of the main diagonal of the matrix \c *this
       *
       * This method simply returns the diagonal of the nested expression, thus by-passing the SelfAdjointView decorator.
@@ -287,6 +319,7 @@ public:
 * Implementation of MatrixBase methods
 ***************************************************************************/
 
+/** This is the const version of MatrixBase::selfadjointView() */
 template<typename Derived>
 template<unsigned int UpLo>
 typename MatrixBase<Derived>::template ConstSelfAdjointViewReturnType<UpLo>::Type
@@ -295,6 +328,15 @@ MatrixBase<Derived>::selfadjointView() const
   return typename ConstSelfAdjointViewReturnType<UpLo>::Type(derived());
 }
 
+/** \returns an expression of a symmetric/self-adjoint view extracted from the upper or lower triangular part of the current matrix
+  *
+  * The parameter \a UpLo can be either \c #Upper or \c #Lower
+  *
+  * Example: \include MatrixBase_selfadjointView.cpp
+  * Output: \verbinclude MatrixBase_selfadjointView.out
+  *
+  * \sa class SelfAdjointView
+  */
 template<typename Derived>
 template<unsigned int UpLo>
 typename MatrixBase<Derived>::template SelfAdjointViewReturnType<UpLo>::Type

Eigen/src/Core/SelfCwiseBinaryOp.h

@@ -15,7 +15,7 @@ namespace Eigen {
 // TODO generalize the scalar type of 'other'
 
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::operator*=(const Scalar& other)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::operator*=(const Scalar& other)
 {
   typedef typename Derived::PlainObject PlainObject;
   internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op<Scalar,Scalar>());
@@ -23,7 +23,7 @@ EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::operator*=(const Scalar& other)
 }
 
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator+=(const Scalar& other)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator+=(const Scalar& other)
 {
   typedef typename Derived::PlainObject PlainObject;
   internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::add_assign_op<Scalar,Scalar>());
@@ -31,7 +31,7 @@ EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator+=(const Scalar& other)
 }
 
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator-=(const Scalar& other)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator-=(const Scalar& other)
 {
   typedef typename Derived::PlainObject PlainObject;
   internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::sub_assign_op<Scalar,Scalar>());
@@ -39,7 +39,7 @@ EIGEN_STRONG_INLINE Derived& ArrayBase<Derived>::operator-=(const Scalar& other)
 }
 
 template<typename Derived>
-EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::operator/=(const Scalar& other)
+EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& DenseBase<Derived>::operator/=(const Scalar& other)
 {
   typedef typename Derived::PlainObject PlainObject;
   internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::div_assign_op<Scalar,Scalar>());

Eigen/src/Core/Solve.h

@@ -34,12 +34,12 @@ template<typename Decomposition, typename RhsType,typename StorageKind> struct s
 template<typename Decomposition, typename RhsType>
 struct solve_traits<Decomposition,RhsType,Dense>
 {
-  typedef Matrix<typename RhsType::Scalar,
+  typedef typename make_proper_matrix_type<typename RhsType::Scalar,
                  Decomposition::ColsAtCompileTime,
                  RhsType::ColsAtCompileTime,
                  RhsType::PlainObject::Options,
                  Decomposition::MaxColsAtCompileTime,
-                 RhsType::MaxColsAtCompileTime> PlainObject;  
+                 RhsType::MaxColsAtCompileTime>::type PlainObject;
 };
 
 template<typename Decomposition, typename RhsType>

Eigen/src/Core/SolveTriangular.h

@@ -161,6 +161,7 @@ struct triangular_solver_selector<Lhs,Rhs,OnTheRight,Mode,CompleteUnrolling,1> {
 * TriangularView methods
 ***************************************************************************/
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename MatrixType, unsigned int Mode>
 template<int Side, typename OtherDerived>
 void TriangularViewImpl<MatrixType,Mode,Dense>::solveInPlace(const MatrixBase<OtherDerived>& _other) const
@@ -188,6 +189,7 @@ TriangularViewImpl<Derived,Mode,Dense>::solve(const MatrixBase<Other>& other) co
 {
   return internal::triangular_solve_retval<Side,TriangularViewType,Other>(derived(), other.derived());
 }
+#endif
 
 namespace internal {
 

Eigen/src/Core/StableNorm.h

@@ -170,7 +170,8 @@ MatrixBase<Derived>::stableNorm() const
   enum {
     CanAlign = (   (int(DerivedCopyClean::Flags)&DirectAccessBit)
                 || (int(internal::evaluator<DerivedCopyClean>::Alignment)>0) // FIXME Alignment)>0 might not be enough
-               ) && (blockSize*sizeof(Scalar)*2<EIGEN_STACK_ALLOCATION_LIMIT) // ifwe cannot allocate on the stack, then let's not bother about this optimization
+               ) && (blockSize*sizeof(Scalar)*2<EIGEN_STACK_ALLOCATION_LIMIT)
+                 && (EIGEN_MAX_STATIC_ALIGN_BYTES>0) // if we cannot allocate on the stack, then let's not bother about this optimization
   };
   typedef typename internal::conditional<CanAlign, Ref<const Matrix<Scalar,Dynamic,1,0,blockSize,1>, internal::evaluator<DerivedCopyClean>::Alignment>,
                                                    typename DerivedCopyClean::ConstSegmentReturnType>::type SegmentWrapper;

Eigen/src/Core/TriangularMatrix.h

@@ -470,6 +470,8 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
       * \a Side==OnTheLeft (the default), or the right-inverse-multiply  \a other * inverse(\c *this) if
       * \a Side==OnTheRight.
       *
+      * Note that the template parameter \c Side can be ommitted, in which case \c Side==OnTheLeft
+      *
       * The matrix \c *this must be triangular and invertible (i.e., all the coefficients of the
       * diagonal must be non zero). It works as a forward (resp. backward) substitution if \c *this
       * is an upper (resp. lower) triangular matrix.
@@ -495,6 +497,8 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
       * \warning The parameter is only marked 'const' to make the C++ compiler accept a temporary expression here.
       * This function will const_cast it, so constness isn't honored here.
       *
+      * Note that the template parameter \c Side can be ommitted, in which case \c Side==OnTheLeft
+      *
       * See TriangularView:solve() for the details.
       */
     template<int Side, typename OtherDerived>
@@ -539,13 +543,14 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
 
     template<typename ProductType>
     EIGEN_DEVICE_FUNC
-    EIGEN_STRONG_INLINE TriangularViewType& _assignProduct(const ProductType& prod, const Scalar& alpha);
+    EIGEN_STRONG_INLINE TriangularViewType& _assignProduct(const ProductType& prod, const Scalar& alpha, bool beta);
 };
 
 /***************************************************************************
 * Implementation of triangular evaluation/assignment
 ***************************************************************************/
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 // FIXME should we keep that possibility
 template<typename MatrixType, unsigned int Mode>
 template<typename OtherDerived>
@@ -583,6 +588,7 @@ void TriangularViewImpl<MatrixType, Mode, Dense>::lazyAssign(const TriangularBas
   eigen_assert(Mode == int(OtherDerived::Mode));
   internal::call_assignment_no_alias(derived(), other.derived());
 }
+#endif
 
 /***************************************************************************
 * Implementation of TriangularBase methods
@@ -944,8 +950,7 @@ struct Assignment<DstXprType, Product<Lhs,Rhs,DefaultProduct>, internal::assign_
     if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
       dst.resize(dstRows, dstCols);
 
-    dst.setZero();
-    dst._assignProduct(src, 1);
+    dst._assignProduct(src, 1, 0);
   }
 };
 
@@ -956,7 +961,7 @@ struct Assignment<DstXprType, Product<Lhs,Rhs,DefaultProduct>, internal::add_ass
   typedef Product<Lhs,Rhs,DefaultProduct> SrcXprType;
   static void run(DstXprType &dst, const SrcXprType &src, const internal::add_assign_op<Scalar,typename SrcXprType::Scalar> &)
   {
-    dst._assignProduct(src, 1);
+    dst._assignProduct(src, 1, 1);
   }
 };
 
@@ -967,7 +972,7 @@ struct Assignment<DstXprType, Product<Lhs,Rhs,DefaultProduct>, internal::sub_ass
   typedef Product<Lhs,Rhs,DefaultProduct> SrcXprType;
   static void run(DstXprType &dst, const SrcXprType &src, const internal::sub_assign_op<Scalar,typename SrcXprType::Scalar> &)
   {
-    dst._assignProduct(src, -1);
+    dst._assignProduct(src, -1, 1);
   }
 };
 

Eigen/src/Core/Visitor.h

@@ -194,7 +194,8 @@ struct functor_traits<max_coeff_visitor<Scalar> > {
 
 } // end namespace internal
 
-/** \returns the minimum of all coefficients of *this and puts in *row and *col its location.
+/** \fn DenseBase<Derived>::minCoeff(IndexType* rowId, IndexType* colId) const
+  * \returns the minimum of all coefficients of *this and puts in *row and *col its location.
   * \warning the result is undefined if \c *this contains NaN.
   *
   * \sa DenseBase::minCoeff(Index*), DenseBase::maxCoeff(Index*,Index*), DenseBase::visit(), DenseBase::minCoeff()
@@ -230,7 +231,8 @@ DenseBase<Derived>::minCoeff(IndexType* index) const
   return minVisitor.res;
 }
 
-/** \returns the maximum of all coefficients of *this and puts in *row and *col its location.
+/** \fn DenseBase<Derived>::maxCoeff(IndexType* rowId, IndexType* colId) const
+  * \returns the maximum of all coefficients of *this and puts in *row and *col its location.
   * \warning the result is undefined if \c *this contains NaN. 
   *
   * \sa DenseBase::minCoeff(IndexType*,IndexType*), DenseBase::visit(), DenseBase::maxCoeff()

Eigen/src/Core/arch/AVX/PacketMath.h

@@ -395,14 +395,11 @@ template<> EIGEN_STRONG_INLINE Packet4d preduxp<Packet4d>(const Packet4d* vecs)
 
 template<> EIGEN_STRONG_INLINE float predux<Packet8f>(const Packet8f& a)
 {
-  Packet8f tmp0 = _mm256_hadd_ps(a,_mm256_permute2f128_ps(a,a,1));
-  tmp0 = _mm256_hadd_ps(tmp0,tmp0);
-  return pfirst(_mm256_hadd_ps(tmp0, tmp0));
+  return predux(Packet4f(_mm_add_ps(_mm256_castps256_ps128(a),_mm256_extractf128_ps(a,1))));
 }
 template<> EIGEN_STRONG_INLINE double predux<Packet4d>(const Packet4d& a)
 {
-  Packet4d tmp0 = _mm256_hadd_pd(a,_mm256_permute2f128_pd(a,a,1));
-  return pfirst(_mm256_hadd_pd(tmp0,tmp0));
+  return predux(Packet2d(_mm_add_pd(_mm256_castpd256_pd128(a),_mm256_extractf128_pd(a,1))));
 }
 
 template<> EIGEN_STRONG_INLINE Packet4f predux_downto4<Packet8f>(const Packet8f& a)

Eigen/src/Core/arch/AltiVec/Complex.h

@@ -15,14 +15,14 @@ namespace Eigen {
 
 namespace internal {
 
-static Packet4ui  p4ui_CONJ_XOR = vec_mergeh((Packet4ui)p4i_ZERO, (Packet4ui)p4f_ZERO_);//{ 0x00000000, 0x80000000, 0x00000000, 0x80000000 };
+static Packet4ui  p4ui_CONJ_XOR = vec_mergeh((Packet4ui)p4i_ZERO, (Packet4ui)p4f_MZERO);//{ 0x00000000, 0x80000000, 0x00000000, 0x80000000 };
 #ifdef __VSX__
 #if defined(_BIG_ENDIAN)
-static Packet2ul  p2ul_CONJ_XOR1 = (Packet2ul) vec_sld((Packet4ui) p2d_ZERO_, (Packet4ui) p2l_ZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
-static Packet2ul  p2ul_CONJ_XOR2 = (Packet2ul) vec_sld((Packet4ui) p2l_ZERO,  (Packet4ui) p2d_ZERO_, 8);//{ 0x8000000000000000, 0x0000000000000000 };
+static Packet2ul  p2ul_CONJ_XOR1 = (Packet2ul) vec_sld((Packet4ui) p2d_MZERO, (Packet4ui) p2l_ZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
+static Packet2ul  p2ul_CONJ_XOR2 = (Packet2ul) vec_sld((Packet4ui) p2l_ZERO,  (Packet4ui) p2d_MZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
 #else
-static Packet2ul  p2ul_CONJ_XOR1 = (Packet2ul) vec_sld((Packet4ui) p2l_ZERO,  (Packet4ui) p2d_ZERO_, 8);//{ 0x8000000000000000, 0x0000000000000000 };
-static Packet2ul  p2ul_CONJ_XOR2 = (Packet2ul) vec_sld((Packet4ui) p2d_ZERO_, (Packet4ui) p2l_ZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
+static Packet2ul  p2ul_CONJ_XOR1 = (Packet2ul) vec_sld((Packet4ui) p2l_ZERO,  (Packet4ui) p2d_MZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
+static Packet2ul  p2ul_CONJ_XOR2 = (Packet2ul) vec_sld((Packet4ui) p2d_MZERO, (Packet4ui) p2l_ZERO, 8);//{ 0x8000000000000000, 0x0000000000000000 };
 #endif
 #endif
 
@@ -65,7 +65,7 @@ template<> struct unpacket_traits<Packet2cf> { typedef std::complex<float> type;
 template<> EIGEN_STRONG_INLINE Packet2cf pset1<Packet2cf>(const std::complex<float>&  from)
 {
   Packet2cf res;
-  if((ptrdiff_t(&from) % 16) == 0)
+  if((std::ptrdiff_t(&from) % 16) == 0)
     res.v = pload<Packet4f>((const float *)&from);
   else
     res.v = ploadu<Packet4f>((const float *)&from);

Eigen/src/Core/arch/AltiVec/MathFunctions.h

@@ -84,8 +84,10 @@ static _EIGEN_DECLARE_CONST_Packet2d(cephes_exp_q3, 2.00000000000000000009e0);
 static _EIGEN_DECLARE_CONST_Packet2d(cephes_exp_C1, 0.693145751953125);
 static _EIGEN_DECLARE_CONST_Packet2d(cephes_exp_C2, 1.42860682030941723212e-6);
 
+#ifdef __POWER8_VECTOR__
 static Packet2l p2l_1023 = { 1023, 1023 };
 static Packet2ul p2ul_52 = { 52, 52 };
+#endif
 
 #endif
 

Eigen/src/Core/arch/AltiVec/PacketMath.h

@@ -72,7 +72,7 @@ static _EIGEN_DECLARE_CONST_FAST_Packet4i(ZERO, 0); //{ 0, 0, 0, 0,}
 static _EIGEN_DECLARE_CONST_FAST_Packet4i(ONE,1); //{ 1, 1, 1, 1}
 static _EIGEN_DECLARE_CONST_FAST_Packet4i(MINUS16,-16); //{ -16, -16, -16, -16}
 static _EIGEN_DECLARE_CONST_FAST_Packet4i(MINUS1,-1); //{ -1, -1, -1, -1}
-static Packet4f p4f_ZERO_ = (Packet4f) vec_sl((Packet4ui)p4i_MINUS1, (Packet4ui)p4i_MINUS1); //{ 0x80000000, 0x80000000, 0x80000000, 0x80000000}
+static Packet4f p4f_MZERO = (Packet4f) vec_sl((Packet4ui)p4i_MINUS1, (Packet4ui)p4i_MINUS1); //{ 0x80000000, 0x80000000, 0x80000000, 0x80000000}
 #ifndef __VSX__
 static Packet4f p4f_ONE = vec_ctf(p4i_ONE, 0); //{ 1.0, 1.0, 1.0, 1.0}
 #endif
@@ -90,7 +90,7 @@ static Packet16uc p16uc_DUPLICATE32_HI = { 0,1,2,3, 0,1,2,3, 4,5,6,7, 4,5,6,7 };
 #define _EIGEN_MASK_ALIGNMENT	0xfffffff0
 #endif
 
-#define _EIGEN_ALIGNED_PTR(x)	((ptrdiff_t)(x) & _EIGEN_MASK_ALIGNMENT)
+#define _EIGEN_ALIGNED_PTR(x)	((std::ptrdiff_t)(x) & _EIGEN_MASK_ALIGNMENT)
 
 // Handle endianness properly while loading constants
 // Define global static constants:
@@ -358,7 +358,7 @@ template<> EIGEN_STRONG_INLINE Packet4i pnegate(const Packet4i& a) { return p4i_
 template<> EIGEN_STRONG_INLINE Packet4f pconj(const Packet4f& a) { return a; }
 template<> EIGEN_STRONG_INLINE Packet4i pconj(const Packet4i& a) { return a; }
 
-template<> EIGEN_STRONG_INLINE Packet4f pmul<Packet4f>(const Packet4f& a, const Packet4f& b) { return vec_madd(a,b, p4f_ZERO); }
+template<> EIGEN_STRONG_INLINE Packet4f pmul<Packet4f>(const Packet4f& a, const Packet4f& b) { return vec_madd(a,b, p4f_MZERO); }
 template<> EIGEN_STRONG_INLINE Packet4i pmul<Packet4i>(const Packet4i& a, const Packet4i& b) { return a * b; }
 
 template<> EIGEN_STRONG_INLINE Packet4f pdiv<Packet4f>(const Packet4f& a, const Packet4f& b)
@@ -373,7 +373,7 @@ template<> EIGEN_STRONG_INLINE Packet4f pdiv<Packet4f>(const Packet4f& a, const
   t   = vec_nmsub(y_0, b, p4f_ONE);
   y_1 = vec_madd(y_0, t, y_0);
 
-  return vec_madd(a, y_1, p4f_ZERO);
+  return vec_madd(a, y_1, p4f_MZERO);
 #else
   return vec_div(a, b);
 #endif
@@ -450,15 +450,15 @@ template<> EIGEN_STRONG_INLINE Packet4f ploadu<Packet4f>(const float* from)
 template<> EIGEN_STRONG_INLINE Packet4f ploaddup<Packet4f>(const float*   from)
 {
   Packet4f p;
-  if((ptrdiff_t(from) % 16) == 0)  p = pload<Packet4f>(from);
-  else                             p = ploadu<Packet4f>(from);
+  if((std::ptrdiff_t(from) % 16) == 0)  p = pload<Packet4f>(from);
+  else                                  p = ploadu<Packet4f>(from);
   return vec_perm(p, p, p16uc_DUPLICATE32_HI);
 }
 template<> EIGEN_STRONG_INLINE Packet4i ploaddup<Packet4i>(const int*     from)
 {
   Packet4i p;
-  if((ptrdiff_t(from) % 16) == 0)  p = pload<Packet4i>(from);
-  else                             p = ploadu<Packet4i>(from);
+  if((std::ptrdiff_t(from) % 16) == 0)  p = pload<Packet4i>(from);
+  else                                  p = ploadu<Packet4i>(from);
   return vec_perm(p, p, p16uc_DUPLICATE32_HI);
 }
 
@@ -766,7 +766,7 @@ static Packet2l  p2l_ONE  = { 1, 1 };
 static Packet2l  p2l_ZERO = reinterpret_cast<Packet2l>(p4i_ZERO);
 static Packet2d  p2d_ONE  = { 1.0, 1.0 }; 
 static Packet2d  p2d_ZERO = reinterpret_cast<Packet2d>(p4f_ZERO);
-static Packet2d  p2d_ZERO_ = { -0.0, -0.0 };
+static Packet2d  p2d_MZERO = { -0.0, -0.0 };
 
 #ifdef _BIG_ENDIAN
 static Packet2d p2d_COUNTDOWN = reinterpret_cast<Packet2d>(vec_sld(reinterpret_cast<Packet4f>(p2d_ZERO), reinterpret_cast<Packet4f>(p2d_ONE), 8));
@@ -904,7 +904,7 @@ template<> EIGEN_STRONG_INLINE Packet2d pnegate(const Packet2d& a) { return p2d_
 
 template<> EIGEN_STRONG_INLINE Packet2d pconj(const Packet2d& a) { return a; }
 
-template<> EIGEN_STRONG_INLINE Packet2d pmul<Packet2d>(const Packet2d& a, const Packet2d& b) { return vec_madd(a,b,p2d_ZERO); }
+template<> EIGEN_STRONG_INLINE Packet2d pmul<Packet2d>(const Packet2d& a, const Packet2d& b) { return vec_madd(a,b,p2d_MZERO); }
 template<> EIGEN_STRONG_INLINE Packet2d pdiv<Packet2d>(const Packet2d& a, const Packet2d& b) { return vec_div(a,b); }
 
 // for some weird raisons, it has to be overloaded for packet of integers
@@ -935,8 +935,8 @@ template<> EIGEN_STRONG_INLINE Packet2d ploadu<Packet2d>(const double* from)
 template<> EIGEN_STRONG_INLINE Packet2d ploaddup<Packet2d>(const double*   from)
 {
   Packet2d p;
-  if((ptrdiff_t(from) % 16) == 0)  p = pload<Packet2d>(from);
-  else                             p = ploadu<Packet2d>(from);
+  if((std::ptrdiff_t(from) % 16) == 0)  p = pload<Packet2d>(from);
+  else                                  p = ploadu<Packet2d>(from);
   return vec_splat_dbl<0>(p);
 }
 

Eigen/src/Core/arch/CUDA/Half.h

@@ -13,7 +13,7 @@
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted.
 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-// “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 // HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
@@ -474,9 +474,59 @@ template<> struct is_arithmetic<half> { enum { value = true }; };
 
 } // end namespace internal
 
+}  // end namespace Eigen
+
+namespace std {
+template<>
+struct numeric_limits<Eigen::half> {
+  static const bool is_specialized = true;
+  static const bool is_signed = true;
+  static const bool is_integer = false;
+  static const bool is_exact = false;
+  static const bool has_infinity = true;
+  static const bool has_quiet_NaN = true;
+  static const bool has_signaling_NaN = true;
+  static const float_denorm_style has_denorm = denorm_present;
+  static const bool has_denorm_loss = false;
+  static const std::float_round_style round_style = std::round_to_nearest;
+  static const bool is_iec559 = false;
+  static const bool is_bounded = false;
+  static const bool is_modulo = false;
+  static const int digits = 11;
+  static const int digits10 = 2;
+  //static const int max_digits10 = ;
+  static const int radix = 2;
+  static const int min_exponent = -13;
+  static const int min_exponent10 = -4;
+  static const int max_exponent = 16;
+  static const int max_exponent10 = 4;
+  static const bool traps = true;
+  static const bool tinyness_before = false;
+
+  static Eigen::half (min)() { return Eigen::half_impl::raw_uint16_to_half(0x400); }
+  static Eigen::half lowest() { return Eigen::half_impl::raw_uint16_to_half(0xfbff); }
+  static Eigen::half (max)() { return Eigen::half_impl::raw_uint16_to_half(0x7bff); }
+  static Eigen::half epsilon() { return Eigen::half_impl::raw_uint16_to_half(0x0800); }
+  static Eigen::half round_error() { return Eigen::half(0.5); }
+  static Eigen::half infinity() { return Eigen::half_impl::raw_uint16_to_half(0x7c00); }
+  static Eigen::half quiet_NaN() { return Eigen::half_impl::raw_uint16_to_half(0x7e00); }
+  static Eigen::half signaling_NaN() { return Eigen::half_impl::raw_uint16_to_half(0x7e00); }
+  static Eigen::half denorm_min() { return Eigen::half_impl::raw_uint16_to_half(0x1); }
+};
+}
+
+namespace Eigen {
+
 template<> struct NumTraits<Eigen::half>
     : GenericNumTraits<Eigen::half>
 {
+  enum {
+    IsSigned = true,
+    IsInteger = false,
+    IsComplex = false,
+    RequireInitialization = false
+  };
+
   EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE Eigen::half epsilon() {
     return half_impl::raw_uint16_to_half(0x0800);
   }

Eigen/src/Core/arch/CUDA/PacketMath.h

@@ -291,7 +291,7 @@ template<> EIGEN_DEVICE_FUNC inline double2 pabs<double2>(const double2& a) {
 
 EIGEN_DEVICE_FUNC inline void
 ptranspose(PacketBlock<float4,4>& kernel) {
-  double tmp = kernel.packet[0].y;
+  float tmp = kernel.packet[0].y;
   kernel.packet[0].y = kernel.packet[1].x;
   kernel.packet[1].x = tmp;
 

Eigen/src/Core/arch/NEON/PacketMath.h

@@ -28,11 +28,13 @@ namespace internal {
 #define EIGEN_HAS_SINGLE_INSTRUCTION_CJMADD
 #endif
 
-// FIXME NEON has 16 quad registers, but since the current register allocator
-// is so bad, it is much better to reduce it to 8
 #ifndef EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS
+#if EIGEN_ARCH_ARM64
+#define EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS 32
+#else
 #define EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS 16 
 #endif
+#endif
 
 typedef float32x2_t Packet2f;
 typedef float32x4_t Packet4f;
@@ -44,19 +46,22 @@ typedef uint32x4_t  Packet4ui;
   const Packet4f p4f_##NAME = pset1<Packet4f>(X)
 
 #define _EIGEN_DECLARE_CONST_Packet4f_FROM_INT(NAME,X) \
-  const Packet4f p4f_##NAME = vreinterpretq_f32_u32(pset1<int>(X))
+  const Packet4f p4f_##NAME = vreinterpretq_f32_u32(pset1<int32_t>(X))
 
 #define _EIGEN_DECLARE_CONST_Packet4i(NAME,X) \
   const Packet4i p4i_##NAME = pset1<Packet4i>(X)
 
-// arm64 does have the pld instruction. If available, let's trust the __builtin_prefetch built-in function
-// which available on LLVM and GCC (at least)
-#if EIGEN_HAS_BUILTIN(__builtin_prefetch) || EIGEN_COMP_GNUC
+#if EIGEN_ARCH_ARM64
+  // __builtin_prefetch tends to do nothing on ARM64 compilers because the
+  // prefetch instructions there are too detailed for __builtin_prefetch to map
+  // meaningfully to them.
+  #define EIGEN_ARM_PREFETCH(ADDR)  __asm__ __volatile__("prfm pldl1keep, [%[addr]]\n" ::[addr] "r"(ADDR) : );
+#elif EIGEN_HAS_BUILTIN(__builtin_prefetch) || EIGEN_COMP_GNUC
   #define EIGEN_ARM_PREFETCH(ADDR) __builtin_prefetch(ADDR);
 #elif defined __pld
   #define EIGEN_ARM_PREFETCH(ADDR) __pld(ADDR)
-#elif !EIGEN_ARCH_ARM64
-  #define EIGEN_ARM_PREFETCH(ADDR) __asm__ __volatile__ ( "   pld [%[addr]]\n" :: [addr] "r" (ADDR) : "cc" );
+#elif EIGEN_ARCH_ARM32
+  #define EIGEN_ARM_PREFETCH(ADDR) __asm__ __volatile__ ("pld [%[addr]]\n" :: [addr] "r" (ADDR) : );
 #else
   // by default no explicit prefetching
   #define EIGEN_ARM_PREFETCH(ADDR)
@@ -81,7 +86,7 @@ template<> struct packet_traits<float>  : default_packet_traits
     HasSqrt = 0
   };
 };
-template<> struct packet_traits<int>    : default_packet_traits
+template<> struct packet_traits<int32_t>    : default_packet_traits
 {
   typedef Packet4i type;
   typedef Packet4i half; // Packet2i intrinsics not implemented yet
@@ -103,19 +108,19 @@ EIGEN_STRONG_INLINE void        vst1q_f32(float* to, float32x4_t from) { ::vst1q
 EIGEN_STRONG_INLINE void        vst1_f32 (float* to, float32x2_t from) { ::vst1_f32 ((float32_t*)to,from); }
 #endif
 
-template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
-template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
+template<> struct unpacket_traits<Packet4f> { typedef float   type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
+template<> struct unpacket_traits<Packet4i> { typedef int32_t type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
 
 template<> EIGEN_STRONG_INLINE Packet4f pset1<Packet4f>(const float&  from) { return vdupq_n_f32(from); }
-template<> EIGEN_STRONG_INLINE Packet4i pset1<Packet4i>(const int&    from)   { return vdupq_n_s32(from); }
+template<> EIGEN_STRONG_INLINE Packet4i pset1<Packet4i>(const int32_t&    from)   { return vdupq_n_s32(from); }
 
 template<> EIGEN_STRONG_INLINE Packet4f plset<Packet4f>(const float& a)
 {
-  const float32_t f[] = {0, 1, 2, 3};
+  const float f[] = {0, 1, 2, 3};
   Packet4f countdown = vld1q_f32(f);
   return vaddq_f32(pset1<Packet4f>(a), countdown);
 }
-template<> EIGEN_STRONG_INLINE Packet4i plset<Packet4i>(const int& a)
+template<> EIGEN_STRONG_INLINE Packet4i plset<Packet4i>(const int32_t& a)
 {
   const int32_t i[] = {0, 1, 2, 3};
   Packet4i countdown = vld1q_s32(i);
@@ -238,20 +243,20 @@ template<> EIGEN_STRONG_INLINE Packet4f pandnot<Packet4f>(const Packet4f& a, con
 }
 template<> EIGEN_STRONG_INLINE Packet4i pandnot<Packet4i>(const Packet4i& a, const Packet4i& b) { return vbicq_s32(a,b); }
 
-template<> EIGEN_STRONG_INLINE Packet4f pload<Packet4f>(const float* from) { EIGEN_DEBUG_ALIGNED_LOAD return vld1q_f32(from); }
-template<> EIGEN_STRONG_INLINE Packet4i pload<Packet4i>(const int*   from) { EIGEN_DEBUG_ALIGNED_LOAD return vld1q_s32(from); }
+template<> EIGEN_STRONG_INLINE Packet4f pload<Packet4f>(const float*    from) { EIGEN_DEBUG_ALIGNED_LOAD return vld1q_f32(from); }
+template<> EIGEN_STRONG_INLINE Packet4i pload<Packet4i>(const int32_t*  from) { EIGEN_DEBUG_ALIGNED_LOAD return vld1q_s32(from); }
 
-template<> EIGEN_STRONG_INLINE Packet4f ploadu<Packet4f>(const float* from) { EIGEN_DEBUG_UNALIGNED_LOAD return vld1q_f32(from); }
-template<> EIGEN_STRONG_INLINE Packet4i ploadu<Packet4i>(const int* from)   { EIGEN_DEBUG_UNALIGNED_LOAD return vld1q_s32(from); }
+template<> EIGEN_STRONG_INLINE Packet4f ploadu<Packet4f>(const float*   from) { EIGEN_DEBUG_UNALIGNED_LOAD return vld1q_f32(from); }
+template<> EIGEN_STRONG_INLINE Packet4i ploadu<Packet4i>(const int32_t* from) { EIGEN_DEBUG_UNALIGNED_LOAD return vld1q_s32(from); }
 
-template<> EIGEN_STRONG_INLINE Packet4f ploaddup<Packet4f>(const float*   from)
+template<> EIGEN_STRONG_INLINE Packet4f ploaddup<Packet4f>(const float* from)
 {
   float32x2_t lo, hi;
   lo = vld1_dup_f32(from);
   hi = vld1_dup_f32(from+1);
   return vcombine_f32(lo, hi);
 }
-template<> EIGEN_STRONG_INLINE Packet4i ploaddup<Packet4i>(const int*     from)
+template<> EIGEN_STRONG_INLINE Packet4i ploaddup<Packet4i>(const int32_t* from)
 {
   int32x2_t lo, hi;
   lo = vld1_dup_s32(from);
@@ -259,11 +264,11 @@ template<> EIGEN_STRONG_INLINE Packet4i ploaddup<Packet4i>(const int*     from)
   return vcombine_s32(lo, hi);
 }
 
-template<> EIGEN_STRONG_INLINE void pstore<float>(float*   to, const Packet4f& from) { EIGEN_DEBUG_ALIGNED_STORE vst1q_f32(to, from); }
-template<> EIGEN_STRONG_INLINE void pstore<int>(int*       to, const Packet4i& from) { EIGEN_DEBUG_ALIGNED_STORE vst1q_s32(to, from); }
+template<> EIGEN_STRONG_INLINE void pstore<float>  (float*    to, const Packet4f& from) { EIGEN_DEBUG_ALIGNED_STORE vst1q_f32(to, from); }
+template<> EIGEN_STRONG_INLINE void pstore<int32_t>(int32_t*  to, const Packet4i& from) { EIGEN_DEBUG_ALIGNED_STORE vst1q_s32(to, from); }
 
-template<> EIGEN_STRONG_INLINE void pstoreu<float>(float*  to, const Packet4f& from) { EIGEN_DEBUG_UNALIGNED_STORE vst1q_f32(to, from); }
-template<> EIGEN_STRONG_INLINE void pstoreu<int>(int*      to, const Packet4i& from) { EIGEN_DEBUG_UNALIGNED_STORE vst1q_s32(to, from); }
+template<> EIGEN_STRONG_INLINE void pstoreu<float>  (float*   to, const Packet4f& from) { EIGEN_DEBUG_UNALIGNED_STORE vst1q_f32(to, from); }
+template<> EIGEN_STRONG_INLINE void pstoreu<int32_t>(int32_t* to, const Packet4i& from) { EIGEN_DEBUG_UNALIGNED_STORE vst1q_s32(to, from); }
 
 template<> EIGEN_DEVICE_FUNC inline Packet4f pgather<float, Packet4f>(const float* from, Index stride)
 {
@@ -274,7 +279,7 @@ template<> EIGEN_DEVICE_FUNC inline Packet4f pgather<float, Packet4f>(const floa
   res = vsetq_lane_f32(from[3*stride], res, 3);
   return res;
 }
-template<> EIGEN_DEVICE_FUNC inline Packet4i pgather<int, Packet4i>(const int* from, Index stride)
+template<> EIGEN_DEVICE_FUNC inline Packet4i pgather<int32_t, Packet4i>(const int32_t* from, Index stride)
 {
   Packet4i res = pset1<Packet4i>(0);
   res = vsetq_lane_s32(from[0*stride], res, 0);
@@ -291,7 +296,7 @@ template<> EIGEN_DEVICE_FUNC inline void pscatter<float, Packet4f>(float* to, co
   to[stride*2] = vgetq_lane_f32(from, 2);
   to[stride*3] = vgetq_lane_f32(from, 3);
 }
-template<> EIGEN_DEVICE_FUNC inline void pscatter<int, Packet4i>(int* to, const Packet4i& from, Index stride)
+template<> EIGEN_DEVICE_FUNC inline void pscatter<int32_t, Packet4i>(int32_t* to, const Packet4i& from, Index stride)
 {
   to[stride*0] = vgetq_lane_s32(from, 0);
   to[stride*1] = vgetq_lane_s32(from, 1);
@@ -299,12 +304,12 @@ template<> EIGEN_DEVICE_FUNC inline void pscatter<int, Packet4i>(int* to, const
   to[stride*3] = vgetq_lane_s32(from, 3);
 }
 
-template<> EIGEN_STRONG_INLINE void prefetch<float>(const float* addr) { EIGEN_ARM_PREFETCH(addr); }
-template<> EIGEN_STRONG_INLINE void prefetch<int>(const int*     addr) { EIGEN_ARM_PREFETCH(addr); }
+template<> EIGEN_STRONG_INLINE void prefetch<float>  (const float*    addr) { EIGEN_ARM_PREFETCH(addr); }
+template<> EIGEN_STRONG_INLINE void prefetch<int32_t>(const int32_t*  addr) { EIGEN_ARM_PREFETCH(addr); }
 
 // FIXME only store the 2 first elements ?
-template<> EIGEN_STRONG_INLINE float  pfirst<Packet4f>(const Packet4f& a) { float EIGEN_ALIGN16 x[4]; vst1q_f32(x, a); return x[0]; }
-template<> EIGEN_STRONG_INLINE int    pfirst<Packet4i>(const Packet4i& a) { int   EIGEN_ALIGN16 x[4]; vst1q_s32(x, a); return x[0]; }
+template<> EIGEN_STRONG_INLINE float   pfirst<Packet4f>(const Packet4f& a) { float   EIGEN_ALIGN16 x[4]; vst1q_f32(x, a); return x[0]; }
+template<> EIGEN_STRONG_INLINE int32_t pfirst<Packet4i>(const Packet4i& a) { int32_t EIGEN_ALIGN16 x[4]; vst1q_s32(x, a); return x[0]; }
 
 template<> EIGEN_STRONG_INLINE Packet4f preverse(const Packet4f& a) {
   float32x2_t a_lo, a_hi;
@@ -359,7 +364,7 @@ template<> EIGEN_STRONG_INLINE Packet4f preduxp<Packet4f>(const Packet4f* vecs)
   return sum;
 }
 
-template<> EIGEN_STRONG_INLINE int predux<Packet4i>(const Packet4i& a)
+template<> EIGEN_STRONG_INLINE int32_t predux<Packet4i>(const Packet4i& a)
 {
   int32x2_t a_lo, a_hi, sum;
 
@@ -406,7 +411,7 @@ template<> EIGEN_STRONG_INLINE float predux_mul<Packet4f>(const Packet4f& a)
 
   return vget_lane_f32(prod, 0);
 }
-template<> EIGEN_STRONG_INLINE int predux_mul<Packet4i>(const Packet4i& a)
+template<> EIGEN_STRONG_INLINE int32_t predux_mul<Packet4i>(const Packet4i& a)
 {
   int32x2_t a_lo, a_hi, prod;
 
@@ -434,7 +439,7 @@ template<> EIGEN_STRONG_INLINE float predux_min<Packet4f>(const Packet4f& a)
   return vget_lane_f32(min, 0);
 }
 
-template<> EIGEN_STRONG_INLINE int predux_min<Packet4i>(const Packet4i& a)
+template<> EIGEN_STRONG_INLINE int32_t predux_min<Packet4i>(const Packet4i& a)
 {
   int32x2_t a_lo, a_hi, min;
 
@@ -459,7 +464,7 @@ template<> EIGEN_STRONG_INLINE float predux_max<Packet4f>(const Packet4f& a)
   return vget_lane_f32(max, 0);
 }
 
-template<> EIGEN_STRONG_INLINE int predux_max<Packet4i>(const Packet4i& a)
+template<> EIGEN_STRONG_INLINE int32_t predux_max<Packet4i>(const Packet4i& a)
 {
   int32x2_t a_lo, a_hi, max;
 

Eigen/src/Core/arch/SSE/PacketMath.h

@@ -28,7 +28,7 @@ namespace internal {
 #endif
 #endif
 
-#if (defined EIGEN_VECTORIZE_AVX) && EIGEN_COMP_GNUC_STRICT && (__GXX_ABI_VERSION < 1004)
+#if (defined EIGEN_VECTORIZE_AVX) && (EIGEN_COMP_GNUC_STRICT || EIGEN_COMP_MINGW) && (__GXX_ABI_VERSION < 1004)
 // With GCC's default ABI version, a __m128 or __m256 are the same types and therefore we cannot
 // have overloads for both types without linking error.
 // One solution is to increase ABI version using -fabi-version=4 (or greater).
@@ -504,30 +504,13 @@ template<> EIGEN_STRONG_INLINE Packet4f preduxp<Packet4f>(const Packet4f* vecs)
 {
   return _mm_hadd_ps(_mm_hadd_ps(vecs[0], vecs[1]),_mm_hadd_ps(vecs[2], vecs[3]));
 }
+
 template<> EIGEN_STRONG_INLINE Packet2d preduxp<Packet2d>(const Packet2d* vecs)
 {
   return _mm_hadd_pd(vecs[0], vecs[1]);
 }
 
-template<> EIGEN_STRONG_INLINE float predux<Packet4f>(const Packet4f& a)
-{
-  Packet4f tmp0 = _mm_hadd_ps(a,a);
-  return pfirst<Packet4f>(_mm_hadd_ps(tmp0, tmp0));
-}
-
-template<> EIGEN_STRONG_INLINE double predux<Packet2d>(const Packet2d& a) { return pfirst<Packet2d>(_mm_hadd_pd(a, a)); }
 #else
-// SSE2 versions
-template<> EIGEN_STRONG_INLINE float predux<Packet4f>(const Packet4f& a)
-{
-  Packet4f tmp = _mm_add_ps(a, _mm_movehl_ps(a,a));
-  return pfirst<Packet4f>(_mm_add_ss(tmp, _mm_shuffle_ps(tmp,tmp, 1)));
-}
-template<> EIGEN_STRONG_INLINE double predux<Packet2d>(const Packet2d& a)
-{
-  return pfirst<Packet2d>(_mm_add_sd(a, _mm_unpackhi_pd(a,a)));
-}
-
 template<> EIGEN_STRONG_INLINE Packet4f preduxp<Packet4f>(const Packet4f* vecs)
 {
   Packet4f tmp0, tmp1, tmp2;
@@ -548,6 +531,29 @@ template<> EIGEN_STRONG_INLINE Packet2d preduxp<Packet2d>(const Packet2d* vecs)
 }
 #endif  // SSE3
 
+template<> EIGEN_STRONG_INLINE float predux<Packet4f>(const Packet4f& a)
+{
+  // Disable SSE3 _mm_hadd_pd that is extremely slow on all existing Intel's architectures
+  // (from Nehalem to Haswell)
+// #ifdef EIGEN_VECTORIZE_SSE3
+//   Packet4f tmp = _mm_add_ps(a, vec4f_swizzle1(a,2,3,2,3));
+//   return pfirst<Packet4f>(_mm_hadd_ps(tmp, tmp));
+// #else
+  Packet4f tmp = _mm_add_ps(a, _mm_movehl_ps(a,a));
+  return pfirst<Packet4f>(_mm_add_ss(tmp, _mm_shuffle_ps(tmp,tmp, 1)));
+// #endif
+}
+
+template<> EIGEN_STRONG_INLINE double predux<Packet2d>(const Packet2d& a)
+{
+  // Disable SSE3 _mm_hadd_pd that is extremely slow on all existing Intel's architectures
+  // (from Nehalem to Haswell)
+// #ifdef EIGEN_VECTORIZE_SSE3
+//   return pfirst<Packet2d>(_mm_hadd_pd(a, a));
+// #else
+  return pfirst<Packet2d>(_mm_add_sd(a, _mm_unpackhi_pd(a,a)));
+// #endif
+}
 
 #ifdef EIGEN_VECTORIZE_SSSE3
 template<> EIGEN_STRONG_INLINE Packet4i preduxp<Packet4i>(const Packet4i* vecs)

Eigen/src/Core/arch/ZVector/PacketMath.h

@@ -100,7 +100,7 @@ static Packet16uc p16uc_DUPLICATE32_HI = { 0,1,2,3, 0,1,2,3, 4,5,6,7, 4,5,6,7 };
 // Mask alignment
 #define _EIGEN_MASK_ALIGNMENT	0xfffffffffffffff0
 
-#define _EIGEN_ALIGNED_PTR(x)	((ptrdiff_t)(x) & _EIGEN_MASK_ALIGNMENT)
+#define _EIGEN_ALIGNED_PTR(x)	((std::ptrdiff_t)(x) & _EIGEN_MASK_ALIGNMENT)
 
 // Handle endianness properly while loading constants
 // Define global static constants:

Eigen/src/Core/functors/AssignmentFunctors.h

@@ -28,7 +28,7 @@ template<typename DstScalar,typename SrcScalar> struct assign_op {
   { internal::pstoret<DstScalar,Packet,Alignment>(a,b); }
 };
 
-// Empty overload for void type (used by PermutationMatrix
+// Empty overload for void type (used by PermutationMatrix)
 template<typename DstScalar> struct assign_op<DstScalar,void> {};
 
 template<typename DstScalar,typename SrcScalar>

Eigen/src/Core/functors/NullaryFunctors.h

@@ -44,16 +44,16 @@ struct linspaced_op_impl<Scalar,Packet,/*IsInteger*/false>
 {
   linspaced_op_impl(const Scalar& low, const Scalar& high, Index num_steps) :
     m_low(low), m_high(high), m_size1(num_steps==1 ? 1 : num_steps-1), m_step(num_steps==1 ? Scalar() : (high-low)/Scalar(num_steps-1)),
-    m_interPacket(plset<Packet>(0)),
     m_flip(numext::abs(high)<numext::abs(low))
   {}
 
   template<typename IndexType>
   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator() (IndexType i) const {
+    typedef typename NumTraits<Scalar>::Real RealScalar;
     if(m_flip)
-      return (i==0)? m_low : (m_high - (m_size1-i)*m_step);
+      return (i==0)? m_low : (m_high - RealScalar(m_size1-i)*m_step);
     else
-      return (i==m_size1)? m_high : (m_low + i*m_step);
+      return (i==m_size1)? m_high : (m_low + RealScalar(i)*m_step);
   }
 
   template<typename IndexType>
@@ -63,7 +63,7 @@ struct linspaced_op_impl<Scalar,Packet,/*IsInteger*/false>
     // [low, ..., low] + ( [step, ..., step] * ( [i, ..., i] + [0, ..., size] ) )
     if(m_flip)
     {
-      Packet pi = padd(pset1<Packet>(Scalar(i-m_size1)),m_interPacket);
+      Packet pi = plset<Packet>(Scalar(i-m_size1));
       Packet res = padd(pset1<Packet>(m_high), pmul(pset1<Packet>(m_step), pi));
       if(i==0)
         res = pinsertfirst(res, m_low);
@@ -71,7 +71,7 @@ struct linspaced_op_impl<Scalar,Packet,/*IsInteger*/false>
     }
     else
     {
-      Packet pi = padd(pset1<Packet>(Scalar(i)),m_interPacket);
+      Packet pi = plset<Packet>(Scalar(i));
       Packet res = padd(pset1<Packet>(m_low), pmul(pset1<Packet>(m_step), pi));
       if(i==m_size1-unpacket_traits<Packet>::size+1)
         res = pinsertlast(res, m_high);
@@ -83,7 +83,6 @@ struct linspaced_op_impl<Scalar,Packet,/*IsInteger*/false>
   const Scalar m_high;
   const Index m_size1;
   const Scalar m_step;
-  const Packet m_interPacket;
   const bool m_flip;
 };
 
@@ -93,8 +92,8 @@ struct linspaced_op_impl<Scalar,Packet,/*IsInteger*/true>
   linspaced_op_impl(const Scalar& low, const Scalar& high, Index num_steps) :
     m_low(low),
     m_multiplier((high-low)/convert_index<Scalar>(num_steps<=1 ? 1 : num_steps-1)),
-    m_divisor(convert_index<Scalar>(num_steps+high-low)/(high-low+1)),
-    m_use_divisor((high+1)<(low+num_steps))
+    m_divisor(convert_index<Scalar>((high>=low?num_steps:-num_steps)+(high-low))/((numext::abs(high-low)+1)==0?1:(numext::abs(high-low)+1))),
+    m_use_divisor(num_steps>1 && (numext::abs(high-low)+1)<num_steps)
   {}
 
   template<typename IndexType>

Eigen/src/Core/functors/StlFunctors.h

@@ -72,7 +72,7 @@ template<typename T>
 struct functor_traits<std::not_equal_to<T> >
 { enum { Cost = 1, PacketAccess = false }; };
 
-#if(__cplusplus < 201103L)
+#if (__cplusplus < 201103L) && (EIGEN_COMP_MSVC <= 1900)
 // std::binder* are deprecated since c++11 and will be removed in c++17
 template<typename T>
 struct functor_traits<std::binder2nd<T> >

Eigen/src/Core/products/GeneralMatrixMatrix.h

@@ -83,8 +83,8 @@ static void run(Index rows, Index cols, Index depth,
   if(info)
   {
     // this is the parallel version!
-    Index tid = omp_get_thread_num();
-    Index threads = omp_get_num_threads();
+    int tid = omp_get_thread_num();
+    int threads = omp_get_num_threads();
 
     LhsScalar* blockA = blocking.blockA();
     eigen_internal_assert(blockA!=0);
@@ -116,9 +116,9 @@ static void run(Index rows, Index cols, Index depth,
       info[tid].sync = k;
 
       // Computes C_i += A' * B' per A'_i
-      for(Index shift=0; shift<threads; ++shift)
+      for(int shift=0; shift<threads; ++shift)
       {
-        Index i = (tid+shift)%threads;
+        int i = (tid+shift)%threads;
 
         // At this point we have to make sure that A'_i has been updated by the thread i,
         // we use testAndSetOrdered to mimic a volatile access.

Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h

@@ -148,7 +148,7 @@ struct tribb_kernel
     ResMapper res(_res, resStride);
     gebp_kernel<LhsScalar, RhsScalar, Index, ResMapper, mr, nr, ConjLhs, ConjRhs> gebp_kernel;
 
-    Matrix<ResScalar,BlockSize,BlockSize,ColMajor> buffer;
+    Matrix<ResScalar,BlockSize,BlockSize,ColMajor> buffer((internal::constructor_without_unaligned_array_assert()));
 
     // let's process the block per panel of actual_mc x BlockSize,
     // again, each is split into three parts, etc.
@@ -199,7 +199,7 @@ struct general_product_to_triangular_selector;
 template<typename MatrixType, typename ProductType, int UpLo>
 struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,true>
 {
-  static void run(MatrixType& mat, const ProductType& prod, const typename MatrixType::Scalar& alpha)
+  static void run(MatrixType& mat, const ProductType& prod, const typename MatrixType::Scalar& alpha, bool beta)
   {
     typedef typename MatrixType::Scalar Scalar;
     
@@ -217,6 +217,9 @@ struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,true>
 
     Scalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs().derived()) * RhsBlasTraits::extractScalarFactor(prod.rhs().derived());
 
+    if(!beta)
+      mat.template triangularView<UpLo>().setZero();
+
     enum {
       StorageOrder = (internal::traits<MatrixType>::Flags&RowMajorBit) ? RowMajor : ColMajor,
       UseLhsDirectly = _ActualLhs::InnerStrideAtCompileTime==1,
@@ -244,7 +247,7 @@ struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,true>
 template<typename MatrixType, typename ProductType, int UpLo>
 struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,false>
 {
-  static void run(MatrixType& mat, const ProductType& prod, const typename MatrixType::Scalar& alpha)
+  static void run(MatrixType& mat, const ProductType& prod, const typename MatrixType::Scalar& alpha, bool beta)
   {
     typedef typename internal::remove_all<typename ProductType::LhsNested>::type Lhs;
     typedef internal::blas_traits<Lhs> LhsBlasTraits;
@@ -260,13 +263,19 @@ struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,false>
 
     typename ProductType::Scalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs().derived()) * RhsBlasTraits::extractScalarFactor(prod.rhs().derived());
 
+    if(!beta)
+      mat.template triangularView<UpLo>().setZero();
+
     enum {
       IsRowMajor = (internal::traits<MatrixType>::Flags&RowMajorBit) ? 1 : 0,
       LhsIsRowMajor = _ActualLhs::Flags&RowMajorBit ? 1 : 0,
-      RhsIsRowMajor = _ActualRhs::Flags&RowMajorBit ? 1 : 0
+      RhsIsRowMajor = _ActualRhs::Flags&RowMajorBit ? 1 : 0,
+      SkipDiag = (UpLo&(UnitDiag|ZeroDiag))!=0
     };
 
     Index size = mat.cols();
+    if(SkipDiag)
+      size--;
     Index depth = actualLhs.cols();
 
     typedef internal::gemm_blocking_space<IsRowMajor ? RowMajor : ColMajor,typename Lhs::Scalar,typename Rhs::Scalar,
@@ -277,20 +286,22 @@ struct general_product_to_triangular_selector<MatrixType,ProductType,UpLo,false>
     internal::general_matrix_matrix_triangular_product<Index,
       typename Lhs::Scalar, LhsIsRowMajor ? RowMajor : ColMajor, LhsBlasTraits::NeedToConjugate,
       typename Rhs::Scalar, RhsIsRowMajor ? RowMajor : ColMajor, RhsBlasTraits::NeedToConjugate,
-      IsRowMajor ? RowMajor : ColMajor, UpLo>
+      IsRowMajor ? RowMajor : ColMajor, UpLo&(Lower|Upper)>
       ::run(size, depth,
-            &actualLhs.coeffRef(0,0), actualLhs.outerStride(), &actualRhs.coeffRef(0,0), actualRhs.outerStride(),
-            mat.data(), mat.outerStride(), actualAlpha, blocking);
+            &actualLhs.coeffRef(SkipDiag&&(UpLo&Lower)==Lower ? 1 : 0,0), actualLhs.outerStride(),
+            &actualRhs.coeffRef(0,SkipDiag&&(UpLo&Upper)==Upper ? 1 : 0), actualRhs.outerStride(),
+            mat.data() + (SkipDiag ? (bool(IsRowMajor) != ((UpLo&Lower)==Lower) ? 1 : mat.outerStride() ) : 0), mat.outerStride(), actualAlpha, blocking);
   }
 };
 
 template<typename MatrixType, unsigned int UpLo>
 template<typename ProductType>
-TriangularView<MatrixType,UpLo>& TriangularViewImpl<MatrixType,UpLo,Dense>::_assignProduct(const ProductType& prod, const Scalar& alpha)
+TriangularView<MatrixType,UpLo>& TriangularViewImpl<MatrixType,UpLo,Dense>::_assignProduct(const ProductType& prod, const Scalar& alpha, bool beta)
 {
+  EIGEN_STATIC_ASSERT((UpLo&UnitDiag)==0, WRITING_TO_TRIANGULAR_PART_WITH_UNIT_DIAGONAL_IS_NOT_SUPPORTED);
   eigen_assert(derived().nestedExpression().rows() == prod.rows() && derived().cols() == prod.cols());
   
-  general_product_to_triangular_selector<MatrixType, ProductType, UpLo, internal::traits<ProductType>::InnerSize==1>::run(derived().nestedExpression().const_cast_derived(), prod, alpha);
+  general_product_to_triangular_selector<MatrixType, ProductType, UpLo, internal::traits<ProductType>::InnerSize==1>::run(derived().nestedExpression().const_cast_derived(), prod, alpha, beta);
   
   return derived();
 }

Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h

@@ -33,7 +33,7 @@
 #ifndef EIGEN_GENERAL_MATRIX_MATRIX_TRIANGULAR_BLAS_H
 #define EIGEN_GENERAL_MATRIX_MATRIX_TRIANGULAR_BLAS_H
 
-namespace Eigen { 
+namespace Eigen {
 
 namespace internal {
 
@@ -52,7 +52,7 @@ struct general_matrix_matrix_triangular_product<Index,Scalar,LhsStorageOrder,Con
   static EIGEN_STRONG_INLINE void run(Index size, Index depth,const Scalar* lhs, Index lhsStride, \
                           const Scalar* rhs, Index rhsStride, Scalar* res, Index resStride, Scalar alpha, level3_blocking<Scalar, Scalar>& blocking) \
   { \
-    if (lhs==rhs) { \
+    if ( lhs==rhs && ((UpLo&(Lower|Upper)==UpLo)) ) { \
       general_matrix_matrix_rankupdate<Index,Scalar,LhsStorageOrder,ConjugateLhs,ColMajor,UpLo> \
       ::run(size,depth,lhs,lhsStride,rhs,rhsStride,res,resStride,alpha,blocking); \
     } else { \
@@ -86,8 +86,8 @@ struct general_matrix_matrix_rankupdate<Index,EIGTYPE,AStorageOrder,ConjugateA,C
   /* typedef Matrix<EIGTYPE, Dynamic, Dynamic, RhsStorageOrder> MatrixRhs;*/ \
 \
    BlasIndex lda=convert_index<BlasIndex>(lhsStride), ldc=convert_index<BlasIndex>(resStride), n=convert_index<BlasIndex>(size), k=convert_index<BlasIndex>(depth); \
-   char uplo=(IsLower) ? 'L' : 'U', trans=(AStorageOrder==RowMajor) ? 'T':'N'; \
-   EIGTYPE beta; \
+   char uplo=((IsLower) ? 'L' : 'U'), trans=((AStorageOrder==RowMajor) ? 'T':'N'); \
+   EIGTYPE beta(1); \
    BLASFUNC(&uplo, &trans, &n, &k, &numext::real_ref(alpha), lhs, &lda, &numext::real_ref(beta), res, &ldc); \
   } \
 };
@@ -107,7 +107,7 @@ struct general_matrix_matrix_rankupdate<Index,EIGTYPE,AStorageOrder,ConjugateA,C
    typedef Matrix<EIGTYPE, Dynamic, Dynamic, AStorageOrder> MatrixType; \
 \
    BlasIndex lda=convert_index<BlasIndex>(lhsStride), ldc=convert_index<BlasIndex>(resStride), n=convert_index<BlasIndex>(size), k=convert_index<BlasIndex>(depth); \
-   char uplo=(IsLower) ? 'L' : 'U', trans=(AStorageOrder==RowMajor) ? 'C':'N'; \
+   char uplo=((IsLower) ? 'L' : 'U'), trans=((AStorageOrder==RowMajor) ? 'C':'N'); \
    RTYPE alpha_, beta_; \
    const EIGTYPE* a_ptr; \
 \

Eigen/src/Core/products/Parallelizer.h

@@ -75,7 +75,7 @@ template<typename Index> struct GemmParallelInfo
 {
   GemmParallelInfo() : sync(-1), users(0), lhs_start(0), lhs_length(0) {}
 
-  int volatile sync;
+  Index volatile sync;
   int volatile users;
 
   Index lhs_start;
@@ -104,13 +104,14 @@ void parallelize_gemm(const Functor& func, Index rows, Index cols, Index depth,
   // - the sizes are large enough
 
   // compute the maximal number of threads from the size of the product:
-  // FIXME this has to be fine tuned
+  // This first heuristic takes into account that the product kernel is fully optimized when working with nr columns at once.
   Index size = transpose ? rows : cols;
-  Index pb_max_threads = std::max<Index>(1,size / 32);
+  Index pb_max_threads = std::max<Index>(1,size / Functor::Traits::nr);
+
   // compute the maximal number of threads from the total amount of work:
   double work = static_cast<double>(rows) * static_cast<double>(cols) *
       static_cast<double>(depth);
-  double kMinTaskSize = 50000;  // Heuristic.
+  double kMinTaskSize = 50000;  // FIXME improve this heuristic.
   pb_max_threads = std::max<Index>(1, std::min<Index>(pb_max_threads, work / kMinTaskSize));
 
   // compute the number of threads we are going to use

Eigen/src/Core/products/SelfadjointMatrixVector.h

@@ -83,10 +83,10 @@ EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrd
     Scalar t3(0);
     Packet ptmp3 = pset1<Packet>(t3);
 
-    size_t starti = FirstTriangular ? 0 : j+2;
-    size_t endi   = FirstTriangular ? j : size;
-    size_t alignedStart = (starti) + internal::first_default_aligned(&res[starti], endi-starti);
-    size_t alignedEnd = alignedStart + ((endi-alignedStart)/(PacketSize))*(PacketSize);
+    Index starti = FirstTriangular ? 0 : j+2;
+    Index endi   = FirstTriangular ? j : size;
+    Index alignedStart = (starti) + internal::first_default_aligned(&res[starti], endi-starti);
+    Index alignedEnd = alignedStart + ((endi-alignedStart)/(PacketSize))*(PacketSize);
 
     res[j]   += cjd.pmul(numext::real(A0[j]), t0);
     res[j+1] += cjd.pmul(numext::real(A1[j+1]), t1);
@@ -101,7 +101,7 @@ EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrd
       t2 += cj1.pmul(A0[j+1], rhs[j+1]);
     }
 
-    for (size_t i=starti; i<alignedStart; ++i)
+    for (Index i=starti; i<alignedStart; ++i)
     {
       res[i] += cj0.pmul(A0[i], t0) + cj0.pmul(A1[i],t1);
       t2 += cj1.pmul(A0[i], rhs[i]);
@@ -113,7 +113,7 @@ EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrd
     const Scalar* EIGEN_RESTRICT a1It  = A1  + alignedStart;
     const Scalar* EIGEN_RESTRICT rhsIt = rhs + alignedStart;
           Scalar* EIGEN_RESTRICT resIt = res + alignedStart;
-    for (size_t i=alignedStart; i<alignedEnd; i+=PacketSize)
+    for (Index i=alignedStart; i<alignedEnd; i+=PacketSize)
     {
       Packet A0i = ploadu<Packet>(a0It);  a0It  += PacketSize;
       Packet A1i = ploadu<Packet>(a1It);  a1It  += PacketSize;
@@ -125,7 +125,7 @@ EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrd
       ptmp3 = pcj1.pmadd(A1i,  Bi, ptmp3);
       pstore(resIt,Xi); resIt += PacketSize;
     }
-    for (size_t i=alignedEnd; i<endi; i++)
+    for (Index i=alignedEnd; i<endi; i++)
     {
       res[i] += cj0.pmul(A0[i], t0) + cj0.pmul(A1[i],t1);
       t2 += cj1.pmul(A0[i], rhs[i]);

Eigen/src/Core/products/TriangularMatrixMatrix.h

@@ -137,7 +137,7 @@ EIGEN_DONT_INLINE void product_triangular_matrix_matrix<Scalar,Index,Mode,true,
     ei_declare_aligned_stack_constructed_variable(Scalar, blockA, sizeA, blocking.blockA());
     ei_declare_aligned_stack_constructed_variable(Scalar, blockB, sizeB, blocking.blockB());
 
-    Matrix<Scalar,SmallPanelWidth,SmallPanelWidth,LhsStorageOrder> triangularBuffer;
+    Matrix<Scalar,SmallPanelWidth,SmallPanelWidth,LhsStorageOrder> triangularBuffer((internal::constructor_without_unaligned_array_assert()));
     triangularBuffer.setZero();
     if((Mode&ZeroDiag)==ZeroDiag)
       triangularBuffer.diagonal().setZero();
@@ -284,7 +284,7 @@ EIGEN_DONT_INLINE void product_triangular_matrix_matrix<Scalar,Index,Mode,false,
     ei_declare_aligned_stack_constructed_variable(Scalar, blockA, sizeA, blocking.blockA());
     ei_declare_aligned_stack_constructed_variable(Scalar, blockB, sizeB, blocking.blockB());
 
-    Matrix<Scalar,SmallPanelWidth,SmallPanelWidth,RhsStorageOrder> triangularBuffer;
+    Matrix<Scalar,SmallPanelWidth,SmallPanelWidth,RhsStorageOrder> triangularBuffer((internal::constructor_without_unaligned_array_assert()));
     triangularBuffer.setZero();
     if((Mode&ZeroDiag)==ZeroDiag)
       triangularBuffer.diagonal().setZero();

Eigen/src/Core/products/TriangularSolverMatrix.h

@@ -183,7 +183,7 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheLeft,Mode,Conju
     }
   }
 
-/* Optimized triangular solver with multiple left hand sides and the trinagular matrix on the right
+/* Optimized triangular solver with multiple left hand sides and the triangular matrix on the right
  */
 template <typename Scalar, typename Index, int Mode, bool Conjugate, int TriStorageOrder>
 struct triangular_solve_matrix<Scalar,Index,OnTheRight,Mode,Conjugate,TriStorageOrder,ColMajor>
@@ -202,6 +202,7 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheRight,Mode,Conj
     level3_blocking<Scalar,Scalar>& blocking)
   {
     Index rows = otherSize;
+    typedef typename NumTraits<Scalar>::Real RealScalar;
 
     typedef blas_data_mapper<Scalar, Index, ColMajor> LhsMapper;
     typedef const_blas_data_mapper<Scalar, Index, TriStorageOrder> RhsMapper;
@@ -306,9 +307,9 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheRight,Mode,Conj
               }
               if((Mode & UnitDiag)==0)
               {
-                Scalar b = conj(rhs(j,j));
+                Scalar inv_rjj = RealScalar(1)/conj(rhs(j,j));
                 for (Index i=0; i<actual_mc; ++i)
-                  r[i] /= b;
+                  r[i] *= inv_rjj;
               }
             }
 

Eigen/src/Core/util/Macros.h

@@ -13,7 +13,7 @@
 
 #define EIGEN_WORLD_VERSION 3
 #define EIGEN_MAJOR_VERSION 3
-#define EIGEN_MINOR_VERSION 1
+#define EIGEN_MINOR_VERSION 4
 
 #define EIGEN_VERSION_AT_LEAST(x,y,z) (EIGEN_WORLD_VERSION>x || (EIGEN_WORLD_VERSION>=x && \
                                       (EIGEN_MAJOR_VERSION>y || (EIGEN_MAJOR_VERSION>=y && \
@@ -80,8 +80,8 @@
 //  2015   14      1900
 //  "15"   15      1900
 
-/// \internal EIGEN_COMP_MSVC_STRICT set to 1 if the compiler is really Microsoft Visual C++ and not ,e.g., ICC
-#if EIGEN_COMP_MSVC && !(EIGEN_COMP_ICC)
+/// \internal EIGEN_COMP_MSVC_STRICT set to 1 if the compiler is really Microsoft Visual C++ and not ,e.g., ICC or clang-cl
+#if EIGEN_COMP_MSVC && !(EIGEN_COMP_ICC || EIGEN_COMP_LLVM || EIGEN_COMP_CLANG)
   #define EIGEN_COMP_MSVC_STRICT _MSC_VER
 #else
   #define EIGEN_COMP_MSVC_STRICT 0
@@ -356,7 +356,7 @@
 #define EIGEN_MAX_CPP_VER 99
 #endif
 
-#if EIGEN_MAX_CPP_VER>=11 && defined(__cplusplus) && (__cplusplus >= 201103L)
+#if EIGEN_MAX_CPP_VER>=11 && (defined(__cplusplus) && (__cplusplus >= 201103L) || EIGEN_COMP_MSVC >= 1900)
 #define EIGEN_HAS_CXX11 1
 #else
 #define EIGEN_HAS_CXX11 0
@@ -497,10 +497,11 @@
 // attribute to maximize inlining. This should only be used when really necessary: in particular,
 // it uses __attribute__((always_inline)) on GCC, which most of the time is useless and can severely harm compile times.
 // FIXME with the always_inline attribute,
-// gcc 3.4.x reports the following compilation error:
+// gcc 3.4.x and 4.1 reports the following compilation error:
 //   Eval.h:91: sorry, unimplemented: inlining failed in call to 'const Eigen::Eval<Derived> Eigen::MatrixBase<Scalar, Derived>::eval() const'
 //    : function body not available
-#if EIGEN_GNUC_AT_LEAST(4,0)
+//   See also bug 1367
+#if EIGEN_GNUC_AT_LEAST(4,2)
 #define EIGEN_ALWAYS_INLINE __attribute__((always_inline)) inline
 #else
 #define EIGEN_ALWAYS_INLINE EIGEN_STRONG_INLINE
@@ -811,7 +812,7 @@ namespace Eigen {
 // just an empty macro !
 #define EIGEN_EMPTY
 
-#if EIGEN_COMP_MSVC_STRICT && (EIGEN_COMP_MSVC < 1900 ||  __CUDACC_VER__) // for older MSVC versions, as well as 1900 && CUDA 8, using the base operator is sufficient (cf Bugs 1000, 1324)
+#if EIGEN_COMP_MSVC_STRICT && (EIGEN_COMP_MSVC < 1900 ||  defined(__CUDACC_VER__)) // for older MSVC versions, as well as 1900 && CUDA 8, using the base operator is sufficient (cf Bugs 1000, 1324)
   #define EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) \
     using Base::operator =;
 #elif EIGEN_COMP_CLANG // workaround clang bug (see http://forum.kde.org/viewtopic.php?f=74&t=102653)

Eigen/src/Core/util/Memory.h

@@ -150,7 +150,7 @@ EIGEN_DEVICE_FUNC inline void check_that_malloc_is_allowed()
 /** \internal Allocates \a size bytes. The returned pointer is guaranteed to have 16 or 32 bytes alignment depending on the requirements.
   * On allocation error, the returned pointer is null, and std::bad_alloc is thrown.
   */
-EIGEN_DEVICE_FUNC inline void* aligned_malloc(size_t size)
+EIGEN_DEVICE_FUNC inline void* aligned_malloc(std::size_t size)
 {
   check_that_malloc_is_allowed();
 
@@ -185,7 +185,7 @@ EIGEN_DEVICE_FUNC inline void aligned_free(void *ptr)
   * \brief Reallocates an aligned block of memory.
   * \throws std::bad_alloc on allocation failure
   */
-inline void* aligned_realloc(void *ptr, size_t new_size, size_t old_size)
+inline void* aligned_realloc(void *ptr, std::size_t new_size, std::size_t old_size)
 {
   EIGEN_UNUSED_VARIABLE(old_size);
 
@@ -209,12 +209,12 @@ inline void* aligned_realloc(void *ptr, size_t new_size, size_t old_size)
 /** \internal Allocates \a size bytes. If Align is true, then the returned ptr is 16-byte-aligned.
   * On allocation error, the returned pointer is null, and a std::bad_alloc is thrown.
   */
-template<bool Align> EIGEN_DEVICE_FUNC inline void* conditional_aligned_malloc(size_t size)
+template<bool Align> EIGEN_DEVICE_FUNC inline void* conditional_aligned_malloc(std::size_t size)
 {
   return aligned_malloc(size);
 }
 
-template<> EIGEN_DEVICE_FUNC inline void* conditional_aligned_malloc<false>(size_t size)
+template<> EIGEN_DEVICE_FUNC inline void* conditional_aligned_malloc<false>(std::size_t size)
 {
   check_that_malloc_is_allowed();
 
@@ -235,12 +235,12 @@ template<> EIGEN_DEVICE_FUNC inline void conditional_aligned_free<false>(void *p
   std::free(ptr);
 }
 
-template<bool Align> inline void* conditional_aligned_realloc(void* ptr, size_t new_size, size_t old_size)
+template<bool Align> inline void* conditional_aligned_realloc(void* ptr, std::size_t new_size, std::size_t old_size)
 {
   return aligned_realloc(ptr, new_size, old_size);
 }
 
-template<> inline void* conditional_aligned_realloc<false>(void* ptr, size_t new_size, size_t)
+template<> inline void* conditional_aligned_realloc<false>(void* ptr, std::size_t new_size, std::size_t)
 {
   return std::realloc(ptr, new_size);
 }
@@ -252,7 +252,7 @@ template<> inline void* conditional_aligned_realloc<false>(void* ptr, size_t new
 /** \internal Destructs the elements of an array.
   * The \a size parameters tells on how many objects to call the destructor of T.
   */
-template<typename T> EIGEN_DEVICE_FUNC inline void destruct_elements_of_array(T *ptr, size_t size)
+template<typename T> EIGEN_DEVICE_FUNC inline void destruct_elements_of_array(T *ptr, std::size_t size)
 {
   // always destruct an array starting from the end.
   if(ptr)
@@ -262,9 +262,9 @@ template<typename T> EIGEN_DEVICE_FUNC inline void destruct_elements_of_array(T
 /** \internal Constructs the elements of an array.
   * The \a size parameter tells on how many objects to call the constructor of T.
   */
-template<typename T> EIGEN_DEVICE_FUNC inline T* construct_elements_of_array(T *ptr, size_t size)
+template<typename T> EIGEN_DEVICE_FUNC inline T* construct_elements_of_array(T *ptr, std::size_t size)
 {
-  size_t i;
+  std::size_t i;
   EIGEN_TRY
   {
       for (i = 0; i < size; ++i) ::new (ptr + i) T;
@@ -283,9 +283,9 @@ template<typename T> EIGEN_DEVICE_FUNC inline T* construct_elements_of_array(T *
 *****************************************************************************/
 
 template<typename T>
-EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void check_size_for_overflow(size_t size)
+EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void check_size_for_overflow(std::size_t size)
 {
-  if(size > size_t(-1) / sizeof(T))
+  if(size > std::size_t(-1) / sizeof(T))
     throw_std_bad_alloc();
 }
 
@@ -293,7 +293,7 @@ EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void check_size_for_overflow(size_t size)
   * On allocation error, the returned pointer is undefined, but a std::bad_alloc is thrown.
   * The default constructor of T is called.
   */
-template<typename T> EIGEN_DEVICE_FUNC inline T* aligned_new(size_t size)
+template<typename T> EIGEN_DEVICE_FUNC inline T* aligned_new(std::size_t size)
 {
   check_size_for_overflow<T>(size);
   T *result = reinterpret_cast<T*>(aligned_malloc(sizeof(T)*size));
@@ -309,7 +309,7 @@ template<typename T> EIGEN_DEVICE_FUNC inline T* aligned_new(size_t size)
   return result;
 }
 
-template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_new(size_t size)
+template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_new(std::size_t size)
 {
   check_size_for_overflow<T>(size);
   T *result = reinterpret_cast<T*>(conditional_aligned_malloc<Align>(sizeof(T)*size));
@@ -328,7 +328,7 @@ template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned
 /** \internal Deletes objects constructed with aligned_new
   * The \a size parameters tells on how many objects to call the destructor of T.
   */
-template<typename T> EIGEN_DEVICE_FUNC inline void aligned_delete(T *ptr, size_t size)
+template<typename T> EIGEN_DEVICE_FUNC inline void aligned_delete(T *ptr, std::size_t size)
 {
   destruct_elements_of_array<T>(ptr, size);
   aligned_free(ptr);
@@ -337,13 +337,13 @@ template<typename T> EIGEN_DEVICE_FUNC inline void aligned_delete(T *ptr, size_t
 /** \internal Deletes objects constructed with conditional_aligned_new
   * The \a size parameters tells on how many objects to call the destructor of T.
   */
-template<typename T, bool Align> EIGEN_DEVICE_FUNC inline void conditional_aligned_delete(T *ptr, size_t size)
+template<typename T, bool Align> EIGEN_DEVICE_FUNC inline void conditional_aligned_delete(T *ptr, std::size_t size)
 {
   destruct_elements_of_array<T>(ptr, size);
   conditional_aligned_free<Align>(ptr);
 }
 
-template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_realloc_new(T* pts, size_t new_size, size_t old_size)
+template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_realloc_new(T* pts, std::size_t new_size, std::size_t old_size)
 {
   check_size_for_overflow<T>(new_size);
   check_size_for_overflow<T>(old_size);
@@ -366,7 +366,7 @@ template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned
 }
 
 
-template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_new_auto(size_t size)
+template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned_new_auto(std::size_t size)
 {
   if(size==0)
     return 0; // short-cut. Also fixes Bug 884
@@ -387,7 +387,7 @@ template<typename T, bool Align> EIGEN_DEVICE_FUNC inline T* conditional_aligned
   return result;
 }
 
-template<typename T, bool Align> inline T* conditional_aligned_realloc_new_auto(T* pts, size_t new_size, size_t old_size)
+template<typename T, bool Align> inline T* conditional_aligned_realloc_new_auto(T* pts, std::size_t new_size, std::size_t old_size)
 {
   check_size_for_overflow<T>(new_size);
   check_size_for_overflow<T>(old_size);
@@ -409,7 +409,7 @@ template<typename T, bool Align> inline T* conditional_aligned_realloc_new_auto(
   return result;
 }
 
-template<typename T, bool Align> EIGEN_DEVICE_FUNC inline void conditional_aligned_delete_auto(T *ptr, size_t size)
+template<typename T, bool Align> EIGEN_DEVICE_FUNC inline void conditional_aligned_delete_auto(T *ptr, std::size_t size)
 {
   if(NumTraits<T>::RequireInitialization)
     destruct_elements_of_array<T>(ptr, size);
@@ -561,7 +561,7 @@ template<typename T> class aligned_stack_memory_handler : noncopyable
      * In this case, the buffer elements will also be destructed when this handler will be destructed.
      * Finally, if \a dealloc is true, then the pointer \a ptr is freed.
      **/
-    aligned_stack_memory_handler(T* ptr, size_t size, bool dealloc)
+    aligned_stack_memory_handler(T* ptr, std::size_t size, bool dealloc)
       : m_ptr(ptr), m_size(size), m_deallocate(dealloc)
     {
       if(NumTraits<T>::RequireInitialization && m_ptr)
@@ -576,7 +576,7 @@ template<typename T> class aligned_stack_memory_handler : noncopyable
     }
   protected:
     T* m_ptr;
-    size_t m_size;
+    std::size_t m_size;
     bool m_deallocate;
 };
 
@@ -655,15 +655,15 @@ template<typename T> void swap(scoped_array<T> &a,scoped_array<T> &b)
 
 #if EIGEN_MAX_ALIGN_BYTES!=0
   #define EIGEN_MAKE_ALIGNED_OPERATOR_NEW_NOTHROW(NeedsToAlign) \
-      void* operator new(size_t size, const std::nothrow_t&) EIGEN_NO_THROW { \
+      void* operator new(std::size_t size, const std::nothrow_t&) EIGEN_NO_THROW { \
         EIGEN_TRY { return Eigen::internal::conditional_aligned_malloc<NeedsToAlign>(size); } \
         EIGEN_CATCH (...) { return 0; } \
       }
   #define EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign) \
-      void *operator new(size_t size) { \
+      void *operator new(std::size_t size) { \
         return Eigen::internal::conditional_aligned_malloc<NeedsToAlign>(size); \
       } \
-      void *operator new[](size_t size) { \
+      void *operator new[](std::size_t size) { \
         return Eigen::internal::conditional_aligned_malloc<NeedsToAlign>(size); \
       } \
       void operator delete(void * ptr) EIGEN_NO_THROW { Eigen::internal::conditional_aligned_free<NeedsToAlign>(ptr); } \
@@ -673,8 +673,8 @@ template<typename T> void swap(scoped_array<T> &a,scoped_array<T> &b)
       /* in-place new and delete. since (at least afaik) there is no actual   */ \
       /* memory allocated we can safely let the default implementation handle */ \
       /* this particular case. */ \
-      static void *operator new(size_t size, void *ptr) { return ::operator new(size,ptr); } \
-      static void *operator new[](size_t size, void* ptr) { return ::operator new[](size,ptr); } \
+      static void *operator new(std::size_t size, void *ptr) { return ::operator new(size,ptr); } \
+      static void *operator new[](std::size_t size, void* ptr) { return ::operator new[](size,ptr); } \
       void operator delete(void * memory, void *ptr) EIGEN_NO_THROW { return ::operator delete(memory,ptr); } \
       void operator delete[](void * memory, void *ptr) EIGEN_NO_THROW { return ::operator delete[](memory,ptr); } \
       /* nothrow-new (returns zero instead of std::bad_alloc) */ \
@@ -713,7 +713,7 @@ template<class T>
 class aligned_allocator : public std::allocator<T>
 {
 public:
-  typedef size_t          size_type;
+  typedef std::size_t     size_type;
   typedef std::ptrdiff_t  difference_type;
   typedef T*              pointer;
   typedef const T*        const_pointer;

Eigen/src/Core/util/XprHelper.h

@@ -532,6 +532,15 @@ template <typename B, typename Functor>                   struct cwise_promote_s
 template <typename Functor>                               struct cwise_promote_storage_type<Sparse,Dense,Functor>                             { typedef Sparse ret; };
 template <typename Functor>                               struct cwise_promote_storage_type<Dense,Sparse,Functor>                             { typedef Sparse ret; };
 
+template <typename LhsKind, typename RhsKind, int LhsOrder, int RhsOrder> struct cwise_promote_storage_order {
+  enum { value = LhsOrder };
+};
+
+template <typename LhsKind, int LhsOrder, int RhsOrder>   struct cwise_promote_storage_order<LhsKind,Sparse,LhsOrder,RhsOrder>                { enum { value = RhsOrder }; };
+template <typename RhsKind, int LhsOrder, int RhsOrder>   struct cwise_promote_storage_order<Sparse,RhsKind,LhsOrder,RhsOrder>                { enum { value = LhsOrder }; };
+template <int Order>                                      struct cwise_promote_storage_order<Sparse,Sparse,Order,Order>                       { enum { value = Order }; };
+
+
 /** \internal Specify the "storage kind" of multiplying an expression of kind A with kind B.
   * The template parameter ProductTag permits to specialize the resulting storage kind wrt to
   * some compile-time properties of the product: GemmProduct, GemvProduct, OuterProduct, InnerProduct.
@@ -629,7 +638,7 @@ struct plain_constant_type
 template<typename ExpressionType>
 struct is_lvalue
 {
-  enum { value = !bool(is_const<ExpressionType>::value) &&
+  enum { value = (!bool(is_const<ExpressionType>::value)) &&
                  bool(traits<ExpressionType>::Flags & LvalueBit) };
 };
 

Eigen/src/Eigenvalues/ComplexEigenSolver.h

@@ -250,7 +250,7 @@ template<typename _MatrixType> class ComplexEigenSolver
     EigenvectorType m_matX;
 
   private:
-    void doComputeEigenvectors(const RealScalar& matrixnorm);
+    void doComputeEigenvectors(RealScalar matrixnorm);
     void sortEigenvalues(bool computeEigenvectors);
 };
 
@@ -284,10 +284,12 @@ ComplexEigenSolver<MatrixType>::compute(const EigenBase<InputType>& matrix, bool
 
 
 template<typename MatrixType>
-void ComplexEigenSolver<MatrixType>::doComputeEigenvectors(const RealScalar& matrixnorm)
+void ComplexEigenSolver<MatrixType>::doComputeEigenvectors(RealScalar matrixnorm)
 {
   const Index n = m_eivalues.size();
 
+  matrixnorm = numext::maxi(matrixnorm,(std::numeric_limits<RealScalar>::min)());
+
   // Compute X such that T = X D X^(-1), where D is the diagonal of T.
   // The matrix X is unit triangular.
   m_matX = EigenvectorType::Zero(n, n);

Eigen/src/Eigenvalues/RealSchur.h

@@ -248,12 +248,24 @@ template<typename MatrixType>
 template<typename InputType>
 RealSchur<MatrixType>& RealSchur<MatrixType>::compute(const EigenBase<InputType>& matrix, bool computeU)
 {
+  const Scalar considerAsZero = (std::numeric_limits<Scalar>::min)();
+
   eigen_assert(matrix.cols() == matrix.rows());
   Index maxIters = m_maxIters;
   if (maxIters == -1)
     maxIters = m_maxIterationsPerRow * matrix.rows();
 
   Scalar scale = matrix.derived().cwiseAbs().maxCoeff();
+  if(scale<considerAsZero)
+  {
+    m_matT.setZero(matrix.rows(),matrix.cols());
+    if(computeU)
+      m_matU.setIdentity(matrix.rows(),matrix.cols());
+    m_info = Success;
+    m_isInitialized = true;
+    m_matUisUptodate = computeU;
+    return *this;
+  }
 
   // Step 1. Reduce to Hessenberg form
   m_hess.compute(matrix.derived()/scale);

Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h

@@ -414,7 +414,8 @@ SelfAdjointEigenSolver<MatrixType>& SelfAdjointEigenSolver<MatrixType>
 
   if(n==1)
   {
-    m_eivalues.coeffRef(0,0) = numext::real(matrix.diagonal()[0]);
+    m_eivec = matrix;
+    m_eivalues.coeffRef(0,0) = numext::real(m_eivec.coeff(0,0));
     if(computeEigenvectors)
       m_eivec.setOnes(n,n);
     m_info = Success;

Eigen/src/Geometry/Hyperplane.h

@@ -217,7 +217,10 @@ public:
   EIGEN_DEVICE_FUNC inline Hyperplane& transform(const MatrixBase<XprType>& mat, TransformTraits traits = Affine)
   {
     if (traits==Affine)
+    {
       normal() = mat.inverse().transpose() * normal();
+      m_coeffs /= normal().norm();
+    }
     else if (traits==Isometry)
       normal() = mat * normal();
     else

Eigen/src/Geometry/Quaternion.h

@@ -423,7 +423,7 @@ typedef Map<Quaternion<double>, Aligned>  QuaternionMapAlignedd;
 // Generic Quaternion * Quaternion product
 // This product can be specialized for a given architecture via the Arch template argument.
 namespace internal {
-template<int Arch, class Derived1, class Derived2, typename Scalar, int _Options> struct quat_product
+template<int Arch, class Derived1, class Derived2, typename Scalar> struct quat_product
 {
   EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE Quaternion<Scalar> run(const QuaternionBase<Derived1>& a, const QuaternionBase<Derived2>& b){
     return Quaternion<Scalar>
@@ -446,8 +446,7 @@ QuaternionBase<Derived>::operator* (const QuaternionBase<OtherDerived>& other) c
   EIGEN_STATIC_ASSERT((internal::is_same<typename Derived::Scalar, typename OtherDerived::Scalar>::value),
    YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
   return internal::quat_product<Architecture::Target, Derived, OtherDerived,
-                         typename internal::traits<Derived>::Scalar,
-                         EIGEN_PLAIN_ENUM_MIN(internal::traits<Derived>::Alignment, internal::traits<OtherDerived>::Alignment)>::run(*this, other);
+                         typename internal::traits<Derived>::Scalar>::run(*this, other);
 }
 
 /** \sa operator*(Quaternion) */
@@ -672,7 +671,7 @@ EIGEN_DEVICE_FUNC inline Quaternion<typename internal::traits<Derived>::Scalar>
 
 // Generic conjugate of a Quaternion
 namespace internal {
-template<int Arch, class Derived, typename Scalar, int _Options> struct quat_conj
+template<int Arch, class Derived, typename Scalar> struct quat_conj
 {
   EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE Quaternion<Scalar> run(const QuaternionBase<Derived>& q){
     return Quaternion<Scalar>(q.w(),-q.x(),-q.y(),-q.z());
@@ -691,8 +690,7 @@ EIGEN_DEVICE_FUNC inline Quaternion<typename internal::traits<Derived>::Scalar>
 QuaternionBase<Derived>::conjugate() const
 {
   return internal::quat_conj<Architecture::Target, Derived,
-                         typename internal::traits<Derived>::Scalar,
-                         internal::traits<Derived>::Alignment>::run(*this);
+                         typename internal::traits<Derived>::Scalar>::run(*this);
                          
 }
 

Eigen/src/Geometry/arch/Geometry_SSE.h

@@ -16,17 +16,23 @@ namespace Eigen {
 namespace internal {
 
 template<class Derived, class OtherDerived>
-struct quat_product<Architecture::SSE, Derived, OtherDerived, float, Aligned16>
+struct quat_product<Architecture::SSE, Derived, OtherDerived, float>
 {
+  enum {
+    AAlignment = traits<Derived>::Alignment,
+    BAlignment = traits<OtherDerived>::Alignment,
+    ResAlignment = traits<Quaternion<float> >::Alignment
+  };
   static inline Quaternion<float> run(const QuaternionBase<Derived>& _a, const QuaternionBase<OtherDerived>& _b)
   {
     Quaternion<float> res;
     const __m128 mask = _mm_setr_ps(0.f,0.f,0.f,-0.f);
-    __m128 a = _a.coeffs().template packet<Aligned16>(0);
-    __m128 b = _b.coeffs().template packet<Aligned16>(0);
+    __m128 a = _a.coeffs().template packet<AAlignment>(0);
+    __m128 b = _b.coeffs().template packet<BAlignment>(0);
     __m128 s1 = _mm_mul_ps(vec4f_swizzle1(a,1,2,0,2),vec4f_swizzle1(b,2,0,1,2));
     __m128 s2 = _mm_mul_ps(vec4f_swizzle1(a,3,3,3,1),vec4f_swizzle1(b,0,1,2,1));
-    pstore(&res.x(),
+    pstoret<float,Packet4f,ResAlignment>(
+              &res.x(),
               _mm_add_ps(_mm_sub_ps(_mm_mul_ps(a,vec4f_swizzle1(b,3,3,3,3)),
                                     _mm_mul_ps(vec4f_swizzle1(a,2,0,1,0),
                                                vec4f_swizzle1(b,1,2,0,0))),
@@ -36,14 +42,17 @@ struct quat_product<Architecture::SSE, Derived, OtherDerived, float, Aligned16>
   }
 };
 
-template<class Derived, int Alignment>
-struct quat_conj<Architecture::SSE, Derived, float, Alignment>
+template<class Derived>
+struct quat_conj<Architecture::SSE, Derived, float>
 {
+  enum {
+    ResAlignment = traits<Quaternion<float> >::Alignment
+  };
   static inline Quaternion<float> run(const QuaternionBase<Derived>& q)
   {
     Quaternion<float> res;
     const __m128 mask = _mm_setr_ps(-0.f,-0.f,-0.f,0.f);
-    pstore(&res.x(), _mm_xor_ps(mask, q.coeffs().template packet<Alignment>(0)));
+    pstoret<float,Packet4f,ResAlignment>(&res.x(), _mm_xor_ps(mask, q.coeffs().template packet<traits<Derived>::Alignment>(0)));
     return res;
   }
 };
@@ -52,6 +61,9 @@ struct quat_conj<Architecture::SSE, Derived, float, Alignment>
 template<typename VectorLhs,typename VectorRhs>
 struct cross3_impl<Architecture::SSE,VectorLhs,VectorRhs,float,true>
 {
+  enum {
+    ResAlignment = traits<typename plain_matrix_type<VectorLhs>::type>::Alignment
+  };
   static inline typename plain_matrix_type<VectorLhs>::type
   run(const VectorLhs& lhs, const VectorRhs& rhs)
   {
@@ -60,7 +72,7 @@ struct cross3_impl<Architecture::SSE,VectorLhs,VectorRhs,float,true>
     __m128 mul1=_mm_mul_ps(vec4f_swizzle1(a,1,2,0,3),vec4f_swizzle1(b,2,0,1,3));
     __m128 mul2=_mm_mul_ps(vec4f_swizzle1(a,2,0,1,3),vec4f_swizzle1(b,1,2,0,3));
     typename plain_matrix_type<VectorLhs>::type res;
-    pstore(&res.x(),_mm_sub_ps(mul1,mul2));
+    pstoret<float,Packet4f,ResAlignment>(&res.x(),_mm_sub_ps(mul1,mul2));
     return res;
   }
 };
@@ -68,9 +80,14 @@ struct cross3_impl<Architecture::SSE,VectorLhs,VectorRhs,float,true>
 
 
 
-template<class Derived, class OtherDerived, int Alignment>
-struct quat_product<Architecture::SSE, Derived, OtherDerived, double, Alignment>
+template<class Derived, class OtherDerived>
+struct quat_product<Architecture::SSE, Derived, OtherDerived, double>
 {
+  enum {
+    BAlignment = traits<OtherDerived>::Alignment,
+    ResAlignment = traits<Quaternion<double> >::Alignment
+  };
+
   static inline Quaternion<double> run(const QuaternionBase<Derived>& _a, const QuaternionBase<OtherDerived>& _b)
   {
   const Packet2d mask = _mm_castsi128_pd(_mm_set_epi32(0x0,0x0,0x80000000,0x0));
@@ -78,8 +95,8 @@ struct quat_product<Architecture::SSE, Derived, OtherDerived, double, Alignment>
   Quaternion<double> res;
 
   const double* a = _a.coeffs().data();
-  Packet2d b_xy = _b.coeffs().template packet<Alignment>(0);
-  Packet2d b_zw = _b.coeffs().template packet<Alignment>(2);
+  Packet2d b_xy = _b.coeffs().template packet<BAlignment>(0);
+  Packet2d b_zw = _b.coeffs().template packet<BAlignment>(2);
   Packet2d a_xx = pset1<Packet2d>(a[0]);
   Packet2d a_yy = pset1<Packet2d>(a[1]);
   Packet2d a_zz = pset1<Packet2d>(a[2]);
@@ -97,9 +114,9 @@ struct quat_product<Architecture::SSE, Derived, OtherDerived, double, Alignment>
   t2 = psub(pmul(a_zz, b_xy), pmul(a_xx, b_zw));
 #ifdef EIGEN_VECTORIZE_SSE3
   EIGEN_UNUSED_VARIABLE(mask)
-  pstore(&res.x(), _mm_addsub_pd(t1, preverse(t2)));
+  pstoret<double,Packet2d,ResAlignment>(&res.x(), _mm_addsub_pd(t1, preverse(t2)));
 #else
-  pstore(&res.x(), padd(t1, pxor(mask,preverse(t2))));
+  pstoret<double,Packet2d,ResAlignment>(&res.x(), padd(t1, pxor(mask,preverse(t2))));
 #endif
   
   /*
@@ -111,25 +128,28 @@ struct quat_product<Architecture::SSE, Derived, OtherDerived, double, Alignment>
   t2 = padd(pmul(a_zz, b_zw), pmul(a_xx, b_xy));
 #ifdef EIGEN_VECTORIZE_SSE3
   EIGEN_UNUSED_VARIABLE(mask)
-  pstore(&res.z(), preverse(_mm_addsub_pd(preverse(t1), t2)));
+  pstoret<double,Packet2d,ResAlignment>(&res.z(), preverse(_mm_addsub_pd(preverse(t1), t2)));
 #else
-  pstore(&res.z(), psub(t1, pxor(mask,preverse(t2))));
+  pstoret<double,Packet2d,ResAlignment>(&res.z(), psub(t1, pxor(mask,preverse(t2))));
 #endif
 
   return res;
 }
 };
 
-template<class Derived, int Alignment>
-struct quat_conj<Architecture::SSE, Derived, double, Alignment>
+template<class Derived>
+struct quat_conj<Architecture::SSE, Derived, double>
 {
+  enum {
+    ResAlignment = traits<Quaternion<double> >::Alignment
+  };
   static inline Quaternion<double> run(const QuaternionBase<Derived>& q)
   {
     Quaternion<double> res;
     const __m128d mask0 = _mm_setr_pd(-0.,-0.);
     const __m128d mask2 = _mm_setr_pd(-0.,0.);
-    pstore(&res.x(), _mm_xor_pd(mask0, q.coeffs().template packet<Alignment>(0)));
-    pstore(&res.z(), _mm_xor_pd(mask2, q.coeffs().template packet<Alignment>(2)));
+    pstoret<double,Packet2d,ResAlignment>(&res.x(), _mm_xor_pd(mask0, q.coeffs().template packet<traits<Derived>::Alignment>(0)));
+    pstoret<double,Packet2d,ResAlignment>(&res.z(), _mm_xor_pd(mask2, q.coeffs().template packet<traits<Derived>::Alignment>(2)));
     return res;
   }
 };

Eigen/src/Householder/BlockHouseholder.h

@@ -87,7 +87,8 @@ void apply_block_householder_on_the_left(MatrixType& mat, const VectorsType& vec
   const TriangularView<const VectorsType, UnitLower> V(vectors);
 
   // A -= V T V^* A
-  Matrix<typename MatrixType::Scalar,VectorsType::ColsAtCompileTime,MatrixType::ColsAtCompileTime,0,
+  Matrix<typename MatrixType::Scalar,VectorsType::ColsAtCompileTime,MatrixType::ColsAtCompileTime,
+         (VectorsType::MaxColsAtCompileTime==1 && MatrixType::MaxColsAtCompileTime!=1)?RowMajor:ColMajor,
          VectorsType::MaxColsAtCompileTime,MatrixType::MaxColsAtCompileTime> tmp = V.adjoint() * mat;
   // FIXME add .noalias() once the triangular product can work inplace
   if(forward) tmp = T.template triangularView<Upper>()           * tmp;

Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h

@@ -152,13 +152,28 @@ class LeastSquareDiagonalPreconditioner : public DiagonalPreconditioner<_Scalar>
     {
       // Compute the inverse squared-norm of each column of mat
       m_invdiag.resize(mat.cols());
-      for(Index j=0; j<mat.outerSize(); ++j)
+      if(MatType::IsRowMajor)
       {
-        RealScalar sum = mat.innerVector(j).squaredNorm();
-        if(sum>0)
-          m_invdiag(j) = RealScalar(1)/sum;
-        else
-          m_invdiag(j) = RealScalar(1);
+        m_invdiag.setZero();
+        for(Index j=0; j<mat.outerSize(); ++j)
+        {
+          for(typename MatType::InnerIterator it(mat,j); it; ++it)
+            m_invdiag(it.index()) += numext::abs2(it.value());
+        }
+        for(Index j=0; j<mat.cols(); ++j)
+          if(numext::real(m_invdiag(j))>RealScalar(0))
+            m_invdiag(j) = RealScalar(1)/numext::real(m_invdiag(j));
+      }
+      else
+      {
+        for(Index j=0; j<mat.outerSize(); ++j)
+        {
+          RealScalar sum = mat.innerVector(j).squaredNorm();
+          if(sum>RealScalar(0))
+            m_invdiag(j) = RealScalar(1)/sum;
+          else
+            m_invdiag(j) = RealScalar(1);
+        }
       }
       Base::m_isInitialized = true;
       return *this;

Eigen/src/Jacobi/Jacobi.h

@@ -302,8 +302,12 @@ template<typename VectorX, typename VectorY, typename OtherScalar>
 void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x, DenseBase<VectorY>& xpr_y, const JacobiRotation<OtherScalar>& j)
 {
   typedef typename VectorX::Scalar Scalar;
-  enum { PacketSize = packet_traits<Scalar>::size };
+  enum {
+    PacketSize = packet_traits<Scalar>::size,
+    OtherPacketSize = packet_traits<OtherScalar>::size
+  };
   typedef typename packet_traits<Scalar>::type Packet;
+  typedef typename packet_traits<OtherScalar>::type OtherPacket;
   eigen_assert(xpr_x.size() == xpr_y.size());
   Index size = xpr_x.size();
   Index incrx = xpr_x.derived().innerStride();
@@ -321,6 +325,7 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
 
   if(VectorX::SizeAtCompileTime == Dynamic &&
     (VectorX::Flags & VectorY::Flags & PacketAccessBit) &&
+    (PacketSize == OtherPacketSize) &&
     ((incrx==1 && incry==1) || PacketSize == 1))
   {
     // both vectors are sequentially stored in memory => vectorization
@@ -329,9 +334,10 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
     Index alignedStart = internal::first_default_aligned(y, size);
     Index alignedEnd = alignedStart + ((size-alignedStart)/PacketSize)*PacketSize;
 
-    const Packet pc = pset1<Packet>(c);
-    const Packet ps = pset1<Packet>(s);
-    conj_helper<Packet,Packet,NumTraits<Scalar>::IsComplex,false> pcj;
+    const OtherPacket pc = pset1<OtherPacket>(c);
+    const OtherPacket ps = pset1<OtherPacket>(s);
+    conj_helper<OtherPacket,Packet,NumTraits<OtherScalar>::IsComplex,false> pcj;
+    conj_helper<OtherPacket,Packet,false,false> pm;
 
     for(Index i=0; i<alignedStart; ++i)
     {
@@ -350,8 +356,8 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
       {
         Packet xi = pload<Packet>(px);
         Packet yi = pload<Packet>(py);
-        pstore(px, padd(pmul(pc,xi),pcj.pmul(ps,yi)));
-        pstore(py, psub(pcj.pmul(pc,yi),pmul(ps,xi)));
+        pstore(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
+        pstore(py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
         px += PacketSize;
         py += PacketSize;
       }
@@ -365,10 +371,10 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
         Packet xi1  = ploadu<Packet>(px+PacketSize);
         Packet yi   = pload <Packet>(py);
         Packet yi1  = pload <Packet>(py+PacketSize);
-        pstoreu(px, padd(pmul(pc,xi),pcj.pmul(ps,yi)));
-        pstoreu(px+PacketSize, padd(pmul(pc,xi1),pcj.pmul(ps,yi1)));
-        pstore (py, psub(pcj.pmul(pc,yi),pmul(ps,xi)));
-        pstore (py+PacketSize, psub(pcj.pmul(pc,yi1),pmul(ps,xi1)));
+        pstoreu(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
+        pstoreu(px+PacketSize, padd(pm.pmul(pc,xi1),pcj.pmul(ps,yi1)));
+        pstore (py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
+        pstore (py+PacketSize, psub(pcj.pmul(pc,yi1),pm.pmul(ps,xi1)));
         px += Peeling*PacketSize;
         py += Peeling*PacketSize;
       }
@@ -376,8 +382,8 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
       {
         Packet xi = ploadu<Packet>(x+peelingEnd);
         Packet yi = pload <Packet>(y+peelingEnd);
-        pstoreu(x+peelingEnd, padd(pmul(pc,xi),pcj.pmul(ps,yi)));
-        pstore (y+peelingEnd, psub(pcj.pmul(pc,yi),pmul(ps,xi)));
+        pstoreu(x+peelingEnd, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
+        pstore (y+peelingEnd, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
       }
     }
 
@@ -393,19 +399,21 @@ void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x
   /*** fixed-size vectorized path ***/
   else if(VectorX::SizeAtCompileTime != Dynamic &&
           (VectorX::Flags & VectorY::Flags & PacketAccessBit) &&
+          (PacketSize == OtherPacketSize) &&
           (EIGEN_PLAIN_ENUM_MIN(evaluator<VectorX>::Alignment, evaluator<VectorY>::Alignment)>0)) // FIXME should be compared to the required alignment
   {
-    const Packet pc = pset1<Packet>(c);
-    const Packet ps = pset1<Packet>(s);
-    conj_helper<Packet,Packet,NumTraits<Scalar>::IsComplex,false> pcj;
+    const OtherPacket pc = pset1<OtherPacket>(c);
+    const OtherPacket ps = pset1<OtherPacket>(s);
+    conj_helper<OtherPacket,Packet,NumTraits<OtherPacket>::IsComplex,false> pcj;
+    conj_helper<OtherPacket,Packet,false,false> pm;
     Scalar* EIGEN_RESTRICT px = x;
     Scalar* EIGEN_RESTRICT py = y;
     for(Index i=0; i<size; i+=PacketSize)
     {
       Packet xi = pload<Packet>(px);
       Packet yi = pload<Packet>(py);
-      pstore(px, padd(pmul(pc,xi),pcj.pmul(ps,yi)));
-      pstore(py, psub(pcj.pmul(pc,yi),pmul(ps,xi)));
+      pstore(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
+      pstore(py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
       px += PacketSize;
       py += PacketSize;
     }

Eigen/src/OrderingMethods/Eigen_Colamd.h

@@ -1004,7 +1004,7 @@ static IndexType find_ordering /* return the number of garbage collections */
     COLAMD_ASSERT (head [min_score] >= COLAMD_EMPTY) ;
 
     /* get pivot column from head of minimum degree list */
-    while (head [min_score] == COLAMD_EMPTY && min_score < n_col)
+    while (min_score < n_col && head [min_score] == COLAMD_EMPTY)
     {
       min_score++ ;
     }

Eigen/src/QR/ColPivHouseholderQR.h

@@ -506,8 +506,8 @@ void ColPivHouseholderQR<MatrixType>::computeInPlace()
     m_colNormsUpdated.coeffRef(k) = m_colNormsDirect.coeffRef(k);
   }
 
-  RealScalar threshold_helper =  numext::abs2<Scalar>(m_colNormsUpdated.maxCoeff() * NumTraits<Scalar>::epsilon()) / RealScalar(rows);
-  RealScalar norm_downdate_threshold = numext::sqrt(NumTraits<Scalar>::epsilon());
+  RealScalar threshold_helper =  numext::abs2<RealScalar>(m_colNormsUpdated.maxCoeff() * NumTraits<RealScalar>::epsilon()) / RealScalar(rows);
+  RealScalar norm_downdate_threshold = numext::sqrt(NumTraits<RealScalar>::epsilon());
 
   m_nonzero_pivots = size; // the generic case is that in which all pivots are nonzero (invertible case)
   m_maxpivot = RealScalar(0);
@@ -553,12 +553,12 @@ void ColPivHouseholderQR<MatrixType>::computeInPlace()
       // http://www.netlib.org/lapack/lawnspdf/lawn176.pdf
       // and used in LAPACK routines xGEQPF and xGEQP3.
       // See lines 278-297 in http://www.netlib.org/lapack/explore-html/dc/df4/sgeqpf_8f_source.html
-      if (m_colNormsUpdated.coeffRef(j) != 0) {
+      if (m_colNormsUpdated.coeffRef(j) != RealScalar(0)) {
         RealScalar temp = abs(m_qr.coeffRef(k, j)) / m_colNormsUpdated.coeffRef(j);
         temp = (RealScalar(1) + temp) * (RealScalar(1) - temp);
-        temp = temp < 0 ? 0 : temp;
-        RealScalar temp2 = temp * numext::abs2<Scalar>(m_colNormsUpdated.coeffRef(j) /
-                                                       m_colNormsDirect.coeffRef(j));
+        temp = temp <  RealScalar(0) ? RealScalar(0) : temp;
+        RealScalar temp2 = temp * numext::abs2<RealScalar>(m_colNormsUpdated.coeffRef(j) /
+                                                           m_colNormsDirect.coeffRef(j));
         if (temp2 <= norm_downdate_threshold) {
           // The updated norm has become too inaccurate so re-compute the column
           // norm directly.

Eigen/src/QR/CompleteOrthogonalDecomposition.h

@@ -138,7 +138,7 @@ class CompleteOrthogonalDecomposition {
    * problem \f[\mathrm{minimize} \|A X - B\|, \f] where \b A is the matrix of
    * which \c *this is the complete orthogonal decomposition.
    *
-   * \param B the right-hand sides of the problem to solve.
+   * \param b the right-hand sides of the problem to solve.
    *
    * \returns a solution.
    *

Eigen/src/SVD/BDCSVD.h

@@ -77,6 +77,7 @@ public:
   typedef _MatrixType MatrixType;
   typedef typename MatrixType::Scalar Scalar;
   typedef typename NumTraits<typename MatrixType::Scalar>::Real RealScalar;
+  typedef typename NumTraits<RealScalar>::Literal Literal;
   enum {
     RowsAtCompileTime = MatrixType::RowsAtCompileTime, 
     ColsAtCompileTime = MatrixType::ColsAtCompileTime, 
@@ -259,7 +260,7 @@ BDCSVD<MatrixType>& BDCSVD<MatrixType>::compute(const MatrixType& matrix, unsign
   
   //**** step 0 - Copy the input matrix and apply scaling to reduce over/under-flows
   RealScalar scale = matrix.cwiseAbs().maxCoeff();
-  if(scale==RealScalar(0)) scale = RealScalar(1);
+  if(scale==Literal(0)) scale = Literal(1);
   MatrixX copy;
   if (m_isTranspose) copy = matrix.adjoint()/scale;
   else               copy = matrix/scale;
@@ -351,13 +352,13 @@ void BDCSVD<MatrixType>::structured_update(Block<MatrixXr,Dynamic,Dynamic> A, co
     Index k1=0, k2=0;
     for(Index j=0; j<n; ++j)
     {
-      if( (A.col(j).head(n1).array()!=0).any() )
+      if( (A.col(j).head(n1).array()!=Literal(0)).any() )
       {
         A1.col(k1) = A.col(j).head(n1);
         B1.row(k1) = B.row(j);
         ++k1;
       }
-      if( (A.col(j).tail(n2).array()!=0).any() )
+      if( (A.col(j).tail(n2).array()!=Literal(0)).any() )
       {
         A2.col(k2) = A.col(j).tail(n2);
         B2.row(k2) = B.row(j);
@@ -449,11 +450,11 @@ void BDCSVD<MatrixType>::divide (Index firstCol, Index lastCol, Index firstRowW,
     l = m_naiveU.row(1).segment(firstCol, k);
     f = m_naiveU.row(0).segment(firstCol + k + 1, n - k - 1);
   }
-  if (m_compV) m_naiveV(firstRowW+k, firstColW) = 1;
+  if (m_compV) m_naiveV(firstRowW+k, firstColW) = Literal(1);
   if (r0<considerZero)
   {
-    c0 = 1;
-    s0 = 0;
+    c0 = Literal(1);
+    s0 = Literal(0);
   }
   else
   {
@@ -574,7 +575,7 @@ void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, Vec
   ArrayRef col0 = m_computed.col(firstCol).segment(firstCol, n);
   m_workspace.head(n) =  m_computed.block(firstCol, firstCol, n, n).diagonal();
   ArrayRef diag = m_workspace.head(n);
-  diag(0) = 0;
+  diag(0) = Literal(0);
 
   // Allocate space for singular values and vectors
   singVals.resize(n);
@@ -590,7 +591,7 @@ void BDCSVD<MatrixType>::computeSVDofM(Index firstCol, Index n, MatrixXr& U, Vec
   // but others are interleaved and we must ignore them at this stage.
   // To this end, let's compute a permutation skipping them:
   Index actual_n = n;
-  while(actual_n>1 && diag(actual_n-1)==0) --actual_n;
+  while(actual_n>1 && diag(actual_n-1)==Literal(0)) --actual_n;
   Index m = 0; // size of the deflated problem
   for(Index k=0;k<actual_n;++k)
     if(abs(col0(k))>considerZero)
@@ -691,7 +692,7 @@ template <typename MatrixType>
 typename BDCSVD<MatrixType>::RealScalar BDCSVD<MatrixType>::secularEq(RealScalar mu, const ArrayRef& col0, const ArrayRef& diag, const IndicesRef &perm, const ArrayRef& diagShifted, RealScalar shift)
 {
   Index m = perm.size();
-  RealScalar res = 1;
+  RealScalar res = Literal(1);
   for(Index i=0; i<m; ++i)
   {
     Index j = perm(i);
@@ -710,16 +711,16 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
 
   Index n = col0.size();
   Index actual_n = n;
-  while(actual_n>1 && col0(actual_n-1)==0) --actual_n;
+  while(actual_n>1 && col0(actual_n-1)==Literal(0)) --actual_n;
 
   for (Index k = 0; k < n; ++k)
   {
-    if (col0(k) == 0 || actual_n==1)
+    if (col0(k) == Literal(0) || actual_n==1)
     {
       // if col0(k) == 0, then entry is deflated, so singular value is on diagonal
       // if actual_n==1, then the deflated problem is already diagonalized
       singVals(k) = k==0 ? col0(0) : diag(k);
-      mus(k) = 0;
+      mus(k) = Literal(0);
       shifts(k) = k==0 ? col0(0) : diag(k);
       continue;
     } 
@@ -733,13 +734,13 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
     {
       // Skip deflated singular values
       Index l = k+1;
-      while(col0(l)==0) { ++l; eigen_internal_assert(l<actual_n); }
+      while(col0(l)==Literal(0)) { ++l; eigen_internal_assert(l<actual_n); }
       right = diag(l);
     }
 
     // first decide whether it's closer to the left end or the right end
-    RealScalar mid = left + (right-left) / 2;
-    RealScalar fMid = secularEq(mid, col0, diag, perm, diag, 0);
+    RealScalar mid = left + (right-left) / Literal(2);
+    RealScalar fMid = secularEq(mid, col0, diag, perm, diag, Literal(0));
 #ifdef EIGEN_BDCSVD_DEBUG_VERBOSE
     std::cout << right-left << "\n";
     std::cout << "fMid = " << fMid << " " << secularEq(mid-left, col0, diag, perm, diag-left, left) << " " << secularEq(mid-right, col0, diag, perm, diag-right, right)   << "\n";
@@ -755,7 +756,7 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
               << " "       << secularEq(0.8*(left+right), col0, diag, perm, diag, 0)
               << " "       << secularEq(0.9*(left+right), col0, diag, perm, diag, 0) << "\n";
 #endif
-    RealScalar shift = (k == actual_n-1 || fMid > 0) ? left : right;
+    RealScalar shift = (k == actual_n-1 || fMid > Literal(0)) ? left : right;
     
     // measure everything relative to shift
     Map<ArrayXr> diagShifted(m_workspace.data()+4*n, n);
@@ -785,13 +786,13 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
 
     // rational interpolation: fit a function of the form a / mu + b through the two previous
     // iterates and use its zero to compute the next iterate
-    bool useBisection = fPrev*fCur>0;
-    while (fCur!=0 && abs(muCur - muPrev) > 8 * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(abs(muCur), abs(muPrev)) && abs(fCur - fPrev)>NumTraits<RealScalar>::epsilon() && !useBisection)
+    bool useBisection = fPrev*fCur>Literal(0);
+    while (fCur!=Literal(0) && abs(muCur - muPrev) > Literal(8) * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(abs(muCur), abs(muPrev)) && abs(fCur - fPrev)>NumTraits<RealScalar>::epsilon() && !useBisection)
     {
       ++m_numIters;
 
       // Find a and b such that the function f(mu) = a / mu + b matches the current and previous samples.
-      RealScalar a = (fCur - fPrev) / (1/muCur - 1/muPrev);
+      RealScalar a = (fCur - fPrev) / (Literal(1)/muCur - Literal(1)/muPrev);
       RealScalar b = fCur - a / muCur;
       // And find mu such that f(mu)==0:
       RealScalar muZero = -a/b;
@@ -803,8 +804,8 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
       fCur = fZero;
       
       
-      if (shift == left  && (muCur < 0 || muCur > right - left)) useBisection = true;
-      if (shift == right && (muCur < -(right - left) || muCur > 0)) useBisection = true;
+      if (shift == left  && (muCur < Literal(0) || muCur > right - left)) useBisection = true;
+      if (shift == right && (muCur < -(right - left) || muCur > Literal(0))) useBisection = true;
       if (abs(fCur)>abs(fPrev)) useBisection = true;
     }
 
@@ -841,13 +842,13 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
         std::cout << k << " : " <<  fLeft << " * " << fRight << " == " << fLeft * fRight << "  ;  " << left << " - " << right << " -> " <<  leftShifted << " " << rightShifted << "   shift=" << shift << "\n";
       }
 #endif
-      eigen_internal_assert(fLeft * fRight < 0);
+      eigen_internal_assert(fLeft * fRight < Literal(0));
       
-      while (rightShifted - leftShifted > 2 * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(abs(leftShifted), abs(rightShifted)))
+      while (rightShifted - leftShifted > Literal(2) * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(abs(leftShifted), abs(rightShifted)))
       {
-        RealScalar midShifted = (leftShifted + rightShifted) / 2;
+        RealScalar midShifted = (leftShifted + rightShifted) / Literal(2);
         fMid = secularEq(midShifted, col0, diag, perm, diagShifted, shift);
-        if (fLeft * fMid < 0)
+        if (fLeft * fMid < Literal(0))
         {
           rightShifted = midShifted;
         }
@@ -858,7 +859,7 @@ void BDCSVD<MatrixType>::computeSingVals(const ArrayRef& col0, const ArrayRef& d
         }
       }
 
-      muCur = (leftShifted + rightShifted) / 2;
+      muCur = (leftShifted + rightShifted) / Literal(2);
     }
       
     singVals[k] = shift + muCur;
@@ -892,8 +893,8 @@ void BDCSVD<MatrixType>::perturbCol0
   // The offset permits to skip deflated entries while computing zhat
   for (Index k = 0; k < n; ++k)
   {
-    if (col0(k) == 0) // deflated
-      zhat(k) = 0;
+    if (col0(k) == Literal(0)) // deflated
+      zhat(k) = Literal(0);
     else
     {
       // see equation (3.6)
@@ -918,7 +919,7 @@ void BDCSVD<MatrixType>::perturbCol0
       std::cout << "zhat(" << k << ") =  sqrt( " << prod << ")  ;  " << (singVals(last) + dk) << " * " << mus(last) + shifts(last) << " - " << dk << "\n";
 #endif
       RealScalar tmp = sqrt(prod);
-      zhat(k) = col0(k) > 0 ? tmp : -tmp;
+      zhat(k) = col0(k) > Literal(0) ? tmp : -tmp;
     }
   }
 }
@@ -934,7 +935,7 @@ void BDCSVD<MatrixType>::computeSingVecs
   
   for (Index k = 0; k < n; ++k)
   {
-    if (zhat(k) == 0)
+    if (zhat(k) == Literal(0))
     {
       U.col(k) = VectorType::Unit(n+1, k);
       if (m_compV) V.col(k) = VectorType::Unit(n, k);
@@ -947,7 +948,7 @@ void BDCSVD<MatrixType>::computeSingVecs
         Index i = perm(l);
         U(i,k) = zhat(i)/(((diag(i) - shifts(k)) - mus(k)) )/( (diag(i) + singVals[k]));
       }
-      U(n,k) = 0;      
+      U(n,k) = Literal(0);
       U.col(k).normalize();
     
       if (m_compV)
@@ -958,7 +959,7 @@ void BDCSVD<MatrixType>::computeSingVecs
           Index i = perm(l);
           V(i,k) = diag(i) * zhat(i) / (((diag(i) - shifts(k)) - mus(k)) )/( (diag(i) + singVals[k]));
         }
-        V(0,k) = -1;
+        V(0,k) = Literal(-1);
         V.col(k).normalize();
       }
     }
@@ -980,14 +981,14 @@ void BDCSVD<MatrixType>::deflation43(Index firstCol, Index shift, Index i, Index
   RealScalar c = m_computed(start, start);
   RealScalar s = m_computed(start+i, start);
   RealScalar r = sqrt(numext::abs2(c) + numext::abs2(s));
-  if (r == 0)
+  if (r == Literal(0))
   {
-    m_computed(start+i, start+i) = 0;
+    m_computed(start+i, start+i) = Literal(0);
     return;
   }
   m_computed(start,start) = r;  
-  m_computed(start+i, start) = 0;
-  m_computed(start+i, start+i) = 0;
+  m_computed(start+i, start) = Literal(0);
+  m_computed(start+i, start+i) = Literal(0);
   
   JacobiRotation<RealScalar> J(c/r,-s/r);
   if (m_compU)  m_naiveU.middleRows(firstCol, size+1).applyOnTheRight(firstCol, firstCol+i, J);
@@ -1020,7 +1021,7 @@ void BDCSVD<MatrixType>::deflation44(Index firstColu , Index firstColm, Index fi
     << m_computed(firstColm + i+1, firstColm+i+1) << " "
     << m_computed(firstColm + i+2, firstColm+i+2) << "\n";
 #endif
-  if (r==0)
+  if (r==Literal(0))
   {
     m_computed(firstColm + i, firstColm + i) = m_computed(firstColm + j, firstColm + j);
     return;
@@ -1029,7 +1030,7 @@ void BDCSVD<MatrixType>::deflation44(Index firstColu , Index firstColm, Index fi
   s/=r;
   m_computed(firstColm + i, firstColm) = r;  
   m_computed(firstColm + j, firstColm + j) = m_computed(firstColm + i, firstColm + i);
-  m_computed(firstColm + j, firstColm) = 0;
+  m_computed(firstColm + j, firstColm) = Literal(0);
 
   JacobiRotation<RealScalar> J(c,-s);
   if (m_compU)  m_naiveU.middleRows(firstColu, size+1).applyOnTheRight(firstColu + i, firstColu + j, J);
@@ -1053,7 +1054,7 @@ void BDCSVD<MatrixType>::deflation(Index firstCol, Index lastCol, Index k, Index
   const RealScalar considerZero = (std::numeric_limits<RealScalar>::min)();
   RealScalar maxDiag = diag.tail((std::max)(Index(1),length-1)).cwiseAbs().maxCoeff();
   RealScalar epsilon_strict = numext::maxi<RealScalar>(considerZero,NumTraits<RealScalar>::epsilon() * maxDiag);
-  RealScalar epsilon_coarse = 8 * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(col0.cwiseAbs().maxCoeff(), maxDiag);
+  RealScalar epsilon_coarse = Literal(8) * NumTraits<RealScalar>::epsilon() * numext::maxi<RealScalar>(col0.cwiseAbs().maxCoeff(), maxDiag);
   
 #ifdef EIGEN_BDCSVD_SANITY_CHECKS
   assert(m_naiveU.allFinite());
@@ -1081,7 +1082,7 @@ void BDCSVD<MatrixType>::deflation(Index firstCol, Index lastCol, Index k, Index
 #ifdef  EIGEN_BDCSVD_DEBUG_VERBOSE
       std::cout << "deflation 4.2, set z(" << i << ") to zero because " << abs(col0(i)) << " < " << epsilon_strict << "  (diag(" << i << ")=" << diag(i) << ")\n";
 #endif
-      col0(i) = 0;
+      col0(i) = Literal(0);
     }
 
   //condition 4.3

Eigen/src/SVD/JacobiSVD.h

@@ -112,9 +112,11 @@ public:
     ColsAtCompileTime = MatrixType::ColsAtCompileTime,
     MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
     MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime,
-    Options = MatrixType::Options
+    TrOptions = RowsAtCompileTime==1 ? (MatrixType::Options & ~(RowMajor))
+              : ColsAtCompileTime==1 ? (MatrixType::Options |   RowMajor)
+              : MatrixType::Options
   };
-  typedef Matrix<Scalar, ColsAtCompileTime, RowsAtCompileTime, Options, MaxColsAtCompileTime, MaxRowsAtCompileTime>
+  typedef Matrix<Scalar, ColsAtCompileTime, RowsAtCompileTime, TrOptions, MaxColsAtCompileTime, MaxRowsAtCompileTime>
           TransposeTypeWithSameStorageOrder;
 
   void allocate(const JacobiSVD<MatrixType, FullPivHouseholderQRPreconditioner>& svd)
@@ -200,10 +202,12 @@ public:
     ColsAtCompileTime = MatrixType::ColsAtCompileTime,
     MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
     MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime,
-    Options = MatrixType::Options
+    TrOptions = RowsAtCompileTime==1 ? (MatrixType::Options & ~(RowMajor))
+              : ColsAtCompileTime==1 ? (MatrixType::Options |   RowMajor)
+              : MatrixType::Options
   };
 
-  typedef Matrix<Scalar, ColsAtCompileTime, RowsAtCompileTime, Options, MaxColsAtCompileTime, MaxRowsAtCompileTime>
+  typedef Matrix<Scalar, ColsAtCompileTime, RowsAtCompileTime, TrOptions, MaxColsAtCompileTime, MaxRowsAtCompileTime>
           TransposeTypeWithSameStorageOrder;
 
   void allocate(const JacobiSVD<MatrixType, ColPivHouseholderQRPreconditioner>& svd)

Eigen/src/SVD/UpperBidiagonalization.h

@@ -159,6 +159,8 @@ void upperbidiagonalization_blocked_helper(MatrixType& A,
                                                       traits<MatrixType>::Flags & RowMajorBit> > Y)
 {
   typedef typename MatrixType::Scalar Scalar;
+  typedef typename MatrixType::RealScalar RealScalar;
+  typedef typename NumTraits<RealScalar>::Literal Literal;
   enum { StorageOrder = traits<MatrixType>::Flags & RowMajorBit };
   typedef InnerStride<int(StorageOrder) == int(ColMajor) ? 1 : Dynamic> ColInnerStride;
   typedef InnerStride<int(StorageOrder) == int(ColMajor) ? Dynamic : 1> RowInnerStride;
@@ -263,7 +265,7 @@ void upperbidiagonalization_blocked_helper(MatrixType& A,
     SubMatType A10( A.block(bs,0, brows-bs,bs) );
     SubMatType A01( A.block(0,bs, bs,bcols-bs) );
     Scalar tmp = A01(bs-1,0);
-    A01(bs-1,0) = 1;
+    A01(bs-1,0) = Literal(1);
     A11.noalias() -= A10 * Y.topLeftCorner(bcols,bs).bottomRows(bcols-bs).adjoint();
     A11.noalias() -= X.topLeftCorner(brows,bs).bottomRows(brows-bs) * A01;
     A01(bs-1,0) = tmp;

Eigen/src/SparseCore/AmbiVector.h

@@ -336,7 +336,7 @@ class AmbiVector<_Scalar,_StorageIndex>::Iterator
       {
         do {
           ++m_cachedIndex;
-        } while (m_cachedIndex<m_vector.m_end && abs(m_vector.m_buffer[m_cachedIndex])<m_epsilon);
+        } while (m_cachedIndex<m_vector.m_end && abs(m_vector.m_buffer[m_cachedIndex])<=m_epsilon);
         if (m_cachedIndex<m_vector.m_end)
           m_cachedValue = m_vector.m_buffer[m_cachedIndex];
         else
@@ -347,7 +347,7 @@ class AmbiVector<_Scalar,_StorageIndex>::Iterator
         ListEl* EIGEN_RESTRICT llElements = reinterpret_cast<ListEl*>(m_vector.m_buffer);
         do {
           m_currentEl = llElements[m_currentEl].next;
-        } while (m_currentEl>=0 && abs(llElements[m_currentEl].value)<m_epsilon);
+        } while (m_currentEl>=0 && abs(llElements[m_currentEl].value)<=m_epsilon);
         if (m_currentEl<0)
         {
           m_cachedIndex = -1;
@@ -363,9 +363,9 @@ class AmbiVector<_Scalar,_StorageIndex>::Iterator
 
   protected:
     const AmbiVector& m_vector; // the target vector
-    StorageIndex m_currentEl;            // the current element in sparse/linked-list mode
+    StorageIndex m_currentEl;   // the current element in sparse/linked-list mode
     RealScalar m_epsilon;       // epsilon used to prune zero coefficients
-    StorageIndex m_cachedIndex;          // current coordinate
+    StorageIndex m_cachedIndex; // current coordinate
     Scalar m_cachedValue;       // current value
     bool m_isDense;             // mode of the vector
 };

Eigen/src/SparseCore/SparseAssign.h

@@ -143,10 +143,7 @@ struct Assignment<DstXprType, SrcXprType, Functor, Sparse2Dense>
       dst.setZero();
     
     internal::evaluator<SrcXprType> srcEval(src);
-    Index dstRows = src.rows();
-    Index dstCols = src.cols();
-    if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
-      dst.resize(dstRows, dstCols);
+    resize_if_allowed(dst, src, func);
     internal::evaluator<DstXprType> dstEval(dst);
     
     const Index outerEvaluationSize = (internal::evaluator<SrcXprType>::Flags&RowMajorBit) ? src.rows() : src.cols();

Eigen/src/SparseCore/SparseCompressedBase.h

@@ -279,11 +279,11 @@ struct evaluator<SparseCompressedBase<Derived> >
     Flags = Derived::Flags
   };
   
-  evaluator() : m_matrix(0)
+  evaluator() : m_matrix(0), m_zero(0)
   {
     EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
   }
-  explicit evaluator(const Derived &mat) : m_matrix(&mat)
+  explicit evaluator(const Derived &mat) : m_matrix(&mat), m_zero(0)
   {
     EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
   }
@@ -296,26 +296,42 @@ struct evaluator<SparseCompressedBase<Derived> >
   operator const Derived&() const { return *m_matrix; }
   
   typedef typename DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
-  Scalar coeff(Index row, Index col) const
-  { return m_matrix->coeff(row,col); }
-  
+  const Scalar& coeff(Index row, Index col) const
+  {
+    Index p = find(row,col);
+
+    if(p==Dynamic)
+      return m_zero;
+    else
+      return m_matrix->const_cast_derived().valuePtr()[p];
+  }
+
   Scalar& coeffRef(Index row, Index col)
+  {
+    Index p = find(row,col);
+    eigen_assert(p!=Dynamic && "written coefficient does not exist");
+    return m_matrix->const_cast_derived().valuePtr()[p];
+  }
+
+protected:
+
+  Index find(Index row, Index col) const
   {
     eigen_internal_assert(row>=0 && row<m_matrix->rows() && col>=0 && col<m_matrix->cols());
-      
+
     const Index outer = Derived::IsRowMajor ? row : col;
     const Index inner = Derived::IsRowMajor ? col : row;
 
     Index start = m_matrix->outerIndexPtr()[outer];
     Index end = m_matrix->isCompressed() ? m_matrix->outerIndexPtr()[outer+1] : m_matrix->outerIndexPtr()[outer] + m_matrix->innerNonZeroPtr()[outer];
-    eigen_assert(end>start && "you are using a non finalized sparse matrix or written coefficient does not exist");
-    const Index p =   std::lower_bound(m_matrix->innerIndexPtr()+start, m_matrix->innerIndexPtr()+end,inner)
-                    - m_matrix->innerIndexPtr();
-    eigen_assert((p<end) && (m_matrix->innerIndexPtr()[p]==inner) && "written coefficient does not exist");
-    return m_matrix->const_cast_derived().valuePtr()[p];
+    eigen_assert(end>=start && "you are using a non finalized sparse matrix or written coefficient does not exist");
+    const Index p = std::lower_bound(m_matrix->innerIndexPtr()+start, m_matrix->innerIndexPtr()+end,inner) - m_matrix->innerIndexPtr();
+
+    return ((p<end) && (m_matrix->innerIndexPtr()[p]==inner)) ? p : Dynamic;
   }
 
   const Derived *m_matrix;
+  const Scalar m_zero;
 };
 
 }

Eigen/src/SparseCore/SparseCwiseBinaryOp.h

@@ -45,7 +45,7 @@ class CwiseBinaryOpImpl<BinaryOp, Lhs, Rhs, Sparse>
       EIGEN_STATIC_ASSERT((
                 (!internal::is_same<typename internal::traits<Lhs>::StorageKind,
                                     typename internal::traits<Rhs>::StorageKind>::value)
-            ||  ((Lhs::Flags&RowMajorBit) == (Rhs::Flags&RowMajorBit))),
+            ||  ((internal::evaluator<Lhs>::Flags&RowMajorBit) == (internal::evaluator<Rhs>::Flags&RowMajorBit))),
             THE_STORAGE_ORDER_OF_BOTH_SIDES_MUST_MATCH);
     }
 };
@@ -110,6 +110,7 @@ public:
     EIGEN_STRONG_INLINE Scalar value() const { return m_value; }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
+    EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return Lhs::IsRowMajor ? m_lhsIter.row() : index(); }
     EIGEN_STRONG_INLINE Index col() const { return Lhs::IsRowMajor ? index() : m_lhsIter.col(); }
 
@@ -193,6 +194,7 @@ public:
     EIGEN_STRONG_INLINE Scalar value() const { eigen_internal_assert(m_id<m_innerSize); return m_value; }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
+    EIGEN_STRONG_INLINE Index outer() const { return m_rhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return IsRowMajor ? m_rhsIter.outer() : m_id; }
     EIGEN_STRONG_INLINE Index col() const { return IsRowMajor ? m_id : m_rhsIter.outer(); }
 
@@ -280,6 +282,7 @@ public:
     EIGEN_STRONG_INLINE Scalar value() const { eigen_internal_assert(m_id<m_innerSize); return m_value; }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
+    EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return IsRowMajor ? m_lhsIter.outer() : m_id; }
     EIGEN_STRONG_INLINE Index col() const { return IsRowMajor ? m_id : m_lhsIter.outer(); }
 
@@ -356,6 +359,16 @@ struct binary_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs>, Itera
   explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
 };
 
+// "sparse ./ dense"
+template<typename T1, typename T2, typename Lhs, typename Rhs>
+struct binary_evaluator<CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs>, IteratorBased, IndexBased>
+  : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs> >
+{
+  typedef CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs> XprType;
+  typedef sparse_conjunction_evaluator<XprType> Base;
+  explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
+};
+
 // "sparse && sparse"
 template<typename Lhs, typename Rhs>
 struct binary_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs>, IteratorBased, IteratorBased>
@@ -432,6 +445,7 @@ public:
     EIGEN_STRONG_INLINE Scalar value() const { return m_functor(m_lhsIter.value(), m_rhsIter.value()); }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_lhsIter.index(); }
+    EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return m_lhsIter.row(); }
     EIGEN_STRONG_INLINE Index col() const { return m_lhsIter.col(); }
 
@@ -503,6 +517,7 @@ public:
     { return m_functor(m_lhsEval.coeff(IsRowMajor?m_outer:m_rhsIter.index(),IsRowMajor?m_rhsIter.index():m_outer), m_rhsIter.value()); }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_rhsIter.index(); }
+    EIGEN_STRONG_INLINE Index outer() const { return m_rhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return m_rhsIter.row(); }
     EIGEN_STRONG_INLINE Index col() const { return m_rhsIter.col(); }
 
@@ -577,6 +592,7 @@ public:
                        m_rhsEval.coeff(IsRowMajor?m_outer:m_lhsIter.index(),IsRowMajor?m_lhsIter.index():m_outer)); }
 
     EIGEN_STRONG_INLINE StorageIndex index() const { return m_lhsIter.index(); }
+    EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
     EIGEN_STRONG_INLINE Index row() const { return m_lhsIter.row(); }
     EIGEN_STRONG_INLINE Index col() const { return m_lhsIter.col(); }
 
@@ -621,6 +637,22 @@ protected:
 * Implementation of SparseMatrixBase and SparseCwise functions/operators
 ***************************************************************************/
 
+template<typename Derived>
+template<typename OtherDerived>
+Derived& SparseMatrixBase<Derived>::operator+=(const EigenBase<OtherDerived> &other)
+{
+  call_assignment(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
+  return derived();
+}
+
+template<typename Derived>
+template<typename OtherDerived>
+Derived& SparseMatrixBase<Derived>::operator-=(const EigenBase<OtherDerived> &other)
+{
+  call_assignment(derived(), other.derived(), internal::assign_op<Scalar,typename OtherDerived::Scalar>());
+  return derived();
+}
+
 template<typename Derived>
 template<typename OtherDerived>
 EIGEN_STRONG_INLINE Derived &

Eigen/src/SparseCore/SparseCwiseUnaryOp.h

@@ -123,8 +123,10 @@ template<typename Derived>
 EIGEN_STRONG_INLINE Derived&
 SparseMatrixBase<Derived>::operator*=(const Scalar& other)
 {
+  typedef typename internal::evaluator<Derived>::InnerIterator EvalIterator;
+  internal::evaluator<Derived> thisEval(derived());
   for (Index j=0; j<outerSize(); ++j)
-    for (typename Derived::InnerIterator i(derived(),j); i; ++i)
+    for (EvalIterator i(thisEval,j); i; ++i)
       i.valueRef() *= other;
   return derived();
 }
@@ -133,8 +135,10 @@ template<typename Derived>
 EIGEN_STRONG_INLINE Derived&
 SparseMatrixBase<Derived>::operator/=(const Scalar& other)
 {
+  typedef typename internal::evaluator<Derived>::InnerIterator EvalIterator;
+  internal::evaluator<Derived> thisEval(derived());
   for (Index j=0; j<outerSize(); ++j)
-    for (typename Derived::InnerIterator i(derived(),j); i; ++i)
+    for (EvalIterator i(thisEval,j); i; ++i)
       i.valueRef() /= other;
   return derived();
 }

Eigen/src/SparseCore/SparseDiagonalProduct.h

@@ -80,6 +80,8 @@ public:
   sparse_diagonal_product_evaluator(const SparseXprType &sparseXpr, const DiagonalCoeffType &diagCoeff)
     : m_sparseXprImpl(sparseXpr), m_diagCoeffImpl(diagCoeff)
   {}
+
+  Index nonZerosEstimate() const { return m_sparseXprImpl.nonZerosEstimate(); }
     
 protected:
   evaluator<SparseXprType> m_sparseXprImpl;
@@ -121,6 +123,8 @@ struct sparse_diagonal_product_evaluator<SparseXprType, DiagCoeffType, SDP_AsCwi
   sparse_diagonal_product_evaluator(const SparseXprType &sparseXpr, const DiagCoeffType &diagCoeff)
     : m_sparseXprEval(sparseXpr), m_diagCoeffNested(diagCoeff)
   {}
+
+  Index nonZerosEstimate() const { return m_sparseXprEval.nonZerosEstimate(); }
     
 protected:
   evaluator<SparseXprType> m_sparseXprEval;

Eigen/src/SparseCore/SparseMatrix.h

@@ -32,18 +32,22 @@ namespace Eigen {
   * \tparam _Scalar the scalar type, i.e. the type of the coefficients
   * \tparam _Options Union of bit flags controlling the storage scheme. Currently the only possibility
   *                 is ColMajor or RowMajor. The default is 0 which means column-major.
-  * \tparam _Index the type of the indices. It has to be a \b signed type (e.g., short, int, std::ptrdiff_t). Default is \c int.
+  * \tparam _StorageIndex the type of the indices. It has to be a \b signed type (e.g., short, int, std::ptrdiff_t). Default is \c int.
+  *
+  * \warning In %Eigen 3.2, the undocumented type \c SparseMatrix::Index was improperly defined as the storage index type (e.g., int),
+  *          whereas it is now (starting from %Eigen 3.3) deprecated and always defined as Eigen::Index.
+  *          Codes making use of \c SparseMatrix::Index, might thus likely have to be changed to use \c SparseMatrix::StorageIndex instead.
   *
   * This class can be extended with the help of the plugin mechanism described on the page
   * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_SPARSEMATRIX_PLUGIN.
   */
 
 namespace internal {
-template<typename _Scalar, int _Options, typename _Index>
-struct traits<SparseMatrix<_Scalar, _Options, _Index> >
+template<typename _Scalar, int _Options, typename _StorageIndex>
+struct traits<SparseMatrix<_Scalar, _Options, _StorageIndex> >
 {
   typedef _Scalar Scalar;
-  typedef _Index StorageIndex;
+  typedef _StorageIndex StorageIndex;
   typedef Sparse StorageKind;
   typedef MatrixXpr XprKind;
   enum {
@@ -56,16 +60,16 @@ struct traits<SparseMatrix<_Scalar, _Options, _Index> >
   };
 };
 
-template<typename _Scalar, int _Options, typename _Index, int DiagIndex>
-struct traits<Diagonal<SparseMatrix<_Scalar, _Options, _Index>, DiagIndex> >
+template<typename _Scalar, int _Options, typename _StorageIndex, int DiagIndex>
+struct traits<Diagonal<SparseMatrix<_Scalar, _Options, _StorageIndex>, DiagIndex> >
 {
-  typedef SparseMatrix<_Scalar, _Options, _Index> MatrixType;
+  typedef SparseMatrix<_Scalar, _Options, _StorageIndex> MatrixType;
   typedef typename ref_selector<MatrixType>::type MatrixTypeNested;
   typedef typename remove_reference<MatrixTypeNested>::type _MatrixTypeNested;
 
   typedef _Scalar Scalar;
   typedef Dense StorageKind;
-  typedef _Index StorageIndex;
+  typedef _StorageIndex StorageIndex;
   typedef MatrixXpr XprKind;
 
   enum {
@@ -77,9 +81,9 @@ struct traits<Diagonal<SparseMatrix<_Scalar, _Options, _Index>, DiagIndex> >
   };
 };
 
-template<typename _Scalar, int _Options, typename _Index, int DiagIndex>
-struct traits<Diagonal<const SparseMatrix<_Scalar, _Options, _Index>, DiagIndex> >
- : public traits<Diagonal<SparseMatrix<_Scalar, _Options, _Index>, DiagIndex> >
+template<typename _Scalar, int _Options, typename _StorageIndex, int DiagIndex>
+struct traits<Diagonal<const SparseMatrix<_Scalar, _Options, _StorageIndex>, DiagIndex> >
+ : public traits<Diagonal<SparseMatrix<_Scalar, _Options, _StorageIndex>, DiagIndex> >
 {
   enum {
     Flags = 0
@@ -88,13 +92,13 @@ struct traits<Diagonal<const SparseMatrix<_Scalar, _Options, _Index>, DiagIndex>
 
 } // end namespace internal
 
-template<typename _Scalar, int _Options, typename _Index>
+template<typename _Scalar, int _Options, typename _StorageIndex>
 class SparseMatrix
-  : public SparseCompressedBase<SparseMatrix<_Scalar, _Options, _Index> >
+  : public SparseCompressedBase<SparseMatrix<_Scalar, _Options, _StorageIndex> >
 {
     typedef SparseCompressedBase<SparseMatrix> Base;
     using Base::convert_index;
-    friend class SparseVector<_Scalar,0,_Index>;
+    friend class SparseVector<_Scalar,0,_StorageIndex>;
   public:
     using Base::isCompressed;
     using Base::nonZeros;
@@ -984,11 +988,11 @@ void set_from_triplets(const InputIterator& begin, const InputIterator& end, Spa
   * an abstract iterator over a complex data-structure that would be expensive to evaluate. The triplets should rather
   * be explicitely stored into a std::vector for instance.
   */
-template<typename Scalar, int _Options, typename _Index>
+template<typename Scalar, int _Options, typename _StorageIndex>
 template<typename InputIterators>
-void SparseMatrix<Scalar,_Options,_Index>::setFromTriplets(const InputIterators& begin, const InputIterators& end)
+void SparseMatrix<Scalar,_Options,_StorageIndex>::setFromTriplets(const InputIterators& begin, const InputIterators& end)
 {
-  internal::set_from_triplets<InputIterators, SparseMatrix<Scalar,_Options,_Index> >(begin, end, *this, internal::scalar_sum_op<Scalar,Scalar>());
+  internal::set_from_triplets<InputIterators, SparseMatrix<Scalar,_Options,_StorageIndex> >(begin, end, *this, internal::scalar_sum_op<Scalar,Scalar>());
 }
 
 /** The same as setFromTriplets but when duplicates are met the functor \a dup_func is applied:
@@ -1000,17 +1004,17 @@ void SparseMatrix<Scalar,_Options,_Index>::setFromTriplets(const InputIterators&
   * mat.setFromTriplets(triplets.begin(), triplets.end(), [] (const Scalar&,const Scalar &b) { return b; });
   * \endcode
   */
-template<typename Scalar, int _Options, typename _Index>
+template<typename Scalar, int _Options, typename _StorageIndex>
 template<typename InputIterators,typename DupFunctor>
-void SparseMatrix<Scalar,_Options,_Index>::setFromTriplets(const InputIterators& begin, const InputIterators& end, DupFunctor dup_func)
+void SparseMatrix<Scalar,_Options,_StorageIndex>::setFromTriplets(const InputIterators& begin, const InputIterators& end, DupFunctor dup_func)
 {
-  internal::set_from_triplets<InputIterators, SparseMatrix<Scalar,_Options,_Index>, DupFunctor>(begin, end, *this, dup_func);
+  internal::set_from_triplets<InputIterators, SparseMatrix<Scalar,_Options,_StorageIndex>, DupFunctor>(begin, end, *this, dup_func);
 }
 
 /** \internal */
-template<typename Scalar, int _Options, typename _Index>
+template<typename Scalar, int _Options, typename _StorageIndex>
 template<typename DupFunctor>
-void SparseMatrix<Scalar,_Options,_Index>::collapseDuplicates(DupFunctor dup_func)
+void SparseMatrix<Scalar,_Options,_StorageIndex>::collapseDuplicates(DupFunctor dup_func)
 {
   eigen_assert(!isCompressed());
   // TODO, in practice we should be able to use m_innerNonZeros for that task
@@ -1048,9 +1052,9 @@ void SparseMatrix<Scalar,_Options,_Index>::collapseDuplicates(DupFunctor dup_fun
   m_data.resize(m_outerIndex[m_outerSize]);
 }
 
-template<typename Scalar, int _Options, typename _Index>
+template<typename Scalar, int _Options, typename _StorageIndex>
 template<typename OtherDerived>
-EIGEN_DONT_INLINE SparseMatrix<Scalar,_Options,_Index>& SparseMatrix<Scalar,_Options,_Index>::operator=(const SparseMatrixBase<OtherDerived>& other)
+EIGEN_DONT_INLINE SparseMatrix<Scalar,_Options,_StorageIndex>& SparseMatrix<Scalar,_Options,_StorageIndex>::operator=(const SparseMatrixBase<OtherDerived>& other)
 {
   EIGEN_STATIC_ASSERT((internal::is_same<Scalar, typename OtherDerived::Scalar>::value),
         YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
@@ -1121,8 +1125,8 @@ EIGEN_DONT_INLINE SparseMatrix<Scalar,_Options,_Index>& SparseMatrix<Scalar,_Opt
   }
 }
 
-template<typename _Scalar, int _Options, typename _Index>
-typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& SparseMatrix<_Scalar,_Options,_Index>::insert(Index row, Index col)
+template<typename _Scalar, int _Options, typename _StorageIndex>
+typename SparseMatrix<_Scalar,_Options,_StorageIndex>::Scalar& SparseMatrix<_Scalar,_Options,_StorageIndex>::insert(Index row, Index col)
 {
   eigen_assert(row>=0 && row<rows() && col>=0 && col<cols());
   
@@ -1241,8 +1245,8 @@ typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& SparseMatrix<_Scalar,_Op
   return insertUncompressed(row,col);
 }
     
-template<typename _Scalar, int _Options, typename _Index>
-EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& SparseMatrix<_Scalar,_Options,_Index>::insertUncompressed(Index row, Index col)
+template<typename _Scalar, int _Options, typename _StorageIndex>
+EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_StorageIndex>::Scalar& SparseMatrix<_Scalar,_Options,_StorageIndex>::insertUncompressed(Index row, Index col)
 {
   eigen_assert(!isCompressed());
 
@@ -1273,8 +1277,8 @@ EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& Sparse
   return (m_data.value(p) = 0);
 }
 
-template<typename _Scalar, int _Options, typename _Index>
-EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& SparseMatrix<_Scalar,_Options,_Index>::insertCompressed(Index row, Index col)
+template<typename _Scalar, int _Options, typename _StorageIndex>
+EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_StorageIndex>::Scalar& SparseMatrix<_Scalar,_Options,_StorageIndex>::insertCompressed(Index row, Index col)
 {
   eigen_assert(isCompressed());
 
@@ -1297,11 +1301,11 @@ EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& Sparse
   // starts with: [ 0 0 0 0 0 1 ...] and we are inserted in, e.g.,
   // the 2nd inner vector...
   bool isLastVec = (!(previousOuter==-1 && m_data.size()!=0))
-                && (size_t(m_outerIndex[outer+1]) == m_data.size());
+                && (std::size_t(m_outerIndex[outer+1]) == m_data.size());
 
-  size_t startId = m_outerIndex[outer];
-  // FIXME let's make sure sizeof(long int) == sizeof(size_t)
-  size_t p = m_outerIndex[outer+1];
+  std::size_t startId = m_outerIndex[outer];
+  // FIXME let's make sure sizeof(long int) == sizeof(std::size_t)
+  std::size_t p = m_outerIndex[outer+1];
   ++m_outerIndex[outer+1];
 
   double reallocRatio = 1;
@@ -1382,12 +1386,12 @@ EIGEN_DONT_INLINE typename SparseMatrix<_Scalar,_Options,_Index>::Scalar& Sparse
 
 namespace internal {
 
-template<typename _Scalar, int _Options, typename _Index>
-struct evaluator<SparseMatrix<_Scalar,_Options,_Index> >
-  : evaluator<SparseCompressedBase<SparseMatrix<_Scalar,_Options,_Index> > >
+template<typename _Scalar, int _Options, typename _StorageIndex>
+struct evaluator<SparseMatrix<_Scalar,_Options,_StorageIndex> >
+  : evaluator<SparseCompressedBase<SparseMatrix<_Scalar,_Options,_StorageIndex> > >
 {
-  typedef evaluator<SparseCompressedBase<SparseMatrix<_Scalar,_Options,_Index> > > Base;
-  typedef SparseMatrix<_Scalar,_Options,_Index> SparseMatrixType;
+  typedef evaluator<SparseCompressedBase<SparseMatrix<_Scalar,_Options,_StorageIndex> > > Base;
+  typedef SparseMatrix<_Scalar,_Options,_StorageIndex> SparseMatrixType;
   evaluator() : Base() {}
   explicit evaluator(const SparseMatrixType &mat) : Base(mat) {}
 };

Eigen/src/SparseCore/SparseMatrixBase.h

@@ -37,7 +37,11 @@ template<typename Derived> class SparseMatrixBase
     
     typedef typename internal::packet_traits<Scalar>::type PacketScalar;
     typedef typename internal::traits<Derived>::StorageKind StorageKind;
+
+    /** The integer type used to \b store indices within a SparseMatrix.
+      * For a \c SparseMatrix<Scalar,Options,IndexType> it an alias of the third template parameter \c IndexType. */
     typedef typename internal::traits<Derived>::StorageIndex StorageIndex;
+
     typedef typename internal::add_const_on_value_type_if_arithmetic<
                          typename internal::packet_traits<Scalar>::type
                      >::type PacketReturnType;
@@ -213,7 +217,7 @@ template<typename Derived> class SparseMatrixBase
 
       if (Flags&RowMajorBit)
       {
-        const Nested nm(m.derived());
+        Nested nm(m.derived());
         internal::evaluator<NestedCleaned> thisEval(nm);
         for (Index row=0; row<nm.outerSize(); ++row)
         {
@@ -232,7 +236,7 @@ template<typename Derived> class SparseMatrixBase
       }
       else
       {
-        const Nested nm(m.derived());
+        Nested nm(m.derived());
         internal::evaluator<NestedCleaned> thisEval(nm);
         if (m.cols() == 1) {
           Index row = 0;
@@ -265,6 +269,11 @@ template<typename Derived> class SparseMatrixBase
     template<typename OtherDerived>
     Derived& operator-=(const DiagonalBase<OtherDerived>& other);
 
+    template<typename OtherDerived>
+    Derived& operator+=(const EigenBase<OtherDerived> &other);
+    template<typename OtherDerived>
+    Derived& operator-=(const EigenBase<OtherDerived> &other);
+
     Derived& operator*=(const Scalar& other);
     Derived& operator/=(const Scalar& other);
 

Eigen/src/SparseCore/SparseSelfAdjointView.h

@@ -47,6 +47,7 @@ template<typename MatrixType, unsigned int _Mode> class SparseSelfAdjointView
     
     enum {
       Mode = _Mode,
+      TransposeMode = ((Mode & Upper) ? Lower : 0) | ((Mode & Lower) ? Upper : 0),
       RowsAtCompileTime = internal::traits<SparseSelfAdjointView>::RowsAtCompileTime,
       ColsAtCompileTime = internal::traits<SparseSelfAdjointView>::ColsAtCompileTime
     };
@@ -222,14 +223,43 @@ template< typename DstXprType, typename SrcXprType, typename Functor>
 struct Assignment<DstXprType, SrcXprType, Functor, SparseSelfAdjoint2Sparse>
 {
   typedef typename DstXprType::StorageIndex StorageIndex;
+  typedef internal::assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> AssignOpType;
+
   template<typename DestScalar,int StorageOrder>
-  static void run(SparseMatrix<DestScalar,StorageOrder,StorageIndex> &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> &/*func*/)
+  static void run(SparseMatrix<DestScalar,StorageOrder,StorageIndex> &dst, const SrcXprType &src, const AssignOpType&/*func*/)
   {
     internal::permute_symm_to_fullsymm<SrcXprType::Mode>(src.matrix(), dst);
   }
+
+  // FIXME: the handling of += and -= in sparse matrices should be cleanup so that next two overloads could be reduced to:
+  template<typename DestScalar,int StorageOrder,typename AssignFunc>
+  static void run(SparseMatrix<DestScalar,StorageOrder,StorageIndex> &dst, const SrcXprType &src, const AssignFunc& func)
+  {
+    SparseMatrix<DestScalar,StorageOrder,StorageIndex> tmp(src.rows(),src.cols());
+    run(tmp, src, AssignOpType());
+    call_assignment_no_alias_no_transpose(dst, tmp, func);
+  }
+
+  template<typename DestScalar,int StorageOrder>
+  static void run(SparseMatrix<DestScalar,StorageOrder,StorageIndex> &dst, const SrcXprType &src,
+                  const internal::add_assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar>& /* func */)
+  {
+    SparseMatrix<DestScalar,StorageOrder,StorageIndex> tmp(src.rows(),src.cols());
+    run(tmp, src, AssignOpType());
+    dst += tmp;
+  }
+
+  template<typename DestScalar,int StorageOrder>
+  static void run(SparseMatrix<DestScalar,StorageOrder,StorageIndex> &dst, const SrcXprType &src,
+                  const internal::sub_assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar>& /* func */)
+  {
+    SparseMatrix<DestScalar,StorageOrder,StorageIndex> tmp(src.rows(),src.cols());
+    run(tmp, src, AssignOpType());
+    dst -= tmp;
+  }
   
   template<typename DestScalar>
-  static void run(DynamicSparseMatrix<DestScalar,ColMajor,StorageIndex>& dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> &/*func*/)
+  static void run(DynamicSparseMatrix<DestScalar,ColMajor,StorageIndex>& dst, const SrcXprType &src, const AssignOpType&/*func*/)
   {
     // TODO directly evaluate into dst;
     SparseMatrix<DestScalar,ColMajor,StorageIndex> tmp(dst.rows(),dst.cols());
@@ -339,7 +369,7 @@ struct generic_product_impl<Lhs, RhsView, DenseShape, SparseSelfAdjointShape, Pr
     
     // transpose everything
     Transpose<Dest> dstT(dst);
-    internal::sparse_selfadjoint_time_dense_product<RhsView::Mode>(rhsNested.transpose(), lhsNested.transpose(), dstT, alpha);
+    internal::sparse_selfadjoint_time_dense_product<RhsView::TransposeMode>(rhsNested.transpose(), lhsNested.transpose(), dstT, alpha);
   }
 };
 

Eigen/src/SparseCore/SparseTriangularView.h

@@ -55,7 +55,10 @@ template<typename MatrixType, unsigned int Mode> class TriangularViewImpl<Matrix
       this->solveInPlace(dst);
     }
 
+    /** Applies the inverse of \c *this to the dense vector or matrix \a other, "in-place" */
     template<typename OtherDerived> void solveInPlace(MatrixBase<OtherDerived>& other) const;
+
+    /** Applies the inverse of \c *this to the sparse vector or matrix \a other, "in-place" */
     template<typename OtherDerived> void solveInPlace(SparseMatrixBase<OtherDerived>& other) const;
   
 };

Eigen/src/SparseCore/SparseView.h

@@ -27,6 +27,20 @@ struct traits<SparseView<MatrixType> > : traits<MatrixType>
 
 } // end namespace internal
 
+/** \ingroup SparseCore_Module
+  * \class SparseView
+  *
+  * \brief Expression of a dense or sparse matrix with zero or too small values removed
+  *
+  * \tparam MatrixType the type of the object of which we are removing the small entries
+  *
+  * This class represents an expression of a given dense or sparse matrix with
+  * entries smaller than \c reference * \c epsilon are removed.
+  * It is the return type of MatrixBase::sparseView() and SparseMatrixBase::pruned()
+  * and most of the time this is the only way it is used.
+  *
+  * \sa MatrixBase::sparseView(), SparseMatrixBase::pruned()
+  */
 template<typename MatrixType>
 class SparseView : public SparseMatrixBase<SparseView<MatrixType> >
 {
@@ -190,6 +204,23 @@ struct unary_evaluator<SparseView<ArgType>, IndexBased>
 
 } // end namespace internal
 
+/** \ingroup SparseCore_Module
+  *
+  * \returns a sparse expression of the dense expression \c *this with values smaller than
+  * \a reference * \a epsilon removed.
+  *
+  * This method is typically used when prototyping to convert a quickly assembled dense Matrix \c D to a SparseMatrix \c S:
+  * \code
+  * MatrixXd D(n,m);
+  * SparseMatrix<double> S;
+  * S = D.sparseView();             // suppress numerical zeros (exact)
+  * S = D.sparseView(reference);
+  * S = D.sparseView(reference,epsilon);
+  * \endcode
+  * where \a reference is a meaningful non zero reference value,
+  * and \a epsilon is a tolerance factor defaulting to NumTraits<Scalar>::dummy_precision().
+  *
+  * \sa SparseMatrixBase::pruned(), class SparseView */
 template<typename Derived>
 const SparseView<Derived> MatrixBase<Derived>::sparseView(const Scalar& reference,
                                                           const typename NumTraits<Scalar>::Real& epsilon) const
@@ -198,7 +229,7 @@ const SparseView<Derived> MatrixBase<Derived>::sparseView(const Scalar& referenc
 }
 
 /** \returns an expression of \c *this with values smaller than
-  * \a reference * \a epsilon are removed.
+  * \a reference * \a epsilon removed.
   *
   * This method is typically used in conjunction with the product of two sparse matrices
   * to automatically prune the smallest values as follows:

Eigen/src/SparseCore/TriangularSolver.h

@@ -171,6 +171,8 @@ struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Upper,ColMajor>
 
 } // end namespace internal
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+
 template<typename ExpressionType,unsigned int Mode>
 template<typename OtherDerived>
 void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(MatrixBase<OtherDerived>& other) const
@@ -189,6 +191,7 @@ void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(MatrixBase<Oth
   if (copy)
     other = otherCopy;
 }
+#endif
 
 // pure sparse path
 
@@ -286,6 +289,7 @@ struct sparse_solve_triangular_sparse_selector<Lhs,Rhs,Mode,UpLo,ColMajor>
 
 } // end namespace internal
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename ExpressionType,unsigned int Mode>
 template<typename OtherDerived>
 void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(SparseMatrixBase<OtherDerived>& other) const
@@ -304,6 +308,7 @@ void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(SparseMatrixBa
 //   if (copy)
 //     other = otherCopy;
 }
+#endif
 
 } // end namespace Eigen
 

Eigen/src/SparseLU/SparseLU.h

@@ -748,7 +748,7 @@ struct SparseLUMatrixUReturnType : internal::no_assignment_operator
       else
       {
         Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(m_mapL.valuePtr()[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
+        Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
         U = A.template triangularView<Upper>().solve(U);
       }
 

Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h

@@ -239,7 +239,7 @@ void MappedSuperNodalMatrix<Scalar,Index_>::solveInPlace( MatrixBase<Dest>&X) co
     Index n    = int(X.rows());
     Index nrhs = Index(X.cols());
     const Scalar * Lval = valuePtr();                 // Nonzero values 
-    Matrix<Scalar,Dynamic,Dynamic, ColMajor> work(n, nrhs);     // working vector
+    Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor> work(n, nrhs);     // working vector
     work.setZero();
     for (Index k = 0; k <= nsuper(); k ++)
     {
@@ -271,12 +271,12 @@ void MappedSuperNodalMatrix<Scalar,Index_>::solveInPlace( MatrixBase<Dest>&X) co
         
         // Triangular solve 
         Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > A( &(Lval[luptr]), nsupc, nsupc, OuterStride<>(lda) );
-        Map< Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) ); 
+        Map< Matrix<Scalar,Dynamic,Dest::ColsAtCompileTime, ColMajor>, 0, OuterStride<> > U (&(X(fsupc,0)), nsupc, nrhs, OuterStride<>(n) );
         U = A.template triangularView<UnitLower>().solve(U); 
         
         // Matrix-vector product 
         new (&A) Map<const Matrix<Scalar,Dynamic,Dynamic, ColMajor>, 0, OuterStride<> > ( &(Lval[luptr+nsupc]), nrow, nsupc, OuterStride<>(lda) );
-        work.block(0, 0, nrow, nrhs) = A * U; 
+        work.topRows(nrow).noalias() = A * U;
         
         //Begin Scatter 
         for (Index j = 0; j < nrhs; j++)

Eigen/src/StlSupport/details.h

@@ -22,13 +22,13 @@ namespace Eigen {
   class aligned_allocator_indirection : public EIGEN_ALIGNED_ALLOCATOR<T>
   {
   public:
-    typedef size_t    size_type;
-    typedef ptrdiff_t difference_type;
-    typedef T*        pointer;
-    typedef const T*  const_pointer;
-    typedef T&        reference;
-    typedef const T&  const_reference;
-    typedef T         value_type;
+    typedef std::size_t     size_type;
+    typedef std::ptrdiff_t  difference_type;
+    typedef T*              pointer;
+    typedef const T*        const_pointer;
+    typedef T&              reference;
+    typedef const T&        const_reference;
+    typedef T               value_type;
 
     template<class U>
     struct rebind

Eigen/src/SuperLUSupport/SuperLUSupport.h

@@ -967,6 +967,7 @@ void SuperILU<MatrixType>::factorize(const MatrixType& a)
   m_factorizationIsOk = true;
 }
 
+#ifndef EIGEN_PARSED_BY_DOXYGEN
 template<typename MatrixType>
 template<typename Rhs,typename Dest>
 void SuperILU<MatrixType>::_solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest>& x) const
@@ -1019,6 +1020,8 @@ void SuperILU<MatrixType>::_solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest
 }
 #endif
 
+#endif
+
 } // end namespace Eigen
 
 #endif // EIGEN_SUPERLUSUPPORT_H

Eigen/src/UmfPackSupport/UmfPackSupport.h

@@ -10,19 +10,37 @@
 #ifndef EIGEN_UMFPACKSUPPORT_H
 #define EIGEN_UMFPACKSUPPORT_H
 
-namespace Eigen { 
+namespace Eigen {
 
 /* TODO extract L, extract U, compute det, etc... */
 
 // generic double/complex<double> wrapper functions:
 
 
-inline void umfpack_defaults(double control[UMFPACK_CONTROL], double) 
+inline void umfpack_defaults(double control[UMFPACK_CONTROL], double)
 { umfpack_di_defaults(control); }
 
-inline void umfpack_defaults(double control[UMFPACK_CONTROL], std::complex<double>) 
+inline void umfpack_defaults(double control[UMFPACK_CONTROL], std::complex<double>)
 { umfpack_zi_defaults(control); }
 
+inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], double)
+{ umfpack_di_report_info(control, info);}
+
+inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], std::complex<double>)
+{ umfpack_zi_report_info(control, info);}
+
+inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, double)
+{ umfpack_di_report_status(control, status);}
+
+inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, std::complex<double>)
+{ umfpack_zi_report_status(control, status);}
+
+inline void umfpack_report_control(double control[UMFPACK_CONTROL], double)
+{ umfpack_di_report_control(control);}
+
+inline void umfpack_report_control(double control[UMFPACK_CONTROL], std::complex<double>)
+{ umfpack_zi_report_control(control);}
+
 inline void umfpack_free_numeric(void **Numeric, double)
 { umfpack_di_free_numeric(Numeric); *Numeric = 0; }
 
@@ -156,6 +174,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
   public:
 
     typedef Array<double, UMFPACK_CONTROL, 1> UmfpackControl;
+    typedef Array<double, UMFPACK_INFO, 1> UmfpackInfo;
 
     UmfPackLU()
       : m_dummy(0,0), mp_matrix(m_dummy)
@@ -215,7 +234,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
       return m_q;
     }
 
-    /** Computes the sparse Cholesky decomposition of \a matrix 
+    /** Computes the sparse Cholesky decomposition of \a matrix
      *  Note that the matrix should be column-major, and in compressed format for best performance.
      *  \sa SparseMatrix::makeCompressed().
      */
@@ -240,7 +259,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
     {
       if(m_symbolic) umfpack_free_symbolic(&m_symbolic,Scalar());
       if(m_numeric)  umfpack_free_numeric(&m_numeric,Scalar());
-      
+
       grab(matrix.derived());
 
       analyzePattern_impl();
@@ -267,7 +286,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
     {
       return m_control;
     }
-    
+
     /** Provides access to the control settings array used by UmfPack.
       *
       * If this array contains NaN's, the default values are used.
@@ -278,7 +297,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
     {
       return m_control;
     }
-    
+
     /** Performs a numeric decomposition of \a matrix
       *
       * The given matrix must has the same sparcity than the matrix on which the pattern anylysis has been performed.
@@ -293,10 +312,38 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
         umfpack_free_numeric(&m_numeric,Scalar());
 
       grab(matrix.derived());
-      
+
       factorize_impl();
     }
 
+    /** Prints the current UmfPack control settings.
+      *
+      * \sa umfpackControl()
+      */
+    void umfpackReportControl()
+    {
+      umfpack_report_control(m_control.data(), Scalar());
+    }
+
+    /** Prints statistics collected by UmfPack.
+      *
+      * \sa analyzePattern(), compute()
+      */
+    void umfpackReportInfo()
+    {
+      eigen_assert(m_analysisIsOk && "UmfPackLU: you must first call analyzePattern()");
+      umfpack_report_info(m_control.data(), m_umfpackInfo.data(), Scalar());
+    }
+
+    /** Prints the status of the previous factorization operation performed by UmfPack (symbolic or numerical factorization).
+      *
+      * \sa analyzePattern(), compute()
+      */
+    void umfpackReportStatus() {
+      eigen_assert(m_analysisIsOk && "UmfPackLU: you must first call analyzePattern()");
+      umfpack_report_status(m_control.data(), m_fact_errorCode, Scalar());
+    }
+
     /** \internal */
     template<typename BDerived,typename XDerived>
     bool _solve_impl(const MatrixBase<BDerived> &b, MatrixBase<XDerived> &x) const;
@@ -314,41 +361,42 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
       m_numeric               = 0;
       m_symbolic              = 0;
       m_extractedDataAreDirty = true;
+
+      umfpack_defaults(m_control.data(), Scalar());
     }
-    
+
     void analyzePattern_impl()
     {
-      umfpack_defaults(m_control.data(), Scalar());
-      int errorCode = 0;
-      errorCode = umfpack_symbolic(internal::convert_index<int>(mp_matrix.rows()),
-                                   internal::convert_index<int>(mp_matrix.cols()),
-                                   mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
-                                   &m_symbolic, m_control.data(), 0);
+      m_fact_errorCode = umfpack_symbolic(internal::convert_index<int>(mp_matrix.rows()),
+                                          internal::convert_index<int>(mp_matrix.cols()),
+                                          mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
+                                          &m_symbolic, m_control.data(), m_umfpackInfo.data());
 
       m_isInitialized = true;
-      m_info = errorCode ? InvalidInput : Success;
+      m_info = m_fact_errorCode ? InvalidInput : Success;
       m_analysisIsOk = true;
       m_factorizationIsOk = false;
       m_extractedDataAreDirty = true;
     }
-    
+
     void factorize_impl()
     {
+
       m_fact_errorCode = umfpack_numeric(mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
-                                         m_symbolic, &m_numeric, m_control.data(), 0);
+                                         m_symbolic, &m_numeric, m_control.data(), m_umfpackInfo.data());
 
       m_info = m_fact_errorCode == UMFPACK_OK ? Success : NumericalIssue;
       m_factorizationIsOk = true;
       m_extractedDataAreDirty = true;
     }
-    
+
     template<typename MatrixDerived>
     void grab(const EigenBase<MatrixDerived> &A)
     {
       mp_matrix.~UmfpackMatrixRef();
       ::new (&mp_matrix) UmfpackMatrixRef(A.derived());
     }
-    
+
     void grab(const UmfpackMatrixRef &A)
     {
       if(&(A.derived()) != &mp_matrix)
@@ -357,19 +405,20 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
         ::new (&mp_matrix) UmfpackMatrixRef(A);
       }
     }
-  
+
     // cached data to reduce reallocation, etc.
     mutable LUMatrixType m_l;
     int m_fact_errorCode;
     UmfpackControl m_control;
-    
+    mutable UmfpackInfo m_umfpackInfo;
+
     mutable LUMatrixType m_u;
     mutable IntColVectorType m_p;
     mutable IntRowVectorType m_q;
 
     UmfpackMatrixType m_dummy;
     UmfpackMatrixRef mp_matrix;
-  
+
     void* m_numeric;
     void* m_symbolic;
 
@@ -377,7 +426,7 @@ class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
     int m_factorizationIsOk;
     int m_analysisIsOk;
     mutable bool m_extractedDataAreDirty;
-    
+
   private:
     UmfPackLU(const UmfPackLU& ) { }
 };
@@ -427,7 +476,7 @@ bool UmfPackLU<MatrixType>::_solve_impl(const MatrixBase<BDerived> &b, MatrixBas
   eigen_assert((BDerived::Flags&RowMajorBit)==0 && "UmfPackLU backend does not support non col-major rhs yet");
   eigen_assert((XDerived::Flags&RowMajorBit)==0 && "UmfPackLU backend does not support non col-major result yet");
   eigen_assert(b.derived().data() != x.derived().data() && " Umfpack does not support inplace solve");
-  
+
   int errorCode;
   Scalar* x_ptr = 0;
   Matrix<Scalar,Dynamic,1> x_tmp;
@@ -442,7 +491,7 @@ bool UmfPackLU<MatrixType>::_solve_impl(const MatrixBase<BDerived> &b, MatrixBas
       x_ptr = &x.col(j).coeffRef(0);
     errorCode = umfpack_solve(UMFPACK_A,
         mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
-        x_ptr, &b.const_cast_derived().col(j).coeffRef(0), m_numeric, m_control.data(), 0);
+        x_ptr, &b.const_cast_derived().col(j).coeffRef(0), m_numeric, m_control.data(), m_umfpackInfo.data());
     if(x.innerStride()!=1)
       x.col(j) = x_tmp;
     if (errorCode!=0)

Eigen/src/plugins/BlockMethods.h

@@ -818,7 +818,7 @@ inline typename FixedBlockXpr<NRows,NCols>::Type block(Index startRow, Index sta
   return typename FixedBlockXpr<NRows,NCols>::Type(derived(), startRow, startCol, blockRows, blockCols);
 }
 
-/// This is the const version of block<>(Index, Index, Index, Index). */
+/// This is the const version of block<>(Index, Index, Index, Index).
 template<int NRows, int NCols>
 inline const typename ConstFixedBlockXpr<NRows,NCols>::Type block(Index startRow, Index startCol,
                                                               Index blockRows, Index blockCols) const
@@ -832,15 +832,15 @@ inline const typename ConstFixedBlockXpr<NRows,NCols>::Type block(Index startRow
 /// Output: \verbinclude MatrixBase_col.out
 ///
 EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(column-major)
-///
-/// \sa row(), class Block */
+/**
+  * \sa row(), class Block */
 EIGEN_DEVICE_FUNC
 inline ColXpr col(Index i)
 {
   return ColXpr(derived(), i);
 }
 
-/// This is the const version of col(). */
+/// This is the const version of col().
 EIGEN_DEVICE_FUNC
 inline ConstColXpr col(Index i) const
 {
@@ -853,8 +853,8 @@ inline ConstColXpr col(Index i) const
 /// Output: \verbinclude MatrixBase_row.out
 ///
 EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(row-major)
-///
-/// \sa col(), class Block */
+/**
+  * \sa col(), class Block */
 EIGEN_DEVICE_FUNC
 inline RowXpr row(Index i)
 {

README.md

@@ -1,3 +1,3 @@
-**Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.**
-
-For more information go to http://eigen.tuxfamily.org/.
+**Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.**
+
+For more information go to http://eigen.tuxfamily.org/.

bench/spbench/CMakeLists.txt

@@ -38,25 +38,32 @@ if(SUPERLU_FOUND AND BLAS_FOUND)
 endif()
 
 
-find_package(Pastix)
-find_package(Scotch)
-find_package(Metis)
-if(PASTIX_FOUND AND BLAS_FOUND)
+find_package(PASTIX QUIET COMPONENTS METIS SCOTCH)
+# check that the PASTIX found is a version without MPI
+find_path(PASTIX_pastix_nompi.h_INCLUDE_DIRS
+  NAMES pastix_nompi.h
+  HINTS ${PASTIX_INCLUDE_DIRS}
+)
+if (NOT PASTIX_pastix_nompi.h_INCLUDE_DIRS)
+  message(STATUS "A version of Pastix has been found but pastix_nompi.h does not exist in the include directory."
+                 " Because Eigen tests require a version without MPI, we disable the Pastix backend.")
+endif()
+if(PASTIX_FOUND AND PASTIX_pastix_nompi.h_INCLUDE_DIRS AND BLAS_FOUND)
   add_definitions("-DEIGEN_PASTIX_SUPPORT")
-  include_directories(${PASTIX_INCLUDES})
+  include_directories(${PASTIX_INCLUDE_DIRS_DEP})
   if(SCOTCH_FOUND)
-    include_directories(${SCOTCH_INCLUDES})
+    include_directories(${SCOTCH_INCLUDE_DIRS})
     set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${SCOTCH_LIBRARIES})
   elseif(METIS_FOUND)
-    include_directories(${METIS_INCLUDES})
+    include_directories(${METIS_INCLUDE_DIRS})
     set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${METIS_LIBRARIES})  
   endif(SCOTCH_FOUND)
-  set(SPARSE_LIBS ${SPARSE_LIBS} ${PASTIX_LIBRARIES} ${ORDERING_LIBRARIES} ${BLAS_LIBRARIES})
-  set(PASTIX_ALL_LIBS ${PASTIX_LIBRARIES} ${BLAS_LIBRARIES})
+  set(SPARSE_LIBS ${SPARSE_LIBS} ${PASTIX_LIBRARIES_DEP} ${ORDERING_LIBRARIES})
+  set(PASTIX_ALL_LIBS ${PASTIX_LIBRARIES_DEP})
 endif(PASTIX_FOUND AND BLAS_FOUND)
 
 if(METIS_FOUND)
-  include_directories(${METIS_INCLUDES})
+  include_directories(${METIS_INCLUDE_DIRS})
   set (SPARSE_LIBS ${SPARSE_LIBS} ${METIS_LIBRARIES})
   add_definitions("-DEIGEN_METIS_SUPPORT")
 endif(METIS_FOUND)

cmake/FindBLASEXT.cmake

@@ -0,0 +1,380 @@
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2016 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find BLAS EXTENDED for MORSE projects: find include dirs and libraries
+#
+# This module allows to find BLAS libraries by calling the official FindBLAS module
+# and handles the creation of different library lists whether the user wishes to link
+# with a sequential BLAS or a multihreaded (BLAS_SEQ_LIBRARIES and BLAS_PAR_LIBRARIES).
+# BLAS is detected with a FindBLAS call then if the BLAS vendor is Intel10_64lp, ACML
+# or IBMESSLMT then the module attempts to find the corresponding multithreaded libraries.
+#
+# The following variables have been added to manage links with sequential or multithreaded
+# versions:
+#  BLAS_INCLUDE_DIRS  - BLAS include directories
+#  BLAS_LIBRARY_DIRS  - Link directories for BLAS libraries
+#  BLAS_SEQ_LIBRARIES - BLAS component libraries to be linked (sequential)
+#  BLAS_PAR_LIBRARIES - BLAS component libraries to be linked (multithreaded)
+
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013-2016 Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
+
+# macro to factorize this call
+macro(find_package_blas)
+  if(BLASEXT_FIND_REQUIRED)
+    if(BLASEXT_FIND_QUIETLY)
+      find_package(BLAS REQUIRED QUIET)
+    else()
+      find_package(BLAS REQUIRED)
+    endif()
+  else()
+    if(BLASEXT_FIND_QUIETLY)
+      find_package(BLAS QUIET)
+    else()
+      find_package(BLAS)
+    endif()
+  endif()
+endmacro()
+
+# add a cache variable to let the user specify the BLAS vendor
+set(BLA_VENDOR "" CACHE STRING "list of possible BLAS vendor:
+    Open, Eigen, Goto, ATLAS PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, IBMESSLMT,
+    Intel10_32 (intel mkl v10 32 bit),
+    Intel10_64lp (intel mkl v10 64 bit, lp thread model, lp64 model),
+    Intel10_64lp_seq (intel mkl v10 64 bit, sequential code, lp64 model),
+    Intel( older versions of mkl 32 and 64 bit),
+    ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
+
+if(NOT BLASEXT_FIND_QUIETLY)
+  message(STATUS "In FindBLASEXT")
+  message(STATUS "If you want to force the use of one specific library, "
+    "\n   please specify the BLAS vendor by setting -DBLA_VENDOR=blas_vendor_name"
+    "\n   at cmake configure.")
+  message(STATUS "List of possible BLAS vendor: Goto, ATLAS PhiPACK, CXML, "
+    "\n   DXML, SunPerf, SCSL, SGIMATH, IBMESSL, IBMESSLMT, Intel10_32 (intel mkl v10 32 bit),"
+    "\n   Intel10_64lp (intel mkl v10 64 bit, lp thread model, lp64 model),"
+    "\n   Intel10_64lp_seq (intel mkl v10 64 bit, sequential code, lp64 model),"
+    "\n   Intel( older versions of mkl 32 and 64 bit),"
+    "\n   ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
+endif()
+
+if (NOT BLAS_FOUND)
+  # First try to detect two cases:
+  # 1: only SEQ libs are handled
+  # 2: both SEQ and PAR libs are handled
+  find_package_blas()
+endif ()
+
+# detect the cases where SEQ and PAR libs are handled
+if(BLA_VENDOR STREQUAL "All" AND
+    (BLAS_mkl_core_LIBRARY OR BLAS_mkl_core_dll_LIBRARY)
+    )
+  set(BLA_VENDOR "Intel")
+  if(BLAS_mkl_intel_LIBRARY)
+    set(BLA_VENDOR "Intel10_32")
+  endif()
+  if(BLAS_mkl_intel_lp64_LIBRARY)
+    set(BLA_VENDOR "Intel10_64lp")
+  endif()
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "A BLAS library has been found (${BLAS_LIBRARIES}) but we"
+      "\n   have also potentially detected some multithreaded BLAS libraries from the MKL."
+      "\n   We try to find both libraries lists (Sequential/Multithreaded).")
+  endif()
+  set(BLAS_FOUND "")
+elseif(BLA_VENDOR STREQUAL "All" AND BLAS_acml_LIBRARY)
+  set(BLA_VENDOR "ACML")
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "A BLAS library has been found (${BLAS_LIBRARIES}) but we"
+      "\n   have also potentially detected some multithreaded BLAS libraries from the ACML."
+      "\n   We try to find both libraries lists (Sequential/Multithreaded).")
+  endif()
+  set(BLAS_FOUND "")
+elseif(BLA_VENDOR STREQUAL "All" AND BLAS_essl_LIBRARY)
+  set(BLA_VENDOR "IBMESSL")
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "A BLAS library has been found (${BLAS_LIBRARIES}) but we"
+      "\n   have also potentially detected some multithreaded BLAS libraries from the ESSL."
+      "\n   We try to find both libraries lists (Sequential/Multithreaded).")
+  endif()
+  set(BLAS_FOUND "")
+endif()
+
+# Intel case
+if(BLA_VENDOR MATCHES "Intel*")
+
+  ###
+  # look for include path if the BLAS vendor is Intel
+  ###
+
+  # gather system include paths
+  unset(_inc_env)
+  if(WIN32)
+    string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
+  else()
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+  endif()
+  list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+  list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+  set(ENV_MKLROOT "$ENV{MKLROOT}")
+  if (ENV_MKLROOT)
+    list(APPEND _inc_env "${ENV_MKLROOT}/include")
+  endif()
+  list(REMOVE_DUPLICATES _inc_env)
+
+  # find mkl.h inside known include paths
+  set(BLAS_mkl.h_INCLUDE_DIRS "BLAS_mkl.h_INCLUDE_DIRS-NOTFOUND")
+  if(BLAS_INCDIR)
+    set(BLAS_mkl.h_INCLUDE_DIRS "BLAS_mkl.h_INCLUDE_DIRS-NOTFOUND")
+    find_path(BLAS_mkl.h_INCLUDE_DIRS
+      NAMES mkl.h
+      HINTS ${BLAS_INCDIR})
+  else()
+    if(BLAS_DIR)
+      set(BLAS_mkl.h_INCLUDE_DIRS "BLAS_mkl.h_INCLUDE_DIRS-NOTFOUND")
+      find_path(BLAS_mkl.h_INCLUDE_DIRS
+	NAMES mkl.h
+	HINTS ${BLAS_DIR}
+	PATH_SUFFIXES include)
+    else()
+      set(BLAS_mkl.h_INCLUDE_DIRS "BLAS_mkl.h_INCLUDE_DIRS-NOTFOUND")
+      find_path(BLAS_mkl.h_INCLUDE_DIRS
+	NAMES mkl.h
+	HINTS ${_inc_env})
+    endif()
+  endif()
+  mark_as_advanced(BLAS_mkl.h_INCLUDE_DIRS)
+  ## Print status if not found
+  ## -------------------------
+  #if (NOT BLAS_mkl.h_INCLUDE_DIRS AND MORSE_VERBOSE)
+  #    Print_Find_Header_Status(blas mkl.h)
+  #endif ()
+  set(BLAS_INCLUDE_DIRS "")
+  if(BLAS_mkl.h_INCLUDE_DIRS)
+    list(APPEND BLAS_INCLUDE_DIRS "${BLAS_mkl.h_INCLUDE_DIRS}" )
+  endif()
+
+  ###
+  # look for libs
+  ###
+  # if Intel 10 64 bit -> look for sequential and multithreaded versions
+  if(BLA_VENDOR MATCHES "Intel10_64lp*")
+
+    ## look for the sequential version
+    set(BLA_VENDOR "Intel10_64lp_seq")
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "Look for the sequential version Intel10_64lp_seq")
+    endif()
+    find_package_blas()
+    if(BLAS_FOUND)
+      set(BLAS_SEQ_LIBRARIES "${BLAS_LIBRARIES}")
+    else()
+      set(BLAS_SEQ_LIBRARIES "${BLAS_SEQ_LIBRARIES-NOTFOUND}")
+    endif()
+
+    ## look for the multithreaded version
+    set(BLA_VENDOR "Intel10_64lp")
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "Look for the multithreaded version Intel10_64lp")
+    endif()
+    find_package_blas()
+    if(BLAS_FOUND)
+      set(BLAS_PAR_LIBRARIES "${BLAS_LIBRARIES}")
+    else()
+      set(BLAS_PAR_LIBRARIES "${BLAS_PAR_LIBRARIES-NOTFOUND}")
+    endif()
+
+  else()
+
+    if(BLAS_FOUND)
+      set(BLAS_SEQ_LIBRARIES "${BLAS_LIBRARIES}")
+    else()
+      set(BLAS_SEQ_LIBRARIES "${BLAS_SEQ_LIBRARIES-NOTFOUND}")
+    endif()
+
+  endif()
+
+  # ACML case
+elseif(BLA_VENDOR MATCHES "ACML*")
+
+  ## look for the sequential version
+  set(BLA_VENDOR "ACML")
+  find_package_blas()
+  if(BLAS_FOUND)
+    set(BLAS_SEQ_LIBRARIES "${BLAS_LIBRARIES}")
+  else()
+    set(BLAS_SEQ_LIBRARIES "${BLAS_SEQ_LIBRARIES-NOTFOUND}")
+  endif()
+
+  ## look for the multithreaded version
+  set(BLA_VENDOR "ACML_MP")
+  find_package_blas()
+  if(BLAS_FOUND)
+    set(BLAS_PAR_LIBRARIES "${BLAS_LIBRARIES}")
+  else()
+    set(BLAS_PAR_LIBRARIES "${BLAS_PAR_LIBRARIES-NOTFOUND}")
+  endif()
+
+  # IBMESSL case
+elseif(BLA_VENDOR MATCHES "IBMESSL*")
+
+  ## look for the sequential version
+  set(BLA_VENDOR "IBMESSL")
+  find_package_blas()
+  if(BLAS_FOUND)
+    set(BLAS_SEQ_LIBRARIES "${BLAS_LIBRARIES}")
+  else()
+    set(BLAS_SEQ_LIBRARIES "${BLAS_SEQ_LIBRARIES-NOTFOUND}")
+  endif()
+
+  ## look for the multithreaded version
+  set(BLA_VENDOR "IBMESSLMT")
+  find_package_blas()
+  if(BLAS_FOUND)
+    set(BLAS_PAR_LIBRARIES "${BLAS_LIBRARIES}")
+  else()
+    set(BLAS_PAR_LIBRARIES "${BLAS_PAR_LIBRARIES-NOTFOUND}")
+  endif()
+
+else()
+
+  if(BLAS_FOUND)
+    # define the SEQ libs as the BLAS_LIBRARIES
+    set(BLAS_SEQ_LIBRARIES "${BLAS_LIBRARIES}")
+  else()
+    set(BLAS_SEQ_LIBRARIES "${BLAS_SEQ_LIBRARIES-NOTFOUND}")
+  endif()
+  set(BLAS_PAR_LIBRARIES "${BLAS_PAR_LIBRARIES-NOTFOUND}")
+
+endif()
+
+
+if(BLAS_SEQ_LIBRARIES)
+  set(BLAS_LIBRARIES "${BLAS_SEQ_LIBRARIES}")
+endif()
+
+# extract libs paths
+# remark: because it is not given by find_package(BLAS)
+set(BLAS_LIBRARY_DIRS "")
+string(REPLACE " " ";" BLAS_LIBRARIES "${BLAS_LIBRARIES}")
+foreach(blas_lib ${BLAS_LIBRARIES})
+  if (EXISTS "${blas_lib}")
+    get_filename_component(a_blas_lib_dir "${blas_lib}" PATH)
+    list(APPEND BLAS_LIBRARY_DIRS "${a_blas_lib_dir}" )
+  else()
+    string(REPLACE "-L" "" blas_lib "${blas_lib}")
+    if (EXISTS "${blas_lib}")
+      list(APPEND BLAS_LIBRARY_DIRS "${blas_lib}" )
+    else()
+      get_filename_component(a_blas_lib_dir "${blas_lib}" PATH)
+      if (EXISTS "${a_blas_lib_dir}")
+	list(APPEND BLAS_LIBRARY_DIRS "${a_blas_lib_dir}" )
+      endif()
+    endif()
+  endif()
+endforeach()
+if (BLAS_LIBRARY_DIRS)
+  list(REMOVE_DUPLICATES BLAS_LIBRARY_DIRS)
+endif ()
+
+# check that BLAS has been found
+# ---------------------------------
+include(FindPackageHandleStandardArgs)
+if(BLA_VENDOR MATCHES "Intel*")
+  if(BLA_VENDOR MATCHES "Intel10_64lp*")
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "BLAS found is Intel MKL:"
+	"\n   we manage two lists of libs, one sequential and one parallel if found"
+	"\n   (see BLAS_SEQ_LIBRARIES and BLAS_PAR_LIBRARIES)")
+      message(STATUS "BLAS sequential libraries stored in BLAS_SEQ_LIBRARIES")
+    endif()
+    find_package_handle_standard_args(BLAS DEFAULT_MSG
+      BLAS_SEQ_LIBRARIES
+      BLAS_LIBRARY_DIRS
+      BLAS_INCLUDE_DIRS)
+    if(BLAS_PAR_LIBRARIES)
+      if(NOT BLASEXT_FIND_QUIETLY)
+	message(STATUS "BLAS parallel libraries stored in BLAS_PAR_LIBRARIES")
+      endif()
+      find_package_handle_standard_args(BLAS DEFAULT_MSG
+	BLAS_PAR_LIBRARIES)
+    endif()
+  else()
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "BLAS sequential libraries stored in BLAS_SEQ_LIBRARIES")
+    endif()
+    find_package_handle_standard_args(BLAS DEFAULT_MSG
+      BLAS_SEQ_LIBRARIES
+      BLAS_LIBRARY_DIRS
+      BLAS_INCLUDE_DIRS)
+  endif()
+elseif(BLA_VENDOR MATCHES "ACML*")
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "BLAS found is ACML:"
+      "\n   we manage two lists of libs, one sequential and one parallel if found"
+      "\n   (see BLAS_SEQ_LIBRARIES and BLAS_PAR_LIBRARIES)")
+    message(STATUS "BLAS sequential libraries stored in BLAS_SEQ_LIBRARIES")
+  endif()
+  find_package_handle_standard_args(BLAS DEFAULT_MSG
+    BLAS_SEQ_LIBRARIES
+    BLAS_LIBRARY_DIRS)
+  if(BLAS_PAR_LIBRARIES)
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "BLAS parallel libraries stored in BLAS_PAR_LIBRARIES")
+    endif()
+    find_package_handle_standard_args(BLAS DEFAULT_MSG
+      BLAS_PAR_LIBRARIES)
+  endif()
+elseif(BLA_VENDOR MATCHES "IBMESSL*")
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "BLAS found is ESSL:"
+      "\n   we manage two lists of libs, one sequential and one parallel if found"
+      "\n   (see BLAS_SEQ_LIBRARIES and BLAS_PAR_LIBRARIES)")
+    message(STATUS "BLAS sequential libraries stored in BLAS_SEQ_LIBRARIES")
+  endif()
+  find_package_handle_standard_args(BLAS DEFAULT_MSG
+    BLAS_SEQ_LIBRARIES
+    BLAS_LIBRARY_DIRS)
+  if(BLAS_PAR_LIBRARIES)
+    if(NOT BLASEXT_FIND_QUIETLY)
+      message(STATUS "BLAS parallel libraries stored in BLAS_PAR_LIBRARIES")
+    endif()
+    find_package_handle_standard_args(BLAS DEFAULT_MSG
+      BLAS_PAR_LIBRARIES)
+  endif()
+else()
+  if(NOT BLASEXT_FIND_QUIETLY)
+    message(STATUS "BLAS sequential libraries stored in BLAS_SEQ_LIBRARIES")
+  endif()
+  find_package_handle_standard_args(BLAS DEFAULT_MSG
+    BLAS_SEQ_LIBRARIES
+    BLAS_LIBRARY_DIRS)
+endif()

cmake/FindHWLOC.cmake

@@ -0,0 +1,331 @@
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2014 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find HWLOC include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(HWLOC
+#               [REQUIRED]) # Fail with error if hwloc is not found
+#
+# This module finds headers and hwloc library.
+# Results are reported in variables:
+#  HWLOC_FOUND           - True if headers and requested libraries were found
+#  HWLOC_INCLUDE_DIRS    - hwloc include directories
+#  HWLOC_LIBRARY_DIRS    - Link directories for hwloc libraries
+#  HWLOC_LIBRARIES       - hwloc component libraries to be linked
+#
+# The user can give specific paths where to find the libraries adding cmake
+# options at configure (ex: cmake path/to/project -DHWLOC_DIR=path/to/hwloc):
+#  HWLOC_DIR             - Where to find the base directory of hwloc
+#  HWLOC_INCDIR          - Where to find the header files
+#  HWLOC_LIBDIR          - Where to find the library files
+# The module can also look for the following environment variables if paths
+# are not given as cmake variable: HWLOC_DIR, HWLOC_INCDIR, HWLOC_LIBDIR
+
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013      Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
+
+include(CheckStructHasMember)
+include(CheckCSourceCompiles)
+
+if (NOT HWLOC_FOUND)
+  set(HWLOC_DIR "" CACHE PATH "Installation directory of HWLOC library")
+  if (NOT HWLOC_FIND_QUIETLY)
+    message(STATUS "A cache variable, namely HWLOC_DIR, has been set to specify the install directory of HWLOC")
+  endif()
+endif()
+
+set(ENV_HWLOC_DIR "$ENV{HWLOC_DIR}")
+set(ENV_HWLOC_INCDIR "$ENV{HWLOC_INCDIR}")
+set(ENV_HWLOC_LIBDIR "$ENV{HWLOC_LIBDIR}")
+set(HWLOC_GIVEN_BY_USER "FALSE")
+if ( HWLOC_DIR OR ( HWLOC_INCDIR AND HWLOC_LIBDIR) OR ENV_HWLOC_DIR OR (ENV_HWLOC_INCDIR AND ENV_HWLOC_LIBDIR) )
+  set(HWLOC_GIVEN_BY_USER "TRUE")
+endif()
+
+# Optionally use pkg-config to detect include/library dirs (if pkg-config is available)
+# -------------------------------------------------------------------------------------
+include(FindPkgConfig)
+find_package(PkgConfig QUIET)
+if( PKG_CONFIG_EXECUTABLE AND NOT HWLOC_GIVEN_BY_USER )
+
+  pkg_search_module(HWLOC hwloc)
+  if (NOT HWLOC_FIND_QUIETLY)
+    if (HWLOC_FOUND AND HWLOC_LIBRARIES)
+      message(STATUS "Looking for HWLOC - found using PkgConfig")
+      #if(NOT HWLOC_INCLUDE_DIRS)
+      #    message("${Magenta}HWLOC_INCLUDE_DIRS is empty using PkgConfig."
+      #        "Perhaps the path to hwloc headers is already present in your"
+      #        "C(PLUS)_INCLUDE_PATH environment variable.${ColourReset}")
+      #endif()
+    else()
+      message(STATUS "${Magenta}Looking for HWLOC - not found using PkgConfig."
+	"\n   Perhaps you should add the directory containing hwloc.pc to"
+	"\n   the PKG_CONFIG_PATH environment variable.${ColourReset}")
+    endif()
+  endif()
+
+endif( PKG_CONFIG_EXECUTABLE AND NOT HWLOC_GIVEN_BY_USER )
+
+if( (NOT PKG_CONFIG_EXECUTABLE) OR (PKG_CONFIG_EXECUTABLE AND NOT HWLOC_FOUND) OR (HWLOC_GIVEN_BY_USER) )
+
+  if (NOT HWLOC_FIND_QUIETLY)
+    message(STATUS "Looking for HWLOC - PkgConfig not used")
+  endif()
+
+  # Looking for include
+  # -------------------
+
+  # Add system include paths to search include
+  # ------------------------------------------
+  unset(_inc_env)
+  if(ENV_HWLOC_INCDIR)
+    list(APPEND _inc_env "${ENV_HWLOC_INCDIR}")
+  elseif(ENV_HWLOC_DIR)
+    list(APPEND _inc_env "${ENV_HWLOC_DIR}")
+    list(APPEND _inc_env "${ENV_HWLOC_DIR}/include")
+    list(APPEND _inc_env "${ENV_HWLOC_DIR}/include/hwloc")
+  else()
+    if(WIN32)
+      string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
+    else()
+      string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+      list(APPEND _inc_env "${_path_env}")
+      string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+      list(APPEND _inc_env "${_path_env}")
+      string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+      list(APPEND _inc_env "${_path_env}")
+      string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+      list(APPEND _inc_env "${_path_env}")
+    endif()
+  endif()
+  list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+  list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+  list(REMOVE_DUPLICATES _inc_env)
+
+  # set paths where to look for
+  set(PATH_TO_LOOK_FOR "${_inc_env}")
+
+  # Try to find the hwloc header in the given paths
+  # -------------------------------------------------
+  # call cmake macro to find the header path
+  if(HWLOC_INCDIR)
+    set(HWLOC_hwloc.h_DIRS "HWLOC_hwloc.h_DIRS-NOTFOUND")
+    find_path(HWLOC_hwloc.h_DIRS
+      NAMES hwloc.h
+      HINTS ${HWLOC_INCDIR})
+  else()
+    if(HWLOC_DIR)
+      set(HWLOC_hwloc.h_DIRS "HWLOC_hwloc.h_DIRS-NOTFOUND")
+      find_path(HWLOC_hwloc.h_DIRS
+	NAMES hwloc.h
+	HINTS ${HWLOC_DIR}
+	PATH_SUFFIXES "include" "include/hwloc")
+    else()
+      set(HWLOC_hwloc.h_DIRS "HWLOC_hwloc.h_DIRS-NOTFOUND")
+      find_path(HWLOC_hwloc.h_DIRS
+	NAMES hwloc.h
+	HINTS ${PATH_TO_LOOK_FOR}
+	PATH_SUFFIXES "hwloc")
+    endif()
+  endif()
+  mark_as_advanced(HWLOC_hwloc.h_DIRS)
+
+  # Add path to cmake variable
+  # ------------------------------------
+  if (HWLOC_hwloc.h_DIRS)
+    set(HWLOC_INCLUDE_DIRS "${HWLOC_hwloc.h_DIRS}")
+  else ()
+    set(HWLOC_INCLUDE_DIRS "HWLOC_INCLUDE_DIRS-NOTFOUND")
+    if(NOT HWLOC_FIND_QUIETLY)
+      message(STATUS "Looking for hwloc -- hwloc.h not found")
+    endif()
+  endif ()
+
+  if (HWLOC_INCLUDE_DIRS)
+    list(REMOVE_DUPLICATES HWLOC_INCLUDE_DIRS)
+  endif ()
+
+
+  # Looking for lib
+  # ---------------
+
+  # Add system library paths to search lib
+  # --------------------------------------
+  unset(_lib_env)
+  if(ENV_HWLOC_LIBDIR)
+    list(APPEND _lib_env "${ENV_HWLOC_LIBDIR}")
+  elseif(ENV_HWLOC_DIR)
+    list(APPEND _lib_env "${ENV_HWLOC_DIR}")
+    list(APPEND _lib_env "${ENV_HWLOC_DIR}/lib")
+  else()
+    if(WIN32)
+      string(REPLACE ":" ";" _lib_env "$ENV{LIB}")
+    else()
+      if(APPLE)
+	string(REPLACE ":" ";" _lib_env "$ENV{DYLD_LIBRARY_PATH}")
+      else()
+	string(REPLACE ":" ";" _lib_env "$ENV{LD_LIBRARY_PATH}")
+      endif()
+      list(APPEND _lib_env "${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")
+      list(APPEND _lib_env "${CMAKE_C_IMPLICIT_LINK_DIRECTORIES}")
+    endif()
+  endif()
+  list(REMOVE_DUPLICATES _lib_env)
+
+  # set paths where to look for
+  set(PATH_TO_LOOK_FOR "${_lib_env}")
+
+  # Try to find the hwloc lib in the given paths
+  # ----------------------------------------------
+
+  # call cmake macro to find the lib path
+  if(HWLOC_LIBDIR)
+    set(HWLOC_hwloc_LIBRARY "HWLOC_hwloc_LIBRARY-NOTFOUND")
+    find_library(HWLOC_hwloc_LIBRARY
+      NAMES hwloc
+      HINTS ${HWLOC_LIBDIR})
+  else()
+    if(HWLOC_DIR)
+      set(HWLOC_hwloc_LIBRARY "HWLOC_hwloc_LIBRARY-NOTFOUND")
+      find_library(HWLOC_hwloc_LIBRARY
+	NAMES hwloc
+	HINTS ${HWLOC_DIR}
+	PATH_SUFFIXES lib lib32 lib64)
+    else()
+      set(HWLOC_hwloc_LIBRARY "HWLOC_hwloc_LIBRARY-NOTFOUND")
+      find_library(HWLOC_hwloc_LIBRARY
+	NAMES hwloc
+	HINTS ${PATH_TO_LOOK_FOR})
+    endif()
+  endif()
+  mark_as_advanced(HWLOC_hwloc_LIBRARY)
+
+  # If found, add path to cmake variable
+  # ------------------------------------
+  if (HWLOC_hwloc_LIBRARY)
+    get_filename_component(hwloc_lib_path ${HWLOC_hwloc_LIBRARY} PATH)
+    # set cmake variables (respects naming convention)
+    set(HWLOC_LIBRARIES    "${HWLOC_hwloc_LIBRARY}")
+    set(HWLOC_LIBRARY_DIRS "${hwloc_lib_path}")
+  else ()
+    set(HWLOC_LIBRARIES    "HWLOC_LIBRARIES-NOTFOUND")
+    set(HWLOC_LIBRARY_DIRS "HWLOC_LIBRARY_DIRS-NOTFOUND")
+    if(NOT HWLOC_FIND_QUIETLY)
+      message(STATUS "Looking for hwloc -- lib hwloc not found")
+    endif()
+  endif ()
+
+  if (HWLOC_LIBRARY_DIRS)
+    list(REMOVE_DUPLICATES HWLOC_LIBRARY_DIRS)
+  endif ()
+
+  # check a function to validate the find
+  if(HWLOC_LIBRARIES)
+
+    set(REQUIRED_INCDIRS)
+    set(REQUIRED_LIBDIRS)
+    set(REQUIRED_LIBS)
+
+    # HWLOC
+    if (HWLOC_INCLUDE_DIRS)
+      set(REQUIRED_INCDIRS "${HWLOC_INCLUDE_DIRS}")
+    endif()
+    if (HWLOC_LIBRARY_DIRS)
+      set(REQUIRED_LIBDIRS "${HWLOC_LIBRARY_DIRS}")
+    endif()
+    set(REQUIRED_LIBS "${HWLOC_LIBRARIES}")
+
+    # set required libraries for link
+    set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
+    set(CMAKE_REQUIRED_LIBRARIES)
+    foreach(lib_dir ${REQUIRED_LIBDIRS})
+      list(APPEND CMAKE_REQUIRED_LIBRARIES "-L${lib_dir}")
+    endforeach()
+    list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LIBS}")
+    string(REGEX REPLACE "^ -" "-" CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+
+    # test link
+    unset(HWLOC_WORKS CACHE)
+    include(CheckFunctionExists)
+    check_function_exists(hwloc_topology_init HWLOC_WORKS)
+    mark_as_advanced(HWLOC_WORKS)
+
+    if(NOT HWLOC_WORKS)
+      if(NOT HWLOC_FIND_QUIETLY)
+	message(STATUS "Looking for hwloc : test of hwloc_topology_init with hwloc library fails")
+	message(STATUS "CMAKE_REQUIRED_LIBRARIES: ${CMAKE_REQUIRED_LIBRARIES}")
+	message(STATUS "CMAKE_REQUIRED_INCLUDES: ${CMAKE_REQUIRED_INCLUDES}")
+	message(STATUS "Check in CMakeFiles/CMakeError.log to figure out why it fails")
+      endif()
+    endif()
+    set(CMAKE_REQUIRED_INCLUDES)
+    set(CMAKE_REQUIRED_FLAGS)
+    set(CMAKE_REQUIRED_LIBRARIES)
+  endif(HWLOC_LIBRARIES)
+
+endif( (NOT PKG_CONFIG_EXECUTABLE) OR (PKG_CONFIG_EXECUTABLE AND NOT HWLOC_FOUND) OR (HWLOC_GIVEN_BY_USER) )
+
+if (HWLOC_LIBRARIES)
+  if (HWLOC_LIBRARY_DIRS)
+    list(GET HWLOC_LIBRARY_DIRS 0 first_lib_path)
+  else()
+    list(GET HWLOC_LIBRARIES 0 first_lib)
+    get_filename_component(first_lib_path "${first_lib}" PATH)
+  endif()
+  if (${first_lib_path} MATCHES "/lib(32|64)?$")
+    string(REGEX REPLACE "/lib(32|64)?$" "" not_cached_dir "${first_lib_path}")
+    set(HWLOC_DIR_FOUND "${not_cached_dir}" CACHE PATH "Installation directory of HWLOC library" FORCE)
+  else()
+    set(HWLOC_DIR_FOUND "${first_lib_path}" CACHE PATH "Installation directory of HWLOC library" FORCE)
+  endif()
+endif()
+mark_as_advanced(HWLOC_DIR)
+mark_as_advanced(HWLOC_DIR_FOUND)
+
+# check that HWLOC has been found
+# -------------------------------
+include(FindPackageHandleStandardArgs)
+if (PKG_CONFIG_EXECUTABLE AND HWLOC_FOUND)
+  find_package_handle_standard_args(HWLOC DEFAULT_MSG
+    HWLOC_LIBRARIES)
+else()
+  find_package_handle_standard_args(HWLOC DEFAULT_MSG
+    HWLOC_LIBRARIES
+    HWLOC_WORKS)
+endif()
+
+if (HWLOC_FOUND)
+  set(HWLOC_SAVE_CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES})
+  list(APPEND CMAKE_REQUIRED_INCLUDES ${HWLOC_INCLUDE_DIRS})
+
+  # test headers to guess the version
+  check_struct_has_member( "struct hwloc_obj" parent hwloc.h HAVE_HWLOC_PARENT_MEMBER )
+  check_struct_has_member( "struct hwloc_cache_attr_s" size hwloc.h HAVE_HWLOC_CACHE_ATTR )
+  check_c_source_compiles( "#include <hwloc.h>
+	    int main(void) { hwloc_obj_t o; o->type = HWLOC_OBJ_PU; return 0;}" HAVE_HWLOC_OBJ_PU)
+  include(CheckLibraryExists)
+  check_library_exists(${HWLOC_LIBRARIES} hwloc_bitmap_free "" HAVE_HWLOC_BITMAP)
+
+  set(CMAKE_REQUIRED_INCLUDES ${HWLOC_SAVE_CMAKE_REQUIRED_INCLUDES})
+endif()

cmake/FindMetis.cmake

@@ -1,59 +1,264 @@
-# Pastix requires METIS or METIS (partitioning and reordering tools)
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2014 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find METIS include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(METIS
+#               [REQUIRED]             # Fail with error if metis is not found
+#              )
+#
+# This module finds headers and metis library.
+# Results are reported in variables:
+#  METIS_FOUND           - True if headers and requested libraries were found
+#  METIS_INCLUDE_DIRS    - metis include directories
+#  METIS_LIBRARY_DIRS    - Link directories for metis libraries
+#  METIS_LIBRARIES       - metis component libraries to be linked
+#
+# The user can give specific paths where to find the libraries adding cmake
+# options at configure (ex: cmake path/to/project -DMETIS_DIR=path/to/metis):
+#  METIS_DIR             - Where to find the base directory of metis
+#  METIS_INCDIR          - Where to find the header files
+#  METIS_LIBDIR          - Where to find the library files
+# The module can also look for the following environment variables if paths
+# are not given as cmake variable: METIS_DIR, METIS_INCDIR, METIS_LIBDIR
 
-if (METIS_INCLUDES AND METIS_LIBRARIES)
-  set(METIS_FIND_QUIETLY TRUE)
-endif (METIS_INCLUDES AND METIS_LIBRARIES)
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013      Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
 
-find_path(METIS_INCLUDES 
-  NAMES 
-  metis.h 
-  PATHS 
-  $ENV{METISDIR} 
-  ${INCLUDE_INSTALL_DIR} 
-  PATH_SUFFIXES
-  .
-  metis
-  include
-)
-
-macro(_metis_check_version)
-  file(READ "${METIS_INCLUDES}/metis.h" _metis_version_header)
-
-  string(REGEX MATCH "define[ \t]+METIS_VER_MAJOR[ \t]+([0-9]+)" _metis_major_version_match "${_metis_version_header}")
-  set(METIS_MAJOR_VERSION "${CMAKE_MATCH_1}")
-  string(REGEX MATCH "define[ \t]+METIS_VER_MINOR[ \t]+([0-9]+)" _metis_minor_version_match "${_metis_version_header}")
-  set(METIS_MINOR_VERSION "${CMAKE_MATCH_1}")
-  string(REGEX MATCH "define[ \t]+METIS_VER_SUBMINOR[ \t]+([0-9]+)" _metis_subminor_version_match "${_metis_version_header}")
-  set(METIS_SUBMINOR_VERSION "${CMAKE_MATCH_1}")
-  if(NOT METIS_MAJOR_VERSION)
-    message(STATUS "Could not determine Metis version. Assuming version 4.0.0")
-    set(METIS_VERSION 4.0.0)
-  else()
-    set(METIS_VERSION ${METIS_MAJOR_VERSION}.${METIS_MINOR_VERSION}.${METIS_SUBMINOR_VERSION})
+if (NOT METIS_FOUND)
+  set(METIS_DIR "" CACHE PATH "Installation directory of METIS library")
+  if (NOT METIS_FIND_QUIETLY)
+    message(STATUS "A cache variable, namely METIS_DIR, has been set to specify the install directory of METIS")
   endif()
-  if(${METIS_VERSION} VERSION_LESS ${Metis_FIND_VERSION})
-    set(METIS_VERSION_OK FALSE)
+endif()
+
+# Looking for include
+# -------------------
+
+# Add system include paths to search include
+# ------------------------------------------
+unset(_inc_env)
+set(ENV_METIS_DIR "$ENV{METIS_DIR}")
+set(ENV_METIS_INCDIR "$ENV{METIS_INCDIR}")
+if(ENV_METIS_INCDIR)
+  list(APPEND _inc_env "${ENV_METIS_INCDIR}")
+elseif(ENV_METIS_DIR)
+  list(APPEND _inc_env "${ENV_METIS_DIR}")
+  list(APPEND _inc_env "${ENV_METIS_DIR}/include")
+  list(APPEND _inc_env "${ENV_METIS_DIR}/include/metis")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
   else()
-    set(METIS_VERSION_OK TRUE)
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+  endif()
+endif()
+list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(REMOVE_DUPLICATES _inc_env)
+
+
+# Try to find the metis header in the given paths
+# -------------------------------------------------
+# call cmake macro to find the header path
+if(METIS_INCDIR)
+  set(METIS_metis.h_DIRS "METIS_metis.h_DIRS-NOTFOUND")
+  find_path(METIS_metis.h_DIRS
+    NAMES metis.h
+    HINTS ${METIS_INCDIR})
+else()
+  if(METIS_DIR)
+    set(METIS_metis.h_DIRS "METIS_metis.h_DIRS-NOTFOUND")
+    find_path(METIS_metis.h_DIRS
+      NAMES metis.h
+      HINTS ${METIS_DIR}
+      PATH_SUFFIXES "include" "include/metis")
+  else()
+    set(METIS_metis.h_DIRS "METIS_metis.h_DIRS-NOTFOUND")
+    find_path(METIS_metis.h_DIRS
+      NAMES metis.h
+      HINTS ${_inc_env})
+  endif()
+endif()
+mark_as_advanced(METIS_metis.h_DIRS)
+
+
+# If found, add path to cmake variable
+# ------------------------------------
+if (METIS_metis.h_DIRS)
+  set(METIS_INCLUDE_DIRS "${METIS_metis.h_DIRS}")
+else ()
+  set(METIS_INCLUDE_DIRS "METIS_INCLUDE_DIRS-NOTFOUND")
+  if(NOT METIS_FIND_QUIETLY)
+    message(STATUS "Looking for metis -- metis.h not found")
+  endif()
+endif()
+
+
+# Looking for lib
+# ---------------
+
+# Add system library paths to search lib
+# --------------------------------------
+unset(_lib_env)
+set(ENV_METIS_LIBDIR "$ENV{METIS_LIBDIR}")
+if(ENV_METIS_LIBDIR)
+  list(APPEND _lib_env "${ENV_METIS_LIBDIR}")
+elseif(ENV_METIS_DIR)
+  list(APPEND _lib_env "${ENV_METIS_DIR}")
+  list(APPEND _lib_env "${ENV_METIS_DIR}/lib")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _lib_env "$ENV{LIB}")
+  else()
+    if(APPLE)
+      string(REPLACE ":" ";" _lib_env "$ENV{DYLD_LIBRARY_PATH}")
+    else()
+      string(REPLACE ":" ";" _lib_env "$ENV{LD_LIBRARY_PATH}")
+    endif()
+    list(APPEND _lib_env "${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")
+    list(APPEND _lib_env "${CMAKE_C_IMPLICIT_LINK_DIRECTORIES}")
+  endif()
+endif()
+list(REMOVE_DUPLICATES _lib_env)
+
+# Try to find the metis lib in the given paths
+# ----------------------------------------------
+# call cmake macro to find the lib path
+if(METIS_LIBDIR)
+  set(METIS_metis_LIBRARY "METIS_metis_LIBRARY-NOTFOUND")
+  find_library(METIS_metis_LIBRARY
+    NAMES metis
+    HINTS ${METIS_LIBDIR})
+else()
+  if(METIS_DIR)
+    set(METIS_metis_LIBRARY "METIS_metis_LIBRARY-NOTFOUND")
+    find_library(METIS_metis_LIBRARY
+      NAMES metis
+      HINTS ${METIS_DIR}
+      PATH_SUFFIXES lib lib32 lib64)
+  else()
+    set(METIS_metis_LIBRARY "METIS_metis_LIBRARY-NOTFOUND")
+    find_library(METIS_metis_LIBRARY
+      NAMES metis
+      HINTS ${_lib_env})
+  endif()
+endif()
+mark_as_advanced(METIS_metis_LIBRARY)
+
+
+# If found, add path to cmake variable
+# ------------------------------------
+if (METIS_metis_LIBRARY)
+  get_filename_component(metis_lib_path "${METIS_metis_LIBRARY}" PATH)
+  # set cmake variables
+  set(METIS_LIBRARIES    "${METIS_metis_LIBRARY}")
+  set(METIS_LIBRARY_DIRS "${metis_lib_path}")
+else ()
+  set(METIS_LIBRARIES    "METIS_LIBRARIES-NOTFOUND")
+  set(METIS_LIBRARY_DIRS "METIS_LIBRARY_DIRS-NOTFOUND")
+  if(NOT METIS_FIND_QUIETLY)
+    message(STATUS "Looking for metis -- lib metis not found")
+  endif()
+endif ()
+
+# check a function to validate the find
+if(METIS_LIBRARIES)
+
+  set(REQUIRED_INCDIRS)
+  set(REQUIRED_LIBDIRS)
+  set(REQUIRED_LIBS)
+
+  # METIS
+  if (METIS_INCLUDE_DIRS)
+    set(REQUIRED_INCDIRS  "${METIS_INCLUDE_DIRS}")
+  endif()
+  if (METIS_LIBRARY_DIRS)
+    set(REQUIRED_LIBDIRS "${METIS_LIBRARY_DIRS}")
+  endif()
+  set(REQUIRED_LIBS "${METIS_LIBRARIES}")
+  # m
+  find_library(M_LIBRARY NAMES m)
+  mark_as_advanced(M_LIBRARY)
+  if(M_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lm")
   endif()
 
-  if(NOT METIS_VERSION_OK)
-    message(STATUS "Metis version ${METIS_VERSION} found in ${METIS_INCLUDES}, "
-                   "but at least version ${Metis_FIND_VERSION} is required")
-  endif(NOT METIS_VERSION_OK)
-endmacro(_metis_check_version)
+  # set required libraries for link
+  set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
+  set(CMAKE_REQUIRED_LIBRARIES)
+  foreach(lib_dir ${REQUIRED_LIBDIRS})
+    list(APPEND CMAKE_REQUIRED_LIBRARIES "-L${lib_dir}")
+  endforeach()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LIBS}")
+  string(REGEX REPLACE "^ -" "-" CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
 
-  if(METIS_INCLUDES AND Metis_FIND_VERSION)
-    _metis_check_version()
-  else()
-    set(METIS_VERSION_OK TRUE)
+  # test link
+  unset(METIS_WORKS CACHE)
+  include(CheckFunctionExists)
+  check_function_exists(METIS_NodeND METIS_WORKS)
+  mark_as_advanced(METIS_WORKS)
+
+  if(NOT METIS_WORKS)
+    if(NOT METIS_FIND_QUIETLY)
+      message(STATUS "Looking for METIS : test of METIS_NodeND with METIS library fails")
+      message(STATUS "CMAKE_REQUIRED_LIBRARIES: ${CMAKE_REQUIRED_LIBRARIES}")
+      message(STATUS "CMAKE_REQUIRED_INCLUDES: ${CMAKE_REQUIRED_INCLUDES}")
+      message(STATUS "Check in CMakeFiles/CMakeError.log to figure out why it fails")
+    endif()
   endif()
+  set(CMAKE_REQUIRED_INCLUDES)
+  set(CMAKE_REQUIRED_FLAGS)
+  set(CMAKE_REQUIRED_LIBRARIES)
+endif(METIS_LIBRARIES)
 
+if (METIS_LIBRARIES)
+  list(GET METIS_LIBRARIES 0 first_lib)
+  get_filename_component(first_lib_path "${first_lib}" PATH)
+  if (${first_lib_path} MATCHES "/lib(32|64)?$")
+    string(REGEX REPLACE "/lib(32|64)?$" "" not_cached_dir "${first_lib_path}")
+    set(METIS_DIR_FOUND "${not_cached_dir}" CACHE PATH "Installation directory of METIS library" FORCE)
+  else()
+    set(METIS_DIR_FOUND "${first_lib_path}" CACHE PATH "Installation directory of METIS library" FORCE)
+  endif()
+endif()
+mark_as_advanced(METIS_DIR)
+mark_as_advanced(METIS_DIR_FOUND)
 
-find_library(METIS_LIBRARIES metis PATHS $ENV{METISDIR} ${LIB_INSTALL_DIR} PATH_SUFFIXES lib)
-
+# check that METIS has been found
+# ---------------------------------
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(METIS DEFAULT_MSG
-                                  METIS_INCLUDES METIS_LIBRARIES METIS_VERSION_OK)
-
-mark_as_advanced(METIS_INCLUDES METIS_LIBRARIES)
+  METIS_LIBRARIES
+  METIS_WORKS)
+#
+# TODO: Add possibility to check for specific functions in the library
+#

cmake/FindPTSCOTCH.cmake

@@ -0,0 +1,423 @@
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2016 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find PTSCOTCH include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(PTSCOTCH
+#               [REQUIRED]             # Fail with error if ptscotch is not found
+#               [COMPONENTS <comp1> <comp2> ...] # dependencies
+#              )
+#
+#  PTSCOTCH depends on the following libraries:
+#   - Threads
+#   - MPI
+#
+#  COMPONENTS can be some of the following:
+#   - ESMUMPS: to activate detection of PT-Scotch with the esmumps interface
+#
+# This module finds headers and ptscotch library.
+# Results are reported in variables:
+#  PTSCOTCH_FOUND            - True if headers and requested libraries were found
+#  PTSCOTCH_LINKER_FLAGS     - list of required linker flags (excluding -l and -L)
+#  PTSCOTCH_INCLUDE_DIRS     - ptscotch include directories
+#  PTSCOTCH_LIBRARY_DIRS     - Link directories for ptscotch libraries
+#  PTSCOTCH_LIBRARIES        - ptscotch component libraries to be linked
+#  PTSCOTCH_INCLUDE_DIRS_DEP - ptscotch + dependencies include directories
+#  PTSCOTCH_LIBRARY_DIRS_DEP - ptscotch + dependencies link directories
+#  PTSCOTCH_LIBRARIES_DEP    - ptscotch libraries + dependencies
+#  PTSCOTCH_INTSIZE          - Number of octets occupied by a SCOTCH_Num
+#
+# The user can give specific paths where to find the libraries adding cmake
+# options at configure (ex: cmake path/to/project -DPTSCOTCH=path/to/ptscotch):
+#  PTSCOTCH_DIR              - Where to find the base directory of ptscotch
+#  PTSCOTCH_INCDIR           - Where to find the header files
+#  PTSCOTCH_LIBDIR           - Where to find the library files
+# The module can also look for the following environment variables if paths
+# are not given as cmake variable: PTSCOTCH_DIR, PTSCOTCH_INCDIR, PTSCOTCH_LIBDIR
+
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013-2016 Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
+
+if (NOT PTSCOTCH_FOUND)
+  set(PTSCOTCH_DIR "" CACHE PATH "Installation directory of PTSCOTCH library")
+  if (NOT PTSCOTCH_FIND_QUIETLY)
+    message(STATUS "A cache variable, namely PTSCOTCH_DIR, has been set to specify the install directory of PTSCOTCH")
+  endif()
+endif()
+
+# Set the version to find
+set(PTSCOTCH_LOOK_FOR_ESMUMPS OFF)
+
+if( PTSCOTCH_FIND_COMPONENTS )
+  foreach( component ${PTSCOTCH_FIND_COMPONENTS} )
+    if (${component} STREQUAL "ESMUMPS")
+      # means we look for esmumps library
+      set(PTSCOTCH_LOOK_FOR_ESMUMPS ON)
+    endif()
+  endforeach()
+endif()
+
+# PTSCOTCH depends on Threads, try to find it
+if (NOT THREADS_FOUND)
+  if (PTSCOTCH_FIND_REQUIRED)
+    find_package(Threads REQUIRED)
+  else()
+    find_package(Threads)
+  endif()
+endif()
+
+# PTSCOTCH depends on MPI, try to find it
+if (NOT MPI_FOUND)
+  if (PTSCOTCH_FIND_REQUIRED)
+    find_package(MPI REQUIRED)
+  else()
+    find_package(MPI)
+  endif()
+endif()
+
+# Looking for include
+# -------------------
+
+# Add system include paths to search include
+# ------------------------------------------
+unset(_inc_env)
+set(ENV_PTSCOTCH_DIR "$ENV{PTSCOTCH_DIR}")
+set(ENV_PTSCOTCH_INCDIR "$ENV{PTSCOTCH_INCDIR}")
+if(ENV_PTSCOTCH_INCDIR)
+  list(APPEND _inc_env "${ENV_PTSCOTCH_INCDIR}")
+elseif(ENV_PTSCOTCH_DIR)
+  list(APPEND _inc_env "${ENV_PTSCOTCH_DIR}")
+  list(APPEND _inc_env "${ENV_PTSCOTCH_DIR}/include")
+  list(APPEND _inc_env "${ENV_PTSCOTCH_DIR}/include/ptscotch")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
+  else()
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+  endif()
+endif()
+list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(REMOVE_DUPLICATES _inc_env)
+
+
+# Try to find the ptscotch header in the given paths
+# -------------------------------------------------
+
+set(PTSCOTCH_hdrs_to_find "ptscotch.h;scotch.h")
+
+# call cmake macro to find the header path
+if(PTSCOTCH_INCDIR)
+  foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+    set(PTSCOTCH_${ptscotch_hdr}_DIRS "PTSCOTCH_${ptscotch_hdr}_DIRS-NOTFOUND")
+    find_path(PTSCOTCH_${ptscotch_hdr}_DIRS
+      NAMES ${ptscotch_hdr}
+      HINTS ${PTSCOTCH_INCDIR})
+    mark_as_advanced(PTSCOTCH_${ptscotch_hdr}_DIRS)
+  endforeach()
+else()
+  if(PTSCOTCH_DIR)
+    foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+      set(PTSCOTCH_${ptscotch_hdr}_DIRS "PTSCOTCH_${ptscotch_hdr}_DIRS-NOTFOUND")
+      find_path(PTSCOTCH_${ptscotch_hdr}_DIRS
+	NAMES ${ptscotch_hdr}
+	HINTS ${PTSCOTCH_DIR}
+	PATH_SUFFIXES "include" "include/scotch")
+      mark_as_advanced(PTSCOTCH_${ptscotch_hdr}_DIRS)
+    endforeach()
+  else()
+    foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+      set(PTSCOTCH_${ptscotch_hdr}_DIRS "PTSCOTCH_${ptscotch_hdr}_DIRS-NOTFOUND")
+      find_path(PTSCOTCH_${ptscotch_hdr}_DIRS
+	NAMES ${ptscotch_hdr}
+	HINTS ${_inc_env}
+	PATH_SUFFIXES "scotch")
+      mark_as_advanced(PTSCOTCH_${ptscotch_hdr}_DIRS)
+    endforeach()
+  endif()
+endif()
+
+# If found, add path to cmake variable
+# ------------------------------------
+foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+  if (PTSCOTCH_${ptscotch_hdr}_DIRS)
+    list(APPEND PTSCOTCH_INCLUDE_DIRS "${PTSCOTCH_${ptscotch_hdr}_DIRS}")
+  else ()
+    set(PTSCOTCH_INCLUDE_DIRS "PTSCOTCH_INCLUDE_DIRS-NOTFOUND")
+    if (NOT PTSCOTCH_FIND_QUIETLY)
+      message(STATUS "Looking for ptscotch -- ${ptscotch_hdr} not found")
+    endif()
+  endif()
+endforeach()
+list(REMOVE_DUPLICATES PTSCOTCH_INCLUDE_DIRS)
+
+# Looking for lib
+# ---------------
+
+# Add system library paths to search lib
+# --------------------------------------
+unset(_lib_env)
+set(ENV_PTSCOTCH_LIBDIR "$ENV{PTSCOTCH_LIBDIR}")
+if(ENV_PTSCOTCH_LIBDIR)
+  list(APPEND _lib_env "${ENV_PTSCOTCH_LIBDIR}")
+elseif(ENV_PTSCOTCH_DIR)
+  list(APPEND _lib_env "${ENV_PTSCOTCH_DIR}")
+  list(APPEND _lib_env "${ENV_PTSCOTCH_DIR}/lib")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _lib_env "$ENV{LIB}")
+  else()
+    if(APPLE)
+      string(REPLACE ":" ";" _lib_env "$ENV{DYLD_LIBRARY_PATH}")
+    else()
+      string(REPLACE ":" ";" _lib_env "$ENV{LD_LIBRARY_PATH}")
+    endif()
+    list(APPEND _lib_env "${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")
+    list(APPEND _lib_env "${CMAKE_C_IMPLICIT_LINK_DIRECTORIES}")
+  endif()
+endif()
+list(REMOVE_DUPLICATES _lib_env)
+
+# Try to find the ptscotch lib in the given paths
+# ----------------------------------------------
+
+set(PTSCOTCH_libs_to_find "ptscotch;ptscotcherr")
+if (PTSCOTCH_LOOK_FOR_ESMUMPS)
+  list(INSERT PTSCOTCH_libs_to_find 0 "ptesmumps")
+  list(APPEND PTSCOTCH_libs_to_find   "esmumps"  )
+endif()
+list(APPEND PTSCOTCH_libs_to_find "scotch;scotcherr")
+
+# call cmake macro to find the lib path
+if(PTSCOTCH_LIBDIR)
+  foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+    set(PTSCOTCH_${ptscotch_lib}_LIBRARY "PTSCOTCH_${ptscotch_lib}_LIBRARY-NOTFOUND")
+    find_library(PTSCOTCH_${ptscotch_lib}_LIBRARY
+      NAMES ${ptscotch_lib}
+      HINTS ${PTSCOTCH_LIBDIR})
+  endforeach()
+else()
+  if(PTSCOTCH_DIR)
+    foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+      set(PTSCOTCH_${ptscotch_lib}_LIBRARY "PTSCOTCH_${ptscotch_lib}_LIBRARY-NOTFOUND")
+      find_library(PTSCOTCH_${ptscotch_lib}_LIBRARY
+	NAMES ${ptscotch_lib}
+	HINTS ${PTSCOTCH_DIR}
+	PATH_SUFFIXES lib lib32 lib64)
+    endforeach()
+  else()
+    foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+      set(PTSCOTCH_${ptscotch_lib}_LIBRARY "PTSCOTCH_${ptscotch_lib}_LIBRARY-NOTFOUND")
+      find_library(PTSCOTCH_${ptscotch_lib}_LIBRARY
+	NAMES ${ptscotch_lib}
+	HINTS ${_lib_env})
+    endforeach()
+  endif()
+endif()
+
+set(PTSCOTCH_LIBRARIES "")
+set(PTSCOTCH_LIBRARY_DIRS "")
+# If found, add path to cmake variable
+# ------------------------------------
+foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+
+  if (PTSCOTCH_${ptscotch_lib}_LIBRARY)
+    get_filename_component(${ptscotch_lib}_lib_path "${PTSCOTCH_${ptscotch_lib}_LIBRARY}" PATH)
+    # set cmake variables
+    list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+    list(APPEND PTSCOTCH_LIBRARY_DIRS "${${ptscotch_lib}_lib_path}")
+  else ()
+    list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+    if (NOT PTSCOTCH_FIND_QUIETLY)
+      message(STATUS "Looking for ptscotch -- lib ${ptscotch_lib} not found")
+    endif()
+  endif ()
+
+  mark_as_advanced(PTSCOTCH_${ptscotch_lib}_LIBRARY)
+
+endforeach()
+list(REMOVE_DUPLICATES PTSCOTCH_LIBRARY_DIRS)
+
+# check a function to validate the find
+if(PTSCOTCH_LIBRARIES)
+
+  set(REQUIRED_LDFLAGS)
+  set(REQUIRED_INCDIRS)
+  set(REQUIRED_LIBDIRS)
+  set(REQUIRED_LIBS)
+
+  # PTSCOTCH
+  if (PTSCOTCH_INCLUDE_DIRS)
+    set(REQUIRED_INCDIRS  "${PTSCOTCH_INCLUDE_DIRS}")
+  endif()
+  if (PTSCOTCH_LIBRARY_DIRS)
+    set(REQUIRED_LIBDIRS "${PTSCOTCH_LIBRARY_DIRS}")
+  endif()
+  set(REQUIRED_LIBS "${PTSCOTCH_LIBRARIES}")
+  # MPI
+  if (MPI_FOUND)
+    if (MPI_C_INCLUDE_PATH)
+      list(APPEND CMAKE_REQUIRED_INCLUDES "${MPI_C_INCLUDE_PATH}")
+    endif()
+    if (MPI_C_LINK_FLAGS)
+      if (${MPI_C_LINK_FLAGS} MATCHES "  -")
+	string(REGEX REPLACE " -" "-" MPI_C_LINK_FLAGS ${MPI_C_LINK_FLAGS})
+      endif()
+      list(APPEND REQUIRED_LDFLAGS "${MPI_C_LINK_FLAGS}")
+    endif()
+    list(APPEND REQUIRED_LIBS "${MPI_C_LIBRARIES}")
+  endif()
+  # THREADS
+  if(CMAKE_THREAD_LIBS_INIT)
+    list(APPEND REQUIRED_LIBS "${CMAKE_THREAD_LIBS_INIT}")
+  endif()
+  set(Z_LIBRARY "Z_LIBRARY-NOTFOUND")
+  find_library(Z_LIBRARY NAMES z)
+  mark_as_advanced(Z_LIBRARY)
+  if(Z_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lz")
+  endif()
+  set(M_LIBRARY "M_LIBRARY-NOTFOUND")
+  find_library(M_LIBRARY NAMES m)
+  mark_as_advanced(M_LIBRARY)
+  if(M_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lm")
+  endif()
+  set(RT_LIBRARY "RT_LIBRARY-NOTFOUND")
+  find_library(RT_LIBRARY NAMES rt)
+  mark_as_advanced(RT_LIBRARY)
+  if(RT_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lrt")
+  endif()
+
+  # set required libraries for link
+  set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
+  set(CMAKE_REQUIRED_LIBRARIES)
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LDFLAGS}")
+  foreach(lib_dir ${REQUIRED_LIBDIRS})
+    list(APPEND CMAKE_REQUIRED_LIBRARIES "-L${lib_dir}")
+  endforeach()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LIBS}")
+  list(APPEND CMAKE_REQUIRED_FLAGS "${REQUIRED_FLAGS}")
+  string(REGEX REPLACE "^ -" "-" CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+
+  # test link
+  unset(PTSCOTCH_WORKS CACHE)
+  include(CheckFunctionExists)
+  check_function_exists(SCOTCH_dgraphInit PTSCOTCH_WORKS)
+  mark_as_advanced(PTSCOTCH_WORKS)
+
+  if(PTSCOTCH_WORKS)
+    # save link with dependencies
+    set(PTSCOTCH_LIBRARIES_DEP "${REQUIRED_LIBS}")
+    set(PTSCOTCH_LIBRARY_DIRS_DEP "${REQUIRED_LIBDIRS}")
+    set(PTSCOTCH_INCLUDE_DIRS_DEP "${REQUIRED_INCDIRS}")
+    set(PTSCOTCH_LINKER_FLAGS "${REQUIRED_LDFLAGS}")
+    list(REMOVE_DUPLICATES PTSCOTCH_LIBRARY_DIRS_DEP)
+    list(REMOVE_DUPLICATES PTSCOTCH_INCLUDE_DIRS_DEP)
+    list(REMOVE_DUPLICATES PTSCOTCH_LINKER_FLAGS)
+  else()
+    if(NOT PTSCOTCH_FIND_QUIETLY)
+      message(STATUS "Looking for PTSCOTCH : test of SCOTCH_dgraphInit with PTSCOTCH library fails")
+      message(STATUS "CMAKE_REQUIRED_LIBRARIES: ${CMAKE_REQUIRED_LIBRARIES}")
+      message(STATUS "CMAKE_REQUIRED_INCLUDES: ${CMAKE_REQUIRED_INCLUDES}")
+      message(STATUS "Check in CMakeFiles/CMakeError.log to figure out why it fails")
+    endif()
+  endif()
+  set(CMAKE_REQUIRED_INCLUDES)
+  set(CMAKE_REQUIRED_FLAGS)
+  set(CMAKE_REQUIRED_LIBRARIES)
+endif(PTSCOTCH_LIBRARIES)
+
+if (PTSCOTCH_LIBRARIES)
+  list(GET PTSCOTCH_LIBRARIES 0 first_lib)
+  get_filename_component(first_lib_path "${first_lib}" PATH)
+  if (${first_lib_path} MATCHES "/lib(32|64)?$")
+    string(REGEX REPLACE "/lib(32|64)?$" "" not_cached_dir "${first_lib_path}")
+    set(PTSCOTCH_DIR_FOUND "${not_cached_dir}" CACHE PATH "Installation directory of PTSCOTCH library" FORCE)
+  else()
+    set(PTSCOTCH_DIR_FOUND "${first_lib_path}" CACHE PATH "Installation directory of PTSCOTCH library" FORCE)
+  endif()
+endif()
+mark_as_advanced(PTSCOTCH_DIR)
+mark_as_advanced(PTSCOTCH_DIR_FOUND)
+
+# Check the size of SCOTCH_Num
+# ---------------------------------
+set(CMAKE_REQUIRED_INCLUDES ${PTSCOTCH_INCLUDE_DIRS})
+
+include(CheckCSourceRuns)
+#stdio.h and stdint.h should be included by scotch.h directly
+set(PTSCOTCH_C_TEST_SCOTCH_Num_4 "
+#include <stdio.h>
+#include <stdint.h>
+#include <ptscotch.h>
+int main(int argc, char **argv) {
+  if (sizeof(SCOTCH_Num) == 4)
+    return 0;
+  else
+    return 1;
+}
+")
+
+set(PTSCOTCH_C_TEST_SCOTCH_Num_8 "
+#include <stdio.h>
+#include <stdint.h>
+#include <ptscotch.h>
+int main(int argc, char **argv) {
+  if (sizeof(SCOTCH_Num) == 8)
+    return 0;
+  else
+    return 1;
+}
+")
+check_c_source_runs("${PTSCOTCH_C_TEST_SCOTCH_Num_4}" PTSCOTCH_Num_4)
+if(NOT PTSCOTCH_Num_4)
+  check_c_source_runs("${PTSCOTCH_C_TEST_SCOTCH_Num_8}" PTSCOTCH_Num_8)
+  if(NOT PTSCOTCH_Num_8)
+    set(PTSCOTCH_INTSIZE -1)
+  else()
+    set(PTSCOTCH_INTSIZE 8)
+  endif()
+else()
+  set(PTSCOTCH_INTSIZE 4)
+endif()
+set(CMAKE_REQUIRED_INCLUDES "")
+
+# check that PTSCOTCH has been found
+# ---------------------------------
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(PTSCOTCH DEFAULT_MSG
+  PTSCOTCH_LIBRARIES
+  PTSCOTCH_WORKS)
+#
+# TODO: Add possibility to check for specific functions in the library
+#

cmake/FindPastix.cmake

@@ -1,25 +1,704 @@
-# Pastix lib requires linking to a blas library.
-# It is up to the user of this module to find a BLAS and link to it.
-# Pastix requires SCOTCH or METIS (partitioning and reordering tools) as well
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2014 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find PASTIX include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(PASTIX
+#               [REQUIRED] # Fail with error if pastix is not found
+#               [COMPONENTS <comp1> <comp2> ...] # dependencies
+#              )
+#
+#  PASTIX depends on the following libraries:
+#   - Threads, m, rt
+#   - MPI
+#   - HWLOC
+#   - BLAS
+#
+#  COMPONENTS are optional libraries PASTIX could be linked with,
+#  Use it to drive detection of a specific compilation chain
+#  COMPONENTS can be some of the following:
+#   - MPI: to activate detection of the parallel MPI version (default)
+#        it looks for Threads, HWLOC, BLAS, MPI and ScaLAPACK libraries
+#   - SEQ: to activate detection of the sequential version (exclude MPI version)
+#   - STARPU: to activate detection of StarPU version
+#   it looks for MPI version of StarPU (default behaviour)
+#   if SEQ and STARPU are given, it looks for a StarPU without MPI
+#   - STARPU_CUDA: to activate detection of StarPU with CUDA
+#   - STARPU_FXT: to activate detection of StarPU with FxT
+#   - SCOTCH: to activate detection of PASTIX linked with SCOTCH
+#   - PTSCOTCH: to activate detection of PASTIX linked with SCOTCH
+#   - METIS: to activate detection of PASTIX linked with SCOTCH
+#
+# This module finds headers and pastix library.
+# Results are reported in variables:
+#  PASTIX_FOUND            - True if headers and requested libraries were found
+#  PASTIX_LINKER_FLAGS     - list of required linker flags (excluding -l and -L)
+#  PASTIX_INCLUDE_DIRS     - pastix include directories
+#  PASTIX_LIBRARY_DIRS     - Link directories for pastix libraries
+#  PASTIX_LIBRARIES        - pastix libraries
+#  PASTIX_INCLUDE_DIRS_DEP - pastix + dependencies include directories
+#  PASTIX_LIBRARY_DIRS_DEP - pastix + dependencies link directories
+#  PASTIX_LIBRARIES_DEP    - pastix libraries + dependencies
+#
+# The user can give specific paths where to find the libraries adding cmake
+# options at configure (ex: cmake path/to/project -DPASTIX_DIR=path/to/pastix):
+#  PASTIX_DIR              - Where to find the base directory of pastix
+#  PASTIX_INCDIR           - Where to find the header files
+#  PASTIX_LIBDIR           - Where to find the library files
+# The module can also look for the following environment variables if paths
+# are not given as cmake variable: PASTIX_DIR, PASTIX_INCDIR, PASTIX_LIBDIR
 
-if (PASTIX_INCLUDES AND PASTIX_LIBRARIES)
-  set(PASTIX_FIND_QUIETLY TRUE)
-endif (PASTIX_INCLUDES AND PASTIX_LIBRARIES)
-
-find_path(PASTIX_INCLUDES
-  NAMES
-  pastix_nompi.h
-  PATHS
-  $ENV{PASTIXDIR}
-  ${INCLUDE_INSTALL_DIR}
-)
-
-find_library(PASTIX_LIBRARIES pastix PATHS $ENV{PASTIXDIR} ${LIB_INSTALL_DIR})
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013      Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
 
 
+if (NOT PASTIX_FOUND)
+  set(PASTIX_DIR "" CACHE PATH "Installation directory of PASTIX library")
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "A cache variable, namely PASTIX_DIR, has been set to specify the install directory of PASTIX")
+  endif()
+endif()
 
+# Set the version to find
+set(PASTIX_LOOK_FOR_MPI ON)
+set(PASTIX_LOOK_FOR_SEQ OFF)
+set(PASTIX_LOOK_FOR_STARPU OFF)
+set(PASTIX_LOOK_FOR_STARPU_CUDA OFF)
+set(PASTIX_LOOK_FOR_STARPU_FXT OFF)
+set(PASTIX_LOOK_FOR_SCOTCH ON)
+set(PASTIX_LOOK_FOR_PTSCOTCH OFF)
+set(PASTIX_LOOK_FOR_METIS OFF)
+
+if( PASTIX_FIND_COMPONENTS )
+  foreach( component ${PASTIX_FIND_COMPONENTS} )
+    if (${component} STREQUAL "SEQ")
+      # means we look for the sequential version of PaStiX (without MPI)
+      set(PASTIX_LOOK_FOR_SEQ ON)
+      set(PASTIX_LOOK_FOR_MPI OFF)
+    endif()
+    if (${component} STREQUAL "MPI")
+      # means we look for the MPI version of PaStiX (default)
+      set(PASTIX_LOOK_FOR_SEQ OFF)
+      set(PASTIX_LOOK_FOR_MPI ON)
+    endif()
+    if (${component} STREQUAL "STARPU")
+      # means we look for PaStiX with StarPU
+      set(PASTIX_LOOK_FOR_STARPU ON)
+    endif()
+    if (${component} STREQUAL "STARPU_CUDA")
+      # means we look for PaStiX with StarPU + CUDA
+      set(PASTIX_LOOK_FOR_STARPU ON)
+      set(PASTIX_LOOK_FOR_STARPU_CUDA ON)
+    endif()
+    if (${component} STREQUAL "STARPU_FXT")
+      # means we look for PaStiX with StarPU + FxT
+      set(PASTIX_LOOK_FOR_STARPU_FXT ON)
+    endif()
+    if (${component} STREQUAL "SCOTCH")
+      set(PASTIX_LOOK_FOR_SCOTCH ON)
+    endif()
+    if (${component} STREQUAL "SCOTCH")
+      set(PASTIX_LOOK_FOR_PTSCOTCH ON)
+    endif()
+    if (${component} STREQUAL "METIS")
+      set(PASTIX_LOOK_FOR_METIS ON)
+    endif()
+  endforeach()
+endif()
+
+# Dependencies detection
+# ----------------------
+
+
+# Required dependencies
+# ---------------------
+
+if (NOT PASTIX_FIND_QUIETLY)
+  message(STATUS "Looking for PASTIX - Try to detect pthread")
+endif()
+if (PASTIX_FIND_REQUIRED)
+  find_package(Threads REQUIRED QUIET)
+else()
+  find_package(Threads QUIET)
+endif()
+set(PASTIX_EXTRA_LIBRARIES "")
+if( THREADS_FOUND )
+  list(APPEND PASTIX_EXTRA_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+endif ()
+
+# Add math library to the list of extra
+# it normally exists on all common systems provided with a C compiler
+if (NOT PASTIX_FIND_QUIETLY)
+  message(STATUS "Looking for PASTIX - Try to detect libm")
+endif()
+set(PASTIX_M_LIBRARIES "")
+if(UNIX OR WIN32)
+  find_library(
+    PASTIX_M_m_LIBRARY
+    NAMES m
+    )
+  mark_as_advanced(PASTIX_M_m_LIBRARY)
+  if (PASTIX_M_m_LIBRARY)
+    list(APPEND PASTIX_M_LIBRARIES "${PASTIX_M_m_LIBRARY}")
+    list(APPEND PASTIX_EXTRA_LIBRARIES "${PASTIX_M_m_LIBRARY}")
+  else()
+    if (PASTIX_FIND_REQUIRED)
+      message(FATAL_ERROR "Could NOT find libm on your system."
+	"Are you sure to a have a C compiler installed?")
+    endif()
+  endif()
+endif()
+
+# Try to find librt (libposix4 - POSIX.1b Realtime Extensions library)
+# on Unix systems except Apple ones because it does not exist on it
+if (NOT PASTIX_FIND_QUIETLY)
+  message(STATUS "Looking for PASTIX - Try to detect librt")
+endif()
+set(PASTIX_RT_LIBRARIES "")
+if(UNIX AND NOT APPLE)
+  find_library(
+    PASTIX_RT_rt_LIBRARY
+    NAMES rt
+    )
+  mark_as_advanced(PASTIX_RT_rt_LIBRARY)
+  if (PASTIX_RT_rt_LIBRARY)
+    list(APPEND PASTIX_RT_LIBRARIES "${PASTIX_RT_rt_LIBRARY}")
+    list(APPEND PASTIX_EXTRA_LIBRARIES "${PASTIX_RT_rt_LIBRARY}")
+  else()
+    if (PASTIX_FIND_REQUIRED)
+      message(FATAL_ERROR "Could NOT find librt on your system")
+    endif()
+  endif()
+endif()
+
+# PASTIX depends on HWLOC
+#------------------------
+if (NOT PASTIX_FIND_QUIETLY)
+  message(STATUS "Looking for PASTIX - Try to detect HWLOC")
+endif()
+if (PASTIX_FIND_REQUIRED)
+  find_package(HWLOC REQUIRED QUIET)
+else()
+  find_package(HWLOC QUIET)
+endif()
+
+# PASTIX depends on BLAS
+#-----------------------
+if (NOT PASTIX_FIND_QUIETLY)
+  message(STATUS "Looking for PASTIX - Try to detect BLAS")
+endif()
+if (PASTIX_FIND_REQUIRED)
+  find_package(BLASEXT REQUIRED QUIET)
+else()
+  find_package(BLASEXT QUIET)
+endif()
+
+# Optional dependencies
+# ---------------------
+
+# PASTIX may depend on MPI
+#-------------------------
+if (NOT MPI_FOUND AND PASTIX_LOOK_FOR_MPI)
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for PASTIX - Try to detect MPI")
+  endif()
+  # allows to use an external mpi compilation by setting compilers with
+  # -DMPI_C_COMPILER=path/to/mpicc -DMPI_Fortran_COMPILER=path/to/mpif90
+  # at cmake configure
+  if(NOT MPI_C_COMPILER)
+    set(MPI_C_COMPILER mpicc)
+  endif()
+  if (PASTIX_FIND_REQUIRED AND PASTIX_FIND_REQUIRED_MPI)
+    find_package(MPI REQUIRED QUIET)
+  else()
+    find_package(MPI QUIET)
+  endif()
+  if (MPI_FOUND)
+    mark_as_advanced(MPI_LIBRARY)
+    mark_as_advanced(MPI_EXTRA_LIBRARY)
+  endif()
+endif (NOT MPI_FOUND AND PASTIX_LOOK_FOR_MPI)
+
+# PASTIX may depend on STARPU
+#----------------------------
+if( NOT STARPU_FOUND AND PASTIX_LOOK_FOR_STARPU)
+
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for PASTIX - Try to detect StarPU")
+  endif()
+
+  set(PASTIX_STARPU_VERSION "1.1" CACHE STRING "oldest STARPU version desired")
+
+  # create list of components in order to make a single call to find_package(starpu...)
+  # we explicitly need a StarPU version built with hwloc
+  set(STARPU_COMPONENT_LIST "HWLOC")
+
+  # StarPU may depend on MPI
+  # allows to use an external mpi compilation by setting compilers with
+  # -DMPI_C_COMPILER=path/to/mpicc -DMPI_Fortran_COMPILER=path/to/mpif90
+  # at cmake configure
+  if (PASTIX_LOOK_FOR_MPI)
+    if(NOT MPI_C_COMPILER)
+      set(MPI_C_COMPILER mpicc)
+    endif()
+    list(APPEND STARPU_COMPONENT_LIST "MPI")
+  endif()
+  if (PASTIX_LOOK_FOR_STARPU_CUDA)
+    list(APPEND STARPU_COMPONENT_LIST "CUDA")
+  endif()
+  if (PASTIX_LOOK_FOR_STARPU_FXT)
+    list(APPEND STARPU_COMPONENT_LIST "FXT")
+  endif()
+  # set the list of optional dependencies we may discover
+  if (PASTIX_FIND_REQUIRED AND PASTIX_FIND_REQUIRED_STARPU)
+    find_package(STARPU ${PASTIX_STARPU_VERSION} REQUIRED
+      COMPONENTS ${STARPU_COMPONENT_LIST})
+  else()
+    find_package(STARPU ${PASTIX_STARPU_VERSION}
+      COMPONENTS ${STARPU_COMPONENT_LIST})
+  endif()
+
+endif( NOT STARPU_FOUND AND PASTIX_LOOK_FOR_STARPU)
+
+# PASTIX may depends on SCOTCH
+#-----------------------------
+if (NOT SCOTCH_FOUND AND PASTIX_LOOK_FOR_SCOTCH)
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for PASTIX - Try to detect SCOTCH")
+  endif()
+  if (PASTIX_FIND_REQUIRED AND PASTIX_FIND_REQUIRED_SCOTCH)
+    find_package(SCOTCH REQUIRED QUIET)
+  else()
+    find_package(SCOTCH QUIET)
+  endif()
+endif()
+
+# PASTIX may depends on PTSCOTCH
+#-------------------------------
+if (NOT PTSCOTCH_FOUND AND PASTIX_LOOK_FOR_PTSCOTCH)
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for PASTIX - Try to detect PTSCOTCH")
+  endif()
+  if (PASTIX_FIND_REQUIRED AND PASTIX_FIND_REQUIRED_PTSCOTCH)
+    find_package(PTSCOTCH REQUIRED QUIET)
+  else()
+    find_package(PTSCOTCH QUIET)
+  endif()
+endif()
+
+# PASTIX may depends on METIS
+#----------------------------
+if (NOT METIS_FOUND AND PASTIX_LOOK_FOR_METIS)
+  if (NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for PASTIX - Try to detect METIS")
+  endif()
+  if (PASTIX_FIND_REQUIRED AND PASTIX_FIND_REQUIRED_METIS)
+    find_package(METIS REQUIRED QUIET)
+  else()
+    find_package(METIS QUIET)
+  endif()
+endif()
+
+# Error if pastix required and no partitioning lib found
+if (PASTIX_FIND_REQUIRED AND NOT SCOTCH_FOUND AND NOT PTSCOTCH_FOUND AND NOT METIS_FOUND)
+  message(FATAL_ERROR "Could NOT find any partitioning library on your system"
+    " (install scotch, ptscotch or metis)")
+endif()
+
+
+# Looking for PaStiX
+# ------------------
+
+# Looking for include
+# -------------------
+
+# Add system include paths to search include
+# ------------------------------------------
+unset(_inc_env)
+set(ENV_PASTIX_DIR "$ENV{PASTIX_DIR}")
+set(ENV_PASTIX_INCDIR "$ENV{PASTIX_INCDIR}")
+if(ENV_PASTIX_INCDIR)
+  list(APPEND _inc_env "${ENV_PASTIX_INCDIR}")
+elseif(ENV_PASTIX_DIR)
+  list(APPEND _inc_env "${ENV_PASTIX_DIR}")
+  list(APPEND _inc_env "${ENV_PASTIX_DIR}/include")
+  list(APPEND _inc_env "${ENV_PASTIX_DIR}/include/pastix")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
+  else()
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+  endif()
+endif()
+list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(REMOVE_DUPLICATES _inc_env)
+
+
+# Try to find the pastix header in the given paths
+# ---------------------------------------------------
+# call cmake macro to find the header path
+if(PASTIX_INCDIR)
+  set(PASTIX_pastix.h_DIRS "PASTIX_pastix.h_DIRS-NOTFOUND")
+  find_path(PASTIX_pastix.h_DIRS
+    NAMES pastix.h
+    HINTS ${PASTIX_INCDIR})
+else()
+  if(PASTIX_DIR)
+    set(PASTIX_pastix.h_DIRS "PASTIX_pastix.h_DIRS-NOTFOUND")
+    find_path(PASTIX_pastix.h_DIRS
+      NAMES pastix.h
+      HINTS ${PASTIX_DIR}
+      PATH_SUFFIXES "include" "include/pastix")
+  else()
+    set(PASTIX_pastix.h_DIRS "PASTIX_pastix.h_DIRS-NOTFOUND")
+    find_path(PASTIX_pastix.h_DIRS
+      NAMES pastix.h
+      HINTS ${_inc_env}
+      PATH_SUFFIXES "pastix")
+  endif()
+endif()
+mark_as_advanced(PASTIX_pastix.h_DIRS)
+
+# If found, add path to cmake variable
+# ------------------------------------
+if (PASTIX_pastix.h_DIRS)
+  set(PASTIX_INCLUDE_DIRS "${PASTIX_pastix.h_DIRS}")
+else ()
+  set(PASTIX_INCLUDE_DIRS "PASTIX_INCLUDE_DIRS-NOTFOUND")
+  if(NOT PASTIX_FIND_QUIETLY)
+    message(STATUS "Looking for pastix -- pastix.h not found")
+  endif()
+endif()
+
+
+# Looking for lib
+# ---------------
+
+# Add system library paths to search lib
+# --------------------------------------
+unset(_lib_env)
+set(ENV_PASTIX_LIBDIR "$ENV{PASTIX_LIBDIR}")
+if(ENV_PASTIX_LIBDIR)
+  list(APPEND _lib_env "${ENV_PASTIX_LIBDIR}")
+elseif(ENV_PASTIX_DIR)
+  list(APPEND _lib_env "${ENV_PASTIX_DIR}")
+  list(APPEND _lib_env "${ENV_PASTIX_DIR}/lib")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _lib_env "$ENV{LIB}")
+  else()
+    if(APPLE)
+      string(REPLACE ":" ";" _lib_env "$ENV{DYLD_LIBRARY_PATH}")
+    else()
+      string(REPLACE ":" ";" _lib_env "$ENV{LD_LIBRARY_PATH}")
+    endif()
+    list(APPEND _lib_env "${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")
+    list(APPEND _lib_env "${CMAKE_C_IMPLICIT_LINK_DIRECTORIES}")
+  endif()
+endif()
+list(REMOVE_DUPLICATES _lib_env)
+
+# Try to find the pastix lib in the given paths
+# ------------------------------------------------
+
+# create list of libs to find
+set(PASTIX_libs_to_find "pastix_murge;pastix")
+
+# call cmake macro to find the lib path
+if(PASTIX_LIBDIR)
+  foreach(pastix_lib ${PASTIX_libs_to_find})
+    set(PASTIX_${pastix_lib}_LIBRARY "PASTIX_${pastix_lib}_LIBRARY-NOTFOUND")
+    find_library(PASTIX_${pastix_lib}_LIBRARY
+      NAMES ${pastix_lib}
+      HINTS ${PASTIX_LIBDIR})
+  endforeach()
+else()
+  if(PASTIX_DIR)
+    foreach(pastix_lib ${PASTIX_libs_to_find})
+      set(PASTIX_${pastix_lib}_LIBRARY "PASTIX_${pastix_lib}_LIBRARY-NOTFOUND")
+      find_library(PASTIX_${pastix_lib}_LIBRARY
+	NAMES ${pastix_lib}
+	HINTS ${PASTIX_DIR}
+	PATH_SUFFIXES lib lib32 lib64)
+    endforeach()
+  else()
+    foreach(pastix_lib ${PASTIX_libs_to_find})
+      set(PASTIX_${pastix_lib}_LIBRARY "PASTIX_${pastix_lib}_LIBRARY-NOTFOUND")
+      find_library(PASTIX_${pastix_lib}_LIBRARY
+	NAMES ${pastix_lib}
+	HINTS ${_lib_env})
+    endforeach()
+  endif()
+endif()
+
+# If found, add path to cmake variable
+# ------------------------------------
+foreach(pastix_lib ${PASTIX_libs_to_find})
+
+  get_filename_component(${pastix_lib}_lib_path ${PASTIX_${pastix_lib}_LIBRARY} PATH)
+  # set cmake variables (respects naming convention)
+  if (PASTIX_LIBRARIES)
+    list(APPEND PASTIX_LIBRARIES "${PASTIX_${pastix_lib}_LIBRARY}")
+  else()
+    set(PASTIX_LIBRARIES "${PASTIX_${pastix_lib}_LIBRARY}")
+  endif()
+  if (PASTIX_LIBRARY_DIRS)
+    list(APPEND PASTIX_LIBRARY_DIRS "${${pastix_lib}_lib_path}")
+  else()
+    set(PASTIX_LIBRARY_DIRS "${${pastix_lib}_lib_path}")
+  endif()
+  mark_as_advanced(PASTIX_${pastix_lib}_LIBRARY)
+
+endforeach(pastix_lib ${PASTIX_libs_to_find})
+
+# check a function to validate the find
+if(PASTIX_LIBRARIES)
+
+  set(REQUIRED_LDFLAGS)
+  set(REQUIRED_INCDIRS)
+  set(REQUIRED_LIBDIRS)
+  set(REQUIRED_LIBS)
+
+  # PASTIX
+  if (PASTIX_INCLUDE_DIRS)
+    set(REQUIRED_INCDIRS "${PASTIX_INCLUDE_DIRS}")
+  endif()
+  foreach(libdir ${PASTIX_LIBRARY_DIRS})
+    if (libdir)
+      list(APPEND REQUIRED_LIBDIRS "${libdir}")
+    endif()
+  endforeach()
+  set(REQUIRED_LIBS "${PASTIX_LIBRARIES}")
+  # STARPU
+  if (PASTIX_LOOK_FOR_STARPU AND STARPU_FOUND)
+    if (STARPU_INCLUDE_DIRS_DEP)
+      list(APPEND REQUIRED_INCDIRS "${STARPU_INCLUDE_DIRS_DEP}")
+    elseif (STARPU_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${STARPU_INCLUDE_DIRS}")
+    endif()
+    if(STARPU_LIBRARY_DIRS_DEP)
+      list(APPEND REQUIRED_LIBDIRS "${STARPU_LIBRARY_DIRS_DEP}")
+    elseif(STARPU_LIBRARY_DIRS)
+      list(APPEND REQUIRED_LIBDIRS "${STARPU_LIBRARY_DIRS}")
+    endif()
+    if (STARPU_LIBRARIES_DEP)
+      list(APPEND REQUIRED_LIBS "${STARPU_LIBRARIES_DEP}")
+    elseif (STARPU_LIBRARIES)
+      foreach(lib ${STARPU_LIBRARIES})
+	if (EXISTS ${lib} OR ${lib} MATCHES "^-")
+	  list(APPEND REQUIRED_LIBS "${lib}")
+	else()
+	  list(APPEND REQUIRED_LIBS "-l${lib}")
+	endif()
+      endforeach()
+    endif()
+  endif()
+  # CUDA
+  if (PASTIX_LOOK_FOR_STARPU_CUDA AND CUDA_FOUND)
+    if (CUDA_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${CUDA_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${CUDA_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    list(APPEND REQUIRED_LIBS "${CUDA_CUBLAS_LIBRARIES};${CUDA_LIBRARIES}")
+  endif()
+  # MPI
+  if (PASTIX_LOOK_FOR_MPI AND MPI_FOUND)
+    if (MPI_C_INCLUDE_PATH)
+      list(APPEND REQUIRED_INCDIRS "${MPI_C_INCLUDE_PATH}")
+    endif()
+    if (MPI_C_LINK_FLAGS)
+      if (${MPI_C_LINK_FLAGS} MATCHES "  -")
+	string(REGEX REPLACE " -" "-" MPI_C_LINK_FLAGS ${MPI_C_LINK_FLAGS})
+      endif()
+      list(APPEND REQUIRED_LDFLAGS "${MPI_C_LINK_FLAGS}")
+    endif()
+    list(APPEND REQUIRED_LIBS "${MPI_C_LIBRARIES}")
+  endif()
+  # HWLOC
+  if (HWLOC_FOUND)
+    if (HWLOC_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${HWLOC_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${HWLOC_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    foreach(lib ${HWLOC_LIBRARIES})
+      if (EXISTS ${lib} OR ${lib} MATCHES "^-")
+	list(APPEND REQUIRED_LIBS "${lib}")
+      else()
+	list(APPEND REQUIRED_LIBS "-l${lib}")
+      endif()
+    endforeach()
+  endif()
+  # BLAS
+  if (BLAS_FOUND)
+    if (BLAS_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${BLAS_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${BLAS_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    list(APPEND REQUIRED_LIBS "${BLAS_LIBRARIES}")
+    if (BLAS_LINKER_FLAGS)
+      list(APPEND REQUIRED_LDFLAGS "${BLAS_LINKER_FLAGS}")
+    endif()
+  endif()
+  # SCOTCH
+  if (PASTIX_LOOK_FOR_SCOTCH AND SCOTCH_FOUND)
+    if (SCOTCH_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${SCOTCH_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${SCOTCH_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    list(APPEND REQUIRED_LIBS "${SCOTCH_LIBRARIES}")
+  endif()
+  # PTSCOTCH
+  if (PASTIX_LOOK_FOR_PTSCOTCH AND PTSCOTCH_FOUND)
+    if (PTSCOTCH_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${PTSCOTCH_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${PTSCOTCH_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    list(APPEND REQUIRED_LIBS "${PTSCOTCH_LIBRARIES}")
+  endif()
+  # METIS
+  if (PASTIX_LOOK_FOR_METIS AND METIS_FOUND)
+    if (METIS_INCLUDE_DIRS)
+      list(APPEND REQUIRED_INCDIRS "${METIS_INCLUDE_DIRS}")
+    endif()
+    foreach(libdir ${METIS_LIBRARY_DIRS})
+      if (libdir)
+	list(APPEND REQUIRED_LIBDIRS "${libdir}")
+      endif()
+    endforeach()
+    list(APPEND REQUIRED_LIBS "${METIS_LIBRARIES}")
+  endif()
+  # Fortran
+  if (CMAKE_C_COMPILER_ID MATCHES "GNU")
+    find_library(
+      FORTRAN_gfortran_LIBRARY
+      NAMES gfortran
+      HINTS ${_lib_env}
+      )
+    mark_as_advanced(FORTRAN_gfortran_LIBRARY)
+    if (FORTRAN_gfortran_LIBRARY)
+      list(APPEND REQUIRED_LIBS "${FORTRAN_gfortran_LIBRARY}")
+    endif()
+  elseif (CMAKE_C_COMPILER_ID MATCHES "Intel")
+    find_library(
+      FORTRAN_ifcore_LIBRARY
+      NAMES ifcore
+      HINTS ${_lib_env}
+      )
+    mark_as_advanced(FORTRAN_ifcore_LIBRARY)
+    if (FORTRAN_ifcore_LIBRARY)
+      list(APPEND REQUIRED_LIBS "${FORTRAN_ifcore_LIBRARY}")
+    endif()
+  endif()
+  # EXTRA LIBS such that pthread, m, rt
+  list(APPEND REQUIRED_LIBS ${PASTIX_EXTRA_LIBRARIES})
+
+  # set required libraries for link
+  set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
+  set(CMAKE_REQUIRED_LIBRARIES)
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LDFLAGS}")
+  foreach(lib_dir ${REQUIRED_LIBDIRS})
+    list(APPEND CMAKE_REQUIRED_LIBRARIES "-L${lib_dir}")
+  endforeach()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LIBS}")
+  list(APPEND CMAKE_REQUIRED_FLAGS "${REQUIRED_FLAGS}")
+  string(REGEX REPLACE "^ -" "-" CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+
+  # test link
+  unset(PASTIX_WORKS CACHE)
+  include(CheckFunctionExists)
+  check_function_exists(pastix PASTIX_WORKS)
+  mark_as_advanced(PASTIX_WORKS)
+
+  if(PASTIX_WORKS)
+    # save link with dependencies
+    set(PASTIX_LIBRARIES_DEP "${REQUIRED_LIBS}")
+    set(PASTIX_LIBRARY_DIRS_DEP "${REQUIRED_LIBDIRS}")
+    set(PASTIX_INCLUDE_DIRS_DEP "${REQUIRED_INCDIRS}")
+    set(PASTIX_LINKER_FLAGS "${REQUIRED_LDFLAGS}")
+    list(REMOVE_DUPLICATES PASTIX_LIBRARY_DIRS_DEP)
+    list(REMOVE_DUPLICATES PASTIX_INCLUDE_DIRS_DEP)
+    list(REMOVE_DUPLICATES PASTIX_LINKER_FLAGS)
+  else()
+    if(NOT PASTIX_FIND_QUIETLY)
+      message(STATUS "Looking for PASTIX : test of pastix() fails")
+      message(STATUS "CMAKE_REQUIRED_LIBRARIES: ${CMAKE_REQUIRED_LIBRARIES}")
+      message(STATUS "CMAKE_REQUIRED_INCLUDES: ${CMAKE_REQUIRED_INCLUDES}")
+      message(STATUS "Check in CMakeFiles/CMakeError.log to figure out why it fails")
+      message(STATUS "Maybe PASTIX is linked with specific libraries. "
+	"Have you tried with COMPONENTS (MPI/SEQ, STARPU, STARPU_CUDA, SCOTCH, PTSCOTCH, METIS)? "
+	"See the explanation in FindPASTIX.cmake.")
+    endif()
+  endif()
+  set(CMAKE_REQUIRED_INCLUDES)
+  set(CMAKE_REQUIRED_FLAGS)
+  set(CMAKE_REQUIRED_LIBRARIES)
+endif(PASTIX_LIBRARIES)
+
+if (PASTIX_LIBRARIES)
+  list(GET PASTIX_LIBRARIES 0 first_lib)
+  get_filename_component(first_lib_path "${first_lib}" PATH)
+  if (${first_lib_path} MATCHES "/lib(32|64)?$")
+    string(REGEX REPLACE "/lib(32|64)?$" "" not_cached_dir "${first_lib_path}")
+    set(PASTIX_DIR_FOUND "${not_cached_dir}" CACHE PATH "Installation directory of PASTIX library" FORCE)
+  else()
+    set(PASTIX_DIR_FOUND "${first_lib_path}" CACHE PATH "Installation directory of PASTIX library" FORCE)
+  endif()
+endif()
+mark_as_advanced(PASTIX_DIR)
+mark_as_advanced(PASTIX_DIR_FOUND)
+
+# check that PASTIX has been found
+# ---------------------------------
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(PASTIX DEFAULT_MSG
-                                  PASTIX_INCLUDES PASTIX_LIBRARIES)
-
-mark_as_advanced(PASTIX_INCLUDES PASTIX_LIBRARIES)
+  PASTIX_LIBRARIES
+  PASTIX_WORKS)

cmake/FindScotch.cmake

@@ -1,24 +1,369 @@
-# Pastix requires SCOTCH or METIS (partitioning and reordering tools)
+###
+#
+# @copyright (c) 2009-2014 The University of Tennessee and The University
+#                          of Tennessee Research Foundation.
+#                          All rights reserved.
+# @copyright (c) 2012-2014 Inria. All rights reserved.
+# @copyright (c) 2012-2014 Bordeaux INP, CNRS (LaBRI UMR 5800), Inria, Univ. Bordeaux. All rights reserved.
+#
+###
+#
+# - Find SCOTCH include dirs and libraries
+# Use this module by invoking find_package with the form:
+#  find_package(SCOTCH
+#               [REQUIRED]             # Fail with error if scotch is not found
+#               [COMPONENTS <comp1> <comp2> ...] # dependencies
+#              )
+#
+#  COMPONENTS can be some of the following:
+#   - ESMUMPS: to activate detection of Scotch with the esmumps interface
+#
+# This module finds headers and scotch library.
+# Results are reported in variables:
+#  SCOTCH_FOUND           - True if headers and requested libraries were found
+#  SCOTCH_INCLUDE_DIRS    - scotch include directories
+#  SCOTCH_LIBRARY_DIRS    - Link directories for scotch libraries
+#  SCOTCH_LIBRARIES       - scotch component libraries to be linked
+#  SCOTCH_INTSIZE         - Number of octets occupied by a SCOTCH_Num
+#
+# The user can give specific paths where to find the libraries adding cmake
+# options at configure (ex: cmake path/to/project -DSCOTCH=path/to/scotch):
+#  SCOTCH_DIR             - Where to find the base directory of scotch
+#  SCOTCH_INCDIR          - Where to find the header files
+#  SCOTCH_LIBDIR          - Where to find the library files
+# The module can also look for the following environment variables if paths
+# are not given as cmake variable: SCOTCH_DIR, SCOTCH_INCDIR, SCOTCH_LIBDIR
 
-if (SCOTCH_INCLUDES AND SCOTCH_LIBRARIES)
-  set(SCOTCH_FIND_QUIETLY TRUE)
-endif (SCOTCH_INCLUDES AND SCOTCH_LIBRARIES)
+#=============================================================================
+# Copyright 2012-2013 Inria
+# Copyright 2012-2013 Emmanuel Agullo
+# Copyright 2012-2013 Mathieu Faverge
+# Copyright 2012      Cedric Castagnede
+# Copyright 2013      Florent Pruvost
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file MORSE-Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of Morse, substitute the full
+#  License text for the above reference.)
 
-find_path(SCOTCH_INCLUDES 
-  NAMES 
-  scotch.h 
-  PATHS 
-  $ENV{SCOTCHDIR} 
-  ${INCLUDE_INSTALL_DIR} 
-  PATH_SUFFIXES 
-  scotch
-)
+if (NOT SCOTCH_FOUND)
+  set(SCOTCH_DIR "" CACHE PATH "Installation directory of SCOTCH library")
+  if (NOT SCOTCH_FIND_QUIETLY)
+    message(STATUS "A cache variable, namely SCOTCH_DIR, has been set to specify the install directory of SCOTCH")
+  endif()
+endif()
+
+# Set the version to find
+set(SCOTCH_LOOK_FOR_ESMUMPS OFF)
+
+if( SCOTCH_FIND_COMPONENTS )
+  foreach( component ${SCOTCH_FIND_COMPONENTS} )
+    if (${component} STREQUAL "ESMUMPS")
+      # means we look for esmumps library
+      set(SCOTCH_LOOK_FOR_ESMUMPS ON)
+    endif()
+  endforeach()
+endif()
+
+# SCOTCH may depend on Threads, try to find it
+if (NOT THREADS_FOUND)
+  if (SCOTCH_FIND_REQUIRED)
+    find_package(Threads REQUIRED)
+  else()
+    find_package(Threads)
+  endif()
+endif()
+
+# Looking for include
+# -------------------
+
+# Add system include paths to search include
+# ------------------------------------------
+unset(_inc_env)
+set(ENV_SCOTCH_DIR "$ENV{SCOTCH_DIR}")
+set(ENV_SCOTCH_INCDIR "$ENV{SCOTCH_INCDIR}")
+if(ENV_SCOTCH_INCDIR)
+  list(APPEND _inc_env "${ENV_SCOTCH_INCDIR}")
+elseif(ENV_SCOTCH_DIR)
+  list(APPEND _inc_env "${ENV_SCOTCH_DIR}")
+  list(APPEND _inc_env "${ENV_SCOTCH_DIR}/include")
+  list(APPEND _inc_env "${ENV_SCOTCH_DIR}/include/scotch")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _inc_env "$ENV{INCLUDE}")
+  else()
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{C_INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{CPATH}")
+    list(APPEND _inc_env "${_path_env}")
+    string(REPLACE ":" ";" _path_env "$ENV{INCLUDE_PATH}")
+    list(APPEND _inc_env "${_path_env}")
+  endif()
+endif()
+list(APPEND _inc_env "${CMAKE_PLATFORM_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(APPEND _inc_env "${CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES}")
+list(REMOVE_DUPLICATES _inc_env)
 
 
-find_library(SCOTCH_LIBRARIES scotch PATHS $ENV{SCOTCHDIR} ${LIB_INSTALL_DIR})
+# Try to find the scotch header in the given paths
+# -------------------------------------------------
+# call cmake macro to find the header path
+if(SCOTCH_INCDIR)
+  set(SCOTCH_scotch.h_DIRS "SCOTCH_scotch.h_DIRS-NOTFOUND")
+  find_path(SCOTCH_scotch.h_DIRS
+    NAMES scotch.h
+    HINTS ${SCOTCH_INCDIR})
+else()
+  if(SCOTCH_DIR)
+    set(SCOTCH_scotch.h_DIRS "SCOTCH_scotch.h_DIRS-NOTFOUND")
+    find_path(SCOTCH_scotch.h_DIRS
+      NAMES scotch.h
+      HINTS ${SCOTCH_DIR}
+      PATH_SUFFIXES "include" "include/scotch")
+  else()
+    set(SCOTCH_scotch.h_DIRS "SCOTCH_scotch.h_DIRS-NOTFOUND")
+    find_path(SCOTCH_scotch.h_DIRS
+      NAMES scotch.h
+      HINTS ${_inc_env}
+      PATH_SUFFIXES "scotch")
+  endif()
+endif()
+mark_as_advanced(SCOTCH_scotch.h_DIRS)
 
+# If found, add path to cmake variable
+# ------------------------------------
+if (SCOTCH_scotch.h_DIRS)
+  set(SCOTCH_INCLUDE_DIRS "${SCOTCH_scotch.h_DIRS}")
+else ()
+  set(SCOTCH_INCLUDE_DIRS "SCOTCH_INCLUDE_DIRS-NOTFOUND")
+  if (NOT SCOTCH_FIND_QUIETLY)
+    message(STATUS "Looking for scotch -- scotch.h not found")
+  endif()
+endif()
+list(REMOVE_DUPLICATES SCOTCH_INCLUDE_DIRS)
+
+# Looking for lib
+# ---------------
+
+# Add system library paths to search lib
+# --------------------------------------
+unset(_lib_env)
+set(ENV_SCOTCH_LIBDIR "$ENV{SCOTCH_LIBDIR}")
+if(ENV_SCOTCH_LIBDIR)
+  list(APPEND _lib_env "${ENV_SCOTCH_LIBDIR}")
+elseif(ENV_SCOTCH_DIR)
+  list(APPEND _lib_env "${ENV_SCOTCH_DIR}")
+  list(APPEND _lib_env "${ENV_SCOTCH_DIR}/lib")
+else()
+  if(WIN32)
+    string(REPLACE ":" ";" _lib_env "$ENV{LIB}")
+  else()
+    if(APPLE)
+      string(REPLACE ":" ";" _lib_env "$ENV{DYLD_LIBRARY_PATH}")
+    else()
+      string(REPLACE ":" ";" _lib_env "$ENV{LD_LIBRARY_PATH}")
+    endif()
+    list(APPEND _lib_env "${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")
+    list(APPEND _lib_env "${CMAKE_C_IMPLICIT_LINK_DIRECTORIES}")
+  endif()
+endif()
+list(REMOVE_DUPLICATES _lib_env)
+
+# Try to find the scotch lib in the given paths
+# ----------------------------------------------
+
+set(SCOTCH_libs_to_find "scotch;scotcherrexit")
+if (SCOTCH_LOOK_FOR_ESMUMPS)
+  list(INSERT SCOTCH_libs_to_find 0 "esmumps")
+endif()
+
+# call cmake macro to find the lib path
+if(SCOTCH_LIBDIR)
+  foreach(scotch_lib ${SCOTCH_libs_to_find})
+    set(SCOTCH_${scotch_lib}_LIBRARY "SCOTCH_${scotch_lib}_LIBRARY-NOTFOUND")
+    find_library(SCOTCH_${scotch_lib}_LIBRARY
+      NAMES ${scotch_lib}
+      HINTS ${SCOTCH_LIBDIR})
+  endforeach()
+else()
+  if(SCOTCH_DIR)
+    foreach(scotch_lib ${SCOTCH_libs_to_find})
+      set(SCOTCH_${scotch_lib}_LIBRARY "SCOTCH_${scotch_lib}_LIBRARY-NOTFOUND")
+      find_library(SCOTCH_${scotch_lib}_LIBRARY
+	NAMES ${scotch_lib}
+	HINTS ${SCOTCH_DIR}
+	PATH_SUFFIXES lib lib32 lib64)
+    endforeach()
+  else()
+    foreach(scotch_lib ${SCOTCH_libs_to_find})
+      set(SCOTCH_${scotch_lib}_LIBRARY "SCOTCH_${scotch_lib}_LIBRARY-NOTFOUND")
+      find_library(SCOTCH_${scotch_lib}_LIBRARY
+	NAMES ${scotch_lib}
+	HINTS ${_lib_env})
+    endforeach()
+  endif()
+endif()
+
+set(SCOTCH_LIBRARIES "")
+set(SCOTCH_LIBRARY_DIRS "")
+# If found, add path to cmake variable
+# ------------------------------------
+foreach(scotch_lib ${SCOTCH_libs_to_find})
+
+  if (SCOTCH_${scotch_lib}_LIBRARY)
+    get_filename_component(${scotch_lib}_lib_path "${SCOTCH_${scotch_lib}_LIBRARY}" PATH)
+    # set cmake variables
+    list(APPEND SCOTCH_LIBRARIES "${SCOTCH_${scotch_lib}_LIBRARY}")
+    list(APPEND SCOTCH_LIBRARY_DIRS "${${scotch_lib}_lib_path}")
+  else ()
+    list(APPEND SCOTCH_LIBRARIES "${SCOTCH_${scotch_lib}_LIBRARY}")
+    if (NOT SCOTCH_FIND_QUIETLY)
+      message(STATUS "Looking for scotch -- lib ${scotch_lib} not found")
+    endif()
+  endif ()
+
+  mark_as_advanced(SCOTCH_${scotch_lib}_LIBRARY)
+
+endforeach()
+list(REMOVE_DUPLICATES SCOTCH_LIBRARY_DIRS)
+
+# check a function to validate the find
+if(SCOTCH_LIBRARIES)
+
+  set(REQUIRED_INCDIRS)
+  set(REQUIRED_LIBDIRS)
+  set(REQUIRED_LIBS)
+
+  # SCOTCH
+  if (SCOTCH_INCLUDE_DIRS)
+    set(REQUIRED_INCDIRS  "${SCOTCH_INCLUDE_DIRS}")
+  endif()
+  if (SCOTCH_LIBRARY_DIRS)
+    set(REQUIRED_LIBDIRS "${SCOTCH_LIBRARY_DIRS}")
+  endif()
+  set(REQUIRED_LIBS "${SCOTCH_LIBRARIES}")
+  # THREADS
+  if(CMAKE_THREAD_LIBS_INIT)
+    list(APPEND REQUIRED_LIBS "${CMAKE_THREAD_LIBS_INIT}")
+  endif()
+  set(Z_LIBRARY "Z_LIBRARY-NOTFOUND")
+  find_library(Z_LIBRARY NAMES z)
+  mark_as_advanced(Z_LIBRARY)
+  if(Z_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lz")
+  endif()
+  set(M_LIBRARY "M_LIBRARY-NOTFOUND")
+  find_library(M_LIBRARY NAMES m)
+  mark_as_advanced(M_LIBRARY)
+  if(M_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lm")
+  endif()
+  set(RT_LIBRARY "RT_LIBRARY-NOTFOUND")
+  find_library(RT_LIBRARY NAMES rt)
+  mark_as_advanced(RT_LIBRARY)
+  if(RT_LIBRARY)
+    list(APPEND REQUIRED_LIBS "-lrt")
+  endif()
+
+  # set required libraries for link
+  set(CMAKE_REQUIRED_INCLUDES "${REQUIRED_INCDIRS}")
+  set(CMAKE_REQUIRED_LIBRARIES)
+  foreach(lib_dir ${REQUIRED_LIBDIRS})
+    list(APPEND CMAKE_REQUIRED_LIBRARIES "-L${lib_dir}")
+  endforeach()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES "${REQUIRED_LIBS}")
+  string(REGEX REPLACE "^ -" "-" CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
+
+  # test link
+  unset(SCOTCH_WORKS CACHE)
+  include(CheckFunctionExists)
+  check_function_exists(SCOTCH_graphInit SCOTCH_WORKS)
+  mark_as_advanced(SCOTCH_WORKS)
+
+  if(SCOTCH_WORKS)
+    # save link with dependencies
+    set(SCOTCH_LIBRARIES "${REQUIRED_LIBS}")
+  else()
+    if(NOT SCOTCH_FIND_QUIETLY)
+      message(STATUS "Looking for SCOTCH : test of SCOTCH_graphInit with SCOTCH library fails")
+      message(STATUS "CMAKE_REQUIRED_LIBRARIES: ${CMAKE_REQUIRED_LIBRARIES}")
+      message(STATUS "CMAKE_REQUIRED_INCLUDES: ${CMAKE_REQUIRED_INCLUDES}")
+      message(STATUS "Check in CMakeFiles/CMakeError.log to figure out why it fails")
+    endif()
+  endif()
+  set(CMAKE_REQUIRED_INCLUDES)
+  set(CMAKE_REQUIRED_FLAGS)
+  set(CMAKE_REQUIRED_LIBRARIES)
+endif(SCOTCH_LIBRARIES)
+
+if (SCOTCH_LIBRARIES)
+  list(GET SCOTCH_LIBRARIES 0 first_lib)
+  get_filename_component(first_lib_path "${first_lib}" PATH)
+  if (${first_lib_path} MATCHES "/lib(32|64)?$")
+    string(REGEX REPLACE "/lib(32|64)?$" "" not_cached_dir "${first_lib_path}")
+    set(SCOTCH_DIR_FOUND "${not_cached_dir}" CACHE PATH "Installation directory of SCOTCH library" FORCE)
+  else()
+    set(SCOTCH_DIR_FOUND "${first_lib_path}" CACHE PATH "Installation directory of SCOTCH library" FORCE)
+  endif()
+endif()
+mark_as_advanced(SCOTCH_DIR)
+mark_as_advanced(SCOTCH_DIR_FOUND)
+
+# Check the size of SCOTCH_Num
+# ---------------------------------
+set(CMAKE_REQUIRED_INCLUDES ${SCOTCH_INCLUDE_DIRS})
+
+include(CheckCSourceRuns)
+#stdio.h and stdint.h should be included by scotch.h directly
+set(SCOTCH_C_TEST_SCOTCH_Num_4 "
+#include <stdio.h>
+#include <stdint.h>
+#include <scotch.h>
+int main(int argc, char **argv) {
+  if (sizeof(SCOTCH_Num) == 4)
+    return 0;
+  else
+    return 1;
+}
+")
+
+set(SCOTCH_C_TEST_SCOTCH_Num_8 "
+#include <stdio.h>
+#include <stdint.h>
+#include <scotch.h>
+int main(int argc, char **argv) {
+  if (sizeof(SCOTCH_Num) == 8)
+    return 0;
+  else
+    return 1;
+}
+")
+check_c_source_runs("${SCOTCH_C_TEST_SCOTCH_Num_4}" SCOTCH_Num_4)
+if(NOT SCOTCH_Num_4)
+  check_c_source_runs("${SCOTCH_C_TEST_SCOTCH_Num_8}" SCOTCH_Num_8)
+  if(NOT SCOTCH_Num_8)
+    set(SCOTCH_INTSIZE -1)
+  else()
+    set(SCOTCH_INTSIZE 8)
+  endif()
+else()
+  set(SCOTCH_INTSIZE 4)
+endif()
+set(CMAKE_REQUIRED_INCLUDES "")
+
+# check that SCOTCH has been found
+# ---------------------------------
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(SCOTCH DEFAULT_MSG
-                                  SCOTCH_INCLUDES SCOTCH_LIBRARIES)
-
-mark_as_advanced(SCOTCH_INCLUDES SCOTCH_LIBRARIES)
+  SCOTCH_LIBRARIES
+  SCOTCH_WORKS)
+#
+# TODO: Add possibility to check for specific functions in the library
+#