Add CI to build docs

(grafted from 94e8d8902f
)

.gitignore

@@ -0,0 +1,41 @@
+qrc_*cxx
+*.orig
+*.pyc
+*.diff
+diff
+*.save
+save
+*.old
+*.gmo
+*.qm
+core
+core.*
+*.bak
+*~
+*.build*
+*.moc.*
+*.moc
+ui_*
+CMakeCache.txt
+tags
+.*.swp
+activity.png
+*.out
+*.php*
+*.log
+*.orig
+*.rej
+log
+patch
+*.patch
+a
+a.*
+lapack/testing
+lapack/reference
+.*project
+.settings
+Makefile
+!ci/build.gitlab-ci.yml
+!scripts/buildtests.in
+!Eigen/Core
+!Eigen/src/Core

.gitlab-ci.yml

@@ -0,0 +1,28 @@
+# This file is part of Eigen, a lightweight C++ template library
+# for linear algebra.
+#
+# Copyright (C) 2023, The Eigen Authors
+#
+# This Source Code Form is subject to the terms of the Mozilla
+# Public License v. 2.0. If a copy of the MPL was not distributed
+# with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+stages:
+  - build
+  - deploy
+
+variables:
+  # CMake build directory.
+  EIGEN_CI_BUILDDIR: .build
+  # Specify the CMake build target.
+  EIGEN_CI_BUILD_TARGET: ""
+  # If a test regex is specified, that will be selected.
+  # Otherwise, we will try a label if specified.
+  EIGEN_CI_CTEST_REGEX: ""
+  EIGEN_CI_CTEST_LABEL: ""
+  EIGEN_CI_CTEST_ARGS: ""
+
+include:
+  - "/ci/common.gitlab-ci.yml"
+  - "/ci/build.linux.gitlab-ci.yml"
+  - "/ci/deploy.gitlab-ci.yml"

CMakeLists.txt

@@ -1,6 +1,5 @@
 project(Eigen)
-
-cmake_minimum_required(VERSION 2.8.2)
+cmake_minimum_required(VERSION 2.8.5)
 
 # guard against in-source builds
 
@@ -55,6 +54,7 @@ endif(EIGEN_HG_CHANGESET)
 
 
 include(CheckCXXCompilerFlag)
+include(GNUInstallDirs)
 
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 
@@ -288,25 +288,26 @@ option(EIGEN_TEST_C++0x "Enables all C++0x features." OFF)
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 
-# the user modifiable install path for header files
-set(EIGEN_INCLUDE_INSTALL_DIR ${EIGEN_INCLUDE_INSTALL_DIR} CACHE PATH "The directory where we install the header files (optional)")
-
-# set the internal install path for header files which depends on wether the user modifiable
-# EIGEN_INCLUDE_INSTALL_DIR has been set by the user or not.
-if(EIGEN_INCLUDE_INSTALL_DIR)
-  set(INCLUDE_INSTALL_DIR
-    ${EIGEN_INCLUDE_INSTALL_DIR}
-    CACHE INTERNAL
-    "The directory where we install the header files (internal)"
-  )
+# Backward compatibility support for EIGEN_INCLUDE_INSTALL_DIR
+if(EIGEN_INCLUDE_INSTALL_DIR AND NOT INCLUDE_INSTALL_DIR)
+  set(INCLUDE_INSTALL_DIR ${EIGEN_INCLUDE_INSTALL_DIR}
+      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed")
 else()
   set(INCLUDE_INSTALL_DIR
-    "include/eigen3"
-    CACHE INTERNAL
-    "The directory where we install the header files (internal)"
-  )
+      "${CMAKE_INSTALL_INCLUDEDIR}/eigen3"
+      CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen header files are installed"
+      )
 endif()
 
+set(CMAKEPACKAGE_INSTALL_DIR
+    "${CMAKE_INSTALL_LIBDIR}/cmake/eigen3"
+    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where Eigen3Config.cmake is installed"
+    )
+set(PKGCONFIG_INSTALL_DIR
+    "${CMAKE_INSTALL_DATADIR}/pkgconfig"
+    CACHE PATH "The directory relative to CMAKE_PREFIX_PATH where eigen3.pc is installed"
+    )
+
 # similar to set_target_properties but append the property instead of overwriting it
 macro(ei_add_target_property target prop value)
 
@@ -324,21 +325,9 @@ install(FILES
   )
 
 if(EIGEN_BUILD_PKGCONFIG)
-    SET(path_separator ":")
-    STRING(REPLACE ${path_separator} ";" pkg_config_libdir_search "$ENV{PKG_CONFIG_LIBDIR}")
-    message(STATUS "searching for 'pkgconfig' directory in PKG_CONFIG_LIBDIR ( $ENV{PKG_CONFIG_LIBDIR} ), ${CMAKE_INSTALL_PREFIX}/share, and ${CMAKE_INSTALL_PREFIX}/lib")
-    FIND_PATH(pkg_config_libdir pkgconfig ${pkg_config_libdir_search} ${CMAKE_INSTALL_PREFIX}/share ${CMAKE_INSTALL_PREFIX}/lib ${pkg_config_libdir_search})
-    if(pkg_config_libdir)
-        SET(pkg_config_install_dir ${pkg_config_libdir})
-        message(STATUS "found ${pkg_config_libdir}/pkgconfig" )
-    else(pkg_config_libdir)
-        SET(pkg_config_install_dir ${CMAKE_INSTALL_PREFIX}/share)
-        message(STATUS "pkgconfig not found; installing in ${pkg_config_install_dir}" )
-    endif(pkg_config_libdir)
-
-    configure_file(eigen3.pc.in eigen3.pc)
+    configure_file(eigen3.pc.in eigen3.pc @ONLY)
     install(FILES ${CMAKE_CURRENT_BINARY_DIR}/eigen3.pc
-        DESTINATION ${pkg_config_install_dir}/pkgconfig
+        DESTINATION ${PKGCONFIG_INSTALL_DIR}
         )
 endif(EIGEN_BUILD_PKGCONFIG)
 
@@ -401,12 +390,15 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "--------------+--------------------------------------------------------------")
   message(STATUS "Command       |   Description")
   message(STATUS "--------------+--------------------------------------------------------------")
-  message(STATUS "make install  | Install to ${CMAKE_INSTALL_PREFIX}. To change that:")
-  message(STATUS "              |     cmake . -DCMAKE_INSTALL_PREFIX=yourpath")
-  message(STATUS "              |   Eigen headers will then be installed to:")
-  message(STATUS "              |     ${CMAKE_INSTALL_PREFIX}/${INCLUDE_INSTALL_DIR}")
-  message(STATUS "              |   To install Eigen headers to a separate location, do:")
-  message(STATUS "              |     cmake . -DEIGEN_INCLUDE_INSTALL_DIR=yourpath")
+  message(STATUS "make install  | Install Eigen. Headers will be installed to:")
+  message(STATUS "              |     <CMAKE_INSTALL_PREFIX>/<INCLUDE_INSTALL_DIR>")
+  message(STATUS "              |   Using the following values:")
+  message(STATUS "              |     CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
+  message(STATUS "              |     INCLUDE_INSTALL_DIR:  ${INCLUDE_INSTALL_DIR}")
+  message(STATUS "              |   Change the install location of Eigen headers using:")
+  message(STATUS "              |     cmake . -DCMAKE_INSTALL_PREFIX=yourprefix")
+  message(STATUS "              |   Or:")
+  message(STATUS "              |     cmake . -DINCLUDE_INSTALL_DIR=yourdir")
   message(STATUS "make doc      | Generate the API documentation, requires Doxygen & LaTeX")
   message(STATUS "make check    | Build and run the unit-tests. Read this page:")
   message(STATUS "              |   http://eigen.tuxfamily.org/index.php?title=Tests")

Eigen/CholmodSupport

@@ -12,7 +12,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup CholmodSupport_Module CholmodSupport module
   *
-  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the two following main factorization classes:
   * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
   * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).

Eigen/SPQRSupport

@@ -10,7 +10,7 @@
 /** \ingroup Support_modules
   * \defgroup SPQRSupport_Module SuiteSparseQR module
   * 
-  * This module provides an interface to the SPQR library, which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the SPQR library, which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   *
   * \code
   * #include <Eigen/SPQRSupport>

Eigen/UmfPackSupport

@@ -12,7 +12,7 @@ extern "C" {
 /** \ingroup Support_modules
   * \defgroup UmfPackSupport_Module UmfPackSupport module
   *
-  * This module provides an interface to the UmfPack library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * This module provides an interface to the UmfPack library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
   * It provides the following factorization class:
   * - class UmfPackLU: a multifrontal sequential LU factorization.
   *

Eigen/src/CholmodSupport/CholmodSupport.h

@@ -14,34 +14,40 @@ namespace Eigen {
 
 namespace internal {
 
-template<typename Scalar, typename CholmodType>
-void cholmod_configure_matrix(CholmodType& mat)
-{
-  if (internal::is_same<Scalar,float>::value)
-  {
-    mat.xtype = CHOLMOD_REAL;
-    mat.dtype = CHOLMOD_SINGLE;
-  }
-  else if (internal::is_same<Scalar,double>::value)
-  {
+template<typename Scalar> struct cholmod_configure_matrix;
+
+template<> struct cholmod_configure_matrix<double> {
+  template<typename CholmodType>
+  static void run(CholmodType& mat) {
     mat.xtype = CHOLMOD_REAL;
     mat.dtype = CHOLMOD_DOUBLE;
   }
-  else if (internal::is_same<Scalar,std::complex<float> >::value)
-  {
-    mat.xtype = CHOLMOD_COMPLEX;
-    mat.dtype = CHOLMOD_SINGLE;
-  }
-  else if (internal::is_same<Scalar,std::complex<double> >::value)
-  {
+};
+
+template<> struct cholmod_configure_matrix<std::complex<double> > {
+  template<typename CholmodType>
+  static void run(CholmodType& mat) {
     mat.xtype = CHOLMOD_COMPLEX;
     mat.dtype = CHOLMOD_DOUBLE;
   }
-  else
-  {
-    eigen_assert(false && "Scalar type not supported by CHOLMOD");
-  }
-}
+};
+
+// Other scalar types are not yet suppotred by Cholmod
+// template<> struct cholmod_configure_matrix<float> {
+//   template<typename CholmodType>
+//   static void run(CholmodType& mat) {
+//     mat.xtype = CHOLMOD_REAL;
+//     mat.dtype = CHOLMOD_SINGLE;
+//   }
+// };
+//
+// template<> struct cholmod_configure_matrix<std::complex<float> > {
+//   template<typename CholmodType>
+//   static void run(CholmodType& mat) {
+//     mat.xtype = CHOLMOD_COMPLEX;
+//     mat.dtype = CHOLMOD_SINGLE;
+//   }
+// };
 
 } // namespace internal
 
@@ -88,7 +94,7 @@ cholmod_sparse viewAsCholmod(SparseMatrix<_Scalar,_Options,_Index>& mat)
   }
 
   // setup res.xtype
-  internal::cholmod_configure_matrix<_Scalar>(res);
+  internal::cholmod_configure_matrix<_Scalar>::run(res);
   
   res.stype = 0;
   
@@ -131,7 +137,7 @@ cholmod_dense viewAsCholmod(MatrixBase<Derived>& mat)
   res.x      = (void*)(mat.derived().data());
   res.z      = 0;
 
-  internal::cholmod_configure_matrix<Scalar>(res);
+  internal::cholmod_configure_matrix<Scalar>::run(res);
 
   return res;
 }
@@ -172,14 +178,16 @@ class CholmodBase : internal::noncopyable
     CholmodBase()
       : m_cholmodFactor(0), m_info(Success), m_isInitialized(false)
     {
-      m_shiftOffset[0] = m_shiftOffset[1] = RealScalar(0.0);
+      EIGEN_STATIC_ASSERT((internal::is_same<double,RealScalar>::value), CHOLMOD_SUPPORTS_DOUBLE_PRECISION_ONLY);
+      m_shiftOffset[0] = m_shiftOffset[1] = 0.0;
       cholmod_start(&m_cholmod);
     }
 
     CholmodBase(const MatrixType& matrix)
       : m_cholmodFactor(0), m_info(Success), m_isInitialized(false)
     {
-      m_shiftOffset[0] = m_shiftOffset[1] = RealScalar(0.0);
+      EIGEN_STATIC_ASSERT((internal::is_same<double,RealScalar>::value), CHOLMOD_SUPPORTS_DOUBLE_PRECISION_ONLY);
+      m_shiftOffset[0] = m_shiftOffset[1] = 0.0;
       cholmod_start(&m_cholmod);
       compute(matrix);
     }
@@ -277,7 +285,7 @@ class CholmodBase : internal::noncopyable
       eigen_assert(m_analysisIsOk && "You must first call analyzePattern()");
       cholmod_sparse A = viewAsCholmod(matrix.template selfadjointView<UpLo>());
       cholmod_factorize_p(&A, m_shiftOffset, 0, 0, m_cholmodFactor, &m_cholmod);
-      
+
       // If the factorization failed, minor is the column at which it did. On success minor == n.
       this->m_info = (m_cholmodFactor->minor == m_cholmodFactor->n ? Success : NumericalIssue);
       m_factorizationIsOk = true;
@@ -344,7 +352,7 @@ class CholmodBase : internal::noncopyable
       */
     Derived& setShift(const RealScalar& offset)
     {
-      m_shiftOffset[0] = offset;
+      m_shiftOffset[0] = double(offset);
       return derived();
     }
     
@@ -355,7 +363,7 @@ class CholmodBase : internal::noncopyable
   protected:
     mutable cholmod_common m_cholmod;
     cholmod_factor* m_cholmodFactor;
-    RealScalar m_shiftOffset[2];
+    double m_shiftOffset[2];
     mutable ComputationInfo m_info;
     bool m_isInitialized;
     int m_factorizationIsOk;
@@ -378,6 +386,8 @@ class CholmodBase : internal::noncopyable
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
+  * \warning Only double precision real and complex scalar types are supported by Cholmod.
+  *
   * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLLT
   */
 template<typename _MatrixType, int _UpLo = Lower>
@@ -425,6 +435,8 @@ class CholmodSimplicialLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimpl
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
+  * \warning Only double precision real and complex scalar types are supported by Cholmod.
+  *
   * \sa \ref TutorialSparseDirectSolvers, class CholmodSupernodalLLT, class SimplicialLDLT
   */
 template<typename _MatrixType, int _UpLo = Lower>
@@ -470,6 +482,8 @@ class CholmodSimplicialLDLT : public CholmodBase<_MatrixType, _UpLo, CholmodSimp
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
+  * \warning Only double precision real and complex scalar types are supported by Cholmod.
+  *
   * \sa \ref TutorialSparseDirectSolvers
   */
 template<typename _MatrixType, int _UpLo = Lower>
@@ -517,6 +531,8 @@ class CholmodSupernodalLLT : public CholmodBase<_MatrixType, _UpLo, CholmodSuper
   *
   * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; compressed or non compressed.
   *
+  * \warning Only double precision real and complex scalar types are supported by Cholmod.
+  *
   * \sa \ref TutorialSparseDirectSolvers
   */
 template<typename _MatrixType, int _UpLo = Lower>

Eigen/src/Core/Block.h

@@ -66,9 +66,8 @@ struct traits<Block<XprType, BlockRows, BlockCols, InnerPanel> > : traits<XprTyp
                          : ColsAtCompileTime != Dynamic ? int(ColsAtCompileTime)
                          : int(traits<XprType>::MaxColsAtCompileTime),
     XprTypeIsRowMajor = (int(traits<XprType>::Flags)&RowMajorBit) != 0,
-    IsDense = is_same<StorageKind,Dense>::value,
-    IsRowMajor = (IsDense&&MaxRowsAtCompileTime==1&&MaxColsAtCompileTime!=1) ? 1
-               : (IsDense&&MaxColsAtCompileTime==1&&MaxRowsAtCompileTime!=1) ? 0
+    IsRowMajor = (MaxRowsAtCompileTime==1&&MaxColsAtCompileTime!=1) ? 1
+               : (MaxColsAtCompileTime==1&&MaxRowsAtCompileTime!=1) ? 0
                : XprTypeIsRowMajor,
     HasSameStorageOrderAsXprType = (IsRowMajor == XprTypeIsRowMajor),
     InnerSize = IsRowMajor ? int(ColsAtCompileTime) : int(RowsAtCompileTime),

Eigen/src/Core/CommaInitializer.h

@@ -76,9 +76,7 @@ struct CommaInitializer
   template<typename OtherDerived>
   CommaInitializer& operator,(const DenseBase<OtherDerived>& other)
   {
-    if(other.cols()==0 || other.rows()==0)
-      return *this;
-    if (m_col==m_xpr.cols())
+    if (m_col==m_xpr.cols() && (other.cols()!=0 || other.rows()!=m_currentBlockRows))
     {
       m_row+=m_currentBlockRows;
       m_col = 0;
@@ -86,24 +84,18 @@ struct CommaInitializer
       eigen_assert(m_row+m_currentBlockRows<=m_xpr.rows()
         && "Too many rows passed to comma initializer (operator<<)");
     }
-    eigen_assert(m_col<m_xpr.cols()
+    eigen_assert((m_col + other.cols() <= m_xpr.cols())
       && "Too many coefficients passed to comma initializer (operator<<)");
     eigen_assert(m_currentBlockRows==other.rows());
-    if (OtherDerived::SizeAtCompileTime != Dynamic)
-      m_xpr.template block<OtherDerived::RowsAtCompileTime != Dynamic ? OtherDerived::RowsAtCompileTime : 1,
-                              OtherDerived::ColsAtCompileTime != Dynamic ? OtherDerived::ColsAtCompileTime : 1>
-                    (m_row, m_col) = other;
-    else
-      m_xpr.block(m_row, m_col, other.rows(), other.cols()) = other;
+    m_xpr.template block<OtherDerived::RowsAtCompileTime, OtherDerived::ColsAtCompileTime>
+                    (m_row, m_col, other.rows(), other.cols()) = other;
     m_col += other.cols();
     return *this;
   }
 
   inline ~CommaInitializer()
   {
-    eigen_assert((m_row+m_currentBlockRows) == m_xpr.rows()
-         && m_col == m_xpr.cols()
-         && "Too few coefficients passed to comma initializer (operator<<)");
+      finished();
   }
 
   /** \returns the built matrix once all its coefficients have been set.
@@ -113,7 +105,12 @@ struct CommaInitializer
     * quaternion.fromRotationMatrix((Matrix3f() << axis0, axis1, axis2).finished());
     * \endcode
     */
-  inline XprType& finished() { return m_xpr; }
+  inline XprType& finished() {
+      eigen_assert(((m_row+m_currentBlockRows) == m_xpr.rows() || m_xpr.cols() == 0)
+           && m_col == m_xpr.cols()
+           && "Too few coefficients passed to comma initializer (operator<<)");
+      return m_xpr;
+  }
 
   XprType& m_xpr;   // target expression
   Index m_row;              // current row id

Eigen/src/Core/CwiseUnaryView.h

@@ -38,7 +38,7 @@ struct traits<CwiseUnaryView<ViewOp, MatrixType> >
   typedef typename remove_all<MatrixTypeNested>::type _MatrixTypeNested;
   enum {
     Flags = (traits<_MatrixTypeNested>::Flags & (HereditaryBits | LvalueBit | LinearAccessBit | DirectAccessBit)),
-    CoeffReadCost = traits<_MatrixTypeNested>::CoeffReadCost + functor_traits<ViewOp>::Cost,
+    CoeffReadCost = EIGEN_ADD_COST(traits<_MatrixTypeNested>::CoeffReadCost, functor_traits<ViewOp>::Cost),
     MatrixTypeInnerStride =  inner_stride_at_compile_time<MatrixType>::ret,
     // need to cast the sizeof's from size_t to int explicitly, otherwise:
     // "error: no integral type can represent all of the enumerator values

Eigen/src/Core/DiagonalMatrix.h

@@ -44,10 +44,10 @@ class DiagonalBase : public EigenBase<Derived>
     template<typename DenseDerived>
     void evalTo(MatrixBase<DenseDerived> &other) const;
     template<typename DenseDerived>
-    void addTo(MatrixBase<DenseDerived> &other) const
+    inline void addTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() += diagonal(); }
     template<typename DenseDerived>
-    void subTo(MatrixBase<DenseDerived> &other) const
+    inline void subTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() -= diagonal(); }
 
     inline const DiagonalVectorType& diagonal() const { return derived().diagonal(); }
@@ -98,7 +98,7 @@ class DiagonalBase : public EigenBase<Derived>
 
 template<typename Derived>
 template<typename DenseDerived>
-void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
+inline void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
 {
   other.setZero();
   other.diagonal() = diagonal();

Eigen/src/Core/Dot.h

@@ -59,7 +59,7 @@ struct dot_nocheck<T, U, true>
   */
 template<typename Derived>
 template<typename OtherDerived>
-typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
+inline typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
 MatrixBase<Derived>::dot(const MatrixBase<OtherDerived>& other) const
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)

Eigen/src/Core/Functors.h

@@ -969,6 +969,8 @@ template<typename T>
 struct functor_traits<std::not_equal_to<T> >
 { enum { Cost = 1, PacketAccess = false }; };
 
+#if(__cplusplus < 201103L)
+// std::binder* are deprecated since c++11 and will be removed in c++17
 template<typename T>
 struct functor_traits<std::binder2nd<T> >
 { enum { Cost = functor_traits<T>::Cost, PacketAccess = false }; };
@@ -976,6 +978,7 @@ struct functor_traits<std::binder2nd<T> >
 template<typename T>
 struct functor_traits<std::binder1st<T> >
 { enum { Cost = functor_traits<T>::Cost, PacketAccess = false }; };
+#endif
 
 template<typename T>
 struct functor_traits<std::unary_negate<T> >

Eigen/src/Core/GeneralProduct.h

@@ -205,9 +205,6 @@ class GeneralProduct<Lhs, Rhs, InnerProduct>
   public:
     GeneralProduct(const Lhs& lhs, const Rhs& rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
-
       Base::coeffRef(0,0) = (lhs.transpose().cwiseProduct(rhs)).sum();
     }
 
@@ -264,8 +261,6 @@ class GeneralProduct<Lhs, Rhs, OuterProduct>
 
     GeneralProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
     }
     
     struct set  { template<typename Dst, typename Src> void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived()  = src; } };
@@ -425,15 +420,18 @@ template<> struct gemv_selector<OnTheRight,ColMajor,true>
     ResScalar actualAlpha = alpha * LhsBlasTraits::extractScalarFactor(prod.lhs())
                                   * RhsBlasTraits::extractScalarFactor(prod.rhs());
 
+    // make sure Dest is a compile-time vector type (bug 1166)
+    typedef typename conditional<Dest::IsVectorAtCompileTime, Dest, typename Dest::ColXpr>::type ActualDest;
+
     enum {
       // FIXME find a way to allow an inner stride on the result if packet_traits<Scalar>::size==1
       // on, the other hand it is good for the cache to pack the vector anyways...
-      EvalToDestAtCompileTime = Dest::InnerStrideAtCompileTime==1,
+      EvalToDestAtCompileTime = (ActualDest::InnerStrideAtCompileTime==1),
       ComplexByReal = (NumTraits<LhsScalar>::IsComplex) && (!NumTraits<RhsScalar>::IsComplex),
-      MightCannotUseDest = (Dest::InnerStrideAtCompileTime!=1) || ComplexByReal
+      MightCannotUseDest = (ActualDest::InnerStrideAtCompileTime!=1) || ComplexByReal
     };
 
-    gemv_static_vector_if<ResScalar,Dest::SizeAtCompileTime,Dest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
+    gemv_static_vector_if<ResScalar,ActualDest::SizeAtCompileTime,ActualDest::MaxSizeAtCompileTime,MightCannotUseDest> static_dest;
 
     bool alphaIsCompatible = (!ComplexByReal) || (numext::imag(actualAlpha)==RealScalar(0));
     bool evalToDest = EvalToDestAtCompileTime && alphaIsCompatible;
@@ -522,7 +520,7 @@ template<> struct gemv_selector<OnTheRight,RowMajor,true>
         actualLhs.rows(), actualLhs.cols(),
         actualLhs.data(), actualLhs.outerStride(),
         actualRhsPtr, 1,
-        dest.data(), dest.innerStride(),
+        dest.data(), dest.col(0).innerStride(), //NOTE  if dest is not a vector at compile-time, then dest.innerStride() might be wrong. (bug 1166)
         actualAlpha);
   }
 };

Eigen/src/Core/GenericPacketMath.h

@@ -183,8 +183,8 @@ template<typename Scalar, typename Packet> inline void pstoreu(Scalar* to, const
 /** \internal tries to do cache prefetching of \a addr */
 template<typename Scalar> inline void prefetch(const Scalar* addr)
 {
-#if !defined(_MSC_VER)
-__builtin_prefetch(addr);
+#if (!EIGEN_COMP_MSVC) && (EIGEN_COMP_GNUC || EIGEN_COMP_CLANG || EIGEN_COMP_ICC)
+  __builtin_prefetch(addr);
 #endif
 }
 

Eigen/src/Core/MapBase.h

@@ -149,6 +149,10 @@ template<typename Derived> class MapBase<Derived, ReadOnlyAccessors>
       checkSanity();
     }
 
+    #ifdef EIGEN_MAPBASE_PLUGIN
+    #include EIGEN_MAPBASE_PLUGIN
+    #endif
+
   protected:
 
     void checkSanity() const

Eigen/src/Core/MathFunctions.h

@@ -218,8 +218,8 @@ struct conj_retval
 * Implementation of abs2                                                 *
 ****************************************************************************/
 
-template<typename Scalar>
-struct abs2_impl
+template<typename Scalar,bool IsComplex>
+struct abs2_impl_default
 {
   typedef typename NumTraits<Scalar>::Real RealScalar;
   static inline RealScalar run(const Scalar& x)
@@ -228,15 +228,26 @@ struct abs2_impl
   }
 };
 
-template<typename RealScalar>
-struct abs2_impl<std::complex<RealScalar> >
+template<typename Scalar>
+struct abs2_impl_default<Scalar, true> // IsComplex
 {
-  static inline RealScalar run(const std::complex<RealScalar>& x)
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
   {
     return real(x)*real(x) + imag(x)*imag(x);
   }
 };
 
+template<typename Scalar>
+struct abs2_impl
+{
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
+  {
+    return abs2_impl_default<Scalar,NumTraits<Scalar>::IsComplex>::run(x);
+  }
+};
+
 template<typename Scalar>
 struct abs2_retval
 {
@@ -496,11 +507,24 @@ struct floor_log2<n, lower, upper, floor_log2_bogus>
 template<typename Scalar>
 struct random_default_impl<Scalar, false, true>
 {
-  typedef typename NumTraits<Scalar>::NonInteger NonInteger;
-
   static inline Scalar run(const Scalar& x, const Scalar& y)
   {
-    return x + Scalar((NonInteger(y)-x+1) * std::rand() / (RAND_MAX + NonInteger(1)));
+    typedef typename conditional<NumTraits<Scalar>::IsSigned,std::ptrdiff_t,std::size_t>::type ScalarX;
+    if(y<x)
+      return x;
+    // the following difference might overflow on a 32 bits system,
+    // but since y>=x the result converted to an unsigned long is still correct.
+    std::size_t range = ScalarX(y)-ScalarX(x);
+    std::size_t offset = 0;
+    // rejection sampling
+    std::size_t divisor = 1;
+    std::size_t multiplier = 1;
+    if(range<RAND_MAX) divisor = (std::size_t(RAND_MAX)+1)/(range+1);
+    else               multiplier = 1 + range/(std::size_t(RAND_MAX)+1);
+    do {
+      offset = (std::size_t(std::rand()) * multiplier) / divisor;
+    } while (offset > range);
+    return Scalar(ScalarX(x) + offset);
   }
 
   static inline Scalar run()
@@ -707,21 +731,21 @@ struct scalar_fuzzy_impl : scalar_fuzzy_default_impl<Scalar, NumTraits<Scalar>::
 
 template<typename Scalar, typename OtherScalar>
 inline bool isMuchSmallerThan(const Scalar& x, const OtherScalar& y,
-                                   typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                              const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::template isMuchSmallerThan<OtherScalar>(x, y, precision);
 }
 
 template<typename Scalar>
 inline bool isApprox(const Scalar& x, const Scalar& y,
-                          typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                     const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::isApprox(x, y, precision);
 }
 
 template<typename Scalar>
 inline bool isApproxOrLessThan(const Scalar& x, const Scalar& y,
-                                    typename NumTraits<Scalar>::Real precision = NumTraits<Scalar>::dummy_precision())
+                               const typename NumTraits<Scalar>::Real &precision = NumTraits<Scalar>::dummy_precision())
 {
   return scalar_fuzzy_impl<Scalar>::isApproxOrLessThan(x, y, precision);
 }

Eigen/src/Core/PermutationMatrix.h

@@ -584,10 +584,11 @@ struct permut_matrix_product_retval
       const Index n = Side==OnTheLeft ? rows() : cols();
       // FIXME we need an is_same for expression that is not sensitive to constness. For instance
       // is_same_xpr<Block<const Matrix>, Block<Matrix> >::value should be true.
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
       if(    is_same<MatrixTypeNestedCleaned,Dest>::value
           && blas_traits<MatrixTypeNestedCleaned>::HasUsableDirectAccess
           && blas_traits<Dest>::HasUsableDirectAccess
-          && extract_data(dst) == extract_data(m_matrix))
+          && dst_data!=0 && dst_data == extract_data(m_matrix))
       {
         // apply the permutation inplace
         Matrix<bool,PermutationType::RowsAtCompileTime,1,0,PermutationType::MaxRowsAtCompileTime> mask(m_permutation.size());

Eigen/src/Core/PlainObjectBase.h

@@ -315,8 +315,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     EIGEN_STRONG_INLINE void resizeLike(const EigenBase<OtherDerived>& _other)
     {
       const OtherDerived& other = _other.derived();
-      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.rows(), other.cols());
-      const Index othersize = other.rows()*other.cols();
+      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(Index(other.rows()), Index(other.cols()));
+      const Index othersize = Index(other.rows())*Index(other.cols());
       if(RowsAtCompileTime == 1)
       {
         eigen_assert(other.rows() == 1 || other.cols() == 1);
@@ -487,7 +487,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     /** \sa MatrixBase::operator=(const EigenBase<OtherDerived>&) */
     template<typename OtherDerived>
     EIGEN_STRONG_INLINE PlainObjectBase(const EigenBase<OtherDerived> &other)
-      : m_storage(other.derived().rows() * other.derived().cols(), other.derived().rows(), other.derived().cols())
+      : m_storage(Index(other.derived().rows()) * Index(other.derived().cols()), other.derived().rows(), other.derived().cols())
     {
       _check_template_params();
       internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.derived().rows(), other.derived().cols());

Eigen/src/Core/Reverse.h

@@ -76,9 +76,23 @@ template<typename MatrixType, int Direction> class Reverse
     EIGEN_DENSE_PUBLIC_INTERFACE(Reverse)
     using Base::IsRowMajor;
 
-    // next line is necessary because otherwise const version of operator()
-    // is hidden by non-const version defined in this file
-    using Base::operator(); 
+    // The following two operators are provided to worarkound
+    // a MSVC 2013 issue. In theory, we could simply do:
+    //   using Base::operator(); 
+    // to make const version of operator() visible.
+    // Otheriwse, they would be hidden by the non-const versions defined in this file
+    
+    inline CoeffReturnType operator()(Index row, Index col) const
+    {
+      eigen_assert(row >= 0 && row < rows() && col >= 0 && col < cols());
+      return coeff(row, col);
+    }
+
+    inline CoeffReturnType operator()(Index index) const
+    {
+      eigen_assert(index >= 0 && index < m_matrix.size());
+      return coeff(index);
+    }
 
   protected:
     enum {

Eigen/src/Core/SolveTriangular.h

@@ -116,17 +116,17 @@ template<typename Lhs, typename Rhs, int Mode, int Index, int Size>
 struct triangular_solver_unroller<Lhs,Rhs,Mode,Index,Size,false> {
   enum {
     IsLower = ((Mode&Lower)==Lower),
-    I = IsLower ? Index : Size - Index - 1,
-    S = IsLower ? 0     : I+1
+    RowIndex = IsLower ? Index : Size - Index - 1,
+    S = IsLower ? 0     : RowIndex+1
   };
   static void run(const Lhs& lhs, Rhs& rhs)
   {
     if (Index>0)
-      rhs.coeffRef(I) -= lhs.row(I).template segment<Index>(S).transpose()
+      rhs.coeffRef(RowIndex) -= lhs.row(RowIndex).template segment<Index>(S).transpose()
                          .cwiseProduct(rhs.template segment<Index>(S)).sum();
 
     if(!(Mode & UnitDiag))
-      rhs.coeffRef(I) /= lhs.coeff(I,I);
+      rhs.coeffRef(RowIndex) /= lhs.coeff(RowIndex,RowIndex);
 
     triangular_solver_unroller<Lhs,Rhs,Mode,Index+1,Size>::run(lhs,rhs);
   }
@@ -243,7 +243,8 @@ template<int Side, typename TriangularType, typename Rhs> struct triangular_solv
 
   template<typename Dest> inline void evalTo(Dest& dst) const
   {
-    if(!(is_same<RhsNestedCleaned,Dest>::value && extract_data(dst) == extract_data(m_rhs)))
+    const typename Dest::Scalar *dst_data = internal::extract_data(dst);
+    if(!(is_same<RhsNestedCleaned,Dest>::value && dst_data!=0 && extract_data(dst) == extract_data(m_rhs)))
       dst = m_rhs;
     m_triangularMatrix.template solveInPlace<Side>(dst);
   }

Eigen/src/Core/Transpose.h

@@ -331,11 +331,11 @@ inline void MatrixBase<Derived>::adjointInPlace()
 
 namespace internal {
 
-template<typename BinOp,typename NestedXpr,typename Rhs>
-struct blas_traits<SelfCwiseBinaryOp<BinOp,NestedXpr,Rhs> >
- : blas_traits<NestedXpr>
+template<typename BinOp,typename Xpr,typename Rhs>
+struct blas_traits<SelfCwiseBinaryOp<BinOp,Xpr,Rhs> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
-  typedef SelfCwiseBinaryOp<BinOp,NestedXpr,Rhs> XprType;
+  typedef SelfCwiseBinaryOp<BinOp,Xpr,Rhs> XprType;
   static inline const XprType extract(const XprType& x) { return x; }
 };
 
@@ -392,7 +392,6 @@ struct checkTransposeAliasing_impl
                       ::run(extract_data(dst), other))
           && "aliasing detected during transposition, use transposeInPlace() "
              "or evaluate the rhs into a temporary using .eval()");
-
     }
 };
 

Eigen/src/Core/Transpositions.h

@@ -376,7 +376,8 @@ struct transposition_matrix_product_retval
       const int size = m_transpositions.size();
       Index j = 0;
 
-      if(!(is_same<MatrixTypeNestedCleaned,Dest>::value && extract_data(dst) == extract_data(m_matrix)))
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
+      if(!(is_same<MatrixTypeNestedCleaned,Dest>::value && dst_data!=0 && dst_data == extract_data(m_matrix)))
         dst = m_matrix;
 
       for(int k=(Transposed?size-1:0) ; Transposed?k>=0:k<size ; Transposed?--k:++k)

Eigen/src/Core/Visitor.h

@@ -76,14 +76,17 @@ template<typename Derived>
 template<typename Visitor>
 void DenseBase<Derived>::visit(Visitor& visitor) const
 {
+  typedef typename internal::remove_all<typename Derived::Nested>::type ThisNested;
+  typename Derived::Nested thisNested(derived());
+
   enum { unroll = SizeAtCompileTime != Dynamic
                    && CoeffReadCost != Dynamic
                    && (SizeAtCompileTime == 1 || internal::functor_traits<Visitor>::Cost != Dynamic)
                    && SizeAtCompileTime * CoeffReadCost + (SizeAtCompileTime-1) * internal::functor_traits<Visitor>::Cost
                       <= EIGEN_UNROLLING_LIMIT };
-  return internal::visitor_impl<Visitor, Derived,
+  return internal::visitor_impl<Visitor, ThisNested,
       unroll ? int(SizeAtCompileTime) : Dynamic
-    >::run(derived(), visitor);
+    >::run(thisNested, visitor);
 }
 
 namespace internal {

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

@@ -235,63 +235,27 @@ template<> EIGEN_STRONG_INLINE Packet4i pload<Packet4i>(const int*     from) { E
     return _mm_loadu_ps(from);
     #endif
   }
-  template<> EIGEN_STRONG_INLINE Packet2d ploadu<Packet2d>(const double* from) { EIGEN_DEBUG_UNALIGNED_LOAD return _mm_loadu_pd(from); }
-  template<> EIGEN_STRONG_INLINE Packet4i ploadu<Packet4i>(const int*    from) { EIGEN_DEBUG_UNALIGNED_LOAD return _mm_loadu_si128(reinterpret_cast<const Packet4i*>(from)); }
 #else
-// Fast unaligned loads. Note that here we cannot directly use intrinsics: this would
-// require pointer casting to incompatible pointer types and leads to invalid code
-// because of the strict aliasing rule. The "dummy" stuff are required to enforce
-// a correct instruction dependency.
-// TODO: do the same for MSVC (ICC is compatible)
 // NOTE: with the code below, MSVC's compiler crashes!
 
-#if defined(__GNUC__) && defined(__i386__)
-  // bug 195: gcc/i386 emits weird x87 fldl/fstpl instructions for _mm_load_sd
-  #define EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS 1
-#elif defined(__clang__)
-  // bug 201: Segfaults in __mm_loadh_pd with clang 2.8
-  #define EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS 1
-#else
-  #define EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS 0
-#endif
-
 template<> EIGEN_STRONG_INLINE Packet4f ploadu<Packet4f>(const float* from)
 {
   EIGEN_DEBUG_UNALIGNED_LOAD
-#if EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS
   return _mm_loadu_ps(from);
-#else
-  __m128d res;
-  res =  _mm_load_sd((const double*)(from)) ;
-  res =  _mm_loadh_pd(res, (const double*)(from+2)) ;
-  return _mm_castpd_ps(res);
-#endif
 }
+#endif
+
 template<> EIGEN_STRONG_INLINE Packet2d ploadu<Packet2d>(const double* from)
 {
   EIGEN_DEBUG_UNALIGNED_LOAD
-#if EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS
   return _mm_loadu_pd(from);
-#else
-  __m128d res;
-  res = _mm_load_sd(from) ;
-  res = _mm_loadh_pd(res,from+1);
-  return res;
-#endif
 }
 template<> EIGEN_STRONG_INLINE Packet4i ploadu<Packet4i>(const int* from)
 {
   EIGEN_DEBUG_UNALIGNED_LOAD
-#if EIGEN_AVOID_CUSTOM_UNALIGNED_LOADS
-  return _mm_loadu_si128(reinterpret_cast<const Packet4i*>(from));
-#else
-  __m128d res;
-  res =  _mm_load_sd((const double*)(from)) ;
-  res =  _mm_loadh_pd(res, (const double*)(from+2)) ;
-  return _mm_castpd_si128(res);
-#endif
+  return _mm_loadu_si128(reinterpret_cast<const __m128i*>(from));
 }
-#endif
+
 
 template<> EIGEN_STRONG_INLINE Packet4f ploaddup<Packet4f>(const float*   from)
 {

Eigen/src/Core/products/GeneralMatrixMatrix.h

@@ -140,8 +140,10 @@ static void run(Index rows, Index cols, Index depth,
       // Release all the sub blocks B'_j of B' for the current thread,
       // i.e., we simply decrement the number of users by 1
       for(Index j=0; j<threads; ++j)
+      {
         #pragma omp atomic
-        --(info[j].users);
+        info[j].users -= 1;
+      }
     }
   }
   else
@@ -390,13 +392,17 @@ class GeneralProduct<Lhs, Rhs, GemmProduct>
 
     GeneralProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs)
     {
+#if !(defined(EIGEN_NO_STATIC_ASSERT) && defined(EIGEN_NO_DEBUG))
       typedef internal::scalar_product_op<LhsScalar,RhsScalar> BinOp;
       EIGEN_CHECK_BINARY_COMPATIBILIY(BinOp,LhsScalar,RhsScalar);
+#endif
     }
 
     template<typename Dest> void scaleAndAddTo(Dest& dst, const Scalar& alpha) const
     {
       eigen_assert(dst.rows()==m_lhs.rows() && dst.cols()==m_rhs.cols());
+      if(m_lhs.cols()==0 || m_lhs.rows()==0 || m_rhs.cols()==0)
+        return;
 
       typename internal::add_const_on_value_type<ActualLhsType>::type lhs = LhsBlasTraits::extract(m_lhs);
       typename internal::add_const_on_value_type<ActualRhsType>::type rhs = RhsBlasTraits::extract(m_rhs);

Eigen/src/Core/products/TriangularSolverMatrix.h

@@ -81,7 +81,7 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheLeft,Mode,Conju
     // coherence when accessing the rhs elements
     std::ptrdiff_t l1, l2;
     manage_caching_sizes(GetAction, &l1, &l2);
-    Index subcols = cols>0 ? l2/(4 * sizeof(Scalar) * otherStride) : 0;
+    Index subcols = cols>0 ? l2/(4 * sizeof(Scalar) *  std::max<Index>(otherStride,size)) : 0;
     subcols = std::max<Index>((subcols/Traits::nr)*Traits::nr, Traits::nr);
 
     for(Index k2=IsLower ? 0 : size;
@@ -115,8 +115,9 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheLeft,Mode,Conju
           {
             // TODO write a small kernel handling this (can be shared with trsv)
             Index i  = IsLower ? k2+k1+k : k2-k1-k-1;
-            Index s  = IsLower ? k2+k1 : i+1;
             Index rs = actualPanelWidth - k - 1; // remaining size
+            Index s  = TriStorageOrder==RowMajor ? (IsLower ? k2+k1 : i+1)
+                                                 :  IsLower ? i+1 : i-rs;
 
             Scalar a = (Mode & UnitDiag) ? Scalar(1) : Scalar(1)/conj(tri(i,i));
             for (Index j=j2; j<j2+actual_cols; ++j)
@@ -133,7 +134,6 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheLeft,Mode,Conju
               }
               else
               {
-                Index s = IsLower ? i+1 : i-rs;
                 Scalar b = (other(i,j) *= a);
                 Scalar* r = &other(s,j);
                 const Scalar* l = &tri(s,i);

Eigen/src/Core/util/BlasUtil.h

@@ -42,16 +42,29 @@ template<bool Conjugate> struct conj_if;
 
 template<> struct conj_if<true> {
   template<typename T>
-  inline T operator()(const T& x) { return numext::conj(x); }
+  inline T operator()(const T& x) const { return numext::conj(x); }
   template<typename T>
-  inline T pconj(const T& x) { return internal::pconj(x); }
+  inline T pconj(const T& x) const { return internal::pconj(x); }
 };
 
 template<> struct conj_if<false> {
   template<typename T>
-  inline const T& operator()(const T& x) { return x; }
+  inline const T& operator()(const T& x) const { return x; }
   template<typename T>
-  inline const T& pconj(const T& x) { return x; }
+  inline const T& pconj(const T& x) const { return x; }
+};
+
+// Generic implementation for custom complex types.
+template<typename LhsScalar, typename RhsScalar, bool ConjLhs, bool ConjRhs>
+struct conj_helper
+{
+  typedef typename scalar_product_traits<LhsScalar,RhsScalar>::ReturnType Scalar;
+
+  EIGEN_STRONG_INLINE Scalar pmadd(const LhsScalar& x, const RhsScalar& y, const Scalar& c) const
+  { return padd(c, pmul(x,y)); }
+
+  EIGEN_STRONG_INLINE Scalar pmul(const LhsScalar& x, const RhsScalar& y) const
+  { return conj_if<ConjLhs>()(x) *  conj_if<ConjRhs>()(y); }
 };
 
 template<typename Scalar> struct conj_helper<Scalar,Scalar,false,false>
@@ -171,12 +184,13 @@ template<typename XprType> struct blas_traits
 };
 
 // pop conjugate
-template<typename Scalar, typename NestedXpr>
-struct blas_traits<CwiseUnaryOp<scalar_conjugate_op<Scalar>, NestedXpr> >
- : blas_traits<NestedXpr>
+template<typename Scalar, typename Xpr>
+struct blas_traits<CwiseUnaryOp<scalar_conjugate_op<Scalar>, Xpr> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
+  typedef typename internal::remove_all<typename Xpr::Nested>::type NestedXpr;
   typedef blas_traits<NestedXpr> Base;
-  typedef CwiseUnaryOp<scalar_conjugate_op<Scalar>, NestedXpr> XprType;
+  typedef CwiseUnaryOp<scalar_conjugate_op<Scalar>, Xpr> XprType;
   typedef typename Base::ExtractType ExtractType;
 
   enum {
@@ -188,12 +202,13 @@ struct blas_traits<CwiseUnaryOp<scalar_conjugate_op<Scalar>, NestedXpr> >
 };
 
 // pop scalar multiple
-template<typename Scalar, typename NestedXpr>
-struct blas_traits<CwiseUnaryOp<scalar_multiple_op<Scalar>, NestedXpr> >
- : blas_traits<NestedXpr>
+template<typename Scalar, typename Xpr>
+struct blas_traits<CwiseUnaryOp<scalar_multiple_op<Scalar>, Xpr> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
+  typedef typename internal::remove_all<typename Xpr::Nested>::type NestedXpr;
   typedef blas_traits<NestedXpr> Base;
-  typedef CwiseUnaryOp<scalar_multiple_op<Scalar>, NestedXpr> XprType;
+  typedef CwiseUnaryOp<scalar_multiple_op<Scalar>, Xpr> XprType;
   typedef typename Base::ExtractType ExtractType;
   static inline ExtractType extract(const XprType& x) { return Base::extract(x.nestedExpression()); }
   static inline Scalar extractScalarFactor(const XprType& x)
@@ -201,12 +216,13 @@ struct blas_traits<CwiseUnaryOp<scalar_multiple_op<Scalar>, NestedXpr> >
 };
 
 // pop opposite
-template<typename Scalar, typename NestedXpr>
-struct blas_traits<CwiseUnaryOp<scalar_opposite_op<Scalar>, NestedXpr> >
- : blas_traits<NestedXpr>
+template<typename Scalar, typename Xpr>
+struct blas_traits<CwiseUnaryOp<scalar_opposite_op<Scalar>, Xpr> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
+  typedef typename internal::remove_all<typename Xpr::Nested>::type NestedXpr;
   typedef blas_traits<NestedXpr> Base;
-  typedef CwiseUnaryOp<scalar_opposite_op<Scalar>, NestedXpr> XprType;
+  typedef CwiseUnaryOp<scalar_opposite_op<Scalar>, Xpr> XprType;
   typedef typename Base::ExtractType ExtractType;
   static inline ExtractType extract(const XprType& x) { return Base::extract(x.nestedExpression()); }
   static inline Scalar extractScalarFactor(const XprType& x)
@@ -214,13 +230,14 @@ struct blas_traits<CwiseUnaryOp<scalar_opposite_op<Scalar>, NestedXpr> >
 };
 
 // pop/push transpose
-template<typename NestedXpr>
-struct blas_traits<Transpose<NestedXpr> >
- : blas_traits<NestedXpr>
+template<typename Xpr>
+struct blas_traits<Transpose<Xpr> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
+  typedef typename internal::remove_all<typename Xpr::Nested>::type NestedXpr;
   typedef typename NestedXpr::Scalar Scalar;
   typedef blas_traits<NestedXpr> Base;
-  typedef Transpose<NestedXpr> XprType;
+  typedef Transpose<Xpr> XprType;
   typedef Transpose<const typename Base::_ExtractType>  ExtractType; // const to get rid of a compile error; anyway blas traits are only used on the RHS
   typedef Transpose<const typename Base::_ExtractType> _ExtractType;
   typedef typename conditional<bool(Base::HasUsableDirectAccess),

Eigen/src/Core/util/Constants.h

@@ -162,7 +162,7 @@ const unsigned int HereditaryBits = RowMajorBit
 /** \ingroup enums
   * Enum containing possible values for the \p Mode parameter of 
   * MatrixBase::selfadjointView() and MatrixBase::triangularView(). */
-enum {
+enum UpLoType {
   /** View matrix as a lower triangular matrix. */
   Lower=0x1,                      
   /** View matrix as an upper triangular matrix. */
@@ -187,7 +187,7 @@ enum {
 
 /** \ingroup enums
   * Enum for indicating whether an object is aligned or not. */
-enum { 
+enum AlignmentType {
   /** Object is not correctly aligned for vectorization. */
   Unaligned=0, 
   /** Object is aligned for vectorization. */
@@ -217,7 +217,7 @@ enum DirectionType {
 
 /** \internal \ingroup enums
   * Enum to specify how to traverse the entries of a matrix. */
-enum {
+enum TraversalType {
   /** \internal Default traversal, no vectorization, no index-based access */
   DefaultTraversal,
   /** \internal No vectorization, use index-based access to have only one for loop instead of 2 nested loops */
@@ -239,7 +239,7 @@ enum {
 
 /** \internal \ingroup enums
   * Enum to specify whether to unroll loops when traversing over the entries of a matrix. */
-enum {
+enum UnrollingType {
   /** \internal Do not unroll loops. */
   NoUnrolling,
   /** \internal Unroll only the inner loop, but not the outer loop. */
@@ -251,7 +251,7 @@ enum {
 
 /** \internal \ingroup enums
   * Enum to specify whether to use the default (built-in) implementation or the specialization. */
-enum {
+enum SpecializedType {
   Specialized,
   BuiltIn
 };
@@ -259,7 +259,7 @@ enum {
 /** \ingroup enums
   * Enum containing possible values for the \p _Options template parameter of
   * Matrix, Array and BandMatrix. */
-enum {
+enum StorageOptions {
   /** Storage order is column major (see \ref TopicStorageOrders). */
   ColMajor = 0,
   /** Storage order is row major (see \ref TopicStorageOrders). */
@@ -272,7 +272,7 @@ enum {
 
 /** \ingroup enums
   * Enum for specifying whether to apply or solve on the left or right. */
-enum {
+enum SideType {
   /** Apply transformation on the left. */
   OnTheLeft = 1,  
   /** Apply transformation on the right. */
@@ -418,7 +418,7 @@ namespace Architecture
 
 /** \internal \ingroup enums
   * Enum used as template parameter in GeneralProduct. */
-enum { CoeffBasedProductMode, LazyCoeffBasedProductMode, OuterProduct, InnerProduct, GemvProduct, GemmProduct };
+enum ProductImplType { CoeffBasedProductMode, LazyCoeffBasedProductMode, OuterProduct, InnerProduct, GemvProduct, GemmProduct };
 
 /** \internal \ingroup enums
   * Enum used in experimental parallel implementation. */

Eigen/src/Core/util/DisableStupidWarnings.h

@@ -35,6 +35,14 @@
     #pragma clang diagnostic push
   #endif
   #pragma clang diagnostic ignored "-Wconstant-logical-operand"
+
+#elif defined __GNUC__ && __GNUC__>=6
+
+  #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+    #pragma GCC diagnostic push
+  #endif
+  #pragma GCC diagnostic ignored "-Wignored-attributes"
+
 #endif
 
 #endif // not EIGEN_WARNINGS_DISABLED

Eigen/src/Core/util/Macros.h

@@ -13,23 +13,292 @@
 
 #define EIGEN_WORLD_VERSION 3
 #define EIGEN_MAJOR_VERSION 2
-#define EIGEN_MINOR_VERSION 7
+#define EIGEN_MINOR_VERSION 10
 
 #define EIGEN_VERSION_AT_LEAST(x,y,z) (EIGEN_WORLD_VERSION>x || (EIGEN_WORLD_VERSION>=x && \
                                       (EIGEN_MAJOR_VERSION>y || (EIGEN_MAJOR_VERSION>=y && \
                                                                  EIGEN_MINOR_VERSION>=z))))
+
+
+// Compiler identification, EIGEN_COMP_*
+
+/// \internal EIGEN_COMP_GNUC set to 1 for all compilers compatible with GCC
 #ifdef __GNUC__
+  #define EIGEN_COMP_GNUC 1
+#else
+  #define EIGEN_COMP_GNUC 0
+#endif
+
+/// \internal EIGEN_COMP_CLANG set to 1 if the compiler is clang (alias for __clang__)
+#if defined(__clang__)
+  #define EIGEN_COMP_CLANG 1
+#else
+  #define EIGEN_COMP_CLANG 0
+#endif
+
+
+/// \internal EIGEN_COMP_LLVM set to 1 if the compiler backend is llvm
+#if defined(__llvm__)
+  #define EIGEN_COMP_LLVM 1
+#else
+  #define EIGEN_COMP_LLVM 0
+#endif
+
+/// \internal EIGEN_COMP_ICC set to __INTEL_COMPILER if the compiler is Intel compiler, 0 otherwise
+#if defined(__INTEL_COMPILER)
+  #define EIGEN_COMP_ICC __INTEL_COMPILER
+#else
+  #define EIGEN_COMP_ICC 0
+#endif
+
+/// \internal EIGEN_COMP_MINGW set to 1 if the compiler is mingw
+#if defined(__MINGW32__)
+  #define EIGEN_COMP_MINGW 1
+#else
+  #define EIGEN_COMP_MINGW 0
+#endif
+
+/// \internal EIGEN_COMP_SUNCC set to 1 if the compiler is Solaris Studio
+#if defined(__SUNPRO_CC)
+  #define EIGEN_COMP_SUNCC 1
+#else
+  #define EIGEN_COMP_SUNCC 0
+#endif
+
+/// \internal EIGEN_COMP_MSVC set to _MSC_VER if the compiler is Microsoft Visual C++, 0 otherwise.
+#if defined(_MSC_VER)
+  #define EIGEN_COMP_MSVC _MSC_VER
+#else
+  #define EIGEN_COMP_MSVC 0
+#endif
+
+/// \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)
+  #define EIGEN_COMP_MSVC_STRICT _MSC_VER
+#else
+  #define EIGEN_COMP_MSVC_STRICT 0
+#endif
+
+/// \internal EIGEN_COMP_IBM set to 1 if the compiler is IBM XL C++
+#if defined(__IBMCPP__) || defined(__xlc__)
+  #define EIGEN_COMP_IBM 1
+#else
+  #define EIGEN_COMP_IBM 0
+#endif
+
+/// \internal EIGEN_COMP_PGI set to 1 if the compiler is Portland Group Compiler
+#if defined(__PGI)
+  #define EIGEN_COMP_PGI 1
+#else
+  #define EIGEN_COMP_PGI 0
+#endif
+
+/// \internal EIGEN_COMP_ARM set to 1 if the compiler is ARM Compiler
+#if defined(__CC_ARM) || defined(__ARMCC_VERSION)
+  #define EIGEN_COMP_ARM 1
+#else
+  #define EIGEN_COMP_ARM 0
+#endif
+
+
+/// \internal EIGEN_GNUC_STRICT set to 1 if the compiler is really GCC and not a compatible compiler (e.g., ICC, clang, mingw, etc.)
+#if EIGEN_COMP_GNUC && !(EIGEN_COMP_CLANG || EIGEN_COMP_ICC || EIGEN_COMP_MINGW || EIGEN_COMP_PGI || EIGEN_COMP_IBM || EIGEN_COMP_ARM )
+  #define EIGEN_COMP_GNUC_STRICT 1
+#else
+  #define EIGEN_COMP_GNUC_STRICT 0
+#endif
+
+
+#if EIGEN_COMP_GNUC
   #define EIGEN_GNUC_AT_LEAST(x,y) ((__GNUC__==x && __GNUC_MINOR__>=y) || __GNUC__>x)
+  #define EIGEN_GNUC_AT_MOST(x,y)  ((__GNUC__==x && __GNUC_MINOR__<=y) || __GNUC__<x)
+  #define EIGEN_GNUC_AT(x,y)       ( __GNUC__==x && __GNUC_MINOR__==y )
 #else
   #define EIGEN_GNUC_AT_LEAST(x,y) 0
+  #define EIGEN_GNUC_AT_MOST(x,y)  0
+  #define EIGEN_GNUC_AT(x,y)       0
 #endif
- 
-#ifdef __GNUC__
-  #define EIGEN_GNUC_AT_MOST(x,y) ((__GNUC__==x && __GNUC_MINOR__<=y) || __GNUC__<x)
+
+// FIXME: could probably be removed as we do not support gcc 3.x anymore
+#if EIGEN_COMP_GNUC && (__GNUC__ <= 3)
+#define EIGEN_GCC3_OR_OLDER 1
 #else
-  #define EIGEN_GNUC_AT_MOST(x,y) 0
+#define EIGEN_GCC3_OR_OLDER 0
 #endif
 
+
+// Architecture identification, EIGEN_ARCH_*
+
+#if defined(__x86_64__) || defined(_M_X64) || defined(__amd64)
+  #define EIGEN_ARCH_x86_64 1
+#else
+  #define EIGEN_ARCH_x86_64 0
+#endif
+
+#if defined(__i386__) || defined(_M_IX86) || defined(_X86_) || defined(__i386)
+  #define EIGEN_ARCH_i386 1
+#else
+  #define EIGEN_ARCH_i386 0
+#endif
+
+#if EIGEN_ARCH_x86_64 || EIGEN_ARCH_i386
+  #define EIGEN_ARCH_i386_OR_x86_64 1
+#else
+  #define EIGEN_ARCH_i386_OR_x86_64 0
+#endif
+
+/// \internal EIGEN_ARCH_ARM set to 1 if the architecture is ARM
+#if defined(__arm__)
+  #define EIGEN_ARCH_ARM 1
+#else
+  #define EIGEN_ARCH_ARM 0
+#endif
+
+/// \internal EIGEN_ARCH_ARM64 set to 1 if the architecture is ARM64
+#if defined(__aarch64__)
+  #define EIGEN_ARCH_ARM64 1
+#else
+  #define EIGEN_ARCH_ARM64 0
+#endif
+
+#if EIGEN_ARCH_ARM || EIGEN_ARCH_ARM64
+  #define EIGEN_ARCH_ARM_OR_ARM64 1
+#else
+  #define EIGEN_ARCH_ARM_OR_ARM64 0
+#endif
+
+/// \internal EIGEN_ARCH_MIPS set to 1 if the architecture is MIPS
+#if defined(__mips__) || defined(__mips)
+  #define EIGEN_ARCH_MIPS 1
+#else
+  #define EIGEN_ARCH_MIPS 0
+#endif
+
+/// \internal EIGEN_ARCH_SPARC set to 1 if the architecture is SPARC
+#if defined(__sparc__) || defined(__sparc)
+  #define EIGEN_ARCH_SPARC 1
+#else
+  #define EIGEN_ARCH_SPARC 0
+#endif
+
+/// \internal EIGEN_ARCH_IA64 set to 1 if the architecture is Intel Itanium
+#if defined(__ia64__)
+  #define EIGEN_ARCH_IA64 1
+#else
+  #define EIGEN_ARCH_IA64 0
+#endif
+
+/// \internal EIGEN_ARCH_PPC set to 1 if the architecture is PowerPC
+#if defined(__powerpc__) || defined(__ppc__) || defined(_M_PPC)
+  #define EIGEN_ARCH_PPC 1
+#else
+  #define EIGEN_ARCH_PPC 0
+#endif
+
+
+
+// Operating system identification, EIGEN_OS_*
+
+/// \internal EIGEN_OS_UNIX set to 1 if the OS is a unix variant
+#if defined(__unix__) || defined(__unix)
+  #define EIGEN_OS_UNIX 1
+#else
+  #define EIGEN_OS_UNIX 0
+#endif
+
+/// \internal EIGEN_OS_LINUX set to 1 if the OS is based on Linux kernel
+#if defined(__linux__)
+  #define EIGEN_OS_LINUX 1
+#else
+  #define EIGEN_OS_LINUX 0
+#endif
+
+/// \internal EIGEN_OS_ANDROID set to 1 if the OS is Android
+// note: ANDROID is defined when using ndk_build, __ANDROID__ is defined when using a standalone toolchain.
+#if defined(__ANDROID__) || defined(ANDROID)
+  #define EIGEN_OS_ANDROID 1
+#else
+  #define EIGEN_OS_ANDROID 0
+#endif
+
+/// \internal EIGEN_OS_GNULINUX set to 1 if the OS is GNU Linux and not Linux-based OS (e.g., not android)
+#if defined(__gnu_linux__) && !(EIGEN_OS_ANDROID)
+  #define EIGEN_OS_GNULINUX 1
+#else
+  #define EIGEN_OS_GNULINUX 0
+#endif
+
+/// \internal EIGEN_OS_BSD set to 1 if the OS is a BSD variant
+#if defined(__FreeBSD__) || defined(__NetBSD__) || defined(__OpenBSD__) || defined(__bsdi__) || defined(__DragonFly__)
+  #define EIGEN_OS_BSD 1
+#else
+  #define EIGEN_OS_BSD 0
+#endif
+
+/// \internal EIGEN_OS_MAC set to 1 if the OS is MacOS
+#if defined(__APPLE__)
+  #define EIGEN_OS_MAC 1
+#else
+  #define EIGEN_OS_MAC 0
+#endif
+
+/// \internal EIGEN_OS_QNX set to 1 if the OS is QNX
+#if defined(__QNX__)
+  #define EIGEN_OS_QNX 1
+#else
+  #define EIGEN_OS_QNX 0
+#endif
+
+/// \internal EIGEN_OS_WIN set to 1 if the OS is Windows based
+#if defined(_WIN32)
+  #define EIGEN_OS_WIN 1
+#else
+  #define EIGEN_OS_WIN 0
+#endif
+
+/// \internal EIGEN_OS_WIN64 set to 1 if the OS is Windows 64bits
+#if defined(_WIN64)
+  #define EIGEN_OS_WIN64 1
+#else
+  #define EIGEN_OS_WIN64 0
+#endif
+
+/// \internal EIGEN_OS_WINCE set to 1 if the OS is Windows CE
+#if defined(_WIN32_WCE)
+  #define EIGEN_OS_WINCE 1
+#else
+  #define EIGEN_OS_WINCE 0
+#endif
+
+/// \internal EIGEN_OS_CYGWIN set to 1 if the OS is Windows/Cygwin
+#if defined(__CYGWIN__)
+  #define EIGEN_OS_CYGWIN 1
+#else
+  #define EIGEN_OS_CYGWIN 0
+#endif
+
+/// \internal EIGEN_OS_WIN_STRICT set to 1 if the OS is really Windows and not some variants
+#if EIGEN_OS_WIN && !( EIGEN_OS_WINCE || EIGEN_OS_CYGWIN )
+  #define EIGEN_OS_WIN_STRICT 1
+#else
+  #define EIGEN_OS_WIN_STRICT 0
+#endif
+
+/// \internal EIGEN_OS_SUN set to 1 if the OS is SUN
+#if (defined(sun) || defined(__sun)) && !(defined(__SVR4) || defined(__svr4__))
+  #define EIGEN_OS_SUN 1
+#else
+  #define EIGEN_OS_SUN 0
+#endif
+
+/// \internal EIGEN_OS_SOLARIS set to 1 if the OS is Solaris
+#if (defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))
+  #define EIGEN_OS_SOLARIS 1
+#else
+  #define EIGEN_OS_SOLARIS 0
+#endif
+
+
 #if EIGEN_GNUC_AT_MOST(4,3) && !defined(__clang__)
   // see bug 89
   #define EIGEN_SAFE_TO_USE_STANDARD_ASSERT_MACRO 0
@@ -37,12 +306,6 @@
   #define EIGEN_SAFE_TO_USE_STANDARD_ASSERT_MACRO 1
 #endif
 
-#if defined(__GNUC__) && (__GNUC__ <= 3)
-#define EIGEN_GCC3_OR_OLDER 1
-#else
-#define EIGEN_GCC3_OR_OLDER 0
-#endif
-
 // 16 byte alignment is only useful for vectorization. Since it affects the ABI, we need to enable
 // 16 byte alignment on all platforms where vectorization might be enabled. In theory we could always
 // enable alignment, but it can be a cause of problems on some platforms, so we just disable it in
@@ -104,7 +367,7 @@
 
 // Do we support r-value references?
 #if (__has_feature(cxx_rvalue_references) || \
-     defined(__GXX_EXPERIMENTAL_CXX0X__) || \
+     (defined(__cplusplus) && __cplusplus >= 201103L) || \
      (defined(_MSC_VER) && _MSC_VER >= 1600))
   #define EIGEN_HAVE_RVALUE_REFERENCES
 #endif
@@ -149,10 +412,11 @@
 // 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

Eigen/src/Core/util/Memory.h

@@ -507,7 +507,12 @@ template<typename T> void smart_copy(const T* start, const T* end, T* target)
 
 template<typename T> struct smart_copy_helper<T,true> {
   static inline void run(const T* start, const T* end, T* target)
-  { memcpy(target, start, std::ptrdiff_t(end)-std::ptrdiff_t(start)); }
+  {
+    std::ptrdiff_t size = std::ptrdiff_t(end)-std::ptrdiff_t(start);
+    if(size==0) return;
+    eigen_internal_assert(start!=0 && end!=0 && target!=0);
+    memcpy(target, start, size);
+  }
 };
 
 template<typename T> struct smart_copy_helper<T,false> {
@@ -515,7 +520,6 @@ template<typename T> struct smart_copy_helper<T,false> {
   { std::copy(start, end, target); }
 };
 
-
 /*****************************************************************************
 *** Implementation of runtime stack allocation (falling back to malloc)    ***
 *****************************************************************************/
@@ -630,6 +634,8 @@ template<typename T> class aligned_stack_memory_handler
       } \
       void operator delete(void * ptr) throw() { Eigen::internal::conditional_aligned_free<NeedsToAlign>(ptr); } \
       void operator delete[](void * ptr) throw() { Eigen::internal::conditional_aligned_free<NeedsToAlign>(ptr); } \
+      void operator delete(void * ptr, std::size_t /* sz */) throw() { Eigen::internal::conditional_aligned_free<NeedsToAlign>(ptr); } \
+      void operator delete[](void * ptr, std::size_t /* sz */) throw() { Eigen::internal::conditional_aligned_free<NeedsToAlign>(ptr); } \
       /* 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. */ \
@@ -653,99 +659,60 @@ template<typename T> class aligned_stack_memory_handler
 
 /****************************************************************************/
 
+
 /** \class aligned_allocator
-* \ingroup Core_Module
-*
-* \brief STL compatible allocator to use with with 16 byte aligned types
-*
-* Example:
-* \code
-* // Matrix4f requires 16 bytes alignment:
-* std::map< int, Matrix4f, std::less<int>, 
-*           aligned_allocator<std::pair<const int, Matrix4f> > > my_map_mat4;
-* // Vector3f does not require 16 bytes alignment, no need to use Eigen's allocator:
-* std::map< int, Vector3f > my_map_vec3;
-* \endcode
-*
-* \sa \ref TopicStlContainers.
-*/
+  * \ingroup Core_Module
+  *
+  * \brief STL compatible allocator to use with with 16 byte aligned types
+  *
+  * Example:
+  * \code
+  * // Matrix4f requires 16 bytes alignment:
+  * std::map< int, Matrix4f, std::less<int>,
+  *           aligned_allocator<std::pair<const int, Matrix4f> > > my_map_mat4;
+  * // Vector3f does not require 16 bytes alignment, no need to use Eigen's allocator:
+  * std::map< int, Vector3f > my_map_vec3;
+  * \endcode
+  *
+  * \sa \blank \ref TopicStlContainers.
+  */
 template<class T>
-class aligned_allocator
+class aligned_allocator : public std::allocator<T>
 {
 public:
-    typedef 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;
+  typedef 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
-    {
-        typedef aligned_allocator<U> other;
-    };
+  template<class U>
+  struct rebind
+  {
+    typedef aligned_allocator<U> other;
+  };
 
-    pointer address( reference value ) const
-    {
-        return &value;
-    }
+  aligned_allocator() : std::allocator<T>() {}
 
-    const_pointer address( const_reference value ) const
-    {
-        return &value;
-    }
+  aligned_allocator(const aligned_allocator& other) : std::allocator<T>(other) {}
 
-    aligned_allocator()
-    {
-    }
+  template<class U>
+  aligned_allocator(const aligned_allocator<U>& other) : std::allocator<T>(other) {}
 
-    aligned_allocator( const aligned_allocator& )
-    {
-    }
+  ~aligned_allocator() {}
 
-    template<class U>
-    aligned_allocator( const aligned_allocator<U>& )
-    {
-    }
+  pointer allocate(size_type num, const void* /*hint*/ = 0)
+  {
+    internal::check_size_for_overflow<T>(num);
+    return static_cast<pointer>( internal::aligned_malloc(num * sizeof(T)) );
+  }
 
-    ~aligned_allocator()
-    {
-    }
-
-    size_type max_size() const
-    {
-        return (std::numeric_limits<size_type>::max)();
-    }
-
-    pointer allocate( size_type num, const void* hint = 0 )
-    {
-        EIGEN_UNUSED_VARIABLE(hint);
-        internal::check_size_for_overflow<T>(num);
-        return static_cast<pointer>( internal::aligned_malloc( num * sizeof(T) ) );
-    }
-
-    void construct( pointer p, const T& value )
-    {
-        ::new( p ) T( value );
-    }
-
-    void destroy( pointer p )
-    {
-        p->~T();
-    }
-
-    void deallocate( pointer p, size_type /*num*/ )
-    {
-        internal::aligned_free( p );
-    }
-
-    bool operator!=(const aligned_allocator<T>& ) const
-    { return false; }
-
-    bool operator==(const aligned_allocator<T>& ) const
-    { return true; }
+  void deallocate(pointer p, size_type /*num*/)
+  {
+    internal::aligned_free(p);
+  }
 };
 
 //---------- Cache sizes ----------

Eigen/src/Core/util/ReenableStupidWarnings.h

@@ -8,7 +8,10 @@
     #pragma warning pop
   #elif defined __clang__
     #pragma clang diagnostic pop
+  #elif defined __GNUC__ && __GNUC__>=6
+    #pragma GCC diagnostic pop
   #endif
+
 #endif
 
 #endif // EIGEN_WARNINGS_DISABLED

Eigen/src/Core/util/StaticAssert.h

@@ -26,7 +26,7 @@
 
 #ifndef EIGEN_NO_STATIC_ASSERT
 
-  #if defined(__GXX_EXPERIMENTAL_CXX0X__) || (defined(_MSC_VER) && (_MSC_VER >= 1600))
+  #if __has_feature(cxx_static_assert) || (defined(__cplusplus) && __cplusplus >= 201103L) || (EIGEN_COMP_MSVC >= 1600)
 
     // if native static_assert is enabled, let's use it
     #define EIGEN_STATIC_ASSERT(X,MSG) static_assert(X,#MSG);
@@ -92,7 +92,8 @@
         THE_STORAGE_ORDER_OF_BOTH_SIDES_MUST_MATCH,
         OBJECT_ALLOCATED_ON_STACK_IS_TOO_BIG,
         IMPLICIT_CONVERSION_TO_SCALAR_IS_FOR_INNER_PRODUCT_ONLY,
-        STORAGE_LAYOUT_DOES_NOT_MATCH
+        STORAGE_LAYOUT_DOES_NOT_MATCH,
+        CHOLMOD_SUPPORTS_DOUBLE_PRECISION_ONLY
       };
     };
 

Eigen/src/Eigenvalues/ComplexSchur_MKL.h

@@ -45,7 +45,6 @@ ComplexSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >& \
 ComplexSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >::compute(const Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW>& matrix, bool computeU) \
 { \
   typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> MatrixType; \
-  typedef MatrixType::Scalar Scalar; \
   typedef MatrixType::RealScalar RealScalar; \
   typedef std::complex<RealScalar> ComplexScalar; \
 \

Eigen/src/Eigenvalues/GeneralizedEigenSolver.h

@@ -327,13 +327,33 @@ GeneralizedEigenSolver<MatrixType>::compute(const MatrixType& A, const MatrixTyp
       }
       else
       {
-        Scalar p = Scalar(0.5) * (m_matS.coeff(i, i) - m_matS.coeff(i+1, i+1));
-        Scalar z = sqrt(abs(p * p + m_matS.coeff(i+1, i) * m_matS.coeff(i, i+1)));
-        m_alphas.coeffRef(i)   = ComplexScalar(m_matS.coeff(i+1, i+1) + p, z);
-        m_alphas.coeffRef(i+1) = ComplexScalar(m_matS.coeff(i+1, i+1) + p, -z);
+        // We need to extract the generalized eigenvalues of the pair of a general 2x2 block S and a triangular 2x2 block T
+        // From the eigen decomposition of T = U * E * U^-1,
+        // we can extract the eigenvalues of (U^-1 * S * U) / E
+        // Here, we can take advantage that E = diag(T), and U = [ 1 T_01 ; 0 T_11-T_00], and U^-1 = [1 -T_11/(T_11-T_00) ; 0 1/(T_11-T_00)].
+        // Then taking beta=T_00*T_11*(T_11-T_00), we can avoid any division, and alpha is the eigenvalues of A = (U^-1 * S * U) * diag(T_11,T_00) * (T_11-T_00):
+
+        // T =  [a b ; 0 c]
+        // S =  [e f ; g h]
+        RealScalar a = m_realQZ.matrixT().coeff(i, i), b = m_realQZ.matrixT().coeff(i, i+1), c = m_realQZ.matrixT().coeff(i+1, i+1);
+        RealScalar e = m_matS.coeff(i, i), f = m_matS.coeff(i, i+1), g = m_matS.coeff(i+1, i), h = m_matS.coeff(i+1, i+1);
+        RealScalar d = c-a;
+        RealScalar gb = g*b;
+        Matrix<RealScalar,2,2> A;
+        A <<  (e*d-gb)*c,  ((e*b+f*d-h*b)*d-gb*b)*a,
+              g*c       ,  (gb+h*d)*a;
+
+        // NOTE, we could also compute the SVD of T's block during the QZ factorization so that the respective T block is guaranteed to be diagonal,
+        // and then we could directly apply the formula below (while taking care of scaling S columns by T11,T00):
+
+        Scalar p = Scalar(0.5) * (A.coeff(i, i) - A.coeff(i+1, i+1));
+        Scalar z = sqrt(abs(p * p + A.coeff(i+1, i) * A.coeff(i, i+1)));
+        m_alphas.coeffRef(i)   = ComplexScalar(A.coeff(i+1, i+1) + p, z);
+        m_alphas.coeffRef(i+1) = ComplexScalar(A.coeff(i+1, i+1) + p, -z);
+
+        m_betas.coeffRef(i)   =
+        m_betas.coeffRef(i+1) = a*c*d;
 
-        m_betas.coeffRef(i)   = m_realQZ.matrixT().coeff(i,i);
-        m_betas.coeffRef(i+1) = m_realQZ.matrixT().coeff(i,i);
         i += 2;
       }
     }

Eigen/src/Eigenvalues/RealSchur_MKL.h

@@ -44,10 +44,6 @@ template<> inline \
 RealSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >& \
 RealSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >::compute(const Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW>& matrix, bool computeU) \
 { \
-  typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> MatrixType; \
-  typedef MatrixType::Scalar Scalar; \
-  typedef MatrixType::RealScalar RealScalar; \
-\
   eigen_assert(matrix.cols() == matrix.rows()); \
 \
   lapack_int n = matrix.cols(), sdim, info; \

Eigen/src/Eigenvalues/Tridiagonalization.h

@@ -367,10 +367,10 @@ void tridiagonalization_inplace(MatrixType& matA, CoeffVectorType& hCoeffs)
     hCoeffs.tail(n-i-1).noalias() = (matA.bottomRightCorner(remainingSize,remainingSize).template selfadjointView<Lower>()
                                   * (conj(h) * matA.col(i).tail(remainingSize)));
 
-    hCoeffs.tail(n-i-1) += (conj(h)*Scalar(-0.5)*(hCoeffs.tail(remainingSize).dot(matA.col(i).tail(remainingSize)))) * matA.col(i).tail(n-i-1);
+    hCoeffs.tail(n-i-1) += (conj(h)*RealScalar(-0.5)*(hCoeffs.tail(remainingSize).dot(matA.col(i).tail(remainingSize)))) * matA.col(i).tail(n-i-1);
 
     matA.bottomRightCorner(remainingSize, remainingSize).template selfadjointView<Lower>()
-      .rankUpdate(matA.col(i).tail(remainingSize), hCoeffs.tail(remainingSize), -1);
+      .rankUpdate(matA.col(i).tail(remainingSize), hCoeffs.tail(remainingSize), Scalar(-1));
 
     matA.col(i).coeffRef(i+1) = beta;
     hCoeffs.coeffRef(i) = h;

Eigen/src/Geometry/AngleAxis.h

@@ -83,10 +83,17 @@ public:
   template<typename Derived>
   inline explicit AngleAxis(const MatrixBase<Derived>& m) { *this = m; }
 
+  /** \returns the value of the rotation angle in radian */
   Scalar angle() const { return m_angle; }
+  /** \returns a read-write reference to the stored angle in radian */
   Scalar& angle() { return m_angle; }
 
+  /** \returns the rotation axis */
   const Vector3& axis() const { return m_axis; }
+  /** \returns a read-write reference to the stored rotation axis.
+    *
+    * \warning The rotation axis must remain a \b unit vector.
+    */
   Vector3& axis() { return m_axis; }
 
   /** Concatenates two rotations */

Eigen/src/Geometry/Homogeneous.h

@@ -75,7 +75,7 @@ template<typename MatrixType,int _Direction> class Homogeneous
     inline Index rows() const { return m_matrix.rows() + (int(Direction)==Vertical   ? 1 : 0); }
     inline Index cols() const { return m_matrix.cols() + (int(Direction)==Horizontal ? 1 : 0); }
 
-    inline Scalar coeff(Index row, Index col) const
+    inline Scalar coeff(Index row, Index col=0) const
     {
       if(  (int(Direction)==Vertical   && row==m_matrix.rows())
         || (int(Direction)==Horizontal && col==m_matrix.cols()))

Eigen/src/Geometry/Hyperplane.h

@@ -218,7 +218,10 @@ public:
   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/ParametrizedLine.h

@@ -129,7 +129,7 @@ public:
     * determined by \a prec.
     *
     * \sa MatrixBase::isApprox() */
-  bool isApprox(const ParametrizedLine& other, typename NumTraits<Scalar>::Real prec = NumTraits<Scalar>::dummy_precision()) const
+  bool isApprox(const ParametrizedLine& other, const typename NumTraits<Scalar>::Real& prec = NumTraits<Scalar>::dummy_precision()) const
   { return m_origin.isApprox(other.m_origin, prec) && m_direction.isApprox(other.m_direction, prec); }
 
 protected:

Eigen/src/Geometry/Quaternion.h

@@ -276,7 +276,7 @@ public:
   inline Coefficients& coeffs() { return m_coeffs;}
   inline const Coefficients& coeffs() const { return m_coeffs;}
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(IsAligned)
+  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(bool(IsAligned))
 
 protected:
   Coefficients m_coeffs;

Eigen/src/Geometry/Transform.h

@@ -102,15 +102,15 @@ template<int Mode> struct transform_make_affine;
   *
   * However, unlike a plain matrix, the Transform class provides many features
   * simplifying both its assembly and usage. In particular, it can be composed
-  * with any other transformations (Transform,Translation,RotationBase,Matrix)
+  * with any other transformations (Transform,Translation,RotationBase,DiagonalMatrix)
   * and can be directly used to transform implicit homogeneous vectors. All these
   * operations are handled via the operator*. For the composition of transformations,
   * its principle consists to first convert the right/left hand sides of the product
   * to a compatible (Dim+1)^2 matrix and then perform a pure matrix product.
   * Of course, internally, operator* tries to perform the minimal number of operations
   * according to the nature of each terms. Likewise, when applying the transform
-  * to non homogeneous vectors, the latters are automatically promoted to homogeneous
-  * one before doing the matrix product. The convertions to homogeneous representations
+  * to points, the latters are automatically promoted to homogeneous vectors
+  * before doing the matrix product. The conventions to homogeneous representations
   * are performed as follow:
   *
   * \b Translation t (Dim)x(1):
@@ -124,7 +124,7 @@ template<int Mode> struct transform_make_affine;
   * R & 0\\
   * 0\,...\,0 & 1
   * \end{array} \right) \f$
-  *
+  *<!--
   * \b Linear \b Matrix L (Dim)x(Dim):
   * \f$ \left( \begin{array}{cc}
   * L & 0\\
@@ -136,14 +136,20 @@ template<int Mode> struct transform_make_affine;
   * A\\
   * 0\,...\,0\,1
   * \end{array} \right) \f$
+  *-->
+  * \b Scaling \b DiagonalMatrix S (Dim)x(Dim):
+  * \f$ \left( \begin{array}{cc}
+  * S & 0\\
+  * 0\,...\,0 & 1
+  * \end{array} \right) \f$
   *
-  * \b Column \b vector v (Dim)x(1):
+  * \b Column \b point v (Dim)x(1):
   * \f$ \left( \begin{array}{c}
   * v\\
   * 1
   * \end{array} \right) \f$
   *
-  * \b Set \b of \b column \b vectors V1...Vn (Dim)x(n):
+  * \b Set \b of \b column \b points V1...Vn (Dim)x(n):
   * \f$ \left( \begin{array}{ccc}
   * v_1 & ... & v_n\\
   * 1 & ... & 1
@@ -384,26 +390,39 @@ public:
   /** \returns a writable expression of the translation vector of the transformation */
   inline TranslationPart translation() { return TranslationPart(m_matrix,0,Dim); }
 
-  /** \returns an expression of the product between the transform \c *this and a matrix expression \a other
+  /** \returns an expression of the product between the transform \c *this and a matrix expression \a other.
     *
-    * The right hand side \a other might be either:
-    * \li a vector of size Dim,
+    * The right-hand-side \a other can be either:
     * \li an homogeneous vector of size Dim+1,
-    * \li a set of vectors of size Dim x Dynamic,
-    * \li a set of homogeneous vectors of size Dim+1 x Dynamic,
-    * \li a linear transformation matrix of size Dim x Dim,
-    * \li an affine transformation matrix of size Dim x Dim+1,
+    * \li a set of homogeneous vectors of size Dim+1 x N,
     * \li a transformation matrix of size Dim+1 x Dim+1.
+    *
+    * Moreover, if \c *this represents an affine transformation (i.e., Mode!=Projective), then \a other can also be:
+    * \li a point of size Dim (computes: \code this->linear() * other + this->translation()\endcode),
+    * \li a set of N points as a Dim x N matrix (computes: \code (this->linear() * other).colwise() + this->translation()\endcode),
+    *
+    * In all cases, the return type is a matrix or vector of same sizes as the right-hand-side \a other.
+    *
+    * If you want to interpret \a other as a linear or affine transformation, then first convert it to a Transform<> type,
+    * or do your own cooking.
+    *
+    * Finally, if you want to apply Affine transformations to vectors, then explicitly apply the linear part only:
+    * \code
+    * Affine3f A;
+    * Vector3f v1, v2;
+    * v2 = A.linear() * v1;
+    * \endcode
+    *
     */
   // note: this function is defined here because some compilers cannot find the respective declaration
   template<typename OtherDerived>
-  EIGEN_STRONG_INLINE const typename internal::transform_right_product_impl<Transform, OtherDerived>::ResultType
+  EIGEN_STRONG_INLINE const typename OtherDerived::PlainObject
   operator * (const EigenBase<OtherDerived> &other) const
   { return internal::transform_right_product_impl<Transform, OtherDerived>::run(*this,other.derived()); }
 
   /** \returns the product expression of a transformation matrix \a a times a transform \a b
     *
-    * The left hand side \a other might be either:
+    * The left hand side \a other can be either:
     * \li a linear transformation matrix of size Dim x Dim,
     * \li an affine transformation matrix of size Dim x Dim+1,
     * \li a general transformation matrix of size Dim+1 x Dim+1.
@@ -424,7 +443,7 @@ public:
     operator * (const DiagonalBase<DiagonalDerived> &b) const
   {
     TransformTimeDiagonalReturnType res(*this);
-    res.linear() *= b;
+    res.linearExt() *= b;
     return res;
   }
 
@@ -538,7 +557,7 @@ public:
     return res;
   }
 
-  inline Transform& operator*=(const DiagonalMatrix<Scalar,Dim>& s) { linear() *= s; return *this; }
+  inline Transform& operator*=(const DiagonalMatrix<Scalar,Dim>& s) { linearExt() *= s; return *this; }
 
   template<typename Derived>
   inline Transform& operator=(const RotationBase<Derived,Dim>& r);
@@ -809,7 +828,7 @@ Transform<Scalar,Dim,Mode,Options>::prescale(const MatrixBase<OtherDerived> &oth
 {
   EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(OtherDerived,int(Dim))
   EIGEN_STATIC_ASSERT(Mode!=int(Isometry), THIS_METHOD_IS_ONLY_FOR_SPECIFIC_TRANSFORMATIONS)
-  m_matrix.template block<Dim,HDim>(0,0).noalias() = (other.asDiagonal() * m_matrix.template block<Dim,HDim>(0,0));
+  affine().noalias() = (other.asDiagonal() * affine());
   return *this;
 }
 
@@ -1029,7 +1048,7 @@ void Transform<Scalar,Dim,Mode,Options>::computeRotationScaling(RotationMatrixTy
   }
 }
 
-/** decomposes the linear part of the transformation as a product rotation x scaling, the scaling being
+/** decomposes the linear part of the transformation as a product scaling x rotation, the scaling being
   * not necessarily positive.
   *
   * If either pointer is zero, the corresponding computation is skipped.

Eigen/src/Geometry/Translation.h

@@ -130,8 +130,10 @@ public:
   }
 
   /** Applies translation to vector */
-  inline VectorType operator* (const VectorType& other) const
-  { return m_coeffs + other; }
+  template<typename Derived>
+  inline typename internal::enable_if<Derived::IsVectorAtCompileTime,VectorType>::type
+  operator* (const MatrixBase<Derived>& vec) const
+  { return m_coeffs + vec.derived(); }
 
   /** \returns the inverse translation (opposite) */
   Translation inverse() const { return Translation(-m_coeffs); }
@@ -162,7 +164,7 @@ public:
     * determined by \a prec.
     *
     * \sa MatrixBase::isApprox() */
-  bool isApprox(const Translation& other, typename NumTraits<Scalar>::Real prec = NumTraits<Scalar>::dummy_precision()) const
+  bool isApprox(const Translation& other, const typename NumTraits<Scalar>::Real& prec = NumTraits<Scalar>::dummy_precision()) const
   { return m_coeffs.isApprox(other.m_coeffs, prec); }
 
 };

Eigen/src/Householder/Householder.h

@@ -75,8 +75,9 @@ void MatrixBase<Derived>::makeHouseholder(
   
   RealScalar tailSqNorm = size()==1 ? RealScalar(0) : tail.squaredNorm();
   Scalar c0 = coeff(0);
+  const RealScalar tol = (std::numeric_limits<RealScalar>::min)();
 
-  if(tailSqNorm == RealScalar(0) && numext::imag(c0)==RealScalar(0))
+  if(tailSqNorm <= tol && numext::abs2(numext::imag(c0))<=tol)
   {
     tau = RealScalar(0);
     beta = numext::real(c0);

Eigen/src/Householder/HouseholderSequence.h

@@ -237,8 +237,9 @@ template<typename VectorsType, typename CoeffsType, int Side> class HouseholderS
     {
       workspace.resize(rows());
       Index vecs = m_length;
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
       if(    internal::is_same<typename internal::remove_all<VectorsType>::type,Dest>::value
-          && internal::extract_data(dst) == internal::extract_data(m_vectors))
+          && dst_data!=0 && dst_data == internal::extract_data(m_vectors))
       {
         // in-place
         dst.diagonal().setOnes();

Eigen/src/IterativeLinearSolvers/ConjugateGradient.h

@@ -139,6 +139,8 @@ struct traits<ConjugateGradient<_MatrixType,_UpLo,_Preconditioner> >
   * By default the iterations start with x=0 as an initial guess of the solution.
   * One can control the start using the solveWithGuess() method.
   * 
+  * ConjugateGradient can also be used in a matrix-free context, see the following \link MatrixfreeSolverExample example \endlink.
+  *
   * \sa class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
   */
 template< typename _MatrixType, int _UpLo, typename _Preconditioner>

Eigen/src/LU/FullPivLU.h

@@ -688,7 +688,7 @@ struct solve_retval<FullPivLU<_MatrixType>, Rhs>
      */
 
     const Index rows = dec().rows(), cols = dec().cols(),
-              nonzero_pivots = dec().nonzeroPivots();
+              nonzero_pivots = dec().rank();
     eigen_assert(rhs().rows() == rows);
     const Index smalldim = (std::min)(rows, cols);
 

Eigen/src/LU/Inverse.h

@@ -290,7 +290,7 @@ struct inverse_impl : public ReturnByValue<inverse_impl<MatrixType> >
   {
     const int Size = EIGEN_PLAIN_ENUM_MIN(MatrixType::ColsAtCompileTime,Dest::ColsAtCompileTime);
     EIGEN_ONLY_USED_FOR_DEBUG(Size);
-    eigen_assert(( (Size<=1) || (Size>4) || (extract_data(m_matrix)!=extract_data(dst)))
+    eigen_assert(( (Size<=1) || (Size>4) || (extract_data(m_matrix)!=0 && extract_data(m_matrix)!=extract_data(dst)))
               && "Aliasing problem detected in inverse(), you need to do inverse().eval() here.");
 
     compute_inverse<MatrixTypeNestedCleaned, Dest>::run(m_matrix, dst);

Eigen/src/LU/arch/Inverse_SSE.h

@@ -151,10 +151,12 @@ struct compute_inverse_size4<Architecture::SSE, float, MatrixType, ResultType>
     iC = _mm_mul_ps(rd,iC);
     iD = _mm_mul_ps(rd,iD);
 
-    result.template writePacket<ResultAlignment>( 0, _mm_shuffle_ps(iA,iB,0x77));
-    result.template writePacket<ResultAlignment>( 4, _mm_shuffle_ps(iA,iB,0x22));
-    result.template writePacket<ResultAlignment>( 8, _mm_shuffle_ps(iC,iD,0x77));
-    result.template writePacket<ResultAlignment>(12, _mm_shuffle_ps(iC,iD,0x22));
+    DenseIndex res_stride = result.outerStride();
+    float* res = result.data();
+    pstoret<float, Packet4f, ResultAlignment>(res+0,            _mm_shuffle_ps(iA,iB,0x77));
+    pstoret<float, Packet4f, ResultAlignment>(res+res_stride,   _mm_shuffle_ps(iA,iB,0x22));
+    pstoret<float, Packet4f, ResultAlignment>(res+2*res_stride, _mm_shuffle_ps(iC,iD,0x77));
+    pstoret<float, Packet4f, ResultAlignment>(res+3*res_stride, _mm_shuffle_ps(iC,iD,0x22));
   }
 
 };
@@ -311,14 +313,16 @@ struct compute_inverse_size4<Architecture::SSE, double, MatrixType, ResultType>
     iC1 = _mm_sub_pd(_mm_mul_pd(B1, dC), iC1);
     iC2 = _mm_sub_pd(_mm_mul_pd(B2, dC), iC2);
 
-    result.template writePacket<ResultAlignment>( 0, _mm_mul_pd(_mm_shuffle_pd(iA2, iA1, 3), d1));     // iA# / det
-    result.template writePacket<ResultAlignment>( 4, _mm_mul_pd(_mm_shuffle_pd(iA2, iA1, 0), d2));
-    result.template writePacket<ResultAlignment>( 2, _mm_mul_pd(_mm_shuffle_pd(iB2, iB1, 3), d1));     // iB# / det
-    result.template writePacket<ResultAlignment>( 6, _mm_mul_pd(_mm_shuffle_pd(iB2, iB1, 0), d2));
-    result.template writePacket<ResultAlignment>( 8, _mm_mul_pd(_mm_shuffle_pd(iC2, iC1, 3), d1));     // iC# / det
-    result.template writePacket<ResultAlignment>(12, _mm_mul_pd(_mm_shuffle_pd(iC2, iC1, 0), d2));
-    result.template writePacket<ResultAlignment>(10, _mm_mul_pd(_mm_shuffle_pd(iD2, iD1, 3), d1));     // iD# / det
-    result.template writePacket<ResultAlignment>(14, _mm_mul_pd(_mm_shuffle_pd(iD2, iD1, 0), d2));
+    DenseIndex res_stride = result.outerStride();
+    double* res = result.data();
+    pstoret<double, Packet2d, ResultAlignment>(res+0,             _mm_mul_pd(_mm_shuffle_pd(iA2, iA1, 3), d1));
+    pstoret<double, Packet2d, ResultAlignment>(res+res_stride,    _mm_mul_pd(_mm_shuffle_pd(iA2, iA1, 0), d2));
+    pstoret<double, Packet2d, ResultAlignment>(res+2,             _mm_mul_pd(_mm_shuffle_pd(iB2, iB1, 3), d1));
+    pstoret<double, Packet2d, ResultAlignment>(res+res_stride+2,  _mm_mul_pd(_mm_shuffle_pd(iB2, iB1, 0), d2));
+    pstoret<double, Packet2d, ResultAlignment>(res+2*res_stride,  _mm_mul_pd(_mm_shuffle_pd(iC2, iC1, 3), d1));
+    pstoret<double, Packet2d, ResultAlignment>(res+3*res_stride,  _mm_mul_pd(_mm_shuffle_pd(iC2, iC1, 0), d2));
+    pstoret<double, Packet2d, ResultAlignment>(res+2*res_stride+2,_mm_mul_pd(_mm_shuffle_pd(iD2, iD1, 3), d1));
+    pstoret<double, Packet2d, ResultAlignment>(res+3*res_stride+2,_mm_mul_pd(_mm_shuffle_pd(iD2, iD1, 0), d2));
   }
 };
 

Eigen/src/OrderingMethods/Amd.h

@@ -8,7 +8,7 @@
 NOTE: this routine has been adapted from the CSparse library:
 
 Copyright (c) 2006, Timothy A. Davis.
-http://www.cise.ufl.edu/research/sparse/CSparse
+http://www.suitesparse.com
 
 CSparse is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public

Eigen/src/OrderingMethods/Eigen_Colamd.h

@@ -41,12 +41,8 @@
 // 
 //   The colamd/symamd library is available at
 // 
-//       http://www.cise.ufl.edu/research/sparse/colamd/
+//       http://www.suitesparse.com
 
-//   This is the http://www.cise.ufl.edu/research/sparse/colamd/colamd.h
-//   file.  It is required by the colamd.c, colamdmex.c, and symamdmex.c
-//   files, and by any C code that calls the routines whose prototypes are
-//   listed below, or that uses the colamd/symamd definitions listed below.
   
 #ifndef EIGEN_COLAMD_H
 #define EIGEN_COLAMD_H
@@ -102,9 +98,6 @@ namespace internal {
 /* === Definitions ========================================================== */
 /* ========================================================================== */
 
-#define COLAMD_MAX(a,b) (((a) > (b)) ? (a) : (b))
-#define COLAMD_MIN(a,b) (((a) < (b)) ? (a) : (b))
-
 #define ONES_COMPLEMENT(r) (-(r)-1)
 
 /* -------------------------------------------------------------------------- */
@@ -516,7 +509,7 @@ static Index init_rows_cols  /* returns true if OK, or false otherwise */
     Col [col].start = p [col] ;
     Col [col].length = p [col+1] - p [col] ;
 
-    if (Col [col].length < 0)
+    if ((Col [col].length) < 0) // extra parentheses to work-around gcc bug 10200
     {
       /* column pointers must be non-decreasing */
       stats [COLAMD_STATUS] = COLAMD_ERROR_col_length_negative ;
@@ -739,8 +732,8 @@ static void init_scoring
 
   /* === Extract knobs ==================================================== */
 
-  dense_row_count = COLAMD_MAX (0, COLAMD_MIN (knobs [COLAMD_DENSE_ROW] * n_col, n_col)) ;
-  dense_col_count = COLAMD_MAX (0, COLAMD_MIN (knobs [COLAMD_DENSE_COL] * n_row, n_row)) ;
+  dense_row_count = std::max<Index>(0, (std::min)(Index(knobs [COLAMD_DENSE_ROW] * n_col), n_col)) ;
+  dense_col_count = std::max<Index>(0, (std::min)(Index(knobs [COLAMD_DENSE_COL] * n_row), n_row)) ;
   COLAMD_DEBUG1 (("colamd: densecount: %d %d\n", dense_row_count, dense_col_count)) ;
   max_deg = 0 ;
   n_col2 = n_col ;
@@ -804,7 +797,7 @@ static void init_scoring
     else
     {
       /* keep track of max degree of remaining rows */
-      max_deg = COLAMD_MAX (max_deg, deg) ;
+      max_deg = (std::max)(max_deg, deg) ;
     }
   }
   COLAMD_DEBUG1 (("colamd: Dense and null rows killed: %d\n", n_row - n_row2)) ;
@@ -842,7 +835,7 @@ static void init_scoring
       /* add row's external degree */
       score += Row [row].shared1.degree - 1 ;
       /* guard against integer overflow */
-      score = COLAMD_MIN (score, n_col) ;
+      score = (std::min)(score, n_col) ;
     }
     /* determine pruned column length */
     col_length = (Index) (new_cp - &A [Col [c].start]) ;
@@ -914,7 +907,7 @@ static void init_scoring
       head [score] = c ;
 
       /* see if this score is less than current min */
-      min_score = COLAMD_MIN (min_score, score) ;
+      min_score = (std::min)(min_score, score) ;
 
 
     }
@@ -1040,7 +1033,7 @@ static Index find_ordering /* return the number of garbage collections */
 
     /* === Garbage_collection, if necessary ============================= */
 
-    needed_memory = COLAMD_MIN (pivot_col_score, n_col - k) ;
+    needed_memory = (std::min)(pivot_col_score, n_col - k) ;
     if (pfree + needed_memory >= Alen)
     {
       pfree = Eigen::internal::garbage_collection (n_row, n_col, Row, Col, A, &A [pfree]) ;
@@ -1099,7 +1092,7 @@ static Index find_ordering /* return the number of garbage collections */
 
     /* clear tag on pivot column */
     Col [pivot_col].shared1.thickness = pivot_col_thickness ;
-    max_deg = COLAMD_MAX (max_deg, pivot_row_degree) ;
+    max_deg = (std::max)(max_deg, pivot_row_degree) ;
 
 
     /* === Kill all rows used to construct pivot row ==================== */
@@ -1273,7 +1266,7 @@ static Index find_ordering /* return the number of garbage collections */
 	/* add set difference */
 	cur_score += row_mark - tag_mark ;
 	/* integer overflow... */
-	cur_score = COLAMD_MIN (cur_score, n_col) ;
+	cur_score = (std::min)(cur_score, n_col) ;
       }
 
       /* recompute the column's length */
@@ -1386,7 +1379,7 @@ static Index find_ordering /* return the number of garbage collections */
       cur_score -= Col [col].shared1.thickness ;
 
       /* make sure score is less or equal than the max score */
-      cur_score = COLAMD_MIN (cur_score, max_score) ;
+      cur_score = (std::min)(cur_score, max_score) ;
       COLAMD_ASSERT (cur_score >= 0) ;
 
       /* store updated score */
@@ -1409,7 +1402,7 @@ static Index find_ordering /* return the number of garbage collections */
       head [cur_score] = col ;
 
       /* see if this score is less than current min */
-      min_score = COLAMD_MIN (min_score, cur_score) ;
+      min_score = (std::min)(min_score, cur_score) ;
 
     }
 

Eigen/src/PaStiXSupport/PaStiXSupport.h

@@ -10,6 +10,14 @@
 #ifndef EIGEN_PASTIXSUPPORT_H
 #define EIGEN_PASTIXSUPPORT_H
 
+#if defined(DCOMPLEX)
+  #define PASTIX_COMPLEX  COMPLEX
+  #define PASTIX_DCOMPLEX DCOMPLEX
+#else
+  #define PASTIX_COMPLEX  std::complex<float>
+  #define PASTIX_DCOMPLEX std::complex<double>
+#endif
+
 namespace Eigen { 
 
 /** \ingroup PaStiXSupport_Module
@@ -74,14 +82,14 @@ namespace internal
   {
     if (n == 0) { ptr = NULL; idx = NULL; vals = NULL; }
     if (nbrhs == 0) {x = NULL; nbrhs=1;}
-    c_pastix(pastix_data, pastix_comm, n, ptr, idx, reinterpret_cast<COMPLEX*>(vals), perm, invp, reinterpret_cast<COMPLEX*>(x), nbrhs, iparm, dparm); 
+    c_pastix(pastix_data, pastix_comm, n, ptr, idx, reinterpret_cast<PASTIX_COMPLEX*>(vals), perm, invp, reinterpret_cast<PASTIX_COMPLEX*>(x), nbrhs, iparm, dparm);
   }
   
   void eigen_pastix(pastix_data_t **pastix_data, int pastix_comm, int n, int *ptr, int *idx, std::complex<double> *vals, int *perm, int * invp, std::complex<double> *x, int nbrhs, int *iparm, double *dparm)
   {
     if (n == 0) { ptr = NULL; idx = NULL; vals = NULL; }
     if (nbrhs == 0) {x = NULL; nbrhs=1;}
-    z_pastix(pastix_data, pastix_comm, n, ptr, idx, reinterpret_cast<DCOMPLEX*>(vals), perm, invp, reinterpret_cast<DCOMPLEX*>(x), nbrhs, iparm, dparm); 
+    z_pastix(pastix_data, pastix_comm, n, ptr, idx, reinterpret_cast<PASTIX_DCOMPLEX*>(vals), perm, invp, reinterpret_cast<PASTIX_DCOMPLEX*>(x), nbrhs, iparm, dparm);
   }
 
   // Convert the matrix  to Fortran-style Numbering

Eigen/src/PardisoSupport/PardisoSupport.h

@@ -221,11 +221,11 @@ class PardisoImpl
       m_type = type;
       bool symmetric = std::abs(m_type) < 10;
       m_iparm[0] = 1;   // No solver default
-      m_iparm[1] = 3;   // use Metis for the ordering
-      m_iparm[2] = 1;   // Numbers of processors, value of OMP_NUM_THREADS
+      m_iparm[1] = 2;   // use Metis for the ordering
+      m_iparm[2] = 0;   // Reserved. Set to zero. (??Numbers of processors, value of OMP_NUM_THREADS??)
       m_iparm[3] = 0;   // No iterative-direct algorithm
       m_iparm[4] = 0;   // No user fill-in reducing permutation
-      m_iparm[5] = 0;   // Write solution into x
+      m_iparm[5] = 0;   // Write solution into x, b is left unchanged
       m_iparm[6] = 0;   // Not in use
       m_iparm[7] = 2;   // Max numbers of iterative refinement steps
       m_iparm[8] = 0;   // Not in use
@@ -246,7 +246,10 @@ class PardisoImpl
       m_iparm[26] = 0;  // No matrix checker
       m_iparm[27] = (sizeof(RealScalar) == 4) ? 1 : 0;
       m_iparm[34] = 1;  // C indexing
-      m_iparm[59] = 1;  // Automatic switch between In-Core and Out-of-Core modes
+      m_iparm[36] = 0;  // CSR
+      m_iparm[59] = 0;  // 0 - In-Core ; 1 - Automatic switch between In-Core and Out-of-Core modes ; 2 - Out-of-Core
+      
+      memset(m_pt, 0, sizeof(m_pt));
     }
 
   protected:
@@ -384,7 +387,6 @@ bool PardisoImpl<Base>::_solve(const MatrixBase<BDerived> &b, MatrixBase<XDerive
                                                      m_matrix.valuePtr(), m_matrix.outerIndexPtr(), m_matrix.innerIndexPtr(),
                                                      m_perm.data(), nrhs, m_iparm.data(), m_msglvl,
                                                      rhs_ptr, x.derived().data());
-
   return error==0;
 }
 
@@ -397,6 +399,9 @@ bool PardisoImpl<Base>::_solve(const MatrixBase<BDerived> &b, MatrixBase<XDerive
   * using the Intel MKL PARDISO library. The sparse matrix A must be squared and invertible.
   * The vectors or matrices X and B can be either dense or sparse.
   *
+  * By default, it runs in in-core mode. To enable PARDISO's out-of-core feature, set:
+  * \code solver.pardisoParameterArray()[59] = 1; \endcode
+  *
   * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
   *
   * \sa \ref TutorialSparseDirectSolvers
@@ -447,6 +452,9 @@ class PardisoLU : public PardisoImpl< PardisoLU<MatrixType> >
   * using the Intel MKL PARDISO library. The sparse matrix A must be selfajoint and positive definite.
   * The vectors or matrices X and B can be either dense or sparse.
   *
+  * By default, it runs in in-core mode. To enable PARDISO's out-of-core feature, set:
+  * \code solver.pardisoParameterArray()[59] = 1; \endcode
+  *
   * \tparam MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
   * \tparam UpLo can be any bitwise combination of Upper, Lower. The default is Upper, meaning only the upper triangular part has to be used.
   *         Upper|Lower can be used to tell both triangular parts can be used as input.
@@ -507,6 +515,9 @@ class PardisoLLT : public PardisoImpl< PardisoLLT<MatrixType,_UpLo> >
   * For complex matrices, A can also be symmetric only, see the \a Options template parameter.
   * The vectors or matrices X and B can be either dense or sparse.
   *
+  * By default, it runs in in-core mode. To enable PARDISO's out-of-core feature, set:
+  * \code solver.pardisoParameterArray()[59] = 1; \endcode
+  *
   * \tparam MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
   * \tparam Options can be any bitwise combination of Upper, Lower, and Symmetric. The default is Upper, meaning only the upper triangular part has to be used.
   *         Symmetric can be used for symmetric, non-selfadjoint complex matrices, the default being to assume a selfadjoint matrix.

Eigen/src/QR/ColPivHouseholderQR.h

@@ -127,9 +127,6 @@ template<typename _MatrixType> class ColPivHouseholderQR
       *
       * \returns a solution.
       *
-      * \note The case where b is a matrix is not yet implemented. Also, this
-      *       code is space inefficient.
-      *
       * \note_about_checking_solutions
       *
       * \note_about_arbitrary_choice_of_solution

Eigen/src/QR/ColPivHouseholderQR_MKL.h

@@ -49,7 +49,6 @@ ColPivHouseholderQR<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynami
 { \
   using std::abs; \
   typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic> MatrixType; \
-  typedef MatrixType::Scalar Scalar; \
   typedef MatrixType::RealScalar RealScalar; \
   Index rows = matrix.rows();\
   Index cols = matrix.cols();\

Eigen/src/QR/FullPivHouseholderQR.h

@@ -134,9 +134,6 @@ template<typename _MatrixType> class FullPivHouseholderQR
       * \returns the exact or least-square solution if the rank is greater or equal to the number of columns of A,
       * and an arbitrary solution otherwise.
       *
-      * \note The case where b is a matrix is not yet implemented. Also, this
-      *       code is space inefficient.
-      *
       * \note_about_checking_solutions
       *
       * \note_about_arbitrary_choice_of_solution

Eigen/src/QR/HouseholderQR.h

@@ -107,9 +107,6 @@ template<typename _MatrixType> class HouseholderQR
       *
       * \returns a solution.
       *
-      * \note The case where b is a matrix is not yet implemented. Also, this
-      *       code is space inefficient.
-      *
       * \note_about_checking_solutions
       *
       * \note_about_arbitrary_choice_of_solution

Eigen/src/SPQRSupport/SuiteSparseQRSupport.h

@@ -110,16 +110,16 @@ class SPQR
           max2Norm = RealScalar(1);
         pivotThreshold = 20 * (mat.rows() + mat.cols()) * max2Norm * NumTraits<RealScalar>::epsilon();
       }
-      
       cholmod_sparse A; 
       A = viewAsCholmod(mat);
+      m_rows = matrix.rows();
       Index col = matrix.cols();
       m_rank = SuiteSparseQR<Scalar>(m_ordering, pivotThreshold, col, &A, 
                              &m_cR, &m_E, &m_H, &m_HPinv, &m_HTau, &m_cc);
 
       if (!m_cR)
       {
-        m_info = NumericalIssue; 
+        m_info = NumericalIssue;
         m_isInitialized = false;
         return;
       }
@@ -130,7 +130,7 @@ class SPQR
     /** 
      * Get the number of rows of the input matrix and the Q matrix
      */
-    inline Index rows() const {return m_cR->nrow; }
+    inline Index rows() const {return m_rows; }
     
     /** 
      * Get the number of columns of the input matrix. 
@@ -254,6 +254,7 @@ class SPQR
     mutable Index m_rank; // The rank of the matrix
     mutable cholmod_common m_cc; // Workspace and parameters
     bool m_useDefaultThreshold;     // Use default threshold
+    Index m_rows;
     template<typename ,typename > friend struct SPQR_QProduct;
 };
 

Eigen/src/SVD/JacobiSVD.h

@@ -359,29 +359,42 @@ struct svd_precondition_2x2_block_to_be_real<MatrixType, QRPreconditioner, false
 {
   typedef JacobiSVD<MatrixType, QRPreconditioner> SVD;
   typedef typename SVD::Index Index;
-  static void run(typename SVD::WorkMatrixType&, SVD&, Index, Index) {}
+  typedef typename MatrixType::RealScalar RealScalar;
+  static bool run(typename SVD::WorkMatrixType&, SVD&, Index, Index, RealScalar&) { return true; }
 };
 
 template<typename MatrixType, int QRPreconditioner>
 struct svd_precondition_2x2_block_to_be_real<MatrixType, QRPreconditioner, true>
 {
   typedef JacobiSVD<MatrixType, QRPreconditioner> SVD;
+  typedef typename SVD::Index Index;
   typedef typename MatrixType::Scalar Scalar;
   typedef typename MatrixType::RealScalar RealScalar;
-  typedef typename SVD::Index Index;
-  static void run(typename SVD::WorkMatrixType& work_matrix, SVD& svd, Index p, Index q)
+  static bool run(typename SVD::WorkMatrixType& work_matrix, SVD& svd, Index p, Index q, RealScalar& maxDiagEntry)
   {
     using std::sqrt;
+    using std::abs;
+    using std::max;
     Scalar z;
     JacobiRotation<Scalar> rot;
     RealScalar n = sqrt(numext::abs2(work_matrix.coeff(p,p)) + numext::abs2(work_matrix.coeff(q,p)));
-    
+
+    const RealScalar considerAsZero = (std::numeric_limits<RealScalar>::min)();
+    const RealScalar precision = NumTraits<Scalar>::epsilon();
+
     if(n==0)
     {
-      z = abs(work_matrix.coeff(p,q)) / work_matrix.coeff(p,q);
-      work_matrix.row(p) *= z;
-      if(svd.computeU()) svd.m_matrixU.col(p) *= conj(z);
-      if(work_matrix.coeff(q,q)!=Scalar(0))
+      // make sure first column is zero
+      work_matrix.coeffRef(p,p) = work_matrix.coeffRef(q,p) = Scalar(0);
+
+      if(abs(numext::imag(work_matrix.coeff(p,q)))>considerAsZero)
+      {
+        // work_matrix.coeff(p,q) can be zero if work_matrix.coeff(q,p) is not zero but small enough to underflow when computing n
+        z = abs(work_matrix.coeff(p,q)) / work_matrix.coeff(p,q);
+        work_matrix.row(p) *= z;
+        if(svd.computeU()) svd.m_matrixU.col(p) *= conj(z);
+      }
+      if(abs(numext::imag(work_matrix.coeff(q,q)))>considerAsZero)
       {
         z = abs(work_matrix.coeff(q,q)) / work_matrix.coeff(q,q);
         work_matrix.row(q) *= z;
@@ -395,19 +408,25 @@ struct svd_precondition_2x2_block_to_be_real<MatrixType, QRPreconditioner, true>
       rot.s() = work_matrix.coeff(q,p) / n;
       work_matrix.applyOnTheLeft(p,q,rot);
       if(svd.computeU()) svd.m_matrixU.applyOnTheRight(p,q,rot.adjoint());
-      if(work_matrix.coeff(p,q) != Scalar(0))
+      if(abs(numext::imag(work_matrix.coeff(p,q)))>considerAsZero)
       {
-        Scalar z = abs(work_matrix.coeff(p,q)) / work_matrix.coeff(p,q);
+        z = abs(work_matrix.coeff(p,q)) / work_matrix.coeff(p,q);
         work_matrix.col(q) *= z;
         if(svd.computeV()) svd.m_matrixV.col(q) *= z;
       }
-      if(work_matrix.coeff(q,q) != Scalar(0))
+      if(abs(numext::imag(work_matrix.coeff(q,q)))>considerAsZero)
       {
         z = abs(work_matrix.coeff(q,q)) / work_matrix.coeff(q,q);
         work_matrix.row(q) *= z;
         if(svd.computeU()) svd.m_matrixU.col(q) *= conj(z);
       }
     }
+
+    // update largest diagonal entry
+    maxDiagEntry = max EIGEN_EMPTY (maxDiagEntry,max EIGEN_EMPTY (abs(work_matrix.coeff(p,p)), abs(work_matrix.coeff(q,q))));
+    // and check whether the 2x2 block is already diagonal
+    RealScalar threshold = max EIGEN_EMPTY (considerAsZero, precision * maxDiagEntry);
+    return abs(work_matrix.coeff(p,q))>threshold || abs(work_matrix.coeff(q,p)) > threshold;
   }
 };
 
@@ -424,22 +443,23 @@ void real_2x2_jacobi_svd(const MatrixType& matrix, Index p, Index q,
   JacobiRotation<RealScalar> rot1;
   RealScalar t = m.coeff(0,0) + m.coeff(1,1);
   RealScalar d = m.coeff(1,0) - m.coeff(0,1);
-  if(t == RealScalar(0))
+  if(d == RealScalar(0))
   {
-    rot1.c() = RealScalar(0);
-    rot1.s() = d > RealScalar(0) ? RealScalar(1) : RealScalar(-1);
+    rot1.s() = RealScalar(0);
+    rot1.c() = RealScalar(1);
   }
   else
   {
-    RealScalar t2d2 = numext::hypot(t,d);
-    rot1.c() = abs(t)/t2d2;
-    rot1.s() = d/t2d2;
-    if(t<RealScalar(0))
-      rot1.s() = -rot1.s();
+    // If d!=0, then t/d cannot overflow because the magnitude of the
+    // entries forming d are not too small compared to the ones forming t.
+    RealScalar u = t / d;
+    RealScalar tmp = sqrt(RealScalar(1) + numext::abs2(u));
+    rot1.s() = RealScalar(1) / tmp;
+    rot1.c() = u / tmp;
   }
   m.applyOnTheLeft(0,1,rot1);
   j_right->makeJacobi(m,0,1);
-  *j_left  = rot1 * j_right->transpose();
+  *j_left = rot1 * j_right->transpose();
 }
 
 } // end namespace internal
@@ -816,7 +836,7 @@ void JacobiSVD<MatrixType, QRPreconditioner>::allocate(Index rows, Index cols, u
   
   if(m_cols>m_rows)   m_qr_precond_morecols.allocate(*this);
   if(m_rows>m_cols)   m_qr_precond_morerows.allocate(*this);
-  if(m_cols!=m_cols)  m_scaledMatrix.resize(rows,cols);
+  if(m_rows!=m_cols)  m_scaledMatrix.resize(rows,cols);
 }
 
 template<typename MatrixType, int QRPreconditioner>
@@ -826,6 +846,7 @@ JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType& matrix, unsig
   check_template_parameters();
   
   using std::abs;
+  using std::max;
   allocate(matrix.rows(), matrix.cols(), computationOptions);
 
   // currently we stop when we reach precision 2*epsilon as the last bit of precision can require an unreasonable number of iterations,
@@ -857,6 +878,7 @@ JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType& matrix, unsig
   }
 
   /*** step 2. The main Jacobi SVD iteration. ***/
+  RealScalar maxDiagEntry = m_workMatrix.cwiseAbs().diagonal().maxCoeff();
 
   bool finished = false;
   while(!finished)
@@ -872,25 +894,27 @@ JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType& matrix, unsig
         // if this 2x2 sub-matrix is not diagonal already...
         // notice that this comparison will evaluate to false if any NaN is involved, ensuring that NaN's don't
         // keep us iterating forever. Similarly, small denormal numbers are considered zero.
-        using std::max;
-        RealScalar threshold = (max)(considerAsZero, precision * (max)(abs(m_workMatrix.coeff(p,p)),
-                                                                       abs(m_workMatrix.coeff(q,q))));
-        // We compare both values to threshold instead of calling max to be robust to NaN (See bug 791)
+        RealScalar threshold = max EIGEN_EMPTY (considerAsZero, precision * maxDiagEntry);
         if(abs(m_workMatrix.coeff(p,q))>threshold || abs(m_workMatrix.coeff(q,p)) > threshold)
         {
           finished = false;
-
           // perform SVD decomposition of 2x2 sub-matrix corresponding to indices p,q to make it diagonal
-          internal::svd_precondition_2x2_block_to_be_real<MatrixType, QRPreconditioner>::run(m_workMatrix, *this, p, q);
-          JacobiRotation<RealScalar> j_left, j_right;
-          internal::real_2x2_jacobi_svd(m_workMatrix, p, q, &j_left, &j_right);
+          // the complex to real operation returns true is the updated 2x2 block is not already diagonal
+          if(internal::svd_precondition_2x2_block_to_be_real<MatrixType, QRPreconditioner>::run(m_workMatrix, *this, p, q, maxDiagEntry))
+          {
+            JacobiRotation<RealScalar> j_left, j_right;
+            internal::real_2x2_jacobi_svd(m_workMatrix, p, q, &j_left, &j_right);
 
-          // accumulate resulting Jacobi rotations
-          m_workMatrix.applyOnTheLeft(p,q,j_left);
-          if(computeU()) m_matrixU.applyOnTheRight(p,q,j_left.transpose());
+            // accumulate resulting Jacobi rotations
+            m_workMatrix.applyOnTheLeft(p,q,j_left);
+            if(computeU()) m_matrixU.applyOnTheRight(p,q,j_left.transpose());
 
-          m_workMatrix.applyOnTheRight(p,q,j_right);
-          if(computeV()) m_matrixV.applyOnTheRight(p,q,j_right);
+            m_workMatrix.applyOnTheRight(p,q,j_right);
+            if(computeV()) m_matrixV.applyOnTheRight(p,q,j_right);
+
+            // keep track of the largest diagonal coefficient
+            maxDiagEntry = max EIGEN_EMPTY (maxDiagEntry,max EIGEN_EMPTY (abs(m_workMatrix.coeff(p,p)), abs(m_workMatrix.coeff(q,q))));
+          }
         }
       }
     }

Eigen/src/SVD/JacobiSVD_MKL.h

@@ -45,8 +45,8 @@ JacobiSVD<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic>, ColPiv
 JacobiSVD<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic>, ColPivHouseholderQRPreconditioner>::compute(const Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic>& matrix, unsigned int computationOptions) \
 { \
   typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic> MatrixType; \
-  typedef MatrixType::Scalar Scalar; \
-  typedef MatrixType::RealScalar RealScalar; \
+  /*typedef MatrixType::Scalar Scalar;*/ \
+  /*typedef MatrixType::RealScalar RealScalar;*/ \
   allocate(matrix.rows(), matrix.cols(), computationOptions); \
 \
   /*const RealScalar precision = RealScalar(2) * NumTraits<Scalar>::epsilon();*/ \

Eigen/src/SparseCore/CompressedStorage.h

@@ -102,6 +102,11 @@ class CompressedStorage
     inline size_t allocatedSize() const { return m_allocatedSize; }
     inline void clear() { m_size = 0; }
 
+    const Scalar* valuePtr() const { return m_values; }
+    Scalar* valuePtr() { return m_values; }
+    const Index* indexPtr() const { return m_indices; }
+    Index* indexPtr() { return m_indices; }
+
     inline Scalar& value(size_t i) { return m_values[i]; }
     inline const Scalar& value(size_t i) const { return m_values[i]; }
 
@@ -208,8 +213,10 @@ class CompressedStorage
       Index* newIndices = new Index[size];
       size_t copySize = (std::min)(size, m_size);
       // copy
-      internal::smart_copy(m_values, m_values+copySize, newValues);
-      internal::smart_copy(m_indices, m_indices+copySize, newIndices);
+      if (copySize>0) {
+        internal::smart_copy(m_values, m_values+copySize, newValues);
+        internal::smart_copy(m_indices, m_indices+copySize, newIndices);
+      }
       // delete old stuff
       delete[] m_values;
       delete[] m_indices;

Eigen/src/SparseCore/SparseCwiseBinaryOp.h

@@ -55,10 +55,9 @@ class CwiseBinaryOpImpl<BinaryOp, Lhs, Rhs, Sparse>
     EIGEN_SPARSE_PUBLIC_INTERFACE(Derived)
     CwiseBinaryOpImpl()
     {
-      typedef typename internal::traits<Lhs>::StorageKind LhsStorageKind;
-      typedef typename internal::traits<Rhs>::StorageKind RhsStorageKind;
       EIGEN_STATIC_ASSERT((
-                (!internal::is_same<LhsStorageKind,RhsStorageKind>::value)
+                (!internal::is_same<typename internal::traits<Lhs>::StorageKind,
+                                    typename internal::traits<Rhs>::StorageKind>::value)
             ||  ((Lhs::Flags&RowMajorBit) == (Rhs::Flags&RowMajorBit))),
             THE_STORAGE_ORDER_OF_BOTH_SIDES_MUST_MATCH);
     }

Eigen/src/SparseCore/SparseMatrix.h

@@ -128,20 +128,20 @@ class SparseMatrix
     /** \returns a const pointer to the array of values.
       * This function is aimed at interoperability with other libraries.
       * \sa innerIndexPtr(), outerIndexPtr() */
-    inline const Scalar* valuePtr() const { return &m_data.value(0); }
+    inline const Scalar* valuePtr() const { return m_data.valuePtr(); }
     /** \returns a non-const pointer to the array of values.
       * This function is aimed at interoperability with other libraries.
       * \sa innerIndexPtr(), outerIndexPtr() */
-    inline Scalar* valuePtr() { return &m_data.value(0); }
+    inline Scalar* valuePtr() { return m_data.valuePtr(); }
 
     /** \returns a const pointer to the array of inner indices.
       * This function is aimed at interoperability with other libraries.
       * \sa valuePtr(), outerIndexPtr() */
-    inline const Index* innerIndexPtr() const { return &m_data.index(0); }
+    inline const Index* innerIndexPtr() const { return m_data.indexPtr(); }
     /** \returns a non-const pointer to the array of inner indices.
       * This function is aimed at interoperability with other libraries.
       * \sa valuePtr(), outerIndexPtr() */
-    inline Index* innerIndexPtr() { return &m_data.index(0); }
+    inline Index* innerIndexPtr() { return m_data.indexPtr(); }
 
     /** \returns a const pointer to the array of the starting positions of the inner vectors.
       * This function is aimed at interoperability with other libraries.
@@ -697,8 +697,8 @@ class SparseMatrix
     {
       eigen_assert(rows() == cols() && "ONLY FOR SQUARED MATRICES");
       this->m_data.resize(rows());
-      Eigen::Map<Matrix<Index, Dynamic, 1> >(&this->m_data.index(0), rows()).setLinSpaced(0, rows()-1);
-      Eigen::Map<Matrix<Scalar, Dynamic, 1> >(&this->m_data.value(0), rows()).setOnes();
+      Eigen::Map<Matrix<Index, Dynamic, 1> >(this->m_data.indexPtr(), rows()).setLinSpaced(0, rows()-1);
+      Eigen::Map<Matrix<Scalar, Dynamic, 1> >(this->m_data.valuePtr(), rows()).setOnes();
       Eigen::Map<Matrix<Index, Dynamic, 1> >(this->m_outerIndex, rows()+1).setLinSpaced(0, rows());
       std::free(m_innerNonZeros);
       m_innerNonZeros = 0;

Eigen/src/SparseCore/SparseMatrixBase.h

@@ -38,6 +38,7 @@ template<typename Derived> class SparseMatrixBase
     typedef typename internal::packet_traits<Scalar>::type PacketScalar;
     typedef typename internal::traits<Derived>::StorageKind StorageKind;
     typedef typename internal::traits<Derived>::Index Index;
+    typedef typename internal::traits<Derived>::Index StorageIndex;
     typedef typename internal::add_const_on_value_type_if_arithmetic<
                          typename internal::packet_traits<Scalar>::type
                      >::type PacketReturnType;

Eigen/src/SparseCore/SparseRedux.h

@@ -29,7 +29,10 @@ typename internal::traits<SparseMatrix<_Scalar,_Options,_Index> >::Scalar
 SparseMatrix<_Scalar,_Options,_Index>::sum() const
 {
   eigen_assert(rows()>0 && cols()>0 && "you are using a non initialized matrix");
-  return Matrix<Scalar,1,Dynamic>::Map(&m_data.value(0), m_data.size()).sum();
+  if(this->isCompressed())
+    return Matrix<Scalar,1,Dynamic>::Map(m_data.valuePtr(), m_data.size()).sum();
+  else
+    return Base::sum();
 }
 
 template<typename _Scalar, int _Options, typename _Index>
@@ -37,7 +40,7 @@ typename internal::traits<SparseVector<_Scalar,_Options, _Index> >::Scalar
 SparseVector<_Scalar,_Options,_Index>::sum() const
 {
   eigen_assert(rows()>0 && cols()>0 && "you are using a non initialized matrix");
-  return Matrix<Scalar,1,Dynamic>::Map(&m_data.value(0), m_data.size()).sum();
+  return Matrix<Scalar,1,Dynamic>::Map(m_data.valuePtr(), m_data.size()).sum();
 }
 
 } // end namespace Eigen

Eigen/src/SparseCore/SparseSparseProductWithPruning.h

@@ -48,7 +48,7 @@ static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& r
     res.resize(rows, cols);
 
   res.reserve(estimated_nnz_prod);
-  double ratioColRes = double(estimated_nnz_prod)/double(lhs.rows()*rhs.cols());
+  double ratioColRes = double(estimated_nnz_prod)/(double(lhs.rows())*double(rhs.cols()));
   for (Index j=0; j<cols; ++j)
   {
     // FIXME:

Eigen/src/SparseCore/SparseVector.h

@@ -84,12 +84,12 @@ class SparseVector
     EIGEN_STRONG_INLINE Index innerSize() const { return m_size; }
     EIGEN_STRONG_INLINE Index outerSize() const { return 1; }
 
-    EIGEN_STRONG_INLINE const Scalar* valuePtr() const { return &m_data.value(0); }
-    EIGEN_STRONG_INLINE Scalar* valuePtr() { return &m_data.value(0); }
+    EIGEN_STRONG_INLINE const Scalar* valuePtr() const { return m_data.valuePtr(); }
+    EIGEN_STRONG_INLINE Scalar* valuePtr() { return m_data.valuePtr(); }
+
+    EIGEN_STRONG_INLINE const Index* innerIndexPtr() const { return m_data.indexPtr(); }
+    EIGEN_STRONG_INLINE Index* innerIndexPtr() { return m_data.indexPtr(); }
 
-    EIGEN_STRONG_INLINE const Index* innerIndexPtr() const { return &m_data.index(0); }
-    EIGEN_STRONG_INLINE Index* innerIndexPtr() { return &m_data.index(0); }
-    
     /** \internal */
     inline Storage& data() { return m_data; }
     /** \internal */

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> >
 {
@@ -35,9 +49,9 @@ class SparseView : public SparseMatrixBase<SparseView<MatrixType> >
 public:
   EIGEN_SPARSE_PUBLIC_INTERFACE(SparseView)
 
-  SparseView(const MatrixType& mat, const Scalar& m_reference = Scalar(0),
-             typename NumTraits<Scalar>::Real m_epsilon = NumTraits<Scalar>::dummy_precision()) : 
-    m_matrix(mat), m_reference(m_reference), m_epsilon(m_epsilon) {}
+  explicit SparseView(const MatrixType& mat, const Scalar& reference = Scalar(0),
+                      const RealScalar &epsilon = NumTraits<Scalar>::dummy_precision())
+    : m_matrix(mat), m_reference(reference), m_epsilon(epsilon) {}
 
   class InnerIterator;
 
@@ -87,6 +101,25 @@ private:
   }
 };
 
+
+
+/** \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& m_reference,
                                                           const typename NumTraits<Scalar>::Real& m_epsilon) const

Eigen/src/StlSupport/StdDeque.h

@@ -13,32 +13,24 @@
 
 #include "details.h"
 
-// Define the explicit instantiation (e.g. necessary for the Intel compiler)
-#if defined(__INTEL_COMPILER) || defined(__GNUC__)
-  #define EIGEN_EXPLICIT_STL_DEQUE_INSTANTIATION(...) template class std::deque<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> >;
-#else
-  #define EIGEN_EXPLICIT_STL_DEQUE_INSTANTIATION(...)
-#endif
-
 /**
  * This section contains a convenience MACRO which allows an easy specialization of
  * std::deque such that for data types with alignment issues the correct allocator
  * is used automatically.
  */
 #define EIGEN_DEFINE_STL_DEQUE_SPECIALIZATION(...) \
-EIGEN_EXPLICIT_STL_DEQUE_INSTANTIATION(__VA_ARGS__) \
 namespace std \
 { \
-  template<typename _Ay> \
-  class deque<__VA_ARGS__, _Ay>  \
+  template<> \
+  class deque<__VA_ARGS__, std::allocator<__VA_ARGS__> >           \
     : public deque<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> > \
   { \
     typedef deque<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> > deque_base; \
   public: \
     typedef __VA_ARGS__ value_type; \
-    typedef typename deque_base::allocator_type allocator_type; \
-    typedef typename deque_base::size_type size_type;  \
-    typedef typename deque_base::iterator iterator;  \
+    typedef deque_base::allocator_type allocator_type; \
+    typedef deque_base::size_type size_type;  \
+    typedef deque_base::iterator iterator;  \
     explicit deque(const allocator_type& a = allocator_type()) : deque_base(a) {}  \
     template<typename InputIterator> \
     deque(InputIterator first, InputIterator last, const allocator_type& a = allocator_type()) : deque_base(first, last, a) {} \

Eigen/src/StlSupport/StdList.h

@@ -12,32 +12,24 @@
 
 #include "details.h"
 
-// Define the explicit instantiation (e.g. necessary for the Intel compiler)
-#if defined(__INTEL_COMPILER) || defined(__GNUC__)
-  #define EIGEN_EXPLICIT_STL_LIST_INSTANTIATION(...) template class std::list<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> >;
-#else
-  #define EIGEN_EXPLICIT_STL_LIST_INSTANTIATION(...)
-#endif
-
 /**
  * This section contains a convenience MACRO which allows an easy specialization of
  * std::list such that for data types with alignment issues the correct allocator
  * is used automatically.
  */
 #define EIGEN_DEFINE_STL_LIST_SPECIALIZATION(...) \
-EIGEN_EXPLICIT_STL_LIST_INSTANTIATION(__VA_ARGS__) \
 namespace std \
 { \
-  template<typename _Ay> \
-  class list<__VA_ARGS__, _Ay>  \
+  template<> \
+  class list<__VA_ARGS__, std::allocator<__VA_ARGS__> >           \
     : public list<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> > \
   { \
     typedef list<__VA_ARGS__, EIGEN_ALIGNED_ALLOCATOR<__VA_ARGS__> > list_base; \
   public: \
     typedef __VA_ARGS__ value_type; \
-    typedef typename list_base::allocator_type allocator_type; \
-    typedef typename list_base::size_type size_type;  \
-    typedef typename list_base::iterator iterator;  \
+    typedef list_base::allocator_type allocator_type; \
+    typedef list_base::size_type size_type;  \
+    typedef list_base::iterator iterator;  \
     explicit list(const allocator_type& a = allocator_type()) : list_base(a) {}  \
     template<typename InputIterator> \
     list(InputIterator first, InputIterator last, const allocator_type& a = allocator_type()) : list_base(first, last, a) {} \

Eigen/src/UmfPackSupport/UmfPackSupport.h

@@ -148,7 +148,8 @@ class UmfPackLU : internal::noncopyable
 
     UmfPackLU() { init(); }
 
-    UmfPackLU(const MatrixType& matrix)
+    template<typename InputMatrixType>
+    UmfPackLU(const InputMatrixType& matrix)
     {
       init();
       compute(matrix);

bench/btl/generic_bench/btl.hh

@@ -44,15 +44,10 @@
 #define BTL_ASM_COMMENT(X)
 #endif
 
-#if (defined __GNUC__) && (!defined __INTEL_COMPILER) && !defined(__arm__) && !defined(__powerpc__)
-#define BTL_DISABLE_SSE_EXCEPTIONS()  { \
-  int aux; \
-  asm( \
-  "stmxcsr   %[aux]           \n\t" \
-  "orl       $32832, %[aux]   \n\t" \
-  "ldmxcsr   %[aux]           \n\t" \
-  : : [aux] "m" (aux)); \
-}
+#ifdef __SSE__
+#include "xmmintrin.h"
+// This enables flush to zero (FTZ) and denormals are zero (DAZ) modes:
+#define BTL_DISABLE_SSE_EXCEPTIONS()  { _mm_setcsr(_mm_getcsr() | 0x8040); }
 #else
 #define BTL_DISABLE_SSE_EXCEPTIONS()
 #endif

ci/build.linux.gitlab-ci.yml

@@ -0,0 +1,30 @@
+# Base configuration for linux cross-compilation.
+.build:linux:cross:
+  extends: .common:linux:cross
+  stage: build
+  variables:
+    EIGEN_CI_BUILD_TARGET: buildtests
+  script:
+    - . ci/scripts/build.linux.script.sh
+  tags:
+    - saas-linux-2xlarge-amd64
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule" && $CI_PROJECT_NAMESPACE == "libeigen"
+    - if: $CI_PIPELINE_SOURCE == "web" && $CI_PROJECT_NAMESPACE == "libeigen"
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event" && $CI_PROJECT_NAMESPACE == "libeigen" && $CI_MERGE_REQUEST_LABELS =~ "/all-tests/"
+  cache:
+    key: "$CI_JOB_NAME_SLUG-$CI_COMMIT_REF_SLUG-BUILD"
+    paths:
+      - ${EIGEN_CI_BUILDDIR}/
+
+build:linux:docs:
+  extends: .build:linux:cross
+  variables:
+    EIGEN_CI_TARGET_ARCH: any
+    EIGEN_CI_BUILD_TARGET: doc
+    EIGEN_CI_INSTALL: ca-certificates clang flex python3 bison graphviz
+    EIGEN_CI_C_COMPILER: clang
+    EIGEN_CI_CXX_COMPILER: clang++
+    EIGEN_CI_BEFORE_SCRIPT: ". ci/scripts/build_and_install_doxygen.sh Release_1_13_2"
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push" && $CI_PROJECT_NAMESPACE == "libeigen"

ci/common.gitlab-ci.yml

@@ -0,0 +1,24 @@
+# Base configuration for linux builds and tests.
+.common:linux:cross:
+  image: ubuntu:20.04
+  variables:
+    EIGEN_CI_TARGET_ARCH: ""
+    EIGEN_CI_ADDITIONAL_ARGS: ""
+    # If host matches target, use the following:
+    EIGEN_CI_C_COMPILER: ""
+    EIGEN_CI_CXX_COMPILER: ""
+    EIGEN_CI_INSTALL: "${EIGEN_CI_C_COMPILER} ${EIGEN_CI_CXX_COMPILER}"
+    # If host does not match the target, use the following:
+    EIGEN_CI_CROSS_TARGET_TRIPLE: ""
+    EIGEN_CI_CROSS_C_COMPILER: ${EIGEN_CI_C_COMPILER}
+    EIGEN_CI_CROSS_CXX_COMPILER: ${EIGEN_CI_CXX_COMPILER}
+    EIGEN_CI_CROSS_INSTALL: "${EIGEN_CI_CROSS_C_COMPILER} ${EIGEN_CI_CROSS_CXX_COMPILER}"
+  before_script:
+    # Call script in current shell - it sets up some environment variables.
+    - . ci/scripts/common.linux.before_script.sh
+  artifacts:
+    when: always
+    name: "$CI_JOB_NAME_SLUG-$CI_COMMIT_REF_SLUG"
+    paths:
+      - ${EIGEN_CI_BUILDDIR}/
+    expire_in: 5 days

ci/deploy.gitlab-ci.yml

@@ -0,0 +1,25 @@
+# Upload docs if pipeline succeeded.
+deploy:docs:
+  stage: deploy
+  image: busybox
+  dependencies: [ build:linux:docs ]
+  variables:
+    PAGES_PREFIX: docs-nightly
+  script:
+    - echo "Deploying site to $CI_PAGES_URL"
+    - mv ${EIGEN_CI_BUILDDIR}/doc/html public
+  pages:
+    path_prefix: $PAGES_PREFIX
+    expire_in: never
+  artifacts:
+    name: "$CI_JOB_NAME_SLUG-$CI_COMMIT_REF_SLUG"
+    paths:
+      - public
+  tags:
+    - saas-linux-small-amd64
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule" && $CI_PROJECT_NAMESPACE == "libeigen"
+    - if: $CI_PIPELINE_SOURCE == "web" && $CI_PROJECT_NAMESPACE == "libeigen"
+    - if: $CI_PIPELINE_SOURCE == "push" && $CI_PROJECT_NAMESPACE == "libeigen"
+      variables:
+        PAGES_PREFIX: docs-$CI_COMMIT_REF_NAME

ci/scripts/build.linux.script.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -x
+
+# Create and enter build directory.
+rootdir=`pwd`
+mkdir -p ${EIGEN_CI_BUILDDIR}
+cd ${EIGEN_CI_BUILDDIR}
+
+# Configure build.
+cmake -G Ninja                                                   \
+  -DCMAKE_CXX_COMPILER=${EIGEN_CI_CXX_COMPILER}                  \
+  -DCMAKE_C_COMPILER=${EIGEN_CI_C_COMPILER}                      \
+  -DCMAKE_CXX_COMPILER_TARGET=${EIGEN_CI_CXX_COMPILER_TARGET}    \
+  ${EIGEN_CI_ADDITIONAL_ARGS} ${rootdir}
+
+target=""
+if [[ ${EIGEN_CI_BUILD_TARGET} ]]; then
+  target="--target ${EIGEN_CI_BUILD_TARGET}"
+fi
+
+# Builds (particularly gcc) sometimes get killed, potentially when running
+# out of resources.  In that case, keep trying to build the remaining
+# targets (k0), then try to build again with a single thread (j1) to minimize
+# resource use.
+cmake --build . ${target} -- -k0 || cmake --build . ${target} -- -k0 -j1
+
+# Return to root directory.
+cd ${rootdir}
+
+set +x

ci/scripts/build_and_install_doxygen.sh

@@ -0,0 +1,6 @@
+git clone --depth 1 --branch $1 https://github.com/doxygen/doxygen.git
+cmake -B doxygen/.build -G Ninja                                 \
+  -DCMAKE_CXX_COMPILER=${EIGEN_CI_CXX_COMPILER}                  \
+  -DCMAKE_C_COMPILER=${EIGEN_CI_C_COMPILER}                      \
+  doxygen
+cmake --build doxygen/.build -t install

ci/scripts/common.linux.before_script.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+set -x
+
+echo "Running ${CI_JOB_NAME}"
+
+# Get architecture and display CI configuration.
+export ARCH=`uname -m`
+export NPROC=`nproc`
+echo "arch=$ARCH, target=${EIGEN_CI_TARGET_ARCH}"
+echo "Processors: ${NPROC}"
+echo "CI Variables:"
+export | grep EIGEN
+
+# Set noninteractive, otherwise tzdata may be installed and prompt for a
+# geographical region.
+export DEBIAN_FRONTEND=noninteractive
+apt-get update -y > /dev/null
+apt-get install -y --no-install-recommends ninja-build cmake git > /dev/null
+
+# Install required dependencies and set up compilers.
+# These are required even for testing to ensure that dynamic runtime libraries
+# are available.
+if [[ "$ARCH" == "${EIGEN_CI_TARGET_ARCH}" || "${EIGEN_CI_TARGET_ARCH}" == "any" ]]; then
+  apt-get install -y --no-install-recommends ${EIGEN_CI_INSTALL} > /dev/null;
+  export EIGEN_CI_CXX_IMPLICIT_INCLUDE_DIRECTORIES="";
+  export EIGEN_CI_CXX_COMPILER_TARGET="";
+else
+  apt-get install -y --no-install-recommends ${EIGEN_CI_CROSS_INSTALL} > /dev/null;
+  export EIGEN_CI_C_COMPILER=${EIGEN_CI_CROSS_C_COMPILER};
+  export EIGEN_CI_CXX_COMPILER=${EIGEN_CI_CROSS_CXX_COMPILER};
+  export EIGEN_CI_CXX_COMPILER_TARGET=${EIGEN_CI_CROSS_TARGET_TRIPLE};
+  # Tell the compiler where to find headers and libraries if using clang.
+  # NOTE: this breaks GCC since it messes with include path order
+  #       (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129)
+  if [[ "${EIGEN_CI_CROSS_CXX_COMPILER}" == *"clang"* ]]; then
+    export CPLUS_INCLUDE_PATH="/usr/${EIGEN_CI_CROSS_TARGET_TRIPLE}/include";
+    export LIBRARY_PATH="/usr/${EIGEN_CI_CROSS_TARGET_TRIPLE}/lib64";
+  fi
+fi
+
+echo "Compilers: ${EIGEN_CI_C_COMPILER} ${EIGEN_CI_CXX_COMPILER}"
+
+if [ -n "$EIGEN_CI_BEFORE_SCRIPT" ]; then eval "$EIGEN_CI_BEFORE_SCRIPT"; fi
+
+set +x

cmake/EigenConfigureTesting.cmake

@@ -1,7 +1,7 @@
 include(EigenTesting)
 include(CheckCXXSourceCompiles)
 
-# configure the "site" and "buildname" 
+# configure the "site" and "buildname"
 ei_set_sitename()
 
 # retrieve and store the build string
@@ -14,17 +14,10 @@ add_dependencies(check buildtests)
 # check whether /bin/bash exists
 find_file(EIGEN_BIN_BASH_EXISTS "/bin/bash" PATHS "/" NO_DEFAULT_PATH)
 
-# CMake/Ctest does not allow us to change the build command,
-# so we have to workaround by directly editing the generated DartConfiguration.tcl file
-# save CMAKE_MAKE_PROGRAM
-set(CMAKE_MAKE_PROGRAM_SAVE ${CMAKE_MAKE_PROGRAM})
-# and set a fake one
-set(CMAKE_MAKE_PROGRAM "@EIGEN_MAKECOMMAND_PLACEHOLDER@")
-
 # This call activates testing and generates the DartConfiguration.tcl
 include(CTest)
 
-set(EIGEN_TEST_BUILD_FLAGS " " CACHE STRING "Options passed to the build command of unit tests")
+set(EIGEN_TEST_BUILD_FLAGS "" CACHE STRING "Options passed to the build command of unit tests")
 
 # Overwrite default DartConfiguration.tcl such that ctest can build our unit tests.
 # Recall that our unit tests are not in the "all" target, so we have to explicitely ask ctest to build our custom 'buildtests' target.

cmake/EigenDetermineOSVersion.cmake

@@ -26,7 +26,7 @@ function(DetermineShortWindowsName WIN_VERSION win_num_version)
 endfunction()
 
 function(DetermineOSVersion OS_VERSION)
-  if (WIN32)
+  if (WIN32 AND CMAKE_HOST_SYSTEM_NAME MATCHES Windows)
     file (TO_NATIVE_PATH "$ENV{COMSPEC}" SHELL)
     exec_program( ${SHELL} ARGS "/c" "ver" OUTPUT_VARIABLE ver_output)
 				

doc/CMakeLists.txt

@@ -89,6 +89,7 @@ add_dependencies(doc-unsupported-prerequisites unsupported_snippets unsupported_
 add_custom_target(doc ALL
   COMMAND doxygen
   COMMAND doxygen Doxyfile-unsupported
+  COMMAND ${CMAKE_COMMAND} -E copy ${Eigen_BINARY_DIR}/doc/html/group__TopicUnalignedArrayAssert.html ${Eigen_BINARY_DIR}/doc/html/TopicUnalignedArrayAssert.html
   COMMAND ${CMAKE_COMMAND} -E rename html eigen-doc
   COMMAND ${CMAKE_COMMAND} -E remove eigen-doc/eigen-doc.tgz
   COMMAND ${CMAKE_COMMAND} -E tar cfz eigen-doc.tgz eigen-doc

doc/Manual.dox

@@ -121,6 +121,8 @@ namespace Eigen {
     \ingroup Sparse_chapter */
 /** \addtogroup TopicSparseSystems
     \ingroup Sparse_chapter */
+/** \addtogroup MatrixfreeSolverExample
+    \ingroup Sparse_chapter */
 
 /** \addtogroup Sparse_Reference
     \ingroup Sparse_chapter */

doc/MatrixfreeSolverExample.dox

@@ -0,0 +1,21 @@
+
+namespace Eigen {
+
+/**
+
+\eigenManualPage MatrixfreeSolverExample Matrix-free solvers
+
+Iterative solvers such as ConjugateGradient and BiCGSTAB can be used in a matrix free context. To this end, user must provide a wrapper class inheriting EigenBase<> and implementing the following methods:
+ - Index rows() and Index cols(): returns number of rows and columns respectively
+ - operator* with and Eigen dense column vector
+ - resize(rows,cols): needed for source compatibility (can stay empty)
+
+Eigen::internal::traits<> must also be specialized for the wrapper type.
+
+For efficiency purpose, one might also want to provide a custom preconditioner. Here is an example using ConjugateGradient and implementing also a custom Jacobi preconditioner:
+\include matrixfree_cg.cpp
+Output: \verbinclude matrixfree_cg.out
+
+*/
+
+}

doc/PreprocessorDirectives.dox

@@ -91,6 +91,7 @@ following macros are supported; none of them are defined by default.
  - \b EIGEN_MATRIX_PLUGIN - filename of plugin for extending the Matrix class.
  - \b EIGEN_MATRIXBASE_PLUGIN - filename of plugin for extending the MatrixBase class.
  - \b EIGEN_PLAINOBJECTBASE_PLUGIN - filename of plugin for extending the PlainObjectBase class.
+ - \b EIGEN_MAPBASE_PLUGIN - filename of plugin for extending the MapBase class.
  - \b EIGEN_QUATERNIONBASE_PLUGIN - filename of plugin for extending the QuaternionBase class.
  - \b EIGEN_SPARSEMATRIX_PLUGIN - filename of plugin for extending the SparseMatrix class.
  - \b EIGEN_SPARSEMATRIXBASE_PLUGIN - filename of plugin for extending the SparseMatrixBase class.

doc/SparseLinearSystems.dox

@@ -35,17 +35,20 @@ They are summarized in the following table:
     <td>Requires the <a href="http://pastix.gforge.inria.fr">PaStiX</a> package, \b CeCILL-C </td>
     <td>optimized for tough problems and symmetric patterns</td></tr>
 <tr><td>CholmodSupernodalLLT</td><td>\link CholmodSupport_Module CholmodSupport \endlink</td><td>Direct LLt factorization</td><td>SPD</td><td>Fill-in reducing, Leverage fast dense algebra</td>
-    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
+    <td>Requires the <a href="http://www.suitesparse.com">SuiteSparse</a> package, \b GPL </td>
     <td></td></tr>
 <tr><td>UmfPackLU</td><td>\link UmfPackSupport_Module UmfPackSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
-    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
+    <td>Requires the <a href="http://www.suitesparse.com">SuiteSparse</a> package, \b GPL </td>
     <td></td></tr>
 <tr><td>SuperLU</td><td>\link SuperLUSupport_Module SuperLUSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
     <td>Requires the <a href="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/">SuperLU</a> library, (BSD-like)</td>
     <td></td></tr>
 <tr><td>SPQR</td><td>\link SPQRSupport_Module SPQRSupport \endlink  </td> <td> QR factorization </td> 
     <td> Any, rectangular</td><td>fill-in reducing, multithreaded, fast dense algebra</td>
-    <td> requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td><td>recommended for linear least-squares problems, has a rank-revealing feature</tr>
+    <td> requires the <a href="http://www.suitesparse.com">SuiteSparse</a> package, \b GPL </td><td>recommended for linear least-squares problems, has a rank-revealing feature</tr>
+<tr><td>PardisoLLT \n PardisoLDLT \n PardisoLU</td><td>\link PardisoSupport_Module PardisoSupport \endlink</td><td>Direct LLt, LDLt, LU factorizations</td><td>SPD \n SPD \n Square</td><td>Fill-in reducing, Leverage fast dense algebra, Multithreading</td>
+    <td>Requires the <a href="http://eigen.tuxfamily.org/Counter/redirect_to_mkl.php">Intel MKL</a> package, \b Proprietary </td>
+    <td>optimized for tough problems patterns, see also \link TopicUsingIntelMKL using MKL with Eigen \endlink</td></tr>
 </table>
 
 Here \c SPD means symmetric positive definite.

doc/SparseQuickReference.dox

@@ -21,7 +21,7 @@ i.e either row major or column major. The default is column major. Most arithmet
 <td> Resize/Reserve</td>
 <td> 
  \code
-    sm1.resize(m,n);      //Change sm1 to a m x n matrix. 
+    sm1.resize(m,n);      // Change sm1 to a m x n matrix.
     sm1.reserve(nnz);     // Allocate room for nnz nonzeros elements.   
   \endcode 
 </td>
@@ -151,10 +151,10 @@ It is easy to perform arithmetic operations on sparse matrices provided that the
 <td> Permutation </td>
 <td> 
 \code 
-perm.indices(); // Reference to the vector of indices
+perm.indices();      // Reference to the vector of indices
 sm1.twistedBy(perm); // Permute rows and columns
-sm2 = sm1 * perm; //Permute the columns
-sm2 = perm * sm1; // Permute the columns
+sm2 = sm1 * perm;    // Permute the columns
+sm2 = perm * sm1;    // Permute the columns
 \endcode 
 </td>
 <td> 
@@ -181,9 +181,9 @@ sm2 = perm * sm1; // Permute the columns
 
 \section sparseotherops Other supported operations
 <table class="manual">
-<tr><th>Operations</th> <th> Code </th> <th> Notes</th> </tr>
+<tr><th style="min-width:initial"> Code </th> <th> Notes</th> </tr>
+<tr><td colspan="2">Sub-matrices</td></tr>
 <tr>
-<td>Sub-matrices</td> 
 <td> 
 \code 
   sm1.block(startRow, startCol, rows, cols); 
@@ -193,25 +193,31 @@ sm2 = perm * sm1; // Permute the columns
   sm1.bottomLeftCorner( rows, cols);
   sm1.bottomRightCorner( rows, cols);
   \endcode
-</td> <td>  </td>
+</td><td>
+Contrary to dense matrices, here <strong>all these methods are read-only</strong>.\n
+See \ref TutorialSparse_SubMatrices and below for read-write sub-matrices.
+</td>
 </tr>
-<tr> 
-<td> Range </td>
+<tr class="alt"><td colspan="2"> Range </td></tr>
+<tr class="alt">
 <td> 
 \code 
-  sm1.innerVector(outer); 
-  sm1.innerVectors(start, size);
-  sm1.leftCols(size);
-  sm2.rightCols(size);
-  sm1.middleRows(start, numRows);
-  sm1.middleCols(start, numCols);
-  sm1.col(j);
+  sm1.innerVector(outer);           // RW
+  sm1.innerVectors(start, size);    // RW
+  sm1.leftCols(size);               // RW
+  sm2.rightCols(size);              // RO because sm2 is row-major
+  sm1.middleRows(start, numRows);   // RO becasue sm1 is column-major
+  sm1.middleCols(start, numCols);   // RW
+  sm1.col(j);                       // RW
 \endcode
 </td>
-<td>A inner vector is either a row (for row-major) or a column (for column-major). As stated earlier, the evaluation can be done in a matrix with different storage order </td>
+<td>
+A inner vector is either a row (for row-major) or a column (for column-major).\n
+As stated earlier, for a read-write sub-matrix (RW), the evaluation can be done in a matrix with different storage order.
+</td>
 </tr>
+<tr><td colspan="2"> Triangular and selfadjoint views</td></tr>
 <tr>
-<td> Triangular and selfadjoint views</td>
 <td> 
 \code
   sm2 = sm1.triangularview<Lower>();
@@ -222,26 +228,30 @@ sm2 = perm * sm1; // Permute the columns
 \code 
   \endcode </td>
 </tr>
-<tr> 
-<td>Triangular solve </td>
+<tr class="alt"><td colspan="2">Triangular solve </td></tr>
+<tr class="alt">
 <td> 
 \code 
  dv2 = sm1.triangularView<Upper>().solve(dv1);
- dv2 = sm1.topLeftCorner(size, size).triangularView<Lower>().solve(dv1);
+ dv2 = sm1.topLeftCorner(size, size)
+          .triangularView<Lower>().solve(dv1);
 \endcode 
 </td>
 <td> For general sparse solve, Use any suitable module described at \ref TopicSparseSystems </td>
 </tr>
+<tr><td colspan="2"> Low-level API</td></tr>
 <tr>
-<td> Low-level API</td>
 <td>
 \code
-sm1.valuePtr(); // Pointer to the values
-sm1.innerIndextr(); // Pointer to the indices.
-sm1.outerIndexPtr(); //Pointer to the beginning of each inner vector
+sm1.valuePtr();      // Pointer to the values
+sm1.innerIndextr();  // Pointer to the indices.
+sm1.outerIndexPtr(); // Pointer to the beginning of each inner vector
 \endcode
 </td>
-<td> If the matrix is not in compressed form, makeCompressed() should be called before. Note that these functions are mostly provided for interoperability purposes with external libraries. A better access to the values of the matrix is done by using the InnerIterator class as described in \link TutorialSparse the Tutorial Sparse \endlink section</td>
+<td>
+If the matrix is not in compressed form, makeCompressed() should be called before.\n
+Note that these functions are mostly provided for interoperability purposes with external libraries.\n
+A better access to the values of the matrix is done by using the InnerIterator class as described in \link TutorialSparse the Tutorial Sparse \endlink section</td>
 </tr>
 </table>
 */

doc/TopicAssertions.dox

@@ -16,7 +16,7 @@ Both eigen_assert and eigen_plain_assert are defined in Macros.h. Defining eigen
 #include <stdexcept>
 #undef eigen_assert
 #define eigen_assert(x) \
-  if (!x) { throw (std::runtime_error("Put your message here")); }
+  if (!(x)) { throw (std::runtime_error("Put your message here")); }
 \endcode
 
 \subsection DisableAssert Disabling assertions

doc/TutorialSparse.dox

@@ -241,11 +241,11 @@ In the following \em sm denotes a sparse matrix, \em sv a sparse vector, \em dm
 sm1.real()   sm1.imag()   -sm1                    0.5*sm1
 sm1+sm2      sm1-sm2      sm1.cwiseProduct(sm2)
 \endcode
-However, a strong restriction is that the storage orders must match. For instance, in the following example:
+However, <strong>a strong restriction is that the storage orders must match</strong>. For instance, in the following example:
 \code
 sm4 = sm1 + sm2 + sm3;
 \endcode
-sm1, sm2, and sm3 must all be row-major or all column major.
+sm1, sm2, and sm3 must all be row-major or all column-major.
 On the other hand, there is no restriction on the target matrix sm4.
 For instance, this means that for computing \f$ A^T + A \f$, the matrix \f$ A^T \f$ must be evaluated into a temporary matrix of compatible storage order:
 \code
@@ -307,6 +307,26 @@ sm2 = sm1.transpose() * P;
     \endcode
 
 
+\subsection TutorialSparse_SubMatrices Block operations
+
+Regarding read-access, sparse matrices expose the same API than for dense matrices to access to sub-matrices such as blocks, columns, and rows. See \ref TutorialBlockOperations for a detailed introduction.
+However, for performance reasons, writing to a sub-sparse-matrix is much more limited, and currently only contiguous sets of columns (resp. rows) of a column-major (resp. row-major) SparseMatrix are writable. Moreover, this information has to be known at compile-time, leaving out methods such as <tt>block(...)</tt> and <tt>corner*(...)</tt>. The available API for write-access to a SparseMatrix are summarized below:
+\code
+SparseMatrix<double,ColMajor> sm1;
+sm1.col(j) = ...;
+sm1.leftCols(ncols) = ...;
+sm1.middleCols(j,ncols) = ...;
+sm1.rightCols(ncols) = ...;
+
+SparseMatrix<double,RowMajor> sm2;
+sm2.row(i) = ...;
+sm2.topRows(nrows) = ...;
+sm2.middleRows(i,nrows) = ...;
+sm2.bottomRows(nrows) = ...;
+\endcode
+
+In addition, sparse matrices expose the SparseMatrixBase::innerVector() and SparseMatrixBase::innerVectors() methods, which are aliases to the col/middleCols methods for a column-major storage, and to the row/middleRows methods for a row-major storage.
+
 \subsection TutorialSparse_TriangularSelfadjoint Triangular and selfadjoint views
 
 Just as with dense matrices, the triangularView() function can be used to address a triangular part of the matrix, and perform triangular solves with a dense right hand side:

doc/UnalignedArrayAssert.dox

@@ -7,8 +7,8 @@ Hello! You are seeing this webpage because your program terminated on an asserti
 my_program: path/to/eigen/Eigen/src/Core/DenseStorage.h:44:
 Eigen::internal::matrix_array<T, Size, MatrixOptions, Align>::internal::matrix_array()
 [with T = double, int Size = 2, int MatrixOptions = 2, bool Align = true]:
-Assertion `(reinterpret_cast<size_t>(array) & 0xf) == 0 && "this assertion
-is explained here: http://eigen.tuxfamily.org/dox/UnalignedArrayAssert.html
+Assertion `(reinterpret_cast<size_t>(array) & (sizemask)) == 0 && "this assertion
+is explained here: http://eigen.tuxfamily.org/dox/group__TopicUnalignedArrayAssert.html
 **** READ THIS WEB PAGE !!! ****"' failed.
 </pre>
 
@@ -46,9 +46,9 @@ then you need to read this separate page: \ref TopicStructHavingEigenMembers "St
 
 Note that here, Eigen::Vector2d is only used as an example, more generally the issue arises for all \ref TopicFixedSizeVectorizable "fixed-size vectorizable Eigen types".
 
-\section c2 Cause 2: STL Containers
+\section c2 Cause 2: STL Containers or manual memory allocation
 
-If you use STL Containers such as std::vector, std::map, ..., with Eigen objects, or with classes containing Eigen objects, like this,
+If you use STL Containers such as std::vector, std::map, ..., with %Eigen objects, or with classes containing %Eigen objects, like this,
 
 \code
 std::vector<Eigen::Matrix2f> my_vector;
@@ -60,6 +60,8 @@ then you need to read this separate page: \ref TopicStlContainers "Using STL Con
 
 Note that here, Eigen::Matrix2f is only used as an example, more generally the issue arises for all \ref TopicFixedSizeVectorizable "fixed-size vectorizable Eigen types" and \ref TopicStructHavingEigenMembers "structures having such Eigen objects as member".
 
+The same issue will be exhibited by any classes/functions by-passing operator new to allocate memory, that is, by performing custom memory allocation followed by calls to the placement new operator. This is for instance typically the case of \c std::make_shared or \c std::allocate_shared for which is the solution is to use an \ref aligned_allocator "aligned allocator" as detailed in the \ref TopicStlContainers "solution for STL containers".
+
 \section c3 Cause 3: Passing Eigen objects by value
 
 If some function in your code is getting an Eigen object passed by value, like this,
@@ -107,7 +109,10 @@ Two possibilities:
       128-bit alignment code and thus preserves ABI compatibility, but completely disables vectorization.</li>
 </ul>
 
-For more information, see <a href="http://eigen.tuxfamily.org/index.php?title=FAQ#I_disabled_vectorization.2C_but_I.27m_still_getting_annoyed_about_alignment_issues.21">this FAQ</a>.
+If you want to know why defining EIGEN_DONT_VECTORIZE does not by itself disable 128-bit alignment and the assertion, here's the explanation:
+
+It doesn't disable the assertion, because otherwise code that runs fine without vectorization would suddenly crash when enabling vectorization.
+It doesn't disable 128bit alignment, because that would mean that vectorized and non-vectorized code are not mutually ABI-compatible. This ABI compatibility is very important, even for people who develop only an in-house application, as for instance one may want to have in the same application a vectorized path and a non-vectorized path.
 
 */
 

doc/eigendoxy_footer.html.in

@@ -17,18 +17,22 @@ $generatedby &#160;<a href="http://www.doxygen.org/index.html">
 </small></address>
 <!--END !GENERATE_TREEVIEW-->
 
-<!-- Piwik -->
+<!-- Matomo -->
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-</script><script type="text/javascript">
-try {
-var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 20);
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-piwikTracker.enableLinkTracking();
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-<!-- End Piwik Tracking Code -->
+  var _paq = _paq || [];
+  /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+  _paq.push(['trackPageView']);
+  _paq.push(['enableLinkTracking']);
+  (function() {
+    var u="//stats.sylphide-consulting.com/matomo/";
+    _paq.push(['setTrackerUrl', u+'piwik.php']);
+    _paq.push(['setSiteId', '20']);
+    var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
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+</script>
+<noscript><p><img src="//stats.sylphide-consulting.com/matomo/piwik.php?idsite=20&rec=1" style="border:0;" alt="" /></p></noscript>
+<!-- End Matomo Code -->
 
 </body>
 </html>

doc/examples/matrixfree_cg.cpp

@@ -0,0 +1,180 @@
+#include <iostream>
+#include <Eigen/Core>
+#include <Eigen/Dense>
+#include <Eigen/IterativeLinearSolvers>
+
+class MatrixReplacement;
+template<typename Rhs> class MatrixReplacement_ProductReturnType;
+
+namespace Eigen {
+namespace internal {
+  template<>
+  struct traits<MatrixReplacement> :  Eigen::internal::traits<Eigen::SparseMatrix<double> >
+  {};
+
+  template <typename Rhs>
+  struct traits<MatrixReplacement_ProductReturnType<Rhs> > {
+    // The equivalent plain objet type of the product. This type is used if the product needs to be evaluated into a temporary.
+    typedef Eigen::Matrix<typename Rhs::Scalar, Eigen::Dynamic, Rhs::ColsAtCompileTime> ReturnType;
+  };
+}
+}
+
+// Inheriting EigenBase should not be needed in the future.
+class MatrixReplacement : public Eigen::EigenBase<MatrixReplacement> {
+public:
+  // Expose some compile-time information to Eigen:
+  typedef double Scalar;
+  typedef double RealScalar;
+  enum {
+    ColsAtCompileTime = Eigen::Dynamic,
+    RowsAtCompileTime = Eigen::Dynamic,
+    MaxColsAtCompileTime = Eigen::Dynamic,
+    MaxRowsAtCompileTime = Eigen::Dynamic
+  };
+
+  Index rows() const { return 4; }
+  Index cols() const { return 4; }
+
+  void resize(Index a_rows, Index a_cols)
+  {
+    // This method should not be needed in the future.
+    assert(a_rows==0 && a_cols==0 || a_rows==rows() && a_cols==cols());
+  }
+
+  // In the future, the return type should be Eigen::Product<MatrixReplacement,Rhs>
+  template<typename Rhs>
+  MatrixReplacement_ProductReturnType<Rhs> operator*(const Eigen::MatrixBase<Rhs>& x) const {
+    return MatrixReplacement_ProductReturnType<Rhs>(*this, x.derived());
+  }
+
+};
+
+// The proxy class representing the product of a MatrixReplacement with a MatrixBase<>
+template<typename Rhs>
+class MatrixReplacement_ProductReturnType : public Eigen::ReturnByValue<MatrixReplacement_ProductReturnType<Rhs> > {
+public:
+  typedef MatrixReplacement::Index Index;
+  
+  // The ctor store references to the matrix and right-hand-side object (usually a vector).
+  MatrixReplacement_ProductReturnType(const MatrixReplacement& matrix, const Rhs& rhs)
+    : m_matrix(matrix), m_rhs(rhs)
+  {}
+  
+  Index rows() const { return m_matrix.rows(); }
+  Index cols() const { return m_rhs.cols(); }
+
+  // This function is automatically called by Eigen. It must evaluate the product of matrix * rhs into y.
+  template<typename Dest>
+  void evalTo(Dest& y) const
+  {
+    y.setZero(4);
+
+    y(0) += 2 * m_rhs(0); y(1) += 1 * m_rhs(0);
+    y(0) += 1 * m_rhs(1); y(1) += 2 * m_rhs(1); y(2) += 1 * m_rhs(1);
+    y(1) += 1 * m_rhs(2); y(2) += 2 * m_rhs(2); y(3) += 1 * m_rhs(2);
+    y(2) += 1 * m_rhs(3); y(3) += 2 * m_rhs(3);
+  }
+
+protected:
+  const MatrixReplacement& m_matrix;
+  typename Rhs::Nested m_rhs;
+};
+
+
+/*****/
+
+// This class simply warp a diagonal matrix as a Jacobi preconditioner.
+// In the future such simple and generic wrapper should be shipped within Eigen itsel.
+template <typename _Scalar>
+class MyJacobiPreconditioner
+{
+    typedef _Scalar Scalar;
+    typedef Eigen::Matrix<Scalar,Eigen::Dynamic,1> Vector;
+    typedef typename Vector::Index Index;
+
+  public:
+    // this typedef is only to export the scalar type and compile-time dimensions to solve_retval
+    typedef Eigen::Matrix<Scalar,Eigen::Dynamic,Eigen::Dynamic> MatrixType;
+
+    MyJacobiPreconditioner() : m_isInitialized(false) {}
+
+    void setInvDiag(const Eigen::VectorXd &invdiag) {
+      m_invdiag=invdiag;
+      m_isInitialized=true;
+    }
+
+    Index rows() const { return m_invdiag.size(); }
+    Index cols() const { return m_invdiag.size(); }
+    
+    template<typename MatType>
+    MyJacobiPreconditioner& analyzePattern(const MatType& ) { return *this; }
+    
+    template<typename MatType>
+    MyJacobiPreconditioner& factorize(const MatType& mat) { return *this; }
+    
+    template<typename MatType>
+    MyJacobiPreconditioner& compute(const MatType& mat) { return *this; }
+
+    template<typename Rhs, typename Dest>
+    void _solve(const Rhs& b, Dest& x) const
+    {
+      x = m_invdiag.array() * b.array() ;
+    }
+
+    template<typename Rhs> inline const Eigen::internal::solve_retval<MyJacobiPreconditioner, Rhs>
+    solve(const Eigen::MatrixBase<Rhs>& b) const
+    {
+      eigen_assert(m_isInitialized && "MyJacobiPreconditioner is not initialized.");
+      eigen_assert(m_invdiag.size()==b.rows()
+                && "MyJacobiPreconditioner::solve(): invalid number of rows of the right hand side matrix b");
+      return Eigen::internal::solve_retval<MyJacobiPreconditioner, Rhs>(*this, b.derived());
+    }
+
+  protected:
+    Vector m_invdiag;
+    bool m_isInitialized;
+};
+
+namespace Eigen {
+namespace internal {
+
+template<typename _MatrixType, typename Rhs>
+struct solve_retval<MyJacobiPreconditioner<_MatrixType>, Rhs>
+  : solve_retval_base<MyJacobiPreconditioner<_MatrixType>, Rhs>
+{
+  typedef MyJacobiPreconditioner<_MatrixType> Dec;
+  EIGEN_MAKE_SOLVE_HELPERS(Dec,Rhs)
+
+  template<typename Dest> void evalTo(Dest& dst) const
+  {
+    dec()._solve(rhs(),dst);
+  }
+};
+
+}
+}
+
+
+/*****/
+
+
+int main()
+{
+  MatrixReplacement A;
+  Eigen::VectorXd b(4), x;
+  b << 1, 1, 1, 1;
+
+  // solve Ax = b using CG with matrix-free version:
+  Eigen::ConjugateGradient < MatrixReplacement, Eigen::Lower|Eigen::Upper, MyJacobiPreconditioner<double> > cg;
+
+  Eigen::VectorXd invdiag(4);
+  invdiag << 1./3., 1./4., 1./4., 1./3.;
+
+  cg.preconditioner().setInvDiag(invdiag);
+  cg.compute(A);
+  x = cg.solve(b);
+
+  std::cout << "#iterations: " << cg.iterations() << std::endl;
+  std::cout << "estimated error: " << cg.error() << std::endl;
+}

eigen3.pc.in

@@ -1,6 +1,9 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+
 Name: Eigen3
 Description: A C++ template library for linear algebra: vectors, matrices, and related algorithms
 Requires:
-Version: ${EIGEN_VERSION_NUMBER}
+Version: @EIGEN_VERSION_NUMBER@
 Libs:
-Cflags: -I${INCLUDE_INSTALL_DIR}
+Cflags: -I${prefix}/@INCLUDE_INSTALL_DIR@

test/CMakeLists.txt

@@ -125,6 +125,7 @@ endif(TEST_LIB)
 set_property(GLOBAL PROPERTY EIGEN_CURRENT_SUBPROJECT "Official")
 add_custom_target(BuildOfficial)
 
+ei_add_test(rand)
 ei_add_test(meta)
 ei_add_test(sizeof)
 ei_add_test(dynalloc)
@@ -202,7 +203,9 @@ ei_add_test(geo_alignedbox)
 ei_add_test(stdvector)
 ei_add_test(stdvector_overload)
 ei_add_test(stdlist)
+ei_add_test(stdlist_overload)
 ei_add_test(stddeque)
+ei_add_test(stddeque_overload)
 ei_add_test(resize)
 ei_add_test(sparse_vector)
 ei_add_test(sparse_basic)

test/commainitializer.cpp

@@ -9,14 +9,69 @@
 
 #include "main.h"
 
+
+template<int M1, int M2, int N1, int N2>
+void test_blocks()
+{
+  Matrix<int, M1+M2, N1+N2> m_fixed;
+  MatrixXi m_dynamic(M1+M2, N1+N2);
+
+  Matrix<int, M1, N1> mat11; mat11.setRandom();
+  Matrix<int, M1, N2> mat12; mat12.setRandom();
+  Matrix<int, M2, N1> mat21; mat21.setRandom();
+  Matrix<int, M2, N2> mat22; mat22.setRandom();
+
+  MatrixXi matx11 = mat11, matx12 = mat12, matx21 = mat21, matx22 = mat22;
+
+  {
+    VERIFY_IS_EQUAL((m_fixed << mat11, mat12, mat21, matx22).finished(), (m_dynamic << mat11, matx12, mat21, matx22).finished());
+    VERIFY_IS_EQUAL((m_fixed.template topLeftCorner<M1,N1>()), mat11);
+    VERIFY_IS_EQUAL((m_fixed.template topRightCorner<M1,N2>()), mat12);
+    VERIFY_IS_EQUAL((m_fixed.template bottomLeftCorner<M2,N1>()), mat21);
+    VERIFY_IS_EQUAL((m_fixed.template bottomRightCorner<M2,N2>()), mat22);
+    VERIFY_IS_EQUAL((m_fixed << mat12, mat11, matx21, mat22).finished(), (m_dynamic << mat12, matx11, matx21, mat22).finished());
+  }
+
+  if(N1 > 0)
+  {
+    VERIFY_RAISES_ASSERT((m_fixed << mat11, mat12, mat11, mat21, mat22));
+    VERIFY_RAISES_ASSERT((m_fixed << mat11, mat12, mat21, mat21, mat22));
+  }
+  else
+  {
+    // allow insertion of zero-column blocks:
+    VERIFY_IS_EQUAL((m_fixed << mat11, mat12, mat11, mat11, mat21, mat21, mat22).finished(), (m_dynamic << mat12, mat22).finished());
+  }
+  if(M1 != M2)
+  {
+    VERIFY_RAISES_ASSERT((m_fixed << mat11, mat21, mat12, mat22));
+  }
+}
+
+
+template<int N>
+struct test_block_recursion
+{
+  static void run()
+  {
+    test_blocks<(N>>6)&3, (N>>4)&3, (N>>2)&3, N & 3>();
+    test_block_recursion<N-1>::run();
+  }
+};
+
+template<>
+struct test_block_recursion<-1>
+{
+  static void run() { }
+};
+
 void test_commainitializer()
 {
   Matrix3d m3;
   Matrix4d m4;
 
-  VERIFY_RAISES_ASSERT( (m3 << 1, 2, 3, 4, 5, 6, 7, 8) );
-  
   #ifndef _MSC_VER
+  VERIFY_RAISES_ASSERT( (m3 << 1, 2, 3, 4, 5, 6, 7, 8) );
   VERIFY_RAISES_ASSERT( (m3 << 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) );
   #endif
 
@@ -43,4 +98,7 @@ void test_commainitializer()
         4, 5, 6,
         vec[2].transpose();
   VERIFY_IS_APPROX(m3, ref);
+
+  // recursively test all block-sizes from 0 to 3:
+  test_block_recursion<(1<<8) - 1>();
 }

test/cwiseop.cpp

@@ -164,9 +164,12 @@ template<typename MatrixType> void cwiseops(const MatrixType& m)
   VERIFY( (m1.cwise().min(m2).cwise() < (m1+mones)).all() );
   VERIFY( (m1.cwise().max(m2).cwise() > (m1-mones)).all() );
 
+#if(__cplusplus < 201103L)
+// std::binder* are deprecated since c++11 and will be removed in c++17
   VERIFY( (m1.cwise()<m1.unaryExpr(bind2nd(plus<Scalar>(), Scalar(1)))).all() );
   VERIFY( !(m1.cwise()<m1bis.unaryExpr(bind2nd(minus<Scalar>(), Scalar(1)))).all() );
   VERIFY( !(m1.cwise()>m1bis.unaryExpr(bind2nd(plus<Scalar>(), Scalar(1)))).any() );
+#endif
   
   cwiseops_real_only(m1, m2, m3, mones);
 }

test/dynalloc.cpp

@@ -87,6 +87,32 @@ template<typename T> void check_dynaligned()
   delete obj;
 }
 
+template<typename T> void check_custom_new_delete()
+{
+  {
+    T* t = new T;
+    delete t;
+  }
+  
+  {
+    std::size_t N = internal::random<std::size_t>(1,10);
+    T* t = new T[N];
+    delete[] t;
+  }
+  
+#ifdef EIGEN_ALIGN
+  {
+    T* t = static_cast<T *>((T::operator new)(sizeof(T)));
+    (T::operator delete)(t, sizeof(T));
+  }
+  
+  {
+    T* t = static_cast<T *>((T::operator new)(sizeof(T)));
+    (T::operator delete)(t);
+  }
+#endif
+}
+
 void test_dynalloc()
 {
   // low level dynamic memory allocation
@@ -94,7 +120,9 @@ void test_dynalloc()
   CALL_SUBTEST(check_aligned_malloc());
   CALL_SUBTEST(check_aligned_new());
   CALL_SUBTEST(check_aligned_stack_alloc());
-
+  
+  // check static allocation, who knows ?
+  #if EIGEN_ALIGN_STATICALLY
   for (int i=0; i<g_repeat*100; ++i)
   {
     CALL_SUBTEST(check_dynaligned<Vector4f>() );
@@ -102,10 +130,13 @@ void test_dynalloc()
     CALL_SUBTEST(check_dynaligned<Matrix4f>() );
     CALL_SUBTEST(check_dynaligned<Vector4d>() );
     CALL_SUBTEST(check_dynaligned<Vector4i>() );
+    
+    CALL_SUBTEST( check_custom_new_delete<Vector4f>() );
+    CALL_SUBTEST( check_custom_new_delete<Vector2f>() );
+    CALL_SUBTEST( check_custom_new_delete<Matrix4f>() );
+    CALL_SUBTEST( check_custom_new_delete<MatrixXi>() );
   }
-  
-  // check static allocation, who knows ?
-  #if EIGEN_ALIGN_STATICALLY
+
   {
     MyStruct foo0;  VERIFY(size_t(foo0.avec.data())%ALIGNMENT==0);
     MyClassA fooA;  VERIFY(size_t(fooA.avec.data())%ALIGNMENT==0);

test/eigen2/eigen2_cwiseop.cpp

@@ -137,9 +137,12 @@ template<typename MatrixType> void cwiseops(const MatrixType& m)
   VERIFY( (m1.cwise().min(m2).cwise() < (m1+mones)).all() );
   VERIFY( (m1.cwise().max(m2).cwise() > (m1-mones)).all() );
 
+#if(__cplusplus < 201103L)
+// std::binder* are deprecated since c++11 and will be removed in c++17
   VERIFY( (m1.cwise()<m1.unaryExpr(bind2nd(plus<Scalar>(), Scalar(1)))).all() );
   VERIFY( !(m1.cwise()<m1.unaryExpr(bind2nd(minus<Scalar>(), Scalar(1)))).all() );
   VERIFY( !(m1.cwise()>m1.unaryExpr(bind2nd(plus<Scalar>(), Scalar(1)))).any() );
+#endif
 }
 
 void test_eigen2_cwiseop()