Fix csr_matrix_times_vector linker error

stan/math/prim/fun/value_of.hpp

@@ -67,7 +67,7 @@ inline auto value_of(const T& x) {
  * @param[in] M Matrix to be converted
  * @return Matrix of values
  **/
-template <typename EigMat, require_eigen_t<EigMat>* = nullptr,
+template <typename EigMat, require_eigen_dense_base_t<EigMat>* = nullptr,
           require_not_st_arithmetic<EigMat>* = nullptr>
 inline auto value_of(EigMat&& M) {
   return make_holder(
@@ -77,6 +77,28 @@ inline auto value_of(EigMat&& M) {
       std::forward<EigMat>(M));
 }
 
+template <typename EigMat, require_eigen_sparse_base_t<EigMat>* = nullptr,
+          require_not_st_arithmetic<EigMat>* = nullptr>
+inline auto value_of(EigMat&& M) {
+  auto&& M_ref = to_ref(M);
+  using scalar_t = decltype(value_of(std::declval<value_type_t<EigMat>>()));
+  promote_scalar_t<scalar_t, plain_type_t<EigMat>> ret(M_ref.rows(),
+                                                       M_ref.cols());
+  ret.reserve(M_ref.nonZeros());
+  for (int k = 0; k < M_ref.outerSize(); ++k) {
+    for (typename std::decay_t<EigMat>::InnerIterator it(M_ref, k); it; ++it) {
+      ret.insert(it.row(), it.col()) = value_of(it.valueRef());
+    }
+  }
+  ret.makeCompressed();
+  return ret;
+}
+template <typename EigMat, require_eigen_sparse_base_t<EigMat>* = nullptr,
+          require_st_arithmetic<EigMat>* = nullptr>
+inline auto value_of(EigMat&& M) {
+  return std::forward<EigMat>(M);
+}
+
 }  // namespace math
 }  // namespace stan
 

stan/math/prim/meta/is_eigen_dense_base.hpp

@@ -33,6 +33,22 @@ using require_eigen_dense_base_t
     = require_t<is_eigen_dense_base<std::decay_t<T>>>;
 /*! @} */
 
+/*! \ingroup require_eigens_types */
+/*! \defgroup eigen_dense_base_types eigen_dense_base_types  */
+/*! \addtogroup eigen_dense_base_types */
+/*! @{ */
+
+/*! \brief Require type satisfies @ref is_eigen_dense_base */
+/*! and value type satisfies `TypeCheck` */
+/*! @tparam TypeCheck The type trait to check the value type against */
+/*! @tparam Check The type to test @ref is_eigen_dense_base for and whose
+ * @ref value_type is checked with `TypeCheck` */
+template <template <class...> class TypeCheck, class... Check>
+using require_eigen_dense_base_vt
+    = require_t<container_type_check_base<is_eigen_dense_base, value_type_t,
+                                          TypeCheck, Check...>>;
+/*! @} */
+
 }  // namespace stan
 
 #endif

stan/math/prim/meta/promote_scalar_type.hpp

@@ -4,6 +4,8 @@
 #include <stan/math/prim/fun/Eigen.hpp>
 #include <stan/math/prim/meta/is_eigen.hpp>
 #include <stan/math/prim/meta/is_var.hpp>
+#include <stan/math/prim/meta/is_eigen_dense_base.hpp>
+#include <stan/math/prim/meta/is_eigen_sparse_base.hpp>
 #include <vector>
 
 namespace stan {
@@ -80,7 +82,7 @@ struct promote_scalar_type<T, S,
  * @tparam S input matrix type
  */
 template <typename T, typename S>
-struct promote_scalar_type<T, S, require_eigen_t<S>> {
+struct promote_scalar_type<T, S, require_eigen_dense_base_t<S>> {
   /**
    * The promoted type.
    */
@@ -93,6 +95,16 @@ struct promote_scalar_type<T, S, require_eigen_t<S>> {
                    S::RowsAtCompileTime, S::ColsAtCompileTime>>::type;
 };
 
+template <typename T, typename S>
+struct promote_scalar_type<T, S, require_eigen_sparse_base_t<S>> {
+  /**
+   * The promoted type.
+   */
+  using type = Eigen::SparseMatrix<
+      typename promote_scalar_type<T, typename S::Scalar>::type, S::Options,
+      typename S::StorageIndex>;
+};
+
 template <typename... PromotionScalars, typename... UnPromotedTypes>
 struct promote_scalar_type<std::tuple<PromotionScalars...>,
                            std::tuple<UnPromotedTypes...>> {

stan/math/rev/core/arena_matrix.hpp

@@ -6,7 +6,6 @@
 #include <stan/math/rev/core/chainablestack.hpp>
 #include <stan/math/rev/core/var_value_fwd_declare.hpp>
 #include <stan/math/prim/fun/to_ref.hpp>
-
 namespace stan {
 namespace math {
 
@@ -225,8 +224,10 @@ class arena_matrix<MatrixType, require_eigen_sparse_base_t<MatrixType>>
    */
   arena_matrix(const arena_matrix<MatrixType>& other)
       : Base::Map(other.rows(), other.cols(), other.nonZeros(),
-                  other.outerIndexPtr(), other.innerIndexPtr(),
-                  other.valuePtr(), other.innernonZeroPtr()) {}
+                  const_cast<StorageIndex*>(other.outerIndexPtr()),
+                  const_cast<StorageIndex*>(other.innerIndexPtr()),
+                  const_cast<Scalar*>(other.valuePtr()),
+                  const_cast<StorageIndex*>(other.innerNonZeroPtr())) {}
   /**
    * Move constructor.
    * @note Since the memory for the arena matrix sits in Stan's memory arena all
@@ -235,8 +236,10 @@ class arena_matrix<MatrixType, require_eigen_sparse_base_t<MatrixType>>
    */
   arena_matrix(arena_matrix<MatrixType>&& other)
       : Base::Map(other.rows(), other.cols(), other.nonZeros(),
-                  other.outerIndexPtr(), other.innerIndexPtr(),
-                  other.valuePtr(), other.innerNonZeroPtr()) {}
+                  const_cast<StorageIndex*>(other.outerIndexPtr()),
+                  const_cast<StorageIndex*>(other.innerIndexPtr()),
+                  const_cast<Scalar*>(other.valuePtr()),
+                  const_cast<StorageIndex*>(other.innerNonZeroPtr())) {}
   /**
    * Copy constructor. No actual copy is performed
    * @note Since the memory for the arena matrix sits in Stan's memory arena all
@@ -245,8 +248,10 @@ class arena_matrix<MatrixType, require_eigen_sparse_base_t<MatrixType>>
    */
   arena_matrix(arena_matrix<MatrixType>& other)
       : Base::Map(other.rows(), other.cols(), other.nonZeros(),
-                  other.outerIndexPtr(), other.innerIndexPtr(),
-                  other.valuePtr(), other.innerNonZeroPtr()) {}
+                  const_cast<StorageIndex*>(other.outerIndexPtr()),
+                  const_cast<StorageIndex*>(other.innerIndexPtr()),
+                  const_cast<Scalar*>(other.valuePtr()),
+                  const_cast<StorageIndex*>(other.innerNonZeroPtr())) {}
 
   // without this using, compiler prefers combination of implicit construction
   // and copy assignment to the inherited operator when assigned an expression
@@ -259,7 +264,8 @@ class arena_matrix<MatrixType, require_eigen_sparse_base_t<MatrixType>>
    * @return `*this`
    */
   template <typename ArenaMatrix,
-            require_same_t<ArenaMatrix, arena_matrix<MatrixType>>* = nullptr>
+            require_same_t<std::decay_t<ArenaMatrix>,
+                           arena_matrix<MatrixType>>* = nullptr>
   arena_matrix& operator=(ArenaMatrix&& other) {
     // placement new changes what data map points to - there is no allocation
     new (this) Base(other.rows(), other.cols(), other.nonZeros(),
@@ -280,7 +286,7 @@ class arena_matrix<MatrixType, require_eigen_sparse_base_t<MatrixType>>
   template <typename Expr,
             require_not_same_t<Expr, arena_matrix<MatrixType>>* = nullptr>
   arena_matrix& operator=(Expr&& expr) {
-    *this = arena_matrix(std::forward<Expr>(expr));
+    new (this) arena_matrix(std::forward<Expr>(expr));
     return *this;
   }
 

stan/math/rev/core/var.hpp

@@ -418,6 +418,18 @@ class var_value<T, internal::require_matrix_var_value<T>> {
         });
   }
 
+  /**
+   * Construct a `var_value` with premade @ref arena_matrix types.
+   *  The values and adjoint matrices passed here will be shallow copied.
+   * @tparam S type of the value in the `var_value` to assing
+   * @param val The value matrix to go into the vari
+   * @param adj the adjoint matrix to go into the vari
+   */
+  template <typename S, typename T_ = T,
+            require_assignable_t<value_type, S>* = nullptr,
+            require_arena_matrix_t<S>* = nullptr>
+  var_value(const S& val, const S& adj) : vi_(new vari_type(val, adj)) {}
+
   /**
    * Construct a variable from a pointer to a variable implementation.
    * @param vi A vari_value pointer.

stan/math/rev/core/vari.hpp

@@ -821,17 +821,16 @@ class vari_value<T, require_eigen_sparse_base_t<T>> : public vari_base {
    */
   static constexpr int ColsAtCompileTime = T::ColsAtCompileTime;
 
+  /**
+   * The value of this variable.
+   */
+  arena_matrix<PlainObject> val_;
   /**
    * The adjoint of this variable, which is the partial derivative
    * of this variable with respect to the root variable.
    */
   arena_matrix<PlainObject> adj_;
 
-  /**
-   * The value of this variable.
-   */
-  arena_matrix<PlainObject> val_;
-
   /**
    * Construct a variable implementation from a value. The
    * adjoint is initialized to zero.
@@ -847,10 +846,21 @@ class vari_value<T, require_eigen_sparse_base_t<T>> : public vari_base {
    * @param x Value of the constructed variable.
    */
   template <typename S, require_convertible_t<S&, T>* = nullptr>
-  explicit vari_value(S&& x) : adj_(x), val_(std::forward<S>(x)) {
-    this->set_zero_adjoint();
+  explicit vari_value(S&& x)
+      : val_(std::forward<S>(x)),
+        adj_(val_.rows(), val_.cols(), val_.nonZeros(), val_.outerIndexPtr(),
+             val_.innerIndexPtr(),
+             arena_matrix<Eigen::VectorXd>(val_.nonZeros()).setZero().data(),
+             val_.innerNonZeroPtr()) {
+    ChainableStack::instance_->var_stack_.push_back(this);
+  }
+
+  vari_value(const arena_matrix<PlainObject>& val,
+             const arena_matrix<PlainObject>& adj)
+      : val_(val), adj_(adj) {
     ChainableStack::instance_->var_stack_.push_back(this);
   }
+
   /**
    * Construct an sparse Eigen variable implementation from a value. The
    *  adjoint is initialized to zero and if `stacked` is `false` this vari
@@ -869,8 +879,12 @@ class vari_value<T, require_eigen_sparse_base_t<T>> : public vari_base {
    * that its `chain()` method is not called.
    */
   template <typename S, require_convertible_t<S&, T>* = nullptr>
-  vari_value(S&& x, bool stacked) : adj_(x), val_(std::forward<S>(x)) {
-    this->set_zero_adjoint();
+  vari_value(S&& x, bool stacked)
+      : val_(std::forward<S>(x)),
+        adj_(val_.rows(), val_.cols(), val_.nonZeros(), val_.outerIndexPtr(),
+             val_.innerIndexPtr(),
+             arena_matrix<Eigen::VectorXd>(val_.nonZeros()).setZero().data(),
+             val_.innerNonZeroPtr()) {
     if (stacked) {
       ChainableStack::instance_->var_stack_.push_back(this);
     } else {

stan/math/rev/fun.hpp

@@ -183,6 +183,7 @@
 #include <stan/math/rev/fun/tgamma.hpp>
 #include <stan/math/rev/fun/to_var.hpp>
 #include <stan/math/rev/fun/to_arena.hpp>
+#include <stan/math/rev/fun/to_soa_sparse_matrix.hpp>
 #include <stan/math/rev/fun/to_var_value.hpp>
 #include <stan/math/rev/fun/to_vector.hpp>
 #include <stan/math/rev/fun/trace.hpp>

stan/math/rev/fun/csr_matrix_times_vector.hpp

@@ -2,6 +2,7 @@
 #define STAN_MATH_REV_FUN_CSR_MATRIX_TIMES_VECTOR_HPP
 
 #include <stan/math/prim/fun/Eigen.hpp>
+#include <stan/math/rev/fun/to_soa_sparse_matrix.hpp>
 #include <stan/math/rev/core.hpp>
 #include <stan/math/prim/err.hpp>
 #include <stan/math/prim/fun/csr_u_to_z.hpp>
@@ -10,40 +11,6 @@
 namespace stan {
 namespace math {
 
-namespace internal {
-template <typename T1, typename T2, typename Res,
-          require_eigen_t<T1>* = nullptr>
-void update_w(T1& w, int m, int n, std::vector<int, arena_allocator<int>>& u,
-              std::vector<int, arena_allocator<int>>& v, T2&& b, Res&& res) {
-  Eigen::Map<Eigen::SparseMatrix<var, Eigen::RowMajor>> w_mat(
-      m, n, w.size(), u.data(), v.data(), w.data());
-  for (int k = 0; k < w_mat.outerSize(); ++k) {
-    for (Eigen::Map<Eigen::SparseMatrix<var, Eigen::RowMajor>>::InnerIterator
-             it(w_mat, k);
-         it; ++it) {
-      it.valueRef().adj()
-          += res.adj().coeff(it.row()) * value_of(b).coeff(it.col());
-    }
-  }
-}
-
-template <typename T1, typename T2, typename Res,
-          require_var_matrix_t<T1>* = nullptr>
-void update_w(T1& w, int m, int n, std::vector<int, arena_allocator<int>>& u,
-              std::vector<int, arena_allocator<int>>& v, T2&& b, Res&& res) {
-  Eigen::Map<Eigen::SparseMatrix<double, Eigen::RowMajor>> w_mat(
-      m, n, w.size(), u.data(), v.data(), w.adj().data());
-  for (int k = 0; k < w_mat.outerSize(); ++k) {
-    for (Eigen::Map<Eigen::SparseMatrix<double, Eigen::RowMajor>>::InnerIterator
-             it(w_mat, k);
-         it; ++it) {
-      it.valueRef() += res.adj().coeff(it.row()) * value_of(b).coeff(it.col());
-    }
-  }
-}
-
-}  // namespace internal
-
 /**
  * \addtogroup csr_format
  * Return the multiplication of the sparse matrix (specified by
@@ -100,46 +67,49 @@ inline auto csr_matrix_times_vector(int m, int n, const T1& w,
   std::vector<int, arena_allocator<int>> u_arena(u.size());
   std::transform(u.begin(), u.end(), u_arena.begin(),
                  [](auto&& x) { return x - 1; });
+  using sparse_var_value_t
+      = var_value<Eigen::SparseMatrix<double, Eigen::RowMajor>>;
   if (!is_constant<T2>::value && !is_constant<T1>::value) {
     arena_t<promote_scalar_t<var, T2>> b_arena = b;
-    arena_t<promote_scalar_t<var, T1>> w_arena = to_arena(w);
-    auto w_val_arena = to_arena(value_of(w_arena));
-    sparse_val_mat w_val_mat(m, n, w_val_arena.size(), u_arena.data(),
-                             v_arena.data(), w_val_arena.data());
-    arena_t<return_t> res = w_val_mat * value_of(b_arena);
-    reverse_pass_callback(
-        [m, n, w_arena, w_val_arena, v_arena, u_arena, res, b_arena]() mutable {
-          sparse_val_mat w_val_mat(m, n, w_val_arena.size(), u_arena.data(),
-                                   v_arena.data(), w_val_arena.data());
-          internal::update_w(w_arena, m, n, u_arena, v_arena, b_arena, res);
-          b_arena.adj() += w_val_mat.transpose() * res.adj();
-        });
+    sparse_var_value_t w_mat_arena
+        = to_soa_sparse_matrix<Eigen::RowMajor>(m, n, w, u_arena, v_arena);
+    arena_t<return_t> res = w_mat_arena.val() * value_of(b_arena);
+    reverse_pass_callback([res, w_mat_arena, b_arena]() mutable {
+      for (int k = 0; k < w_mat_arena.adj().outerSize(); ++k) {
+        for (typename sparse_var_value_t::vari_type::InnerIterator it(
+                 w_mat_arena.adj(), k);
+             it; ++it) {
+          it.valueRef()
+              += res.adj().coeff(it.row()) * b_arena.val().coeff(it.col());
+        }
+      }
+      b_arena.adj() += w_mat_arena.val().transpose() * res.adj();
+    });
     return return_t(res);
   } else if (!is_constant<T2>::value) {
     arena_t<promote_scalar_t<var, T2>> b_arena = b;
     auto w_val_arena = to_arena(value_of(w));
     sparse_val_mat w_val_mat(m, n, w_val_arena.size(), u_arena.data(),
                              v_arena.data(), w_val_arena.data());
-
     arena_t<return_t> res = w_val_mat * value_of(b_arena);
-    reverse_pass_callback(
-        [m, n, w_val_arena, v_arena, u_arena, res, b_arena]() mutable {
-          sparse_val_mat w_val_mat(m, n, w_val_arena.size(), u_arena.data(),
-                                   v_arena.data(), w_val_arena.data());
-          b_arena.adj() += w_val_mat.transpose() * res.adj();
-        });
+    reverse_pass_callback([w_val_mat, res, b_arena]() mutable {
+      b_arena.adj() += w_val_mat.transpose() * res.adj();
+    });
     return return_t(res);
   } else {
-    arena_t<promote_scalar_t<var, T1>> w_arena = to_arena(w);
-    auto&& w_val = eval(value_of(w_arena));
-    sparse_val_mat w_val_mat(m, n, w_val.size(), u_arena.data(), v_arena.data(),
-                             w_val.data());
+    sparse_var_value_t w_mat_arena
+        = to_soa_sparse_matrix<Eigen::RowMajor>(m, n, w, u_arena, v_arena);
     auto b_arena = to_arena(value_of(b));
-    arena_t<return_t> res = w_val_mat * b_arena;
-    reverse_pass_callback(
-        [m, n, w_arena, v_arena, u_arena, res, b_arena]() mutable {
-          internal::update_w(w_arena, m, n, u_arena, v_arena, b_arena, res);
-        });
+    arena_t<return_t> res = w_mat_arena.val() * b_arena;
+    reverse_pass_callback([res, w_mat_arena, b_arena]() mutable {
+      for (int k = 0; k < w_mat_arena.adj().outerSize(); ++k) {
+        for (typename sparse_var_value_t::vari_type::InnerIterator it(
+                 w_mat_arena.adj(), k);
+             it; ++it) {
+          it.valueRef() += res.adj().coeff(it.row()) * b_arena.coeff(it.col());
+        }
+      }
+    });
     return return_t(res);
   }
 }