From: Martin Kronbichler <kronbichler@lnm.mw.tum.de>
Date: Thu, 14 Apr 2016 14:16:13 +0000 (+0200)
Subject: Implement affinity partitioner for the deal.II vector class
X-Git-Tag: v8.5.0-rc1~1102^2~4
X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=9cf406844e67c2d545acc4c9588ff2289a1ab6a6;p=dealii.git

Implement affinity partitioner for the deal.II vector class
---

diff --git a/include/deal.II/base/parallel.h b/include/deal.II/base/parallel.h
index 164afa8272..2aeab248b3 100644
--- a/include/deal.II/base/parallel.h
+++ b/include/deal.II/base/parallel.h
@@ -21,6 +21,7 @@
 #include <deal.II/base/exceptions.h>
 #include <deal.II/base/template_constraints.h>
 #include <deal.II/base/synchronous_iterator.h>
+#include <deal.II/base/thread_management.h>
 
 #include <deal.II/base/std_cxx11/tuple.h>
 #include <deal.II/base/std_cxx11/bind.h>
@@ -683,6 +684,78 @@ namespace parallel
 #endif
   }
 
+
+// --------------------- for loop affinity partitioner -----------------------
+
+  /**
+   * A class that wraps a TBB affinity partitioner in a thread-safe way. In
+   * Vector, we use a shared pointer to share an affinity partitioner
+   * between different vectors of the same size for improving data (and
+   * NUMA) locality. However, when an outer task does multiple vector
+   * operations, the shared pointer could lead to race conditions. This
+   * class only allows one instance to get a partitioner. The other objects
+   * cannot use that object and need to create their own copy.
+   */
+  namespace internal
+  {
+    class TBBPartitioner
+    {
+    public:
+      /**
+       * Constructor.
+       */
+      TBBPartitioner()
+#ifdef DEAL_II_WITH_THREADS
+        :
+        in_use(false)
+#endif
+      {}
+
+#ifdef DEAL_II_WITH_THREADS
+      /**
+       * Return a pointer to the affinity partitioner in case it is free. If
+       * it is already in use (i.e., someone else called acquire without
+       * releasing it afterwards), the null pointer is returned.
+       */
+      tbb::affinity_partitioner *acquire()
+      {
+        dealii::Threads::Mutex::ScopedLock lock(mutex);
+        if (in_use)
+          return NULL;
+
+        in_use = true;
+        return &partitioner;
+      }
+
+      /**
+       * After using the partitioner in a tbb loop through acquire(), this
+       * call makes the partitioner available again.
+       */
+      void release()
+      {
+        dealii::Threads::Mutex::ScopedLock lock(mutex);
+        in_use = false;
+      }
+
+    private:
+      /**
+       * The stored partitioner
+       */
+      tbb::affinity_partitioner partitioner;
+
+      /**
+       * A flag to indicate whether the partitioner has been acquired but not
+       * released yet, i.e., it is in use somewhere else.
+       */
+      bool in_use;
+
+      /**
+       * A mutex to guard the access to the in_use flag.
+       */
+      dealii::Threads::Mutex mutex;
+#endif
+    };
+  }
 }
 
 
diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h
index e507c90ca8..fea7f5a1ec 100644
--- a/include/deal.II/lac/vector.h
+++ b/include/deal.II/lac/vector.h
@@ -61,6 +61,13 @@ template <typename> class BlockVector;
 
 template <typename> class VectorView;
 
+namespace parallel
+{
+  namespace internal
+  {
+    class TBBPartitioner;
+  }
+}
 
 
 
@@ -984,6 +991,12 @@ protected:
    */
   Number *val;
 
+  /**
+   * For parallel loops with TBB, this member variable stores the affinity
+   * information of loops.
+   */
+  std_cxx11::shared_ptr<parallel::internal::TBBPartitioner> thread_loop_partitioner;
+
   /**
    * Make all other vector types friends.
    */
@@ -1073,92 +1086,6 @@ Vector<Number>::~Vector ()
 
 
 
-template <typename Number>
-inline
-void Vector<Number>::reinit (const size_type n,
-                             const bool omit_zeroing_entries)
-{
-  if (n==0)
-    {
-      if (val) deallocate();
-      val = 0;
-      max_vec_size = vec_size = 0;
-      return;
-    };
-
-  if (n>max_vec_size)
-    {
-      if (val) deallocate();
-      max_vec_size = n;
-      allocate();
-    };
-  vec_size = n;
-  if (omit_zeroing_entries == false)
-    *this = static_cast<Number>(0);
-}
-
-
-
-// declare function that is implemented in vector.templates.h
-namespace internal
-{
-  namespace Vector
-  {
-    template <typename T, typename U>
-    void copy_vector (const dealii::Vector<T> &src,
-                      dealii::Vector<U>       &dst);
-  }
-}
-
-
-
-template <typename Number>
-inline
-Vector<Number> &
-Vector<Number>::operator= (const Vector<Number> &v)
-{
-  dealii::internal::Vector::copy_vector (v, *this);
-  return *this;
-}
-
-
-
-#ifdef DEAL_II_WITH_CXX11
-template <typename Number>
-inline
-Vector<Number> &
-Vector<Number>::operator= (Vector<Number> &&v)
-{
-  Subscriptor::operator=(std::move(v));
-
-  if (val) deallocate();
-
-  vec_size = v.vec_size;
-  max_vec_size = v.max_vec_size;
-  val = v.val;
-
-  v.vec_size = 0;
-  v.max_vec_size = 0;
-  v.val = nullptr;
-
-  return *this;
-}
-#endif
-
-
-
-template <typename Number>
-template <typename Number2>
-inline
-Vector<Number> &
-Vector<Number>::operator= (const Vector<Number2> &v)
-{
-  internal::Vector::copy_vector (v, *this);
-  return *this;
-}
-
-
-
 template <typename Number>
 inline
 std::size_t Vector<Number>::size () const
diff --git a/include/deal.II/lac/vector.templates.h b/include/deal.II/lac/vector.templates.h
index 24f0416fa9..aff70219c6 100644
--- a/include/deal.II/lac/vector.templates.h
+++ b/include/deal.II/lac/vector.templates.h
@@ -120,7 +120,8 @@ namespace internal
 
   template <typename Functor>
   void vectorized_transform(Functor &functor,
-                            size_type vec_size)
+                            size_type vec_size,
+                            parallel::internal::TBBPartitioner *partitioner = NULL)
   {
 #ifdef DEAL_II_WITH_THREADS
     // only go to the parallel function in case there are at least 4 parallel
@@ -128,15 +129,29 @@ namespace internal
     if (vec_size >= 4*internal::Vector::minimum_parallel_grain_size &&
         MultithreadInfo::n_threads() > 1)
       {
+        // in case the partitioner was used by another thread, create a
+        // private partitioner here for use in the loop (we could also use the
+        // auto partitioner of TBB but that increases code size considerably
+        // without major benefit)
+        tbb::affinity_partitioner *tbb_partitioner = (partitioner == NULL) ?
+                                                     NULL : partitioner->acquire();
+        tbb::affinity_partitioner private_partitioner;
+        if (tbb_partitioner == NULL)
+          tbb_partitioner = &private_partitioner;
+
         tbb::parallel_for (tbb::blocked_range<size_type> (0,
                                                           vec_size,
                                                           internal::Vector::minimum_parallel_grain_size),
                            functor,
-                           tbb::auto_partitioner());
+                           *tbb_partitioner);
+        if (partitioner != NULL)
+          partitioner->release();
       }
     else if (vec_size > 0)
-#endif
       functor(0,vec_size);
+#else
+    functor(0,vec_size);
+#endif
   }
 
 
@@ -604,27 +619,6 @@ namespace internal
         }
     }
   };
-
-  // function used in the header file
-  namespace Vector
-  {
-    template <typename T, typename U>
-    void copy_vector (const dealii::Vector<T> &src,
-                      dealii::Vector<U>       &dst)
-    {
-      if (PointerComparison::equal(&src, &dst))
-        return;
-
-      const typename dealii::Vector<T>::size_type vec_size = src.size();
-      const typename dealii::Vector<U>::size_type dst_size = dst.size();
-      if (dst_size != vec_size)
-        dst.reinit (src, true);
-      dealii::internal::Vector_copy<U,T> copier;
-      copier.dst = dst.begin();
-      copier.src = src.begin();
-      internal::vectorized_transform(copier,vec_size);
-    }
-  }
 }
 
 
@@ -653,7 +647,8 @@ Vector<Number>::Vector (Vector<Number> &&v)
   Subscriptor(std::move(v)),
   vec_size(v.vec_size),
   max_vec_size(v.max_vec_size),
-  val(v.val)
+  val(v.val),
+  thread_loop_partitioner(std::move(v.thread_loop_partitioner))
 {
   v.vec_size = 0;
   v.max_vec_size = 0;
@@ -795,12 +790,123 @@ Vector<Number>::Vector (const TrilinosWrappers::Vector &v)
 #endif
 
 
+template <typename Number>
+inline
+Vector<Number> &
+Vector<Number>::operator= (const Vector<Number> &v)
+{
+  if (PointerComparison::equal(this, &v))
+    return *this;
+
+  if (vec_size != v.vec_size)
+    reinit (v, true);
+
+  dealii::internal::Vector_copy<Number,Number> copier;
+  copier.dst = val;
+  copier.src = v.val;
+  internal::vectorized_transform(copier,vec_size,thread_loop_partitioner.get());
+
+  return *this;
+}
+
+
+
+#ifdef DEAL_II_WITH_CXX11
+template <typename Number>
+inline
+Vector<Number> &
+Vector<Number>::operator= (Vector<Number> &&v)
+{
+  Subscriptor::operator=(std::move(v));
+
+  if (val) deallocate();
+
+  vec_size = v.vec_size;
+  max_vec_size = v.max_vec_size;
+  val = v.val;
+  thread_loop_partitioner = std::move(v.thread_loop_partitioner);
+
+  v.vec_size = 0;
+  v.max_vec_size = 0;
+  v.val = nullptr;
+
+  return *this;
+}
+#endif
+
+
+
+template <typename Number>
+template <typename Number2>
+inline
+Vector<Number> &
+Vector<Number>::operator= (const Vector<Number2> &v)
+{
+  if (vec_size != v.vec_size)
+    reinit (v, true);
+
+  dealii::internal::Vector_copy<Number,Number2> copier;
+  copier.dst = val;
+  copier.src = v.val;
+  internal::vectorized_transform(copier,vec_size,thread_loop_partitioner.get());
+
+  return *this;
+}
+
+
+
+template <typename Number>
+inline
+void Vector<Number>::reinit (const size_type n,
+                             const bool omit_zeroing_entries)
+{
+  thread_loop_partitioner.reset();
+  if (n==0)
+    {
+      if (val) deallocate();
+      val = 0;
+      max_vec_size = vec_size = 0;
+      return;
+    };
+
+  if (n>max_vec_size)
+    {
+      if (val) deallocate();
+      max_vec_size = n;
+      allocate();
+    };
+  vec_size = n;
+  thread_loop_partitioner.reset(new parallel::internal::TBBPartitioner());
+  if (omit_zeroing_entries == false)
+    *this = static_cast<Number>(0);
+}
+
+
+
 template <typename Number>
 template <typename Number2>
 void Vector<Number>::reinit (const Vector<Number2> &v,
                              const bool omit_zeroing_entries)
 {
-  reinit (v.size(), omit_zeroing_entries);
+  thread_loop_partitioner = v.thread_loop_partitioner;
+
+  if (v.vec_size==0)
+    {
+      if (val) deallocate();
+      val = 0;
+      max_vec_size = vec_size = 0;
+      return;
+    };
+
+  if (v.vec_size>max_vec_size)
+    {
+      if (val) deallocate();
+      max_vec_size = v.vec_size;
+      allocate();
+    };
+  vec_size = v.vec_size;
+  if (omit_zeroing_entries == false)
+    *this = static_cast<Number>(0);
 }
 
 
@@ -846,7 +952,7 @@ Vector<Number>::operator= (const Number s)
   setter.dst = val;
   setter.value = s;
 
-  internal::vectorized_transform(setter,vec_size);
+  internal::vectorized_transform(setter,vec_size,thread_loop_partitioner.get());
 
   return *this;
 }
@@ -881,7 +987,7 @@ Vector<Number> &Vector<Number>::operator *= (const Number factor)
   vector_multiply.val = val;
   vector_multiply.factor = factor;
 
-  internal::vectorized_transform(vector_multiply,vec_size);
+  internal::vectorized_transform(vector_multiply,vec_size,thread_loop_partitioner.get());
 
   return *this;
 }
@@ -902,7 +1008,7 @@ Vector<Number>::add (const Number a,
   vector_add_av.val = val;
   vector_add_av.v_val = v.val;
   vector_add_av.factor = a;
-  internal::vectorized_transform(vector_add_av,vec_size);
+  internal::vectorized_transform(vector_add_av,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -924,7 +1030,7 @@ Vector<Number>::sadd (const Number x,
   vector_sadd_xav.v_val = v.val;
   vector_sadd_xav.a = a;
   vector_sadd_xav.x = x;
-  internal::vectorized_transform(vector_sadd_xav,vec_size);
+  internal::vectorized_transform(vector_sadd_xav,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1540,7 +1646,7 @@ Vector<Number> &Vector<Number>::operator -= (const Vector<Number> &v)
   internal::Vectorization_subtract_v<Number> vector_subtract;
   vector_subtract.val = val;
   vector_subtract.v_val = v.val;
-  internal::vectorized_transform(vector_subtract,vec_size);
+  internal::vectorized_transform(vector_subtract,vec_size,thread_loop_partitioner.get());
 
   return *this;
 }
@@ -1555,7 +1661,7 @@ void Vector<Number>::add (const Number v)
   internal::Vectorization_add_factor<Number> vector_add;
   vector_add.val = val;
   vector_add.factor = v;
-  internal::vectorized_transform(vector_add,vec_size);
+  internal::vectorized_transform(vector_add,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1569,7 +1675,7 @@ void Vector<Number>::add (const Vector<Number> &v)
   internal::Vectorization_add_v<Number> vector_add;
   vector_add.val = val;
   vector_add.v_val = v.val;
-  internal::vectorized_transform(vector_add,vec_size);
+  internal::vectorized_transform(vector_add,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1591,7 +1697,7 @@ void Vector<Number>::add (const Number a, const Vector<Number> &v,
   vector_add.w_val = w.val;
   vector_add.a = a;
   vector_add.b = b;
-  internal::vectorized_transform(vector_add,vec_size);
+  internal::vectorized_transform(vector_add,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1609,7 +1715,7 @@ void Vector<Number>::sadd (const Number x,
   vector_sadd.val = val;
   vector_sadd.v_val = v.val;
   vector_sadd.x = x;
-  internal::vectorized_transform(vector_sadd,vec_size);
+  internal::vectorized_transform(vector_sadd,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1634,7 +1740,7 @@ void Vector<Number>::sadd (const Number x, const Number a,
   vector_sadd.x = x;
   vector_sadd.a = a;
   vector_sadd.b = b;
-  internal::vectorized_transform(vector_sadd,vec_size);
+  internal::vectorized_transform(vector_sadd,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1659,7 +1765,7 @@ void Vector<Number>::scale (const Vector<Number> &s)
   internal::Vectorization_scale<Number> vector_scale;
   vector_scale.val = val;
   vector_scale.v_val = s.val;
-  internal::vectorized_transform(vector_scale,vec_size);
+  internal::vectorized_transform(vector_scale,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1690,7 +1796,7 @@ void Vector<Number>::equ (const Number a,
   vector_equ.val = val;
   vector_equ.u_val = u.val;
   vector_equ.a = a;
-  internal::vectorized_transform(vector_equ,vec_size);
+  internal::vectorized_transform(vector_equ,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1734,7 +1840,7 @@ void Vector<Number>::equ (const Number a, const Vector<Number> &u,
   vector_equ.v_val = v.val;
   vector_equ.a = a;
   vector_equ.b = b;
-  internal::vectorized_transform(vector_equ,vec_size);
+  internal::vectorized_transform(vector_equ,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1756,7 +1862,7 @@ void Vector<Number>::equ (const Number a, const Vector<Number> &u,
   vector_equ.a = a;
   vector_equ.b = b;
   vector_equ.c = c;
-  internal::vectorized_transform(vector_equ,vec_size);
+  internal::vectorized_transform(vector_equ,vec_size,thread_loop_partitioner.get());
 }
 
 
@@ -1776,7 +1882,7 @@ void Vector<Number>::ratio (const Vector<Number> &a,
   vector_ratio.val = val;
   vector_ratio.a_val = a.val;
   vector_ratio.b_val = b.val;
-  internal::vectorized_transform(vector_ratio,vec_size);
+  internal::vectorized_transform(vector_ratio,vec_size,thread_loop_partitioner.get());
 }
 
 
diff --git a/source/lac/vector.cc b/source/lac/vector.cc
index 9da88f6780..e7bf7fbe34 100644
--- a/source/lac/vector.cc
+++ b/source/lac/vector.cc
@@ -21,17 +21,7 @@ DEAL_II_NAMESPACE_OPEN
 
 // instantiate for integers:
 template class Vector<int>;
-namespace internal
-{
-  namespace Vector
-  {
-    template void copy_vector<int,double> (const dealii::Vector<int> &,
-                                           dealii::Vector<double> &);
-
-    template void copy_vector<int,int> (const dealii::Vector<int> &,
-                                        dealii::Vector<int> &);
-  }
-}
+template Vector<double> &Vector<double>::operator=<int> (const dealii::Vector<int> &);
 
 template
 void Vector<int>::reinit<double>(const Vector<double> &, const bool);
@@ -42,8 +32,9 @@ void Vector<int>::reinit<double>(const Vector<double> &, const bool);
 // arguments is covered by the default copy constructor and copy operator that
 // is declared separately)
 
-#define TEMPL_COPY_CONSTRUCTOR(S1,S2)                   \
-  template Vector<S1>::Vector (const Vector<S2> &)
+#define TEMPL_COPY_CONSTRUCTOR(S1,S2)                           \
+  template Vector<S1>::Vector (const Vector<S2> &);             \
+  template Vector<S1>& Vector<S1>::operator=<S2> (const Vector<S2> &)
 
 #ifndef DEAL_II_EXPLICIT_CONSTRUCTOR_BUG
 TEMPL_COPY_CONSTRUCTOR(double,float);
diff --git a/source/lac/vector.inst.in b/source/lac/vector.inst.in
index 4a7b11874b..34078f5d90 100644
--- a/source/lac/vector.inst.in
+++ b/source/lac/vector.inst.in
@@ -22,14 +22,6 @@ for (SCALAR : REAL_SCALARS)
 
 for (S1, S2 : REAL_SCALARS)
   {
-    namespace internal
-    \{
-      namespace Vector
-      \{
-      template void copy_vector<S1,S2> (const dealii::Vector<S1>&,
-                                        dealii::Vector<S2>&);
-      \}
-    \}
     template
       bool
       Vector<S1>::operator==<S2>(const Vector<S2>&) const;
@@ -49,14 +41,6 @@ for (SCALAR : COMPLEX_SCALARS)
 
 for (S1, S2 : COMPLEX_SCALARS)
   {
-    namespace internal
-    \{
-      namespace Vector
-      \{
-      template void copy_vector<S1,S2> (const dealii::Vector<S1>&,
-                                        dealii::Vector<S2>&);
-      \}
-    \}
     template
       bool
       Vector<S1>::operator==<S2>(const Vector<S2>&) const;
@@ -69,11 +53,6 @@ for (S1, S2 : COMPLEX_SCALARS)
 
 for (S1: REAL_SCALARS; S2: COMPLEX_SCALARS)
   {
-    namespace internal
-    \{
-      namespace Vector
-      \{
-      template void copy_vector<S1,S2> (const dealii::Vector<S1>&,
-                                        dealii::Vector<S2>&);
-      \}
-    \}
+    template
+      Vector<S2>& Vector<S2>::operator=<S1> (const Vector<S1> &);
+  }
\ No newline at end of file