Added DefaultInitializationAllocator

Added an allocator that can be used to default initialize elements
of a std::vector on resize(). This is useful to avoid initialization
in performance critical code.

Change-Id: I65bd52a760c68c73555e8bb9e017de353a6e9a81

diff --git a/src/gromacs/utility/defaultinitializationallocator.h b/src/gromacs/utility/defaultinitializationallocator.h
new file mode 100644 (file)
index 0000000..a9e8ac2
--- /dev/null
+++ b/src/gromacs/utility/defaultinitializationallocator.h
@@ -0,0 +1,87 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief Declares an allocator that can use default initialization instead
+ * of values initialization. This is useful for improving performance of
+ * resize() in standard vectors for buffers in performance critical code.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_DEFAULTINITIALIZATIONALLOCATOR_H
+#define GMX_UTILITY_DEFAULTINITIALIZATIONALLOCATOR_H
+
+#include <memory>
+
+namespace gmx
+{
+
+/*! \libinternal \brief Allocator adaptor that interposes construct() calls to
+ * convert value initialization into default initialization.
+ *
+ * This can be used to avoid initialization e.g. on resize() in std::vector.
+ */
+template <typename T, typename A = std::allocator<T> >
+class DefaultInitializationAllocator : public A
+{
+    typedef std::allocator_traits<A> a_t;
+    public:
+        template <typename U> struct rebind {
+            using other =
+                    DefaultInitializationAllocator < U, typename a_t::template rebind_alloc < U>>;
+        };
+
+        using A::A;
+
+        /*! \brief Constructs an object and default initializes */
+        template <typename U>
+        void construct(U* ptr)
+        noexcept(std::is_nothrow_default_constructible<U>::value) {
+            ::new(static_cast<void*>(ptr))U;
+        }
+
+        /*! \brief Constructs an object and value initializes */
+        template <typename U, typename ... Args>
+        void construct(U* ptr, Args && ... args)
+        {
+            a_t::construct(static_cast<A &>(*this),
+                           ptr, std::forward<Args>(args) ...);
+        }
+};
+
+}      // namespace gmx
+
+#endif // GMX_UTILITY_DEFAULTINITIALIZATIONALLOCATOR_H

diff --git a/src/gromacs/utility/tests/CMakeLists.txt b/src/gromacs/utility/tests/CMakeLists.txt
index 6697980f4592d3562b2b3a82fe642e5067acdccb..e917d687cd34e360313bcc01cb842cd3a4a5d660 100644 (file)
--- a/src/gromacs/utility/tests/CMakeLists.txt
+++ b/src/gromacs/utility/tests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -36,6 +36,7 @@ gmx_add_unit_test(UtilityUnitTests utility-test
                   alignedallocator.cpp
                   arrayref.cpp
                   bitmask32.cpp bitmask64.cpp bitmask128.cpp
+                  defaultinitializationallocator.cpp
                   keyvaluetreeserializer.cpp
                   keyvaluetreetransform.cpp
                   gmxregex.cpp

diff --git a/src/gromacs/utility/tests/defaultinitializationallocator.cpp b/src/gromacs/utility/tests/defaultinitializationallocator.cpp
new file mode 100644 (file)
index 0000000..1b517f1
--- /dev/null
+++ b/src/gromacs/utility/tests/defaultinitializationallocator.cpp
@@ -0,0 +1,86 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2019, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for gmx::DefaultInitializationAllocator used in std::vector
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_utility
+ */
+
+#include "gmxpre.h"
+
+#include "gromacs/utility/defaultinitializationallocator.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/gmxassert.h"
+
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+TEST(DefaultInitializationAllocator, PerformsValueInitialization)
+{
+    std::vector < int, DefaultInitializationAllocator < int>> v;
+
+    v.resize(1, 2);
+    EXPECT_EQ(v[0], 2);
+}
+
+TEST(DefaultInitializationAllocator, PerformsNoInitialization)
+{
+    std::vector < int, DefaultInitializationAllocator < int>> v {
+        1, 2, 3
+    };
+
+    const int *oldData = v.data();
+    v.resize(0);
+    v.resize(3);
+    GMX_RELEASE_ASSERT(v.data() == oldData,
+                       "According to the C++ standard std::vector will not reallocate when the capacity is sufficient");
+    // The allocation is the same, so the default initialization should
+    // not have changed the contents
+    EXPECT_EQ(v[0], 1);
+    EXPECT_EQ(v[1], 2);
+    EXPECT_EQ(v[2], 3);
+}
+
+} // namespace
+} // namespace test
+} // namespace gmx