Merge pull request #148 from ecmwf/feature/eckit-sparsematrix-allocators

Feature/eckit sparsematrix allocators reorganization, new in-place allocator

Author: pmaciel

src/eckit/linalg/CMakeLists.txt

@@ -18,6 +18,14 @@ list( APPEND eckit_la_srcs
       Triplet.h
       Vector.cc
       Vector.h
+      allocator/BufferAllocator.cc
+      allocator/BufferAllocator.h
+      allocator/NonOwningAllocator.cc
+      allocator/NonOwningAllocator.h
+      allocator/StandardAllocator.cc
+      allocator/StandardAllocator.h
+      allocator/StandardContainerAllocator.cc
+      allocator/StandardContainerAllocator.h
       dense/LinearAlgebraGeneric.cc
       dense/LinearAlgebraGeneric.h
       sparse/LinearAlgebraGeneric.cc

src/eckit/linalg/SparseMatrix.cc

@@ -23,7 +23,8 @@
 #include "eckit/exception/Exceptions.h"
 #include "eckit/io/AutoCloser.h"
 #include "eckit/io/MemoryHandle.h"
-#include "eckit/log/Bytes.h"
+#include "eckit/linalg/allocator/BufferAllocator.h"
+#include "eckit/linalg/allocator/StandardAllocator.h"
 #include "eckit/log/Log.h"
 #include "eckit/memory/MemoryBuffer.h"
 #include "eckit/serialisation/FileStream.h"
@@ -37,64 +38,6 @@ static_assert(sizeof(Index) == sizeof(SparseMatrix::UIndex), "sizeof(sizeof(Inde
 static constexpr bool littleEndian = eckit_LITTLE_ENDIAN != 0;
 
 
-//----------------------------------------------------------------------------------------------------------------------
-
-namespace detail {
-
-class StandardAllocator : public SparseMatrix::Allocator {
-public:
-    StandardAllocator() : membuff_(0) {}
-
-    SparseMatrix::Layout allocate(SparseMatrix::Shape& shape) override {
-        if (shape.allocSize() > membuff_.size()) {
-            membuff_.resize(shape.allocSize());
-        }
-
-        SparseMatrix::Layout p;
-
-        char* addr = membuff_;
-
-        p.data_  = reinterpret_cast<Scalar*>(addr);
-        p.outer_ = reinterpret_cast<SparseMatrix::UIndex*>(addr + shape.sizeofData());
-        p.inner_ = reinterpret_cast<Index*>(addr + shape.sizeofData() + shape.sizeofOuter());
-
-        return p;
-    }
-
-    void deallocate(SparseMatrix::Layout p, SparseMatrix::Shape) override {}
-    bool inSharedMemory() const override { return false; }
-    void print(std::ostream& out) const override {
-        out << "StandardAllocator[" << Bytes{static_cast<double>(membuff_.size())} << "]";
-    }
-
-    MemoryBuffer membuff_;
-};
-
-
-class BufferAllocator : public SparseMatrix::Allocator {
-public:
-    BufferAllocator(const MemoryBuffer& buffer) : buffer_(buffer, buffer.size()) {}
-
-    SparseMatrix::Layout allocate(SparseMatrix::Shape& shape) override {
-        SparseMatrix::Layout layout;
-
-        SparseMatrix::load(buffer_.data(), buffer_.size(), layout, shape);
-
-        return layout;
-    }
-
-    void deallocate(SparseMatrix::Layout, SparseMatrix::Shape) override {}
-    bool inSharedMemory() const override { return false; }
-    void print(std::ostream& out) const override {
-        out << "BufferAllocator[" << Bytes{static_cast<double>(buffer_.size())} << "]";
-    }
-
-    MemoryBuffer buffer_;
-};
-
-
-}  // namespace detail
-
 //----------------------------------------------------------------------------------------------------------------------
 
 void SparseMatrix::Shape::print(std::ostream& os) const {
@@ -105,19 +48,19 @@ void SparseMatrix::Shape::print(std::ostream& os) const {
 }
 
 
-SparseMatrix::SparseMatrix(Allocator* alloc) : owner_(alloc != nullptr ? alloc : new detail::StandardAllocator) {
+SparseMatrix::SparseMatrix(Allocator* alloc) : owner_(alloc != nullptr ? alloc : new allocator::StandardAllocator) {
     spm_ = owner_->allocate(shape_);
 }
 
 
 SparseMatrix::SparseMatrix(Size rows, Size cols, Allocator* alloc) :
-    owner_(alloc != nullptr ? alloc : new detail::StandardAllocator) {
+    owner_(alloc != nullptr ? alloc : new allocator::StandardAllocator) {
     reserve(rows, cols, 1);
 }
 
 
 SparseMatrix::SparseMatrix(Size rows, Size cols, const std::vector<Triplet>& triplets) :
-    owner_(new detail::StandardAllocator) {
+    owner_(new allocator::StandardAllocator) {
 
     // Count number of non-zeros, allocate memory 1 triplet per non-zero
     Size nnz = std::count_if(triplets.begin(), triplets.end(), [](const auto& tri) { return tri.nonZero(); });
@@ -163,17 +106,17 @@ SparseMatrix::SparseMatrix(Size rows, Size cols, const std::vector<Triplet>& tri
 }
 
 
-SparseMatrix::SparseMatrix(Stream& s) : owner_(new detail::StandardAllocator) {
+SparseMatrix::SparseMatrix(Stream& s) : owner_(new allocator::StandardAllocator) {
     decode(s);
 }
 
 
-SparseMatrix::SparseMatrix(const MemoryBuffer& buffer) : owner_(new detail::BufferAllocator(buffer)) {
+SparseMatrix::SparseMatrix(const MemoryBuffer& buffer) : owner_(new allocator::BufferAllocator(buffer)) {
     spm_ = owner_->allocate(shape_);
 }
 
 
-SparseMatrix::SparseMatrix(const SparseMatrix& other) : owner_(new detail::StandardAllocator) {
+SparseMatrix::SparseMatrix(const SparseMatrix& other) : owner_(new allocator::StandardAllocator) {
     if (!other.empty()) {  // in case we copy an other that was constructed empty
 
         reserve(other.rows(), other.cols(), other.nonZeros());
@@ -539,7 +482,7 @@ void SparseMatrix::decode(Stream& s) {
 
     reset();
 
-    owner_ = std::make_unique<detail::StandardAllocator>();
+    owner_ = std::make_unique<allocator::StandardAllocator>();
 
     reserve(rows, cols, nnz);
 

src/eckit/linalg/allocator/BufferAllocator.cc

@@ -0,0 +1,45 @@
+/*
+ * (C) Copyright 1996- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+#include "eckit/linalg/allocator/BufferAllocator.h"
+
+#include <ostream>
+
+#include "eckit/log/Bytes.h"
+
+
+namespace eckit::linalg::allocator {
+
+
+BufferAllocator::BufferAllocator(const MemoryBuffer& buffer) : buffer_(buffer, buffer.size()) {}
+
+
+SparseMatrix::Layout BufferAllocator::allocate(SparseMatrix::Shape& shape) {
+    SparseMatrix::Layout layout;
+    SparseMatrix::load(buffer_.data(), buffer_.size(), layout, shape);
+    return layout;
+}
+
+
+void BufferAllocator::deallocate(SparseMatrix::Layout, SparseMatrix::Shape) {}
+
+
+bool BufferAllocator::inSharedMemory() const {
+    return false;
+}
+
+
+void BufferAllocator::print(std::ostream& out) const {
+    out << "BufferAllocator[" << Bytes{static_cast<double>(buffer_.size())} << "]";
+}
+
+
+}  // namespace eckit::linalg::allocator

src/eckit/linalg/allocator/BufferAllocator.h

@@ -0,0 +1,36 @@
+/*
+ * (C) Copyright 1996- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+#pragma once
+
+#include "eckit/linalg/SparseMatrix.h"
+
+#include "eckit/memory/MemoryBuffer.h"
+
+
+namespace eckit::linalg::allocator {
+
+
+class BufferAllocator : public SparseMatrix::Allocator {
+public:
+    BufferAllocator(const MemoryBuffer&);
+
+    SparseMatrix::Layout allocate(SparseMatrix::Shape&) override;
+
+    void deallocate(SparseMatrix::Layout, SparseMatrix::Shape) override;
+    bool inSharedMemory() const override;
+    void print(std::ostream&) const override;
+
+    MemoryBuffer buffer_;
+};
+
+
+}  // namespace eckit::linalg::allocator

src/eckit/linalg/allocator/NonOwningAllocator.cc

@@ -0,0 +1,57 @@
+/*
+ * (C) Copyright 2024- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+#include "eckit/linalg/allocator/NonOwningAllocator.h"
+
+#include <ostream>
+
+#include "eckit/exception/Exceptions.h"
+
+
+namespace eckit::linalg::allocator {
+
+
+NonOwningAllocator::NonOwningAllocator(Size Nr, Size Nc, Size nnz, Index* ia, Index* ja, Scalar* a) :
+    Nr_(Nr), Nc_(Nc), nnz_(nnz), ia_(ia), ja_(ja), a_(a) {
+    ASSERT(ia_ != nullptr);
+    ASSERT(ja_ != nullptr);
+    ASSERT(a_ != nullptr);
+}
+
+
+SparseMatrix::Layout NonOwningAllocator::NonOwningAllocator::allocate(SparseMatrix::Shape& shape) {
+    shape.size_ = nnz_;
+    shape.rows_ = Nr_;
+    shape.cols_ = Nc_;
+
+    SparseMatrix::Layout layout;
+    layout.outer_ = reinterpret_cast<decltype(SparseMatrix::Layout::outer_)>(ia_);
+    layout.inner_ = ja_;
+    layout.data_  = a_;
+
+    return layout;
+}
+
+
+void NonOwningAllocator::deallocate(SparseMatrix::Layout, SparseMatrix::Shape) {}
+
+
+bool NonOwningAllocator::inSharedMemory() const {
+    return false;
+}
+
+
+void NonOwningAllocator::print(std::ostream& out) const {
+    out << "NonOwningAllocator[Nr=" << Nr_ << ",Nc=" << Nc_ << ",nnz=" << nnz_ << "]";
+}
+
+
+}  // namespace eckit::linalg::allocator

src/eckit/linalg/allocator/NonOwningAllocator.h

@@ -0,0 +1,44 @@
+/*
+ * (C) Copyright 2024- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+#pragma once
+
+#include "eckit/linalg/SparseMatrix.h"
+
+
+namespace eckit::linalg::allocator {
+
+
+/**
+ * @brief In-place allocator for sparse matrices, directly mapping supporting arrays including from another
+ * SparseMatrix. It is able to provide a "view".
+ */
+class NonOwningAllocator : public SparseMatrix::Allocator {
+public:
+    NonOwningAllocator(Size Nr, Size Nc, Size nnz, Index* ia, Index* ja, Scalar* a);
+
+    SparseMatrix::Layout allocate(SparseMatrix::Shape&) override;
+
+    void deallocate(SparseMatrix::Layout, SparseMatrix::Shape) override;
+    bool inSharedMemory() const override;
+    void print(std::ostream&) const override;
+
+private:
+    const Size Nr_;
+    const Size Nc_;
+    const Size nnz_;
+    Index* ia_;  // NOTE: not owned
+    Index* ja_;  // NOTE: not owned
+    Scalar* a_;  // NOTE: not owned
+};
+
+
+}  // namespace eckit::linalg::allocator

src/eckit/linalg/allocator/StandardAllocator.cc

@@ -0,0 +1,56 @@
+
+/*
+ * (C) Copyright 1996- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+
+#include "eckit/linalg/allocator/StandardAllocator.h"
+
+#include <ostream>
+
+#include "eckit/log/Bytes.h"
+
+
+namespace eckit::linalg::allocator {
+
+
+StandardAllocator::StandardAllocator() : buffer_(0) {}
+
+
+SparseMatrix::Layout StandardAllocator::allocate(SparseMatrix::Shape& shape) {
+    if (shape.allocSize() > buffer_.size()) {
+        buffer_.resize(shape.allocSize());
+    }
+
+    SparseMatrix::Layout layout;
+
+    char* addr = buffer_;
+
+    layout.data_  = reinterpret_cast<Scalar*>(addr);
+    layout.outer_ = reinterpret_cast<SparseMatrix::UIndex*>(addr + shape.sizeofData());
+    layout.inner_ = reinterpret_cast<Index*>(addr + shape.sizeofData() + shape.sizeofOuter());
+
+    return layout;
+}
+
+
+void StandardAllocator::deallocate(SparseMatrix::Layout p, SparseMatrix::Shape) {}
+
+
+bool StandardAllocator::inSharedMemory() const {
+    return false;
+}
+
+
+void StandardAllocator::print(std::ostream& out) const {
+    out << "StandardAllocator[" << Bytes{static_cast<double>(buffer_.size())} << "]";
+}
+
+
+}  // namespace eckit::linalg::allocator