Change index type of number of non-zeros to int64_t

Introduction

Sparse matrices are a key component of the performance critical computations in many numerical simulations. A desire to represent sparse matrices efficiently in memory and optimise , in particular given the evolution of hardware architectures, has over the years led to the development of a plethora of sparse matrix storage formats. Each format is designed to exploit the particular strengths of an architecture or the specific sparsity pattern of a matrix. The choice of the format can be crucial in order to achieve optimal performance. Being able to dynamically select storage formats at runtime is therefore highly desirable.

Morpheus, is a library of sparse matrix storage formats that is designed for efficient and transparent format switching across architectures without introducing prohibitive overheads and that, at the same time, enables the straightforward addition of new storage formats without major application code changes. The library has a functional design which separates the containers that implement the storage formats from the algorithm that implement operations such as multiplication. Each container is aware of the memory space it resides in, and the algorithms require knowledge of the execution space that they will be running in. This design allows Morpheus to target multiple heterogeneous architectures.

To enable efficient yet flexible dynamic switching, Morpheus uses the std::variant introduced in C++17 - hence it requires a C++17 compliant compiler - as a type-safe union. It offers a polymorphic variable called DynamicMatrix which abstracts the notion of sparse matrix storage formats away from users and can hold any of the supported formats internally.

Installation

A very basic installation using CMake is done with:

$ cmake ${srcdir} \
   -DCMAKE_CXX_COMPILER=g++ \
   -DCMAKE_INSTALL_PREFIX=${my_install_folder}
   -DKokkos_ROOT=${kokkos_install_prefix}
$ make
$ make install

which configures, builds and installs a default Morpheus. Note that Morpheus REQUIRES Kokkos v.3.5.0 to be installed. Note that Morpheus inherits the enabled devices and compiler optimization flags from Kokkos.

Once Morpheus is installed In your CMakeLists.txt simply use:

find_package(Morpheus REQUIRED)

Then for every executable or library in your project:

target_link_libraries(myTarget Morpheus::morpheus)

More information can be found at BUILD.md

Documentation

Documentation can be found here.

Supported Formats

Format	Container	Serial	OpenMP	CUDA	HIP	Kokkos
Coo	CooMatrix	yes	yes	yes	yes	no
Csr	CsrMatrix	yes	yes	yes	yes	yes
Dia	DiaMatrix	yes	yes	yes	yes	yes

Specifying a container

To define a container we need to specify four template parameters:

ValueType: The type of the values the container will hold. Valid types must satisfy std::is_arithmetic i.e to be an arithmetic type.
IndexType: The type of the indices the container will hold. Valid types must satisfy std::is_integral i.e to be an integral type.
Layout: Orientation of data in memory. Valid layouts are either Kokkos::LayoutLeft (Column-Major) or Kokkos::LayoutRight (Row-Major).
Space: A memory or execution space supported by Morpheus.
- Valid Memory Spaces are HostSpace, CudaSpace and HIPSpace.
- Valid Execution Spaces are Serial, OpenMP, Cuda and HIP.
- Spaces can be Generic or Custom by specifying the appropriate namespace eg: Morpheus::Generic::HostSpace and Morpheus::Custom::HostSpace represent the generic and custom Host Memory space respectively.
- Note that specifying the execution space will determine in which space each member function will be executed. By not providing a space parameter Morpheus will choose a default one for you.

Note that only ValueType is mandatory. For the rest of the arguments, if not provided, sensible defaults will be selected.

#include <Morpheus_Core.hpp>

int main(){
    /* 
     * ValueType        : double
     * IndexType        : long long
     * Layout           : Kokkos::LayoutRight
     * MemorySpace      : Morpheus::HostSpace 
     */
    Morpheus::CooMatirx<double, long long, Kokkos::LayoutRight, Morpheus::HostSpace> A;  

    /* 
     * ValueType        : double
     * IndexType        : int (Default)
     * Layout           : Kokkos::LayoutRight (Default), 
     * MemorySpace      : Morpheus::DefaultSpace (Default) 
     */
    Morpheus::CsrMatirx<double> B; 
}

Using an Algorithm

For each algorithm the same interface is used across different formats. Algorithms are aware of the execution space they will be executed in and dispatch depends on that too. Currently we support the following algorithms for each of the supported storage formats:

Multiply (Sparse Matrix-Vector Multiplication)
Copy
Convert
Copy by key
Print
Update diagonal
Read/Write matrix market

#include <Morpheus_Core.hpp>

int main(){
    // [ 3.5   *   * ]
    // [  *   1.5  * ]
    Morpheus::CooMatirx<double,  Kokkos::HostSpace> A(2, 3, 2);  
    Morpheus::DenseVector<double,  Kokkos::HostSpace> x(3, 0), y(2, 0); 
    
    // Initializing A
    A.row_indices(0) = 0;
    A.column_indices(0) = 0;
    A.values(0) = 3.5;

    A.row_indices(1) = 1;
    A.column_indices(1) = 1;
    A.values(1) = 1.5;

    // Initializing x
    x(0) = 1; x(1) = 2; x(2) = 3;

    // y = A * x
    Morpheus::Multiply<Morpheus::Serial>(A, x, y);
}

Use of dynamic matrix

The dynamic matrix tries to absrtract away the different supported formats and provide an efficient yet flexible switching mechanism between them. The dynamic matrix follows the same interface as the other containers hence algorithms can be used in the same way.

#include <Morpheus_Core.hpp>

int main(){
    Morpheus::DynamicMatirx<double> A;  // Default format is COO

    A.activate(Morpheus::CSR_FORMAT)    // Active type now is CSR

    A.activate(Morpheus::DIA_FORMAT)    // Active type now is DIA

    A.activate(0)    // Active type now is the first in the DynamicMatrix
}

Building and Running the Tests and Examples

Building the tests and examples requires the GTest testing framework, which ships together with Morpheus.

To build and run the tests add the -DMorpheus_ENABLE_TESTS=On during configuration stage respectively. Note that tests for different devices are enabled based on how Kokkos was configured.

After configuration, to build and run the Serial tests do:

$ cd  ${srcdir}
$ make MorpheusCore_UnitTest_Serial
$ ${srcdir}/core/tests/MorpheusCore_UnitTest_Serial

Same process can be followed for OpenMP, Cuda and HIP.

To build and run the examples add the -DMorpheus_ENABLE_EXAMPLES=On during configuration. Similar process is followed as building the tests.

License

This software is licensed under the Apache License, Version 2.0. See the LICENSE file for details.

	bool exceeds_tolerance(const index_type num_rows,
	const index_type num_entries,
	const index_type num_diagonals) {
	const float max_fill = 10.0;
	const float threshold = 100e6; // 100M entries
	const float size = float(num_diagonals) * float(num_rows);
	const float fill_ratio = size / std::max(1.0f, float(num_entries));

	if (max_fill < fill_ratio && size > threshold) {
	return true;
	} else {
	return false;
	}
	}

	Impl::convert<ExecSpace>(src, temp);
	src.activate(index);
	Impl::convert<ExecSpace>(temp, src);

morpheus-org / morpheus Goto Github PK

morpheus's Introduction

Introduction

Installation

Documentation

Supported Formats

Specifying a container

Using an Algorithm

Use of dynamic matrix

Building and Running the Tests and Examples

License

morpheus's People

Stargazers

Watchers

Forkers

morpheus's Issues

Recommend Projects

Recommend Topics

Recommend Org