10,924 research outputs found
Practical Sparse Matrices in C++ with Hybrid Storage and Template-Based Expression Optimisation
Despite the importance of sparse matrices in numerous fields of science,
software implementations remain difficult to use for non-expert users,
generally requiring the understanding of underlying details of the chosen
sparse matrix storage format. In addition, to achieve good performance, several
formats may need to be used in one program, requiring explicit selection and
conversion between the formats. This can be both tedious and error-prone,
especially for non-expert users. Motivated by these issues, we present a
user-friendly and open-source sparse matrix class for the C++ language, with a
high-level application programming interface deliberately similar to the widely
used MATLAB language. This facilitates prototyping directly in C++ and aids the
conversion of research code into production environments. The class internally
uses two main approaches to achieve efficient execution: (i) a hybrid storage
framework, which automatically and seamlessly switches between three underlying
storage formats (compressed sparse column, Red-Black tree, coordinate list)
depending on which format is best suited and/or available for specific
operations, and (ii) a template-based meta-programming framework to
automatically detect and optimise execution of common expression patterns.
Empirical evaluations on large sparse matrices with various densities of
non-zero elements demonstrate the advantages of the hybrid storage framework
and the expression optimisation mechanism.Comment: extended and revised version of an earlier conference paper
arXiv:1805.0338
Practical Sparse Matrices in C++ with Hybrid Storage and Template-Based Expression Optimisation
Despite the importance of sparse matrices in numerous fields of science,
software implementations remain difficult to use for non-expert users,
generally requiring the understanding of underlying details of the chosen
sparse matrix storage format. In addition, to achieve good performance, several
formats may need to be used in one program, requiring explicit selection and
conversion between the formats. This can be both tedious and error-prone,
especially for non-expert users. Motivated by these issues, we present a
user-friendly and open-source sparse matrix class for the C++ language, with a
high-level application programming interface deliberately similar to the widely
used MATLAB language. This facilitates prototyping directly in C++ and aids the
conversion of research code into production environments. The class internally
uses two main approaches to achieve efficient execution: (i) a hybrid storage
framework, which automatically and seamlessly switches between three underlying
storage formats (compressed sparse column, Red-Black tree, coordinate list)
depending on which format is best suited and/or available for specific
operations, and (ii) a template-based meta-programming framework to
automatically detect and optimise execution of common expression patterns.
Empirical evaluations on large sparse matrices with various densities of
non-zero elements demonstrate the advantages of the hybrid storage framework
and the expression optimisation mechanism.Comment: extended and revised version of an earlier conference paper
arXiv:1805.0338
GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU
High-performance implementations of graph algorithms are challenging to
implement on new parallel hardware such as GPUs because of three challenges:
(1) the difficulty of coming up with graph building blocks, (2) load imbalance
on parallel hardware, and (3) graph problems having low arithmetic intensity.
To address some of these challenges, GraphBLAS is an innovative, on-going
effort by the graph analytics community to propose building blocks based on
sparse linear algebra, which will allow graph algorithms to be expressed in a
performant, succinct, composable and portable manner. In this paper, we examine
the performance challenges of a linear-algebra-based approach to building graph
frameworks and describe new design principles for overcoming these bottlenecks.
Among the new design principles is exploiting input sparsity, which allows
users to write graph algorithms without specifying push and pull direction.
Exploiting output sparsity allows users to tell the backend which values of the
output in a single vectorized computation they do not want computed.
Load-balancing is an important feature for balancing work amongst parallel
workers. We describe the important load-balancing features for handling graphs
with different characteristics. The design principles described in this paper
have been implemented in "GraphBLAST", the first high-performance linear
algebra-based graph framework on NVIDIA GPUs that is open-source. The results
show that on a single GPU, GraphBLAST has on average at least an order of
magnitude speedup over previous GraphBLAS implementations SuiteSparse and GBTL,
comparable performance to the fastest GPU hardwired primitives and
shared-memory graph frameworks Ligra and Gunrock, and better performance than
any other GPU graph framework, while offering a simpler and more concise
programming model.Comment: 50 pages, 14 figures, 14 table
GHOST: Building blocks for high performance sparse linear algebra on heterogeneous systems
While many of the architectural details of future exascale-class high
performance computer systems are still a matter of intense research, there
appears to be a general consensus that they will be strongly heterogeneous,
featuring "standard" as well as "accelerated" resources. Today, such resources
are available as multicore processors, graphics processing units (GPUs), and
other accelerators such as the Intel Xeon Phi. Any software infrastructure that
claims usefulness for such environments must be able to meet their inherent
challenges: massive multi-level parallelism, topology, asynchronicity, and
abstraction. The "General, Hybrid, and Optimized Sparse Toolkit" (GHOST) is a
collection of building blocks that targets algorithms dealing with sparse
matrix representations on current and future large-scale systems. It implements
the "MPI+X" paradigm, has a pure C interface, and provides hybrid-parallel
numerical kernels, intelligent resource management, and truly heterogeneous
parallelism for multicore CPUs, Nvidia GPUs, and the Intel Xeon Phi. We
describe the details of its design with respect to the challenges posed by
modern heterogeneous supercomputers and recent algorithmic developments.
Implementation details which are indispensable for achieving high efficiency
are pointed out and their necessity is justified by performance measurements or
predictions based on performance models. The library code and several
applications are available as open source. We also provide instructions on how
to make use of GHOST in existing software packages, together with a case study
which demonstrates the applicability and performance of GHOST as a component
within a larger software stack.Comment: 32 pages, 11 figure
Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi
Intel Xeon Phi is a recently released high-performance coprocessor which
features 61 cores each supporting 4 hardware threads with 512-bit wide SIMD
registers achieving a peak theoretical performance of 1Tflop/s in double
precision. Many scientific applications involve operations on large sparse
matrices such as linear solvers, eigensolver, and graph mining algorithms. The
core of most of these applications involves the multiplication of a large,
sparse matrix with a dense vector (SpMV). In this paper, we investigate the
performance of the Xeon Phi coprocessor for SpMV. We first provide a
comprehensive introduction to this new architecture and analyze its peak
performance with a number of micro benchmarks. Although the design of a Xeon
Phi core is not much different than those of the cores in modern processors,
its large number of cores and hyperthreading capability allow many application
to saturate the available memory bandwidth, which is not the case for many
cutting-edge processors. Yet, our performance studies show that it is the
memory latency not the bandwidth which creates a bottleneck for SpMV on this
architecture. Finally, our experiments show that Xeon Phi's sparse kernel
performance is very promising and even better than that of cutting-edge general
purpose processors and GPUs
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