9,191 research outputs found
Array programming with NumPy.
Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis
Asynchronous Execution of Python Code on Task Based Runtime Systems
Despite advancements in the areas of parallel and distributed computing, the
complexity of programming on High Performance Computing (HPC) resources has
deterred many domain experts, especially in the areas of machine learning and
artificial intelligence (AI), from utilizing performance benefits of such
systems. Researchers and scientists favor high-productivity languages to avoid
the inconvenience of programming in low-level languages and costs of acquiring
the necessary skills required for programming at this level. In recent years,
Python, with the support of linear algebra libraries like NumPy, has gained
popularity despite facing limitations which prevent this code from distributed
runs. Here we present a solution which maintains both high level programming
abstractions as well as parallel and distributed efficiency. Phylanx, is an
asynchronous array processing toolkit which transforms Python and NumPy
operations into code which can be executed in parallel on HPC resources by
mapping Python and NumPy functions and variables into a dependency tree
executed by HPX, a general purpose, parallel, task-based runtime system written
in C++. Phylanx additionally provides introspection and visualization
capabilities for debugging and performance analysis. We have tested the
foundations of our approach by comparing our implementation of widely used
machine learning algorithms to accepted NumPy standards
cphVB: A System for Automated Runtime Optimization and Parallelization of Vectorized Applications
Modern processor architectures, in addition to having still more cores, also
require still more consideration to memory-layout in order to run at full
capacity. The usefulness of most languages is deprecating as their
abstractions, structures or objects are hard to map onto modern processor
architectures efficiently.
The work in this paper introduces a new abstract machine framework, cphVB,
that enables vector oriented high-level programming languages to map onto a
broad range of architectures efficiently. The idea is to close the gap between
high-level languages and hardware optimized low-level implementations. By
translating high-level vector operations into an intermediate vector bytecode,
cphVB enables specialized vector engines to efficiently execute the vector
operations.
The primary success parameters are to maintain a complete abstraction from
low-level details and to provide efficient code execution across different,
modern, processors. We evaluate the presented design through a setup that
targets multi-core CPU architectures. We evaluate the performance of the
implementation using Python implementations of well-known algorithms: a jacobi
solver, a kNN search, a shallow water simulation and a synthetic stencil
simulation. All demonstrate good performance
HeAT – a Distributed and GPU-accelerated Tensor Framework for Data Analytics
In order to cope with the exponential growth in available data, the efficiency of data analysis and machine learning libraries have recently received increased attention. Although corresponding array-based numerical kernels have been significantly improved, most are limited by the resources available on a single computational node. Consequently, kernels must exploit distributed resources, e.g., distributed memory architectures. To this end, we introduce HeAT, an array-based numerical programming framework for large-scale parallel processing with an easy-to-use NumPy-like API. HeAT utilizes PyTorch as a node-local eager execution engine and distributes the workload via MPI on arbitrarily large high-performance computing systems. It provides both low-level array-based computations, as well as assorted higher-level algorithms. With HeAT, it is possible for a NumPy user to take advantage of their available resources, significantly lowering the barrier to distributed data analysis. Compared with applications written in similar frameworks, HeAT achieves speedups of up to two orders of magnitude
Managing Communication Latency-Hiding at Runtime for Parallel Programming Languages and Libraries
This work introduces a runtime model for managing communication with support
for latency-hiding. The model enables non-computer science researchers to
exploit communication latency-hiding techniques seamlessly. For compiled
languages, it is often possible to create efficient schedules for
communication, but this is not the case for interpreted languages. By
maintaining data dependencies between scheduled operations, it is possible to
aggressively initiate communication and lazily evaluate tasks to allow maximal
time for the communication to finish before entering a wait state. We implement
a heuristic of this model in DistNumPy, an auto-parallelizing version of
numerical Python that allows sequential NumPy programs to run on distributed
memory architectures. Furthermore, we present performance comparisons for eight
benchmarks with and without automatic latency-hiding. The results shows that
our model reduces the time spent on waiting for communication as much as 27
times, from a maximum of 54% to only 2% of the total execution time, in a
stencil application.Comment: PREPRIN
Object-oriented implementations of the MPDATA advection equation solver in C++, Python and Fortran
Three object-oriented implementations of a prototype solver of the advection
equation are introduced. The presented programs are based on Blitz++ (C++),
NumPy (Python), and Fortran's built-in array containers. The solvers include an
implementation of the Multidimensional Positive-Definite Advective Transport
Algorithm (MPDATA). The introduced codes exemplify how the application of
object-oriented programming (OOP) techniques allows to reproduce the
mathematical notation used in the literature within the program code. A
discussion on the tradeoffs of the programming language choice is presented.
The main angles of comparison are code brevity and syntax clarity (and hence
maintainability and auditability) as well as performance. In the case of
Python, a significant performance gain is observed when switching from the
standard interpreter (CPython) to the PyPy implementation of Python. Entire
source code of all three implementations is embedded in the text and is
licensed under the terms of the GNU GPL license
HeAT -- a Distributed and GPU-accelerated Tensor Framework for Data Analytics
To cope with the rapid growth in available data, the efficiency of data
analysis and machine learning libraries has recently received increased
attention. Although great advancements have been made in traditional
array-based computations, most are limited by the resources available on a
single computation node. Consequently, novel approaches must be made to exploit
distributed resources, e.g. distributed memory architectures. To this end, we
introduce HeAT, an array-based numerical programming framework for large-scale
parallel processing with an easy-to-use NumPy-like API. HeAT utilizes PyTorch
as a node-local eager execution engine and distributes the workload on
arbitrarily large high-performance computing systems via MPI. It provides both
low-level array computations, as well as assorted higher-level algorithms. With
HeAT, it is possible for a NumPy user to take full advantage of their available
resources, significantly lowering the barrier to distributed data analysis.
When compared to similar frameworks, HeAT achieves speedups of up to two orders
of magnitude.Comment: 10 pages, 8 figures, 5 listings, 1 tabl
Loo.py: transformation-based code generation for GPUs and CPUs
Today's highly heterogeneous computing landscape places a burden on
programmers wanting to achieve high performance on a reasonably broad
cross-section of machines. To do so, computations need to be expressed in many
different but mathematically equivalent ways, with, in the worst case, one
variant per target machine.
Loo.py, a programming system embedded in Python, meets this challenge by
defining a data model for array-style computations and a library of
transformations that operate on this model. Offering transformations such as
loop tiling, vectorization, storage management, unrolling, instruction-level
parallelism, change of data layout, and many more, it provides a convenient way
to capture, parametrize, and re-unify the growth among code variants. Optional,
deep integration with numpy and PyOpenCL provides a convenient computing
environment where the transition from prototype to high-performance
implementation can occur in a gradual, machine-assisted form
API design for machine learning software: experiences from the scikit-learn project
Scikit-learn is an increasingly popular machine learning li- brary. Written
in Python, it is designed to be simple and efficient, accessible to
non-experts, and reusable in various contexts. In this paper, we present and
discuss our design choices for the application programming interface (API) of
the project. In particular, we describe the simple and elegant interface shared
by all learning and processing units in the library and then discuss its
advantages in terms of composition and reusability. The paper also comments on
implementation details specific to the Python ecosystem and analyzes obstacles
faced by users and developers of the library
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