10,182 research outputs found
AutoParallel: A Python module for automatic parallelization and distributed execution of affine loop nests
The last improvements in programming languages, programming models, and
frameworks have focused on abstracting the users from many programming issues.
Among others, recent programming frameworks include simpler syntax, automatic
memory management and garbage collection, which simplifies code re-usage
through library packages, and easily configurable tools for deployment. For
instance, Python has risen to the top of the list of the programming languages
due to the simplicity of its syntax, while still achieving a good performance
even being an interpreted language. Moreover, the community has helped to
develop a large number of libraries and modules, tuning them to obtain great
performance.
However, there is still room for improvement when preventing users from
dealing directly with distributed and parallel computing issues. This paper
proposes and evaluates AutoParallel, a Python module to automatically find an
appropriate task-based parallelization of affine loop nests to execute them in
parallel in a distributed computing infrastructure. This parallelization can
also include the building of data blocks to increase task granularity in order
to achieve a good execution performance. Moreover, AutoParallel is based on
sequential programming and only contains a small annotation in the form of a
Python decorator so that anyone with little programming skills can scale up an
application to hundreds of cores.Comment: Accepted to the 8th Workshop on Python for High-Performance and
Scientific Computing (PyHPC 2018
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
Solution of the Dirac equation in lattice QCD using a domain decomposition method
Efficient algorithms for the solution of partial differential equations on
parallel computers are often based on domain decomposition methods. Schwarz
preconditioners combined with standard Krylov space solvers are widely used in
this context, and such a combination is shown here to perform very well in the
case of the Wilson--Dirac equation in lattice QCD. In particular, with respect
to even-odd preconditioned solvers, the communication overhead is significantly
reduced, which allows the computational work to be distributed over a large
number of processors with only small parallelization losses.Comment: Plain TeX source, 21 pages, figures include
- …