2,040 research outputs found
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
PaPaS: A Portable, Lightweight, and Generic Framework for Parallel Parameter Studies
The current landscape of scientific research is widely based on modeling and
simulation, typically with complexity in the simulation's flow of execution and
parameterization properties. Execution flows are not necessarily
straightforward since they may need multiple processing tasks and iterations.
Furthermore, parameter and performance studies are common approaches used to
characterize a simulation, often requiring traversal of a large parameter
space. High-performance computers offer practical resources at the expense of
users handling the setup, submission, and management of jobs. This work
presents the design of PaPaS, a portable, lightweight, and generic workflow
framework for conducting parallel parameter and performance studies. Workflows
are defined using parameter files based on keyword-value pairs syntax, thus
removing from the user the overhead of creating complex scripts to manage the
workflow. A parameter set consists of any combination of environment variables,
files, partial file contents, and command line arguments. PaPaS is being
developed in Python 3 with support for distributed parallelization using SSH,
batch systems, and C++ MPI. The PaPaS framework will run as user processes, and
can be used in single/multi-node and multi-tenant computing systems. An example
simulation using the BehaviorSpace tool from NetLogo and a matrix multiply
using OpenMP are presented as parameter and performance studies, respectively.
The results demonstrate that the PaPaS framework offers a simple method for
defining and managing parameter studies, while increasing resource utilization.Comment: 8 pages, 6 figures, PEARC '18: Practice and Experience in Advanced
Research Computing, July 22--26, 2018, Pittsburgh, PA, US
Performance analysis and optimization of the JOREK code for many-core CPUs
This report investigates the performance of the JOREK code on the Intel
Knights Landing and Skylake processor architectures. The OpenMP scaling of the
matrix construction part of the code was analyzed and improved synchronization
methods were implemented. A new switch was implemented to control the number of
threads used for the linear equation solver independently from other parts of
the code. The matrix construction subroutine was vectorized, and the data
locality was also improved. These steps led to a factor of two speedup for the
matrix construction
khmer: Working with Big Data in Bioinformatics
We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source
Application
Theano: new features and speed improvements
Theano is a linear algebra compiler that optimizes a user's
symbolically-specified mathematical computations to produce efficient low-level
implementations. In this paper, we present new features and efficiency
improvements to Theano, and benchmarks demonstrating Theano's performance
relative to Torch7, a recently introduced machine learning library, and to
RNNLM, a C++ library targeted at recurrent neural networks.Comment: Presented at the Deep Learning Workshop, NIPS 201
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