20,123 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
Towards a more realistic sink particle algorithm for the RAMSES code
We present a new sink particle algorithm developed for the Adaptive Mesh
Refinement code RAMSES. Our main addition is the use of a clump finder to
identify density peaks and their associated regions (the peak patches). This
allows us to unambiguously define a discrete set of dense molecular cores as
potential sites for sink particle formation. Furthermore, we develop a new
scheme to decide if the gas in which a sink could potentially form, is indeed
gravitationally bound and rapidly collapsing. This is achieved using a general
integral form of the virial theorem, where we use the curvature in the
gravitational potential to correctly account for the background potential. We
detail all the necessary steps to follow the evolution of sink particles in
turbulent molecular cloud simulations, such as sink production, their
trajectory integration, sink merging and finally the gas accretion rate onto an
existing sink. We compare our new recipe for sink formation to other popular
implementations. Statistical properties such as the sink mass function, the
average sink mass and the sink multiplicity function are used to evaluate the
impact that our new scheme has on accurately predicting fundamental quantities
such as the stellar initial mass function or the stellar multiplicity function.Comment: submitted to MNRAS, 24 pages, 19 figures, 5 table
Design and optimization of a portable LQCD Monte Carlo code using OpenACC
The present panorama of HPC architectures is extremely heterogeneous, ranging
from traditional multi-core CPU processors, supporting a wide class of
applications but delivering moderate computing performance, to many-core GPUs,
exploiting aggressive data-parallelism and delivering higher performances for
streaming computing applications. In this scenario, code portability (and
performance portability) become necessary for easy maintainability of
applications; this is very relevant in scientific computing where code changes
are very frequent, making it tedious and prone to error to keep different code
versions aligned. In this work we present the design and optimization of a
state-of-the-art production-level LQCD Monte Carlo application, using the
directive-based OpenACC programming model. OpenACC abstracts parallel
programming to a descriptive level, relieving programmers from specifying how
codes should be mapped onto the target architecture. We describe the
implementation of a code fully written in OpenACC, and show that we are able to
target several different architectures, including state-of-the-art traditional
CPUs and GPUs, with the same code. We also measure performance, evaluating the
computing efficiency of our OpenACC code on several architectures, comparing
with GPU-specific implementations and showing that a good level of
performance-portability can be reached.Comment: 26 pages, 2 png figures, preprint of an article submitted for
consideration in International Journal of Modern Physics
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