34,975 research outputs found
Hydra: A Parallel Adaptive Grid Code
We describe the first parallel implementation of an adaptive
particle-particle, particle-mesh code with smoothed particle hydrodynamics.
Parallelisation of the serial code, ``Hydra'', is achieved by using CRAFT, a
Cray proprietary language which allows rapid implementation of a serial code on
a parallel machine by allowing global addressing of distributed memory.
The collisionless variant of the code has already completed several 16.8
million particle cosmological simulations on a 128 processor Cray T3D whilst
the full hydrodynamic code has completed several 4.2 million particle combined
gas and dark matter runs. The efficiency of the code now allows parameter-space
explorations to be performed routinely using particles of each species.
A complete run including gas cooling, from high redshift to the present epoch
requires approximately 10 hours on 64 processors.
In this paper we present implementation details and results of the
performance and scalability of the CRAFT version of Hydra under varying degrees
of particle clustering.Comment: 23 pages, LaTex plus encapsulated figure
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Multiscale and inhomogeneous molecular systems are challenging topics in the
field of molecular simulation. In particular, modeling biological systems in
the context of multiscale simulations and exploring material properties are
driving a permanent development of new simulation methods and optimization
algorithms. In computational terms, those methods require parallelization
schemes that make a productive use of computational resources for each
simulation and from its genesis. Here, we introduce the heterogeneous domain
decomposition approach which is a combination of an heterogeneity sensitive
spatial domain decomposition with an \textit{a priori} rearrangement of
subdomain-walls. Within this approach, the theoretical modeling and
scaling-laws for the force computation time are proposed and studied as a
function of the number of particles and the spatial resolution ratio. We also
show the new approach capabilities, by comparing it to both static domain
decomposition algorithms and dynamic load balancing schemes. Specifically, two
representative molecular systems have been simulated and compared to the
heterogeneous domain decomposition proposed in this work. These two systems
comprise an adaptive resolution simulation of a biomolecule solvated in water
and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure
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