53,243 research outputs found
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
Shared-Memory Parallel Maximal Clique Enumeration
We present shared-memory parallel methods for Maximal Clique Enumeration
(MCE) from a graph. MCE is a fundamental and well-studied graph analytics task,
and is a widely used primitive for identifying dense structures in a graph. Due
to its computationally intensive nature, parallel methods are imperative for
dealing with large graphs. However, surprisingly, there do not yet exist
scalable and parallel methods for MCE on a shared-memory parallel machine. In
this work, we present efficient shared-memory parallel algorithms for MCE, with
the following properties: (1) the parallel algorithms are provably
work-efficient relative to a state-of-the-art sequential algorithm (2) the
algorithms have a provably small parallel depth, showing that they can scale to
a large number of processors, and (3) our implementations on a multicore
machine shows a good speedup and scaling behavior with increasing number of
cores, and are substantially faster than prior shared-memory parallel
algorithms for MCE.Comment: 10 pages, 3 figures, proceedings of the 25th IEEE International
Conference on. High Performance Computing, Data, and Analytics (HiPC), 201
High performance computing of explicit schemes for electrofusion jointing process based on message-passing paradigm
The research focused on heterogeneous cluster workstations comprising of a number of CPUs in single and shared architecture platform. The problem statements under consideration involved one dimensional parabolic equations. The thermal process of electrofusion jointing was also discussed. Numerical schemes of explicit type such as AGE, Brian, and Charlies Methods were employed. The parallelization of these methods were based on the domain decomposition technique. Some parallel performance measurement for these methods were also addressed. Temperature profile of the one dimensional radial model of the electrofusion process were also given
Parallel symbolic state-space exploration is difficult, but what is the alternative?
State-space exploration is an essential step in many modeling and analysis
problems. Its goal is to find the states reachable from the initial state of a
discrete-state model described. The state space can used to answer important
questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a
starting point for sophisticated investigations expressed in temporal logic.
Unfortunately, the state space is often so large that ordinary explicit data
structures and sequential algorithms cannot cope, prompting the exploration of
(1) parallel approaches using multiple processors, from simple workstation
networks to shared-memory supercomputers, to satisfy large memory and runtime
requirements and (2) symbolic approaches using decision diagrams to encode the
large structured sets and relations manipulated during state-space generation.
Both approaches have merits and limitations. Parallel explicit state-space
generation is challenging, but almost linear speedup can be achieved; however,
the analysis is ultimately limited by the memory and processors available.
Symbolic methods are a heuristic that can efficiently encode many, but not all,
functions over a structured and exponentially large domain; here the pitfalls
are subtler: their performance varies widely depending on the class of decision
diagram chosen, the state variable order, and obscure algorithmic parameters.
As symbolic approaches are often much more efficient than explicit ones for
many practical models, we argue for the need to parallelize symbolic
state-space generation algorithms, so that we can realize the advantage of both
approaches. This is a challenging endeavor, as the most efficient symbolic
algorithm, Saturation, is inherently sequential. We conclude by discussing
challenges, efforts, and promising directions toward this goal
Computational methods and software systems for dynamics and control of large space structures
Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers
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