55,636 research outputs found
Algorithmic patterns for -matrices on many-core processors
In this work, we consider the reformulation of hierarchical ()
matrix algorithms for many-core processors with a model implementation on
graphics processing units (GPUs). matrices approximate specific
dense matrices, e.g., from discretized integral equations or kernel ridge
regression, leading to log-linear time complexity in dense matrix-vector
products. The parallelization of matrix operations on many-core
processors is difficult due to the complex nature of the underlying algorithms.
While previous algorithmic advances for many-core hardware focused on
accelerating existing matrix CPU implementations by many-core
processors, we here aim at totally relying on that processor type. As main
contribution, we introduce the necessary parallel algorithmic patterns allowing
to map the full matrix construction and the fast matrix-vector
product to many-core hardware. Here, crucial ingredients are space filling
curves, parallel tree traversal and batching of linear algebra operations. The
resulting model GPU implementation hmglib is the, to the best of the authors
knowledge, first entirely GPU-based Open Source matrix library of
this kind. We conclude this work by an in-depth performance analysis and a
comparative performance study against a standard matrix library,
highlighting profound speedups of our many-core parallel approach
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
An Evolutionary Algorithm to Optimize Log/Restore Operations within Optimistic Simulation Platforms
In this work we address state recoverability in advanced optimistic simulation systems by proposing an evolutionary algorithm to optimize at run-time the parameters associated with state log/restore activities. Optimization takes place by adaptively selecting for each simulation object both (i) the best suited log mode (incremental vs non-incremental) and (ii) the corresponding optimal value of the log interval. Our performance optimization approach allows to indirectly cope with hidden effects (e.g., locality) as well as cross-object effects due to the variation of log/restore parameters for different simulation objects (e.g., rollback thrashing). Both of them are not captured by literature solutions based on analytical models of the overhead associated with log/restore tasks. More in detail, our evolutionary algorithm dynamically adjusts the log/restore parameters of distinct simulation objects as a whole, towards a well suited configuration. In such a way, we prevent negative effects on performance due to the biasing of the optimization towards individual simulation objects, which may cause reduced gains (or even decrease) in performance just due to the aforementioned hidden and/or cross-object phenomena. We also present an application-transparent implementation of the evolutionary algorithm within the ROme OpTimistic Simulator (ROOT-Sim), namely an open source, general purpose simulation environment designed according to the optimistic synchronization paradigm
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