258 research outputs found
QR Factorization of Tall and Skinny Matrices in a Grid Computing Environment
Previous studies have reported that common dense linear algebra operations do
not achieve speed up by using multiple geographical sites of a computational
grid. Because such operations are the building blocks of most scientific
applications, conventional supercomputers are still strongly predominant in
high-performance computing and the use of grids for speeding up large-scale
scientific problems is limited to applications exhibiting parallelism at a
higher level. We have identified two performance bottlenecks in the distributed
memory algorithms implemented in ScaLAPACK, a state-of-the-art dense linear
algebra library. First, because ScaLAPACK assumes a homogeneous communication
network, the implementations of ScaLAPACK algorithms lack locality in their
communication pattern. Second, the number of messages sent in the ScaLAPACK
algorithms is significantly greater than other algorithms that trade flops for
communication. In this paper, we present a new approach for computing a QR
factorization -- one of the main dense linear algebra kernels -- of tall and
skinny matrices in a grid computing environment that overcomes these two
bottlenecks. Our contribution is to articulate a recently proposed algorithm
(Communication Avoiding QR) with a topology-aware middleware (QCG-OMPI) in
order to confine intensive communications (ScaLAPACK calls) within the
different geographical sites. An experimental study conducted on the Grid'5000
platform shows that the resulting performance increases linearly with the
number of geographical sites on large-scale problems (and is in particular
consistently higher than ScaLAPACK's).Comment: Accepted at IPDPS10. (IEEE International Parallel & Distributed
Processing Symposium 2010 in Atlanta, GA, USA.
Instability of precession driven Kelvin modes: Evidence of a detuning effect
We report an experimental study of the instability of a nearly-resonant
Kelvin mode forced by precession in a cylindrical vessel. The instability is
detected above a critical precession ratio via the appearance of peaks in the
temporal power spectrum of pressure fluctuations measured at the end-walls of
the cylinder. The corresponding frequencies can be grouped into frequency sets
satisfying resonance conditions with the forced Kelvin mode. We show that one
triad is associated with a parametric resonance of Kelvin modes. For the first
time, we observe a significant frequency variation of the unstable modes with
the precession ratio. We explain this frequency modification by considering a
detuning mechanism due to the slowdown of the background flow. By introducing a
semi-analytical model, we show that the departure of the flow from the solid
body rotation leads to a modification of the dispersion relation of Kelvin
modes and to a detuning of the resonance condition. Our calculations reproduce
the features of experimental measurements. We also show that a second frequency
set, including one very low frequency as observed in the experiment, does not
exhibit the properties of a parametric resonance between Kelvin modes. Our
observations suggest that it may correspond to the instability of a geostrophic
mode.Comment: 26 pages, 17 figures, accepted by Phys. Rev. Fluid
MPI Applications on Grids: A Topology-Aware Approach
Large Grids are build by aggregating smaller parallel machines through a public long-distance interconnection network (such as the Internet). Therefore, their structure is intrinsically hierarchical. Each level of the network hierarchy gives performances which differ from the other levels in terms of latency and bandwidth. MPI is the de facto standard for programming parallel machines, therefore an attractive solution for programming parallel applications on this kind of grids. However, because of the aforementioned differences of communication performances, the application continuously communicates back and forth between clusters, with a significant impact on performances. In this report, we present an extension of the information provided by the run-time environment of an MPI library, a set of efficient collective operations for grids and a methodology to organize communication patterns within applications with respect to the underlying physical topology, and implement it in a geophysics application
MPI Applications on Grids: A Topology-Aware Approach
Large Grids are build by aggregating smaller parallel machines through a public long-distance interconnection network (such as the Internet). Therefore, their structure is intrinsically hierarchical. Each level of the network hierarchy gives performances which differ from the other levels in terms of latency and bandwidth. MPI is the de facto standard for programming parallel machines, therefore an attractive solution for programming parallel applications on this kind of grids. However, because of the aforementioned differences of communication performances, the application continuously communicates back and forth between clusters, with a significant impact on performances. In this report, we present an extension of the information provided by the run-time environment of an MPI library, a set of efficient collective operations for grids and a methodology to organize communication patterns within applications with respect to the underlying physical topology, and implement it in a geophysics application
Distribution, Approximation and Probabilistic Model Checking
AbstractAPMC is a model checker dedicated to the quantitative verification of fully probabilistic systems against LTL formulas. Using a Monte-Carlo method in order to efficiently approximate the verification of probabilistic specifications, it could be used naturally in a distributed framework. We present here the tool and its distribution scheme, together with extensive performance evaluation, showing the scalability of the method, even on clusters containing 500+ heterogeneous workstations
Impact of Event Logger on Causal Message Logging Protocols for Fault Tolerant {MPI}
International audienceFault tolerance in MPI becomes a main issue in the HPC community. Several approaches are envisioned from user or programmer controlled fault tolerance to fully automatic fault detection and handling. For this last approach, several protocols have been proposed in the literature. In a recent paper, we have demonstrated that uncoordinated checkpointing tolerates higher fault frequency than coordinated checkpointing. Moreover causal message logging protocols have been proved the most efficient message logging technique. These protocols consist in piggybacking non deterministic events to computation message. Several protocols have been proposed in the literature. Their merits are usually evaluated from four metrics: a) piggybacking computation cost, b) piggyback size, c) applications performance and d) fault recovery performance. In this paper, we investigate the benefit of using a stable storage for logging message events in causal message logging protocols. To evaluate the advantage of this technique we implemented three protocols: 1) a classical causal message protocol proposed in Manetho, 2) a state of the art protocol known as LogOn, 3) a light computation cost protocol called Vcausal. We demonstrate a major impact of this stable storage for the three protocols, on the four criteria for micro benchmarks as well as for the NAS benchmark
Multi-criteria checkpointing strategies: response-time versus resource utilization
International audienceFailures are increasingly threatening the efficiency of HPC systems, and current projections of Exascale platforms indicate that rollback recovery, the most convenient method for providing fault tolerance to general-purpose applications, reaches its own limits at such scales. One of the reasons explaining this unnerving situation comes from the focus that has been given to per-application completion time, rather than to platform efficiency. In this paper, we discuss the case of uncoordinated rollback recovery where the idle time spent waiting recovering processors is used to progress a different, independent application from the system batch queue. We then propose an extended model of uncoordinated checkpointing that can discriminate between idle time and wasted computation. We instantiate this model in a simulator to demonstrate that, with this strategy, uncoordinated checkpointing per application completion time is unchanged, while it delivers near-perfect platform efficiency.Voir le résumé en anglais
A Multithreaded Communication Substrate for OpenSHMEM
ABSTRACT OpenSHMEM scalability is strongly dependent on the capability of its communication layer to efficiently handle multiple threads. In this paper, we present an early evaluation of the thread safety specification in the Unified Common Communication Substrate (UCCS) employed in OpenSHMEM. Results demonstrate that thread safety can be provided at an acceptable cost and can improve efficiency for some operations, compared to serializing communication
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