326,298 research outputs found
A benchmark study on mantle convection in a 3-D spherical shell using CitcomS
As high-performance computing facilities and sophisticated modeling software become available, modeling mantle convection in a three-dimensional (3-D) spherical shell geometry with realistic physical parameters and processes becomes increasingly feasible. However, there is still a lack of comprehensive benchmark studies for 3-D spherical mantle convection. Here we present benchmark and test calculations using a finite element code CitcomS for 3-D spherical convection. Two classes of model calculations are presented: the Stokes' flow and thermal and thermochemical convection. For Stokes' flow, response functions of characteristic flow velocity, topography, and geoid at the surface and core-mantle boundary (CMB) at different spherical harmonic degrees are computed using CitcomS and are compared with those from analytic solutions using a propagator matrix method. For thermal and thermochemical convection, 24 cases are computed with different model parameters including Rayleigh number (7 × 10^3 or 10^5) and viscosity contrast due to temperature dependence (1 to 10^7). For each case, time-averaged quantities at the steady state are computed, including surface and CMB Nussult numbers, RMS velocity, averaged temperature, and maximum and minimum flow velocity, and temperature at the midmantle depth and their standard deviations. For thermochemical convection cases, in addition to outputs for thermal convection, we also quantified entrainment of an initially dense component of the convection and the relative errors in conserving its volume. For nine thermal convection cases that have small viscosity variations and where previously published results were available, we find that the CitcomS results are mostly consistent with these previously published with less than 1% relative differences in globally averaged quantities including Nussult numbers and RMS velocities. For other 15 cases with either strongly temperature-dependent viscosity or thermochemical convection, no previous calculations are available for comparison, but these 15 test calculations from CitcomS are useful for future code developments and comparisons. We also presented results for parallel efficiency for CitcomS, showing that the code achieves 57% efficiency with 3072 cores on Texas Advanced Computing Center's parallel supercomputer Ranger
Algebraic Methods in the Congested Clique
In this work, we use algebraic methods for studying distance computation and
subgraph detection tasks in the congested clique model. Specifically, we adapt
parallel matrix multiplication implementations to the congested clique,
obtaining an round matrix multiplication algorithm, where
is the exponent of matrix multiplication. In conjunction
with known techniques from centralised algorithmics, this gives significant
improvements over previous best upper bounds in the congested clique model. The
highlight results include:
-- triangle and 4-cycle counting in rounds, improving upon the
triangle detection algorithm of Dolev et al. [DISC 2012],
-- a -approximation of all-pairs shortest paths in
rounds, improving upon the -round -approximation algorithm of Nanongkai [STOC 2014], and
-- computing the girth in rounds, which is the first
non-trivial solution in this model.
In addition, we present a novel constant-round combinatorial algorithm for
detecting 4-cycles.Comment: This is work is a merger of arxiv:1412.2109 and arxiv:1412.266
Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches
Background: Large-scale biological jobs on high-performance computing systems
require manual intervention if one or more computing cores on which they
execute fail. This places not only a cost on the maintenance of the job, but
also a cost on the time taken for reinstating the job and the risk of losing
data and execution accomplished by the job before it failed. Approaches which
can proactively detect computing core failures and take action to relocate the
computing core's job onto reliable cores can make a significant step towards
automating fault tolerance.
Method: This paper describes an experimental investigation into the use of
multi-agent approaches for fault tolerance. Two approaches are studied, the
first at the job level and the second at the core level. The approaches are
investigated for single core failure scenarios that can occur in the execution
of parallel reduction algorithms on computer clusters. A third approach is
proposed that incorporates multi-agent technology both at the job and core
level. Experiments are pursued in the context of genome searching, a popular
computational biology application.
Result: The key conclusion is that the approaches proposed are feasible for
automating fault tolerance in high-performance computing systems with minimal
human intervention. In a typical experiment in which the fault tolerance is
studied, centralised and decentralised checkpointing approaches on an average
add 90% to the actual time for executing the job. On the other hand, in the
same experiment the multi-agent approaches add only 10% to the overall
execution time.Comment: Computers in Biology and Medicin
A domain decomposing parallel sparse linear system solver
The solution of large sparse linear systems is often the most time-consuming
part of many science and engineering applications. Computational fluid
dynamics, circuit simulation, power network analysis, and material science are
just a few examples of the application areas in which large sparse linear
systems need to be solved effectively. In this paper we introduce a new
parallel hybrid sparse linear system solver for distributed memory
architectures that contains both direct and iterative components. We show that
by using our solver one can alleviate the drawbacks of direct and iterative
solvers, achieving better scalability than with direct solvers and more
robustness than with classical preconditioned iterative solvers. Comparisons to
well-known direct and iterative solvers on a parallel architecture are
provided.Comment: To appear in Journal of Computational and Applied Mathematic
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