232 research outputs found
Load Balancing Unstructured Adaptive Grids for CFD Problems
Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. A dynamic load balancing method is presented that balances the workload across all processors with a global view. After each parallel tetrahedral mesh adaption, the method first determines if the new mesh is sufficiently unbalanced to warrant a repartitioning. If so, the adapted mesh is repartitioned, with new partitions assigned to processors so that the redistribution cost is minimized. The new partitions are accepted only if the remapping cost is compensated by the improved load balance. Results indicate that this strategy is effective for large-scale scientific computations on distributed-memory multiprocessors
diBELLA: Distributed Long Read to Long Read Alignment
We present a parallel algorithm and scalable implementation for genome
analysis, specifically the problem of finding overlaps and alignments for data
from "third generation" long read sequencers. While long sequences of DNA offer
enormous advantages for biological analysis and insight, current long read
sequencing instruments have high error rates and therefore require different
approaches to analysis than their short read counterparts. Our work focuses on
an efficient distributed-memory parallelization of an accurate single-node
algorithm for overlapping and aligning long reads. We achieve scalability of
this irregular algorithm by addressing the competing issues of increasing
parallelism, minimizing communication, constraining the memory footprint, and
ensuring good load balance. The resulting application, diBELLA, is the first
distributed memory overlapper and aligner specifically designed for long reads
and parallel scalability. We describe and present analyses for high level
design trade-offs and conduct an extensive empirical analysis that compares
performance characteristics across state-of-the-art HPC systems as well as a
commercial cloud architectures, highlighting the advantages of state-of-the-art
network technologies.Comment: This is the authors' preprint of the article that appears in the
proceedings of ICPP 2019, the 48th International Conference on Parallel
Processin
Performance Evaluation of Plasma and Astrophysics Applications on Modern Parallel Vector Systems
Abstract. The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end computing (HEC) platforms, primarily because of their generality, scalability, and cost effectiveness. However, the growing gap between sustained and peak performance for full-scale scientific applications on such platforms has become major concern in high performance computing. The latest generation of custom-built parallel vector systems have the potential to address this concern for numerical algorithms with sufficient regularity in their computational structure. In this work, we explore two and three dimensional implementations of a plasma physics application, as well as a leading astrophysics package on some of today's most powerful supercomputing platforms. Results compare performance between the the vector-based Cray X1, Earth Simulator, and newly-released NEC SX-8, with the commodity-based superscalar platforms of the IBM Power3, Intel Itanium2, and AMD Opteron. Overall results show that the SX-8 attains unprecedented aggregate performance across our evaluated applications
Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation
Across a variety of scientific disciplines, sparse inverse covariance
estimation is a popular tool for capturing the underlying dependency
relationships in multivariate data. Unfortunately, most estimators are not
scalable enough to handle the sizes of modern high-dimensional data sets (often
on the order of terabytes), and assume Gaussian samples. To address these
deficiencies, we introduce HP-CONCORD, a highly scalable optimization method
for estimating a sparse inverse covariance matrix based on a regularized
pseudolikelihood framework, without assuming Gaussianity. Our parallel proximal
gradient method uses a novel communication-avoiding linear algebra algorithm
and runs across a multi-node cluster with up to 1k nodes (24k cores), achieving
parallel scalability on problems with up to ~819 billion parameters (1.28
million dimensions); even on a single node, HP-CONCORD demonstrates
scalability, outperforming a state-of-the-art method. We also use HP-CONCORD to
estimate the underlying dependency structure of the brain from fMRI data, and
use the result to identify functional regions automatically. The results show
good agreement with a clustering from the neuroscience literature.Comment: Main paper: 15 pages, appendix: 24 page
Recommended from our members
Towards Ultra-High Resolution Models of Climate and Weather
We present a speculative extrapolation of the performance aspects of an atmospheric general circulation model to ultra-high resolution and describe alternative technological paths to realize integration of such a model in the relatively near future. Due to a superlinear scaling of the computational burden dictated by stability criterion, the solution of the equations of motion dominate the calculation at ultra-high resolutions. From this extrapolation, it is estimated that a credible kilometer scale atmospheric model would require at least a sustained ten petaflop computer to provide scientifically useful climate simulations. Our design study portends an alternate strategy for practical power-efficient implementations of petaflop scale systems. Embedded processor technology could be exploited to tailor a custom machine designed to ultra-high climate model specifications at relatively affordable cost and power considerations. The major conceptual changes required by a kilometer scale climate model are certain to be difficult to implement. Although the hardware, software, and algorithms are all equally critical in conducting ultra-high climate resolution studies, it is likely that the necessary petaflop computing technology will be available in advance of a credible kilometer scale climate model
Extreme Scale De Novo Metagenome Assembly
Metagenome assembly is the process of transforming a set of short,
overlapping, and potentially erroneous DNA segments from environmental samples
into the accurate representation of the underlying microbiomes's genomes.
State-of-the-art tools require big shared memory machines and cannot handle
contemporary metagenome datasets that exceed Terabytes in size. In this paper,
we introduce the MetaHipMer pipeline, a high-quality and high-performance
metagenome assembler that employs an iterative de Bruijn graph approach.
MetaHipMer leverages a specialized scaffolding algorithm that produces long
scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is
end-to-end parallelized using the Unified Parallel C language and therefore can
run seamlessly on shared and distributed-memory systems. Experimental results
show that MetaHipMer matches or outperforms the state-of-the-art tools in terms
of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and
is able to assemble previously intractable grand challenge metagenomes. We
demonstrate the unprecedented capability of MetaHipMer by computing the first
full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion
reads - size 2.6 TBytes.Comment: Accepted to SC1
Recommended from our members
Performance Evaluation of Plasma and Astrophysics Applications onModern Parallel Vector Systems
The last decade has witnessed a rapid proliferation ofsuperscalar cache-based microprocessors to build high-endcomputing (HEC)platforms, primarily because of their generality,scalability, and costeffectiveness. However, the growing gap between sustained and peakperformance for full-scale scientific applications on such platforms hasbecome major concern in highperformance computing. The latest generationof custom-built parallel vector systems have the potential to addressthis concern for numerical algorithms with sufficient regularity in theircomputational structure. In this work, we explore two and threedimensional implementations of a plasma physics application, as well as aleading astrophysics package on some of today's most powerfulsupercomputing platforms. Results compare performance between the thevector-based Cray X1, EarthSimulator, and newly-released NEC SX- 8, withthe commodity-based superscalar platforms of the IBM Power3, IntelItanium2, and AMDOpteron. Overall results show that the SX-8 attainsunprecedented aggregate performance across our evaluatedapplications
Efficient Helicopter Aerodynamic and Aeroacoustic Predictions on Parallel Computers
This paper presents parallel implementations of two codes used in a combined CFD/Kirchhoff methodology to predict the aerodynamics and aeroacoustics properties of helicopters. The rotorcraft Navier-Stokes code, TURNS, computes the aerodynamic flowfield near the helicopter blades and the Kirchhoff acoustics code computes the noise in the far field, using the TURNS solution as input. The overall parallel strategy adds MPI message passing calls to the existing serial codes to allow for communication between processors. As a result, the total code modifications required for parallel execution are relatively small. The biggest bottleneck in running the TURNS code in parallel comes from the LU-SGS algorithm that solves the implicit system of equations. We use a new hybrid domain decomposition implementation of LU-SGS to obtain good parallel performance on the SP-2. TURNS demonstrates excellent parallel speedups for quasi-steady and unsteady three-dimensional calculations of a helicopter blade in forward flight. The execution rate attained by the code on 114 processors is six times faster than the same cases run on one processor of the Cray C-90. The parallel Kirchhoff code also shows excellent parallel speedups and fast execution rates. As a performance demonstration, unsteady acoustic pressures are computed at 1886 far-field observer locations for a sample acoustics problem. The calculation requires over two hundred hours of CPU time on one C-90 processor but takes only a few hours on 80 processors of the SP2. The resultant far-field acoustic field is analyzed with state of-the-art audio and video rendering of the propagating acoustic signals
- …