Performance Analysis of Parallel Eigensolvers of Two Libraries on BlueGene/P

نویسندگان

  • Inge Gutheil
  • Tommy Berg
  • Johannes Grotendorst
چکیده

Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT (density functional theory) calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Performance of Parallel Eigensolvers on

Many models employed to solve problems in quantum mechanics, such as electronic structure calculations, result in nonlinear eigenproblems. The solution to these problems typically involves iterative schemes requiring the solution of a large symmetric linear eigenproblem during each iteration. This paper evaluates the performance of various popular and new parallel symmetric linear eigensolvers ...

متن کامل

Scaling of Parallel Software for Biological Sequences Alignment and Homology Search on the Supercomputer BlueGene/P

The goal of this paper is to propose the performance evaluation of the scaling of parallel software for biological sequence alignment and homology searching based on blast algorithm for sequence searching and clustalw algorithm for multiple sequence alignment on the supercomputer BlueGene/P for the case study of influenza virus sequences variability and homology searching with human genome.

متن کامل

Parallel Performance Evaluation of Sequence Nucleotide Alignment on the Supercomputer BlueGene/P

Bioinformatics is a scientific area requiring powerful computing resources for exploring large sets of biological data. Sequence alignment is an important method in DNA and protein analysis. BLAST has become the most popular tool and implements a fast heuristic method for sequence alignment and searching. The goal of this paper is to estimate the scalability of parallel sequence alignment on th...

متن کامل

Fourier Transforms for the BlueGene/L Communication Network

A computational kernel of particular importance for many scientific applications is the Fast Fourier Transform (FFT) of multi-dimensional data. A fundamental challenge is the design and implementation of such parallel numerical algorithms to utilise efficiently thousands of nodes. The BlueGene/L is a massively parallel high performance computer organised as a three-dimensional torus of compute ...

متن کامل

Performance Characteristics of Hybrid MPI/OpenMP Implementations of NAS Parallel Benchmarks SP and BT on Large-Scale Multicore Clusters

The NAS Parallel Benchmarks (NPB) are well-known applications with the fixed algorithms for evaluating parallel systems and tools. Multicore clusters provide a natural programming paradigm for hybrid programs, whereby OpenMP can be used with the data sharing with the multicores that comprise a node and MPI can be used with the communication between nodes. In this paper, we use SP and BT benchma...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2012