No Arabic abstract
Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from loss of orthogonality, and therefore its applicability is usually limited to the estimation of the first few components. Here we present an algorithm based on Gram-Schmidt orthogonalization (called GS-PCA), which eliminates this shortcoming of NIPALS-PCA. Also, we discuss the GPU (Graphics Processing Unit) parallel implementation of both NIPALS-PCA and GS-PCA algorithms. The numerical results show that the GPU parallel optimize
In one of the most important methods in Density Functional Theory - the Full-Potential Linearized Augmented Plane Wave (FLAPW) method - dense generalized eigenproblems are organized in long sequences. Moreover each eigenproblem is strongly correlated to the next one in the sequence. We propose a novel approach which exploits such correlation through the use of an eigensolver based on subspace iteration and accelerated with Chebyshev polynomials. The resulting solver, parallelized using the Elemental library framework, achieves excellent scalability and is competitive with current dense parallel eigensolvers.
We consider the problem of sparse signal recovery from a small number of random projections (measurements). This is a well known NP-hard to solve combinatorial optimization problem. A frequently used approach is based on greedy iterative procedures, such as the Matching Pursuit (MP) algorithm. Here, we discuss a fast GPU implementation of the MP algorithm, based on the recently released NVIDIA CUDA API and CUBLAS library. The results show that the GPU version is substantially faster (up to 31 times) than the highly optimized CPU version based on CBLAS (GNU Scientific Library).
In this paper we describe the research and development activities in the Center for Efficient Exascale Discretization within the US Exascale Computing Project, targeting state-of-the-art high-order finite-element algorithms for high-order applications on GPU-accelerated platforms. We discuss the GPU developments in several components of the CEED software stack, including the libCEED, MAGMA, MFEM, libParanumal, and Nek projects. We report performance and capability improvements in several CEED-enabled applications on both NVIDIA and AMD GPU systems.
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective model combining an energy term and a surface term to gain such complexes. The aim of our model is to provide complexes with a low energy and low surface. This model has been validated with two multi-objective genetic algorithms on instances from the literature dedicated to the docking benchmarking.
The detection of insufficiently resolved or ill-conditioned integrand structures is critical for the reliability assessment of the quadrature rule outputs. We discuss a method of analysis of the profile of the integrand at the quadrature knots which allows inferences approaching the theoretical 100% rate of success, under error estimate sharpening. The proposed procedure is of the highest interest for the solution of parametric integrals arising in complex physical models.