Visualization of large multidimensional data sets by using multi-core CPU, GPU and MPI cluster

Piotr Pawliczek, Witold Dzwinel, David A. Yuen
University of Texas, Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
University of Texas, 2012


   title={Visualization of large multidimensional data sets by using multi-core CPU, GPU and MPI cluster},

   author={Pawliczek, P. and Dzwinel, W. and Yuen, D.A.},



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Multidimensional scaling (MDS) is a very popular and reliable method used in feature extraction and visualization of multidimensional data. The role of MDS is to reconstruct the topology of an original N-dimensional feature space consisting of M feature vectors in target 2-D (3-D) Euclidean space. It can be achieved by minimization of the error – "stress" function – F(||D-d||), where D and d are the MxM dissimilarity matrices in the original and in the target spaces, respectively. However, the stress function is in general a multimodal and multidimensional function for which the complexity of finding global minimum increases exponentially with the number of data. We employ here a robust heuristics based on discrete particle method enabling interactive visualization of data for various types of stress functions. Nevertheless, due to at least O(M^2) memory and time complexity, the method becomes computationally demanding when applied for interactive visualization of data sets involving M~10^4. We present here efficient parallel algorithms developed for various small and pre-medium computer architectures from single and multi-core processors to GPU and multiprocessor MPI clusters. The timings obtained show that the computational efficiency of CUDA implementation of MDS on a PC equipped with a strong GPU board (Tesla M2050 or GeForce 480) is two times greater than its MPI equivalent run on 10 nodes (10x 2xIntel Xeon X5670 = 120 threads) of a professional multiprocessor cluster (HP SL390). We show also that the hybridized two-level MPI/CUDA implementation run on a small cluster of GPU nodes can additionally provide a linear speed-up.
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