Efficient Multithreaded Untransposed, Transposed Or Symmetric Sparse
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Soluciones Para Entornos HPC
Soluciones para entornos HPC Dr. Abel Francisco Paz Gallardo. IT Manager / Project Leader @ CETA-Ciemat [email protected] V Jornadas de Supercomputación y Avances en Tecnología CETA-Ciemat/ Noviembre 2012 Soluciones para entornos HPC Abel Francisco Paz Gallardo EXTREMADURA RESEARCH CENTER FOR ADVANCED TECHNOLOGIES INDICE 1 HPC… ¿Qué? ¿Cómo? . 2 Computación. (GPGPU,. UMA/NUMA,. etc.) 3 Almacenamiento en HPC . 4 Gestión de recursos . Soluciones para entornos HPC CETA-Ciemat/ Noviembre 2012 Soluciones para entornos HPC Abel Francisco Paz Gallardo 2 EXTREMADURA RESEARCH CENTER FOR ADVANCED TECHNOLOGIES 1 HPC… ¿Qué? ¿Cómo? ¿Qué? o HPC – High Performance Computing (Computación de alto rendimiento) o Objetivo principal: Resolución de problemas complejos ¿Cómo? Tres pilares fundamentales: o Procesamiento = Cómputo o Almacenamiento o Gestión de recursos HPC = + + CETA-Ciemat/ Noviembre 2012 Soluciones para entornos HPC Abel Francisco Paz Gallardo EXTREMADURA RESEARCH CENTER FOR ADVANCED TECHNOLOGIES 2 Computación (GPGPU, NUMA, etc.) ¿Qué es una GPU? Primera búsqueda en 2006: - Gas Particulate Unit Unidad de partículas de gas ¿? GPU = Graphics Processing Unit (Unidad de procesamiento gráfico). CETA-Ciemat/ Noviembre 2012 Soluciones para entornos HPC Abel Francisco Paz Gallardo EXTREMADURA RESEARCH CENTER FOR ADVANCED TECHNOLOGIES 2 Computación (GPGPU, NUMA, etc.) La cuestión es… Si una GPU en un videojuego procesa miles de polígonos, texturas y sombras en tiempo real… ¿Por qué no utilizar esta tecnología para procesamiento de datos? CETA-Ciemat/ -
Easybuild Documentation Release 20210907.0
EasyBuild Documentation Release 20210907.0 Ghent University Tue, 07 Sep 2021 08:55:41 Contents 1 What is EasyBuild? 3 2 Concepts and terminology 5 2.1 EasyBuild framework..........................................5 2.2 Easyblocks................................................6 2.3 Toolchains................................................7 2.3.1 system toolchain.......................................7 2.3.2 dummy toolchain (DEPRECATED) ..............................7 2.3.3 Common toolchains.......................................7 2.4 Easyconfig files..............................................7 2.5 Extensions................................................8 3 Typical workflow example: building and installing WRF9 3.1 Searching for available easyconfigs files.................................9 3.2 Getting an overview of planned installations.............................. 10 3.3 Installing a software stack........................................ 11 4 Getting started 13 4.1 Installing EasyBuild........................................... 13 4.1.1 Requirements.......................................... 14 4.1.2 Using pip to Install EasyBuild................................. 14 4.1.3 Installing EasyBuild with EasyBuild.............................. 17 4.1.4 Dependencies.......................................... 19 4.1.5 Sources............................................. 21 4.1.6 In case of installation issues. .................................. 22 4.2 Configuring EasyBuild.......................................... 22 4.2.1 Supported configuration -
Interfacing Epetra to the RSB Sparse Matrix Format for Shared-Memory Performance
Interfacing Epetra to the RSB sparse matrix format for shared-memory performance Michele Martone High Level Support Team Max Planck Institute for Plasma Physics Garching bei M¨unchen,Germany 5th European Trilinos User Group Meeting Garching bei M¨unchen, Germany April 19, 2016 1 / 18 Background: sparse kernels can be performance critical Sparse kernel Operation definition1 SpMV: Matrix-Vector Multiply \y β y + α A x" SpMV-T: (Transposed) \y β y + α AT x" SpSV : Triangular Solve \x α L−1 x" SpSV-T : (Transposed) \x α L−T x" Epetra_... Epetra_CrsMatrix I CRS (Compressed Row Storage) versatile and straightforward I class Epetra CrsMatrix can rely on Intel MKL 1A is a sparse matrix, L sparse triangular, x; y vectors or multi-vectors, α; β scalars. 2 / 18 Background: optimized sparse matrix classes Epetra_... Epetra_CrsMatrix Epetra_OskiMatrix I OSKI (Optimized Sparse Kernels Interface) library, by R.Vuduc I kernels for iterative methods, e.g. SpMV, SpSV I autotuning framework I OSKI + Epetra = class Epetra OskiMatrix, by I.Karlin 3 / 18 Background: librsb I a stable \Sparse BLAS"-like kernels library: I Sparse BLAS API (blas sparse.h) I own API (rsb.h) I LGPLv3 licensed I librsb-1.2 at http://librsb.sourceforge.net/ I OpenMP threaded 2 I C/C++/FORTRAN interface 2ISO-C-BINDING for own and F90 for Sparse BLAS 4 / 18 What can librsb do 3 I can be multiple times faster than Intel MKL's CRS in I symmetric/transposed sparse matrix multiply (SpMV) I multi-RHS (SpMM) I large matrices I threaded SpSV/SpSM (sparse triangular solve) I iterative methods ops: scaling, extraction, update, .. -
Using Machine Learning to Improve Dense and Sparse Matrix Multiplication Kernels
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2019 Using machine learning to improve dense and sparse matrix multiplication kernels Brandon Groth Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Applied Mathematics Commons, and the Computer Sciences Commons Recommended Citation Groth, Brandon, "Using machine learning to improve dense and sparse matrix multiplication kernels" (2019). Graduate Theses and Dissertations. 17688. https://lib.dr.iastate.edu/etd/17688 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Using machine learning to improve dense and sparse matrix multiplication kernels by Brandon Micheal Groth A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Applied Mathematics Program of Study Committee: Glenn R. Luecke, Major Professor James Rossmanith Zhijun Wu Jin Tian Kris De Brabanter The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2019 Copyright c Brandon Micheal Groth, 2019. All rights reserved. ii DEDICATION I would like to dedicate this thesis to my wife Maria and our puppy Tiger. -
Best Practice Guide
Best Practice Guide - Application porting and code-optimization activities for European HPC systems Sebastian Lührs, JSC, Forschungszentrum Jülich GmbH, Germany Björn Dick, HLRS, Germany Chris Johnson, EPCC, United Kingdom Luca Marsella, CSCS, Switzerland Gerald Mathias, LRZ, Germany Cristian Morales, BSC, Spain Lilit Axner, KTH, Sweden Anastasiia Shamakina, HLRS, Germany Hayk Shoukourian, LRZ, Germany 30-04-2020 1 Best Practice Guide - Application porting and code-optimization ac- tivities for European HPC systems Table of Contents 1. Introduction .............................................................................................................................. 3 2. EuroHPC Joint Undertaking ........................................................................................................ 3 3. Application porting and optimization activities in PRACE ................................................................ 4 3.1. Preparatory Access .......................................................................................................... 4 3.1.1. Overview ............................................................................................................ 4 3.1.2. Application and review processes ............................................................................ 4 3.1.3. Project white papers .............................................................................................. 4 3.2. SHAPE ........................................................................................................................ -
Application-Level Fault Tolerance and Resilience in HPC Applications
Doctoral Thesis Application-level Fault Tolerance and Resilience in HPC Applications Nuria Losada 2018 Application-level Fault Tolerance and Resilience in HPC Applications Nuria Losada Doctoral Thesis July 2018 PhD Advisors: Mar´ıaJ. Mart´ın Patricia Gonz´alez PhD Program in Information Technology Research Dra. Mar´ıaJos´eMart´ınSantamar´ıa Dra. Patricia Gonz´alezG´omez Profesora Titular de Universidad Profesora Titular de Universidad Dpto. de Ingenier´ıade Computadores Dpto. de Ingenier´ıade Computadores Universidade da Coru~na Universidade da Coru~na CERTIFICAN Que la memoria titulada \Application-level Fault Tolerance and Resilience in HPC Applications" ha sido realizada por D~na.Nuria Losada L´opez-Valc´arcelbajo nuestra direcci´onen el Departamento de Ingenier´ıade Computadores de la Universidade da Coru~na,y concluye la Tesis Doctoral que presenta para optar al grado de Doctora en Ingenier´ıaInform´aticacon la Menci´onde Doctor Internacional. En A Coru~na,a 26 de Julio de 2018 Fdo.: Mar´ıaJos´eMart´ınSantamar´ıa Fdo.: Patricia Gonz´alezG´omez Directora de la Tesis Doctoral Directora de la Tesis Doctoral Fdo.: Nuria Losada L´opez-Valc´arcel Autora de la Tesis Doctoral A todos los que lo hab´eishecho posible. Acknowledgments I would especially like to thank my advisors, Mar´ıaand Patricia, for all their support, hard work, and all the opportunities they've handed me. I consider my- self very lucky to have worked with them during these years. I would also like to thank Gabriel and Basilio for their collaboration and valuable contributions to the development of this work. I would like to say thanks to all my past and present colleagues in the Computer Architecture Group and in the Faculty of Informatics for their fellowship, support, and all the coffee breaks and dinners we held together. -
Enabling the Deployment of Virtual Clusters on the VCOC Experiment of the Bonfire Federated Cloud
CLOUD COMPUTING 2012 : The Third International Conference on Cloud Computing, GRIDs, and Virtualization Enabling the Deployment of Virtual Clusters on the VCOC Experiment of the BonFIRE Federated Cloud Raul Valin, Luis M. Carril, J. Carlos Mouri˜no, Carmen Cotelo, Andr´es G´omez, and Carlos Fern´andez Supercomputing Centre of Galicia (CESGA) Santiago de Compostela, Spain Email: rvalin,lmcarril,jmourino,carmen,agomez,[email protected] Abstract—The BonFIRE project has developed a federated OpenCirrus. BonFIRE offers an experimenter control of cloud that supports experimentation and testing of innovative available resources. It supports dynamically creating, updat- scenarios from the Internet of Services research community. ing, reading and deleting resources throughout the lifetime Virtual Clusters on federated Cloud sites (VCOC) is one of the supported experiments of the BonFIRE Project whose main of an experiment. Compute resources can be configured with objective is to evaluate the feasibility of using multiple Cloud application-specific contextualisation information that can environments to deploy services which need the allocation provide important configuration information to the virtual of a large pool of CPUs or virtual machines to a single machine (VM); this information is available to software user (as High Throughput Computing or High Performance applications after the machine is started. BonFIRE also Computing). In this work, we describe the experiment agent, a tool developed on the VCOC experiment to facilitate the supports elasticity within an experiment, i.e., dynamically automatic deployment and monitoring of virtual clusters on create, update and destroy resources from a running node of the BonFIRE federated cloud. This tool was employed in the experiment, including cross-testbed elasticity. -
Searching for Genetic Interactions in Complex Disease by Using Distance Correlation
Searching for genetic interactions in complex disease by using distance correlation Fernando Castro-Prado, University and Health Research Institute of Santiago de Compostela, Spain. E-mail: [email protected] Javier Costas Health Research Institute of Santiago de Compostela, Spain. and Wenceslao González-Manteiga and David R. Penas University of Santiago de Compostela, Spain. Summary. Understanding epistasis (genetic interaction) may shed some light on the ge- nomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an association measure that characterises general statistical independence between random variables, not only the linear one. Here, we propose distance correlation as a novel tool for the detection of epistasis from case-control data of single nucleotide polymorphisms (SNPs). This approach will be developed both theoretically (mathematical statistics, in a context of high-dimensional statistical inference) and from an applied point of view (simulations and real datasets). Keywords: Association measures; Distance correlation; Epistasis; Genomics; High- dimensional statistical inference; Schizophrenia 1. Introduction The application field that motivates the present article is going to be explained here- inafter. The starting point is a genomic problem, whose importance and interest will be addressed. In addition, the state of the art on this field of knowledge will be sum- marised; underscoring one of the most recent techniques, which has a strong theoretical basis. Upon this, some hypotheses will be made. arXiv:2012.05285v1 [math.ST] 9 Dec 2020 1.1. Epistasis in complex disease The role of heredity in psychiatry has been studied for almost a century, with Pearson (1931) not having “the least hesitation” in asserting its relevance. -
Enabling Rootless Linux Containers in Multi-User Environments: the Udocker Tool
DESY 17-096 Enabling rootless Linux Containers in multi-user environments: the udocker tool Jorge Gomes1, Emanuele Bagnaschi2, Isabel Campos3, Mario David1, Lu´ısAlves1, Jo~aoMartins1, Jo~aoPina1, Alvaro L´opez-Garc´ıa3, and Pablo Orviz3 1Laborat´oriode Instrumenta¸c~aoe F´ısicaExperimental de Part´ıculas(LIP), Lisboa, Portugal 2Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany 3IFCA, Consejo Superior de Investigaciones Cient´ıficas-CSIC,Santander, Spain June 5, 2018 Abstract Containers are increasingly used as means to distribute and run Linux services and applications. In this paper we describe the architectural design and implementation of udocker, a tool which enables the user to execute Linux containers in user mode. We also present a few practical applications, using a range of scientific codes characterized by different requirements: from single core execution to MPI parallel execution and execution on GPGPUs. 1 Introduction Technologies based on Linux containers have become very popular among soft- ware developers and system administrators. The main reason behind this suc- cess is the flexibility and efficiency that containers offer when it comes to pack- ing, deploying and running software. A given software can be containerized together with all its dependencies in arXiv:1711.01758v2 [cs.SE] 1 Jun 2018 such a way that it can be seamlessly executed regardless of the Linux distribution used by the designated host systems. This is achieved by using advanced features of modern Linux kernels [1], namely control groups and namespaces isolation [2, 3]. Using both features, a set of processes can be placed in a fully isolated environment (using namespaces isolation), with a given amount of resources, such as CPU or RAM, allocated to it (using control groups). -
Auto-Tuning Shared Memory Parallel Sparse BLAS Operations In
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Auto-tuning shared memory parallel Sparse BLAS provided by MPG.PuRe operations in librsb-1.2 Michele MARTONE ([email protected]) Max Planck Institute for Plasma Physics, Garching bei Munchen,¨ Germany Intro 2/9 HCSR 1.5e+04 Sparse BLAS (Basic Linear Algebra Subroutines) [2] speci- • 1/9 HCOO 2.0e+03 fies main kernels for iterative methods: – sparseMultiply byMatrix:“MM” 3/9 HCSR 1.3e+04 4/9 HCOO 2.0e+03 – sparse triangularSolve byMatrix:“SM” Untuned. Tuned for NRHS=1. Tuned for NRHS=3. Tuning example on symmetric matrix audikw 1. • Focus on MM:C C+αop(A) B , with Here only lower triangle, ca.1M 1M, 39M nonzeroes. • ← × • × 5/9 HCOO 9.8e+02 6/9 HCSR 1.0e+04 –A has dimensionsm k and is sparse(nnz nonzeroes) On a machine with 256 KB sized L2 cache. × • T H Left one (625 blocks, avg 491 KB) is before tuning. – op(A) can be either of A, A ,A (parameter transA) 9/9 HCOO 5.0e+03 • { } Middle one (271 blocks, avg 1133 KB) after tuning (1.057x – left hand side(LHS)B isk n, • × speedup, 6436.6 ops to amortize) forMV(MM with NRHS=1). right hand side(RHS)C isn m( n=NRHS), × 7/9 HCSR 8.5e+03 8/9 HCSR 7.0e+03 Right one (1319 blocks, avg 233 KB) after tuning (1.050x both dense (eventually with strided access incB, incC, ...) • speedup, 3996.2 ops to amortize) forMM with NRHS=3. -
Potential Use of Supercomputing Resources in Europe and in Spain for CMS (Including Some Technical Points)
Potential use of supercomputing resources in Europe and in Spain for CMS (including some technical points) Presented by Jesus Marco (IFCA, CSIC-UC, Santander, Spain) on behalf of IFCA team, And with tech contribution from Jorge Gomes, LIP, Lisbon, Portugal @ CMS First Open Resources Computing Workshop CERN 21 June 2016 Some background… The supercomputing node at the University of Cantabria, named ALTAMIRA, is hosted and operated by IFCA It is not large (2500 cores) but it is included in the Supercomputing Network in Spain, that has quite significant resources (more than 80K cores) that will be doubled along next year. As these resources are granted on the basis of the scientific interest of the request, CMS teams in Spain could directly benefit of their use "for free". However the request needs to show the need for HPC resources (multicore architecture in CMS case) and the possibility to run in a “existing" framework (OS, username/passw. access, etc.). My presentation aims to cover these points and ask for experience from other teams/experts on exploiting this possibility. The EU PRACE initiative joins many different supercomputers at different levels (Tier-0, Tier-1) and could also be explored. Evolution of the Spanish Supercomputing Network (RES) See https://www.bsc.es/marenostrum-support-services/res Initially (2005) most of the resources were based on IBM-Power +Myrinet Since 2012 many of the centers evolved to use Intel x86 + Infiniband • First one was ALTAMIRA@UC: – 2.500 Xeon E5 cores with FDR IB to 1PB on GPFS • Next: MareNostrum -
Design of Scalable PGAS Collectives for NUMA and Manycore Systems
Design of Scalable PGAS Collectives for NUMA and Manycore Systems Damian´ Alvarez´ Mallon´ Ph.D. in Information Technology Research University of A Coru~na,Spain Ph.D. in Information Technology Research University of A Coru~na,Spain Doctoral Thesis Design of Scalable PGAS Collectives for NUMA and Manycore Systems Dami´an Alvarez´ Mall´on October 2014 PhD Advisor: Guillermo L´opez Taboada Dr. Guillermo L´opez Taboada Profesor Contratado Doctor Dpto. de Electr´onicay Sistemas Universidade da Coru~na CERTIFICA Que la memoria titulada \Design of Scalable PGAS Collectives for NUMA and Manycore Systems" ha sido realizada por D. Dami´an Alvarez´ Mall´onbajo mi di- recci´onen el Departamento de Electr´onicay Sistemas de la Universidade da Coru~na (UDC) y concluye la Tesis Doctoral que presenta para optar al grado de Doctor por la Universidade da Coru~nacon la Menci´onde Doctor Internacional. En A Coru~na,a Martes 10 de Junio de 2014 Fdo.: Guillermo L´opez Taboada Director de la Tesis Doctoral A todos/as os/as que me ensinaron algo Polo bo e polo malo Acknowledgments Quoting Isaac Newton, but without comparing me with him: \If I have seen further it is by standing on the shoulders of giants". Specifically, one of the giants whose shoulder I have found particularly useful is my Ph.D. advisor, Guillermo L´opez Taboada. His support and dedication are major factors behind this work, and it would not exist without them. I cannot forget Ram´onDoallo and Juan Touri~no, that allowed me become part of the Computer Architecture Group.