A Flexible and Dynamic Page Migration Infrastructure Based on Hardware Counters
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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/ -
Slicing (Draft)
Handling Parallelism in a Concurrency Model Mischael Schill, Sebastian Nanz, and Bertrand Meyer ETH Zurich, Switzerland [email protected] Abstract. Programming models for concurrency are optimized for deal- ing with nondeterminism, for example to handle asynchronously arriving events. To shield the developer from data race errors effectively, such models may prevent shared access to data altogether. However, this re- striction also makes them unsuitable for applications that require data parallelism. We present a library-based approach for permitting parallel access to arrays while preserving the safety guarantees of the original model. When applied to SCOOP, an object-oriented concurrency model, the approach exhibits a negligible performance overhead compared to or- dinary threaded implementations of two parallel benchmark programs. 1 Introduction Writing a multithreaded program can have a variety of very different motiva- tions [1]. Oftentimes, multithreading is a functional requirement: it enables ap- plications to remain responsive to input, for example when using a graphical user interface. Furthermore, it is also an effective program structuring technique that makes it possible to handle nondeterministic events in a modular way; develop- ers take advantage of this fact when designing reactive and event-based systems. In all these cases, multithreading is said to provide concurrency. In contrast to this, the multicore revolution has accentuated the use of multithreading for im- proving performance when executing programs on a multicore machine. In this case, multithreading is said to provide parallelism. Programming models for multithreaded programming generally support ei- ther concurrency or parallelism. For example, the Actor model [2] or Simple Con- current Object-Oriented Programming (SCOOP) [3,4] are typical concurrency models: they are optimized for coordination and event handling, and provide safety guarantees such as absence of data races. -
Assessing Gains from Parallel Computation on a Supercomputer
Volume 35, Issue 1 Assessing gains from parallel computation on a supercomputer Lilia Maliar Stanford University Abstract We assess gains from parallel computation on Backlight supercomputer. The information transfers are expensive. We find that to make parallel computation efficient, a task per core must be sufficiently large, ranging from few seconds to one minute depending on the number of cores employed. For small problems, the shared memory programming (OpenMP) and a hybrid of shared and distributive memory programming (OpenMP&MPI) leads to a higher efficiency of parallelization than the distributive memory programming (MPI) alone. I acknowledge XSEDE grant TG-ASC120048, and I thank Roberto Gomez, Phillip Blood and Rick Costa, scientific specialists from the Pittsburgh Supercomputing Center, for technical support. I also acknowledge support from the Hoover Institution and Department of Economics at Stanford University, University of Alicante, Ivie, and the Spanish Ministry of Science and Innovation under the grant ECO2012- 36719. I thank the editor, two anonymous referees, and Eric Aldrich, Yongyang Cai, Kenneth L. Judd, Serguei Maliar and Rafael Valero for useful comments. Citation: Lilia Maliar, (2015) ''Assessing gains from parallel computation on a supercomputer'', Economics Bulletin, Volume 35, Issue 1, pages 159-167 Contact: Lilia Maliar - [email protected]. Submitted: September 17, 2014. Published: March 11, 2015. 1 Introduction The speed of processors was steadily growing over the last few decades. However, this growth has a natural limit (because the speed of electricity along the conducting material is limited and because a thickness and length of the conducting material is limited). The recent progress in solving computationally intense problems is related to parallel computation. -
HP-CAST 20 Final Agenda V3.0 (Sessions and Chairs Are Subject to Change Without Notice)
HP Consortium for Advanced Scientific and Technical Computing World-Wide User Group Meeting ISS Hyperscale and HPC Organization The Westin Hotel Leipzig HP-CAST 20 Final Agenda V3.0 (Sessions and chairs are subject to change without notice) Supported by: Thursday, June 13th – Registration & Get-Together 18:00 – 22:00 Registration 18:00 – 22:00 Welcome Reception for All Attendees – Sky Bar FALCO at the Westin Hotel Friday, June 14th – Conference Section 08:00 – 18:00 Registration Board Introduction and HP Executive Updates HP-Liaison Frank Baetke, HP 08:15 – 09:20 HP-CAST President Rudolf Lohner, KIT/SCC HP Executive Updates on HPC Trends Paul Santeler, HP Scott Misage, HP Invited Partner Keynotes and Updates 09:20 – 09:50 High-Performance Computing Trends in the Georg Scheuerer, ANSYS Europe Manufacturing Industry 09:50 – 10:00 Making HPC Simulation Access Easier Benoît Vautrin, OVH (Oxalya) France 10:00 – 10:30 Break Invited Customer Keynotes 10:30 – 11:00 IT Infrastructure for HPC and Challenges of HPC Wolfgang Burke, BMW Germany Collocation at BMW 11:00 – 11:20 Deployment of HP Clusters in Iceland Guõbrandur R. Sigurõsson, Opin Kerfi Iceland 11:20 – 11:30 Q&A Session Short Processor Technology Updates Roberto Dognini, AMD Karl Freund, Calxeda (ARM) 11:30 – 12:30 John Hengeveld, Intel Timothy Lanfear, NVIDIA Sanjay Bhal, TI (ARM/DSP) 12:30 – 13:30 Lunch Friday, June 14th – Conference Section Attention: ATTENDANCE RESTRICTIONS APPLY Platforms and Products – #1 In Detail Roadmaps & Updates for Ed Turkel, HP 13:30 – 14:00 - Next Generation -
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. -
Instruction Level Parallelism Example
Instruction Level Parallelism Example Is Jule peaty or weak-minded when highlighting some heckles foreground thenceforth? Homoerotic and commendatory Shelby still pinks his pronephros inly. Overneat Kermit never beams so quaveringly or fecundated any academicians effectively. Summary of parallelism create readable and as with a bit says if we currently being considered to resolve these two machine of a pretty cool explanation. Once plug, it book the parallel grammatical structure which creates a truly memorable phrase. In order to accomplish whereas, a hybrid approach is designed to whatever advantage of streaming SIMD instructions for each faction the awful that executes in parallel on independent cores. For the ILPA, there is one more type of instruction possible, which is the special instruction type for the dedicated hardware units. Advantages and high for example? Two which is already present data is, to process includes comprehensive career related services that instruction level parallelism example how many diverse influences on. Simple uses of parallelism create readable and understandable passages. Also note that a data dependent elements that has to be imported from another core in another processor is much higher than either of the previous two costs. Why the charge of the proton does not transfer to the neutron in the nuclei? The OPENMP code is implemented in advance way leaving each thread can climb up an element from first vector and compare after all the elements in you second vector and forth thread will appear able to execute simultaneously in parallel. To be ready to instruction level parallelism in this allows enormous reduction in memory. -
Presentación De Powerpoint
CENTRO DE SUPERCOMPUTACIÓN DE GALICIA High Scalability Multipole Method. Solving Half Billion of Unknowns J.C. Mouriño¹, A. Gómez¹, J.M. Taboada², L. Landesa², J.M. Bértolo³, F. Obelleiro³, J.L. Rodríguez³ ¹ Supercomputing Center of Galicia (CESGA), Spain ² University of Extremadura, Spain ³ University of Vigo, Spain International Supercomputing Conference Hamburg, June 23th 2009 Outline • Introduction • FMM-FFT algorithm • Parallel implementation • HEMCUVE. Challenge history • Experimental Results • Conclusions 2 Introduction • Numerical solution of the integro-differential electromagnetic equations -> important in industry • High frequency in large objects -> scalability limits – 0.78 m² at 3 GHz -> 15000 unknowns – real car at 79 GHz -> 400 million unknowns • Great effort reducing computational time of MoM • Fast Multipole Method (FMM) -> O(N³/²) good scalability • Multilevel FMM (MLFMA) -> O(N log N) poor scalability • Modern HPC systems have thousands of cores • FMM-FFT reduces complexity preserving scalability 3 Introduction • FMM – The geometry is partitioned into M groups using an oct-tree decomposition algorithm – Parallelization: • k-space samples are independent from one another • The workload can be partitioned in the k-space • MLFMA – The same algorithm can be recursively applied in a hierarchical multilevel oct-tree decomposition – Computational cost reduced to O(N log N) – Parallelization: • k-space samples are not independent due to interpolation/ anterpolation of fields across levels • Usually workload distributed by -
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. -
Efficient Multithreaded Untransposed, Transposed Or Symmetric Sparse
Efficient Multithreaded Untransposed, Transposed or Symmetric Sparse Matrix-Vector Multiplication with the Recursive Sparse Blocks Format Michele Martonea,1,∗ aMax Planck Society Institute for Plasma Physics, Boltzmannstrasse 2, D-85748 Garching bei M¨unchen,Germany Abstract In earlier work we have introduced the \Recursive Sparse Blocks" (RSB) sparse matrix storage scheme oriented towards cache efficient matrix-vector multiplication (SpMV ) and triangular solution (SpSV ) on cache based shared memory parallel computers. Both the transposed (SpMV T ) and symmetric (SymSpMV ) matrix-vector multiply variants are supported. RSB stands for a meta-format: it recursively partitions a rectangular sparse matrix in quadrants; leaf submatrices are stored in an appropriate traditional format | either Compressed Sparse Rows (CSR) or Coordinate (COO). In this work, we compare the performance of our RSB implementation of SpMV, SpMV T, SymSpMV to that of the state-of-the-art Intel Math Kernel Library (MKL) CSR implementation on the recent Intel's Sandy Bridge processor. Our results with a few dozens of real world large matrices suggest the efficiency of the approach: in all of the cases, RSB's SymSpMV (and in most cases, SpMV T as well) took less than half of MKL CSR's time; SpMV 's advantage was smaller. Furthermore, RSB's SpMV T is more scalable than MKL's CSR, in that it performs almost as well as SpMV. Additionally, we include comparisons to the state-of-the art format Compressed Sparse Blocks (CSB) implementation. We observed RSB to be slightly superior to CSB in SpMV T, slightly inferior in SpMV, and better (in most cases by a factor of two or more) in SymSpMV. -
Minimizing Startup Costs for Performance-Critical Threading
Minimizing Startup Costs for Performance-Critical Threading Anthony M. Castaldo R. Clint Whaley Department of Computer Science Department of Computer Science University of Texas at San Antonio University of Texas at San Antonio San Antonio, TX 78249 San Antonio, TX 78249 Email : [email protected] Email : [email protected] Abstract—Using the well-known ATLAS and LAPACK dense on several eight core systems running a standard Linux OS, linear algebra libraries, we demonstrate that the parallel manage- ATLAS produced alarmingly poor parallel performance even ment overhead (PMO) can grow with problem size on even stati- on compute bound, highly parallelizable problems such as cally scheduled parallel programs with minimal task interaction. Therefore, the widely held view that these thread management matrix multiply. issues can be ignored in such computationally intensive libraries is wrong, and leads to substantial slowdown on today’s machines. Dense linear algebra libraries like ATLAS and LAPACK [2] We survey several methods for reducing this overhead, the are almost ideal targets for parallelism: the problems are best of which we have not seen in the literature. Finally, we regular and often easily decomposed into subproblems of equal demonstrate that by applying these techniques at the kernel level, performance in applications such as LU and QR factorizations complexity, minimizing any need for dynamic task scheduling, can be improved by almost 40% for small problems, and as load balancing or coordination. Many have high data reuse much as 15% for large O(N 3) computations. These techniques and therefore require relatively modest data movement. Until are completely general, and should yield significant speedup in recently, ATLAS achieved good parallel speedup using simple almost any performance-critical operation. -
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).