DOCSLIB.ORG

RES Supercomputers

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
RES Supercomputers La RES: una oportunidad XXVI Jornadas de Investigación de las Universidades Españolas Josep M. Martorell, PhD BSC – CNS Associate Director 11/2018 The evolution of the research paradigm • Numerical Reduce expense • Avoid suffering simulation and • Help to build knowledge where Big Data analysis experiments are impossible or not affordable HPC: An enabler for all scientific fields Materials, Engineering Astro, Chemistry & High Energy Nanoscience & Plasma Physics Advances leading to: Life Sciences • Improved Healthcare Earth & Medicine Sciences • Better Climate Forecasting • Superior Materials • More Competitive Industry ALYA RED Biomechanics: Respiratory system Wind Farms Simulation Barcelona Supercomputing Center Centro Nacional de Supercomputación BSC-CNS objectives Supercomputing services R&D in Computer, PhD program, to Spanish and Life, Earth and Technology Transfer, EU researchers Engineering Sciences public engagement Spanish Government 60% BSC-CNS is a consortium Catalan Government 30% that includes Univ. Politècnica de Catalunya (UPC) 10% People Data as of October 31, 2018 BSC Resources 2017 executed budget Distributed Supercomputing Infrastructure 26 members, including 5 Hosting Members (Switzerland, France, Germany, Italy and Spain) Hazel Hen JUWELS 652 scientific projects enabled SuperMUC 110 PFlops/s of peak performance on Curie 7 world-class systems >11.500 people trained by 6 PRACE Piz Daint Advanced Training Centers and others events Marconi MareNostrum Access prace-ri.eu/hpc-acces RES: HPC Services for Spain RES now made up of thirteen supercomputers Finis Terrae II, Centro de Supercomputación de Galicia (CESGA); Pirineus, Consorcio de Servicios Universitarios de Cataluña (CSUC); Lusitania, Fundación Computación y Tecnologías Avanzadas de Extremadura; Caléndula, Centro de Supercomputación de Castilla y León,y Cibeles, Universidad Autónoma de Madrid Access www.res.es RES: HPC Services for Spain •The RES was created in 2006. •It is coordinated by the Barcelona Supercomputing Center (BSC-CNS). •It forms part of the Spanish “Map of Unique Scientific and Technical Infrastructures” (ICTS). RES: HPC Services for Spain • Objective: coordinate and manage high performance computing services to promote the progress of excellent science and innovation in Spain. • It offers HPC services for non-profit, open R&D purposes. • Since 2006, it has granted more than 1,200 Million CPU hours to 2,628 research activities. Research areas Hours granted per area 23% AECT 30% Mathematics, physics Astronomy, space and engineering and earth sciences BCV FI QCM 19% 28% Life and health Chemistry and sciences materials sciences RES: HPC Services for Spain RES is made up of 12 institutions: BSC MareNostrum CESGA FinisTerrae CSUC Pirineus & Canigo BSC MinoTauro UV Tirant UC Altamira UPM Magerit CénitS Lusitania & SandyBridge UMA Picaso IAC La Palma UZ CaesarAugusta SCAYLE Caléndula UAM Cibeles 1 10 100 1000 TFlop/s (logarithmic scale) RES supercomputers BSC (MareNostrum 4) 165888 cores, 11400 Tflops Main processors: Intel(R) Xeon(R) Platinum 8160 Memory: 390 TB Disk: 14 PB UPM (Magerit II) 3920 cores, 103 Tflops Main processors : IBM Power7 3.3 GHz Memory: 7840 GB Disk: 1728 TB UMA (Picasso) 4016 cores, 84Tflops Main processors: Intel SandyBridge-EP E5-2670 Memory: 22400 GB Disk: 720 TB UV (Tirant 3) 5376 cores, 111,8 Tflops Main processors: Intel SandyBridge-EP E5-2670 Memory: 10752 GB Disk: 14 + 10 TB CSUC (Pirineus) 2784 cores, 283,66 Tflops Main processors: Intel(R) Xeon(R) Platinum 8160 Memory: 12000 GB Disk: 200 TB CSUC (Canigo) 384 cores, 33,2 Tflops Main processors: Intel(R) Xeon(R) Platinum 8160 Memory: 9000 GB Disk: 200 TB RES supercomputers CénitS (Lusitania 2) 800 cores, 33 Tflops Main processors Intel Xeon E5-2660v3, 2.6GHz Memory: 10 GB Disk: 328 TB CénitS (SandyBridge) 2688 cores, 56 Tflops Main processors Intel Sandybridge Xeon Memory: 5376 GB Disk: 328 TB BSC (MinoTauro) 624 cores, 251 Tflops Main processor: 39x 2 Intel Xeon E5-2630 v3 Memory: 20 TB Disk: 14PB (shared with MN4) CESGA (FinisTerrae 2) 7712 cores, 328Tflops Main processor: Intel Xeon E5-2680v3 Memory: 40 TB Disk: 960 TB UC (Altamira 2+) 5120 cores, 105 Tflops Main processor: Intel SandyBridge Memory: 15,4 TB Disk: 2PB UZ (Caesaraugusta) 2014 cores, 80.5 Tflops Main processor: Intel E5-2680v3, 2.5GHz Memory: 5400 GB RAM memory Disk: 219TB RES supercomputers SCAYLE (Caléndula) 2432 cores, 50 Tflops Main processor: Intel SandyBridge Xeon Memory: 4864 GB Disk: 600 TB UAM (Cibeles) 368 cores, 14 Tflops Main processor: Intel Xeon E5-2630 v3, 2.40GHz Memory: 896 GB Disk: 80 TB UAM (SandyBridge) – coming soon – 2688 cores, 56Tflops Main processor: Intel SandyBridge Xeon, 2.60GHz Memory: 5376 GB Disk: 80 TB IAC (LaPalma) 4032 cores, 83 Tflops Main processor: Intel SandyBrigde Memory: 8064 GB Disk: 60 TB BSC (CTE - Power) 52 cores, 1485 Tflops Main processor: IBM Power 9 with 20 cores & 4 GPU V100 Memory: 27 TB Disk: 14PB (shared with MN4) More information in https://www.res.es/en/res-sites Resources granted: CPU hours 600 500 400 300 Million hours 200 100 0 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 Requested hours Awarded hours (A+B) How to apply? • RES resources are open to researchers and spin-offs: o Computing resources: CPU hours and storage o Technical support: application analysis, porting of applications, search for the best algorithm… to improve performance and ensure the most effective use of HPC resources. o Free of cost • Three open competitive calls per year. Deadline for Period Starting date applications P1 January 1st March P2 May 1st July P3 September 1st November How to apply? RES intranet: https://www.bsc.es/res-intranet • Researchers present a proposal which includes research project description, technical requirements and research group experience. • Accepted proposals have access to RES supercomputers for 4 months. • Granted time can be: hours with priority (hours A) or without priority (hours B) Who can apply? • RES resources are aimed at open R+D+I activities: o Researchers from academia and public R&D institutions o Spin-offs during their first 3 years from its creation o Collaboration projects between private companies and research groups from academia or public institutions o Open to international applicants, but we recommend the collaboration with researchers from Spanish institutions Proposal evaluation Formal Technical evaluation evaluation Submit Access committee Scientific experts panel Final report of accepted activities Activity length • Accepted proposals have access to RES supercomputers for 4 months. If your activity needs more time to be properly developed, you can ask for a continuation activity: New activity Report dissemination (4 months) information Continuation activity Report dissemination (4 months) information • The application form is simplified • Are preferably allocated to the same machine Continuation activities • In the evaluation, one reviewer is kept from the previous activity and the second reviewer changes Tips to write a strong proposal • Read carefully all the protocols, guides and FAQs in: https://www.res.es/en/access-to-res • Project description section: highlight the importance of your project, not only from the scientific point of view but also from the return to society. Why do you think that your project should deserve the resources requested? Tips to write a strong proposal • Activity description section: specify clearly why do you need supercomputing resources. Write as accurate as possible the flowchart of the simulations. Indicate that you have your own human resources in your group to run and process the output of all the simulations you propose. Why do you need to carry out the simulations in the selected machine? Is the amount of computing resources requested adjusted to your needs and properly justified? • Doubts about software/HPC resources: ask support team! Are your jobs adequate for parallel computing? [email protected] RES events: technical training These workshops are organized by the RES nodes and aim to provide the knowledge and skills needed to use and manage the supercomputing facilities. • Check the agenda in RES website: https://www.res.es/en/events?event_type=technical_training • PATC courses in BSC (PRACE Advanced Training Center): https://www.bsc.es/education/training/patc-courses RES events: networking opportunities Scientific seminars The RES promotes scientific seminars which address supercomputing technology applications in specific scientific areas. These events are mainly organized by RES users and are open to the entire research community. Annual Users’ Meeting This event is a discussion forum to share experiences about the use of supercomputing technologies and to promote the dissemination of research results. Next year edition will be held in Zaragoza. Agenda 2018: www.res.es/en/events Mobility grants for researchers using HPC resources Short stays to visit scientific hosts (3 weeks – 3 months) Eligibility: open to researchers from academia or industry whose research needs HPC Funds for travel and living allowance Access to European HPC facilities http://www.hpc-europa.eu/ Funded by the EC: 2017 - 2021 What is HPC-Europa 3 ? • HPC- Europa3 is a partnership of 9 leading HPC centres and 1 centre of excellence. • The project is funded by Horizon 2020: from May 2017 until April 2021. • Aims to support 1220 international research visits in 4 years. • Around 100 million CPU hours are available in total. • Applications can be created at any time: 4 closing dates / year. • Researchers can visit partner countries (transnational access). • Scientific groups can invite research visitors from other EU countries or Associated States. RES: HPC Services for Spain •The RES was created in 2006. •It is coordinated by the Barcelona Supercomputing Center (BSC-CNS). •It forms part of the Spanish “Map of Unique Scientific and Technical Infrastructures” (ICTS). Visit our website: www.res.es Subscribe to our newsletter Contact us! Follow us in Twitter: @RES_HPC [email protected] [email protected] Thank you e-mail: [email protected] Twitter: @martorellBSC 11/2018.
Load more

Recommended publications
  • 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/
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • Finisterrae: Memory Hierarchy and Mapping
    galicia supercomputing center Applications & Projects Department FinisTerrae: Memory Hierarchy and Mapping Technical Report CESGA-2010-001 Juan Carlos Pichel Tuesday 12th January, 2010 Contents Contents 1 1 Introduction 2 2 Useful Topics about the FinisTerrae Architecture 2 2.1 Itanium2 Montvale Processors . .2 2.2 CPUs Identification . .3 2.3 Coherency Mechanism of a rx7640 node . .4 2.4 Memory Latency . .5 3 Linux NUMA support 6 3.1 The libnuma API.........................................7 3.2 Using numactl in the FinisTerrae ..............................7 3.3 Effects of using explicit data and thread placement . .8 References 11 Technical Report CESGA-2010-001 January / 2010 1 Figure 1: Block diagram of a Dual-Core Intel Itanium2 (Montvale) processor. 1 Introduction In this technical report some topics about the Finisterrae architecture and its influence in the per- formance are covered. In Section 2 a brief description of the Itanium2 Montvale processors is provided. Additionally to this, a method for identifying the CPUs is explained. At the end of this section the mem- ory coherency mechanism of a FinisTerrae node is detailed. Section 3 deals with the tools provided by the Linux kernel to support NUMA architectures. An example of the benefits of using these tools in the FinisTerrae for the sparse matrix-vector product (SpMV) kernel is shown. 2 Useful Topics about the FinisTerrae Architecture FinisTerrae supercomputer consists of 142 HP Integrity rx7640 nodes [1], with 8 1.6GHz Dual-Core Intel Itanium2 (Montvale) processors and 128 GB of memory per node. Additionally, there is a HP Integrity Superdome with 64 1.6GHz Dual-Core Intel Itanium2 (Montvale) processors and 1 TB of main memory (not considered in this report).
    [Show full text]
  • The Udocker Tool
    Computer Physics Communications 232 (2018) 84–97 Contents lists available at ScienceDirect Computer Physics Communications journal homepage: www.elsevier.com/locate/cpc Enabling rootless Linux Containers in multi-user environments: The udocker tool Jorge Gomes a,*, Emanuele Bagnaschi b, Isabel Campos c, Mario David a, Luís Alves a, João Martins a, João Pina a, Alvaro López-García c, Pablo Orviz c a Laboratório de Instrumentação e Física Experimental de Partículas (LIP), Lisboa, Portugal b Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany c IFCA, Consejo Superior de Investigaciones Científicas-CSIC, Santander, Spain article info a b s t r a c t Article history: Containers are increasingly used as means to distribute and run Linux services and applications. In this Received 25 January 2018 paper we describe the architectural design and implementation of udocker, a tool which enables the user Received in revised form 28 May 2018 to execute Linux containers in user mode. We also present a few practical applications, using a range Accepted 31 May 2018 of scientific codes characterized by different requirements: from single core execution to MPI parallel Available online 6 June 2018 execution and execution on GPGPUs. ' 2018 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license Keywords: Linux containers (http://creativecommons.org/licenses/by/4.0/). HPC on cloud Virtualization Phenomenology QCD Biophysics 1. Introduction Technologies based on Linux containers have become very popular among software developers and system administrators. The main reason behind this success is the flexibility and efficiency that containers offer when it comes to packing, deploying and running software.
    [Show full text]
  • 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.
    [Show full text]
  • E-Infrastructures H2020-EINFRA-2016-2017
    E-Infrastructures H2020-EINFRA-2016-2017 EINFRA-11-2016: Support to the next implementation phase of Pan- European High Performance Computing Infrastructure and Services (PRACE) PRACE-5IP PRACE Fifth Implementation Phase Project Grant Agreement Number: EINFRA-730913 D6.4 Development of Prototypal New Services Final Version: 1.0 Author(s): Janez Povh, UL FME Date: 15.04.2019 D6.4 Development of Prototypal New Services Project and Deliverable Information Sheet PRACE Project Project Ref. №: EINFRA-730913 Project Title: PRACE Fifth Implementation Phase Project Project Web Site: http://www.prace-project.eu Deliverable ID: < D6.4 Deliverable Nature: < Report> Dissemination Level: Contractual Date of Delivery: PU * 15 / 04 / 2019 Actual Date of Delivery: 30 / 04 / 2019 EC Project Officer: Leonardo Flores Añover * - The dissemination level are indicated as follows: PU – Public, CO – Confidential, only for members of the consortium (including the Commission Services) CL – Classified, as referred to in Commission Decision 2005/444/EC. Document Control Sheet Title: Development of Prototypal New Services Document ID: D6.4 Version: <1.0> Status: Final Available at: http://www.prace-project.eu Software Tool: Microsoft Word 2013 File(s): D6.4.docx Written by: Janez Povh, UL FME Authorship Contributors: Agnes Ansari, CNRS/IDRIS Abdulrahman Azab, UiO Simone Bna, CINECA Kyriakos Ginis, GRNET Miroslaw Kupczyk, PSNC Frederic Suter, CNRS / CC-IN2P3 Reviewed by: Dimitrios Dellis, GRNET Florian Berberich, JUELICH Approved by: MB/TB Document Status Sheet Version
    [Show full text]