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Penguin Computing / IU Partnership HPC “cluster as a service” and Cloud Services CASC Spring Meeting 2012 Craig A. Stewart Executive Director,

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Presentation on theme: "Penguin Computing / IU Partnership HPC “cluster as a service” and Cloud Services CASC Spring Meeting 2012 Craig A. Stewart Executive Director,"— Presentation transcript:

1 Penguin Computing / IU Partnership HPC “cluster as a service” and Cloud Services CASC Spring Meeting 2012 Craig A. Stewart Executive Director, Pervasive Technology Institute Associate Dean, Research Technologies Matthew Jacobs SVP Corporate Development

2 Please cite as: Stewart, C.A. and M. Jacobs “Penguin Computing / IU Partnership HPC ‘cluster as a service’ and Cloud Services.” Presentation. Presented at Coalition of Academic Scientific Computation, 29 February 2012, Arlington, VA. The image on slide 1 (title slide) and slides 3 – 7 © Penguin Computing Inc. all rights reserved; may not be reused without permission from Penguin Computing Inc. Other slides (except where explicitly noted) are copyright 2011 by the Trustees of Indiana University, and this content is released under the Creative Commons Attribution 3.0 Unported license ( 2

3  On-demand HPC system > Compute, storage, low latency fabrics, GPU, non-virtualized  Robust software infrastructure > Full automation > User and administration space controls > Secure and seamless job migration > Extensible framework > Complete billing infrastructure  Services > Custom product design > Site and workflow integration > Managed services > Application support  HPC support expertise > Skilled HPC administrators > Leverage 13 yrs serving HPC market What is POD Internet (150Mb, burstable to 1Gb) 3

4 Penguin HPC Cloud Services 4

5 Created by POD Developers and Administrators Scyld HPC Cloud Management System Create and Manage User and Group HierarchiesSimultaneously Manage Multiple Collocated ClustersCreate Customer Facing Web PortalsUse Web Services to Integrate with Back-End SystemsDeploy HTML5 Based Cluster Management ToolsSecurely Migrate User WorkloadsEfficiently Schedule and Manage Cluster ResourcesCreate and Deploy Virtual Headnodes for User-Specific Clusters 5

6  Current data centers: Salt Lake City, Indiana University, Mountain View  1,500 cores (AMD and Intel)  240 TB on-demand storage 12 Million Commercial Jobs and Counting… Replaced in-house image analysis cluster with POD and co-located storage Provides cloud analysis services on POD for world- wide bioinformatics customers Replaced Amazon AWS cloud usage with PODTools workflow migration system Nihon ESI provides crash analysis analyses to Honda R&D during Japan’s brown-outs 6

7 Persistent, customized user environment High-speed Intel and AMD compute nodes (physical) Fast access to local storage (data guaranteed to be local) Highly secure (https, shared key authentication, IP matching, VPN) Billed by the fractional core hour HPC expertise included (Penguin’s core business for many years) Cluster software stack included Troubleshooting included in support Collocated storage options available Highly dependable and dynamically scalable The POD Advantage 7

8 Clouds look serene enough - But is ignorance bliss?  In the cloud, do you know: >Where your data are? >What laws prevail over the physical location of your data? >What license you really agreed to? >What is the security (electronic / physical) around your data? >And how exactly do you get to that cloud, or get things out of it? >How secure your provider is financially? (The fact that something seems unimaginable, like cloud provider such-and-such going out of business abruptly, does not mean it is impossible!) Photo by es/z/in/photostream/ 8

9 Penguin Computing & IU partner for “Cluster as a Service”  Just what it says: Cluster as a Service  Cluster physically located on IU’s campus, in IU’s Data Center  Available to anyone at or FFRDC (Federally Funded Research and Development Center)  To use it: >Go to >Fill out registration form >Verify via your >Get out your credit card >Go computing  This builds on Penguin’s experience - currently host Life Technologies' BioScope and LifeScope in the cloud ( 9

10 We know where the data are … and they are secure 10

11 An example of NET+ Services / Campus Bridging  "We are seeing the early emergence of a meta-university — a transcendent, accessible, empowering, dynamic, communally constructed framework of open materials and platforms on which much of higher education worldwide can be constructed or enhanced.” Charles Vest, president emeritus of MIT, 2006  NET+ Goal: achieve economy of scale and retain reasonable measure of controlSee: Brad Wheeler and Shelton Waggener Above-Campus Services: Shaping the Promise of Cloud Computing for Higher Education. EDUCAUSE Review, vol. 44, no. 6 (November/December 2009):  Campus Bridging goal – make it all feel like it’s just a peripheral to your laptop (see 11

12  True On-Demand HPC for Internet2  Creative Public/Private model to address HPC shortfall  Turning lost EC2 dollars into central IT expansion  Tiered channel strategy expansion to EDU sector  Program and discipline-specific enhancements under way  Objective third party resource for collaboration > EDU, Federal and Commercial IU POD – Innovation Through Partnership 12

13 POD IU (Rockhopper) specifications Server Information ArchitecturePenguin Computing Altus 1804 TFLOPS4.4 Clock Speed2.1GHz Nodes11 compute; 2 login; 4 management; 3 servers CPUs4 x 2.1GHz 12-core AMD Opteron 6172 processors per compute node Memory TypeDistributed and Shared Total Memory1408 GB Memory per Node128GB 1333MHz DDR3 ECC Local Scratch Storage6TB locally attached SATA2 Cluster Scratch100TB Lustre Further Details OSCentOS 5 NetworkQDR (40Gb/s) Infiniband, 1Gb/s ethernet Job Management SoftwareSGE Job Scheduling SoftwareSGE Job Scheduling policyFair Share Accesskeybased ssh login to headnodes remote job control via Penguin's PODShell 13

14 Package nameSummary COAMPSCoupled ocean / atmosphere meoscale prediction system Desmond Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. GAMESSGAMESS is a program for ab initio molecular quantum chemistry. GalaxyGalaxy is an open, web-based platform for data intensive biomedical research. GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. HMMER HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. Intelcompilers and libraries LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. MM5 The PSU/NCAR mesoscale model (known as MM5) is a limited-area, nonhydrostatic, terrain-following sigma-coordinate model designed to simulate or predict mesoscale atmospheric circulation. The model is supported by several pre- and post-processing programs, which are referred to collectively as the MM5 modeling system. mpiBLASTmpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. NAMDNAMD is a parallel molecular dynamics code for large biomolecular systems. Available applications at POD IU (Rockhopper) 14

15 Package nameSummary NCBI-Blast The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. OpenAtom OpenAtom is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method. OpenFoam The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenMPIInfinibad based Message Passing Interface - 2 (MPI-2) implementation POP POP is an ocean circulation model derived from earlier models of Bryan, Cox, Semtner and Chervin in which depth is used as the vertical coordinate. The model solves the three-dimensional primitive equations for fluid motions on the sphere under hydrostatic and Boussinesq approximations. Portland Groupcompilers RR is a language and environment for statistical computing and graphics. WRF The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility. Available applications at POD IU (Rockhopper) 15

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