Running applications on interoperable Grid infrastructures, focusing on OMII-UK supported software HPC-BP Interoperability Tutorial OGF 28, Munich s. crouch@omii. ac. uk Steve Crouch, David Wallom, Matteo Turilli, Morris Riedel, Shahbaz Memon, Balazs Konya, Gabor Roczei, Peter Stefan, Andrew Grimshaw, Mark Morgan , Katzushige Saga, Justin Bradley, Richard Boardman Web: www. omii. ac. uk Email: info@omii. ac. uk
Objectives • To give participants practical experience of: o o Using individual middleware clients to submit jobs to HPCBP compliant services Using the HPC-BP interop demo framework, used for previous HPC-BP demos, to submit jobs to HPC-BP compliant services • To give participants opportunity (and starting point) to learn about: o o Basic techniques and approaches for interoperability – what do I need, and how can I do this? Some of the limitations of standards support across middlewares – what can’t I do? Web: www. omii. ac. uk Email: info@omii. ac. uk
Tutorial Approach • ‘Presentation-lite’ • Learn at your own pace via online web tutorial… • …or follow my lead • Pragmatic • Generous in terms of time • Tutorial remains available after OGF 28 • Ask for help! Web: www. omii. ac. uk Email: info@omii. ac. uk
Schedule • Session 1: Using individual clients to invoke HPC-BP services o o o Overview of the demo + demo, Introduction to Grid. SAM Download, Install and Configure Grid. SAM Submit a Trivial Compute-only JSDL Job to HPC-BP Compliant Services Download, Build and Configure the BES++ Client Running the BES++ Client Against HPC-BP Compliant Services • Session 2: Using HPC-BP demo framework to invoke multiple HPC-BP services simultaneously o o o Download, Install and Configure the Demo Framework Running the Demo Against Multiple HPC-BP Compliant Services The Demo in Detail: Adding Another Endpoint to the Demo Web: www. omii. ac. uk Email: info@omii. ac. uk
The Interoperability Demonstrator Web: www. omii. ac. uk Email: info@omii. ac. uk
Background • Motivation: o o o Researchers are often reaching the limits of locally available resources to conduct research They are beginning to realise the potential of using much largerscale resources Compute resources are becoming more numerous and available across Europe • However, using different Grid middleware deployments is traditionally difficult o o Middleware clients for different deployments not compatible Require different security policies/configuration for each Web: www. omii. ac. uk Email: info@omii. ac. uk
Background • Possible solutions: o Maintain infrastructure that enables use of different clients for each middleware – interoperation • Not scalable - user learning curve, operation and maintenance o Each middleware supports a common service interface, enabled through adoption of accepted open standards – interoperability • Need only learn, use and maintain single client infrastructure • Still leaves security! • What can be practically achieved, in terms of interoperability, with middlewares that adopt OGF compute-related standards? o o What is possible? Limitations? • Demonstrate through proof-of-concept, client-side, applicationfocused demo Web: www. omii. ac. uk Email: info@omii. ac. uk
History • Initiated by UK National Grid Service, OMII-UK and FZJ • Initially shown at OGF 27, Banff, Canada, Oct 09 • Super. Computing, Nov 09 • ETSI Plugtests, FZJ, UK AHM, Dec 09 • GIN-CG, OGF 28, Mar 10 • Demonstrators: David Wallom, Peter Stefan, Morris/Shahbaz Memon, Steve Crouch Web: www. omii. ac. uk Video available at http: //www. omii. ac. uk/wiki/Videos Email: info@omii. ac. uk
Compute Related Standards - OGF Architecture OGSA EMS Scenarios (GFD 106) Use Cases Grid Scheduling Use Cases (GFD 64) Job Definition Job Description JSDL (GFD 56/136) Agreement WS-Agreement (GFD 107) Uses Programming Interface DRMAA (GFD 22/133) Supports Produces Application Description SPMD Application (GFD 115) Job Management OGSA-BES (GFD 108) Job Parameterization Parameter Sweep (GFD. 149) File Transfer HPC File Staging (GFD 135) Programming Interface SAGA (GFD 90) Accounting Usage Record (GFD 98) Application Description HPC Application (GFD 111) Extend Education ISV Primer (GFD 141) Describes Profiles Information GLUE Schema 2. 0 (GFD. 147) HPC Domain Specific Profile HPC Basic Profile (GFD 114) Web: www. omii. ac. uk Email: info@omii. ac. uk
Standards/Data Protocols/Security Supported • Standards: o HPC Basic Profile v 1. 0 • OGSA BES (Basic Execution Service) v 1. 0 • JSDL (Job Submission Description Language) v 1. 0 • HPC Profile Application Extension v 1. 0 o HPC File Staging Profile – UNICORE, Grid. SAM • Data protocols: o o UNICORE, ARC, BES++ – ftp Grid. SAM – Grid. FTP • Security: o Direct middleware -> certificate CA trust (just import CAs) Web: www. omii. ac. uk Email: info@omii. ac. uk
Participation • Currently: o o DEISA/FZJ – UNICORE, Su. SE, AMD 64 -bit, 1 core Nordu. Grid/NIIF – ARC NOX Release, Debian Linux, i 686, 16 core UK NGS/OMII-UK – Grid. SAM, Scientific Linux 4. 7, AMD 64 -bit, 256 core NAREGI-NII/Platform Computing – BES++, 2 nodes • Coming soon: o o University of Virginia Campus Grid – GENESIS 2, Ubuntu Linux, i 686, 8 core POZNAN Supercomputing Centre – SMOA Computing • Platform Computing BES++ Client used as interop client Web: www. omii. ac. uk Email: info@omii. ac. uk
Example Application: Plasma Charge Minimization • Provided by David Wallom, NGS • Undergraduate project • Total system energy minimization of point charges around the surface of a sphere • Three different applications o o o Pre processing – generate input files Main processing – parallel distributed processing Post-processing – choose optimal solution Web: www. omii. ac. uk Email: info@omii. ac. uk
System Requirements • System requirements: o o o Linux - see the Linux client pre-requisites in OMII-UK Development Kit supported platforms Sun Java JDK 1. 6 or above C compiler - gcc and related development libraries Lexical analyser - flex Parser generator - bison • Soon to appear on OGF Forge – hopefully by end of week Web: www. omii. ac. uk Email: info@omii. ac. uk
<? xml version="1. 0" ? > <Job. Definition xmlns="http: //schemas. ggf. org/jsdl/2005/11/jsdl"> <Job. Description> <Application> <HPCProfile. Application xmlns="http: //schemas. ggf. org/jsdl/2006/07/jsdl-hpcpa"> <Executable>@MINEM_INSTALL_LOCATION@/up date_file</Executable> <Argument>input. txt</Argument> <Argument>output. txt</Argument> <Output>stdout. txt</Output> <Data. Staging> <Error>stderr. txt</Error> <File. Name>stdout. txt</File. Name> @OPTIONAL_WORKING_DIR_ELEMENT@ <Creation. Flag>overwrite</Creation. Flag> </HPCProfile. Application> <Target> @OPTIONAL_JOBRESOURCE_CREDENTIAL@ <URI>@STDOUT_FILE_URI@</URI> </Application> </Target> @OPTIONAL_HPCFSP_CREDENTIAL@ <Data. Staging> </Data. Staging> <File. Name>input. txt</File. Name> <Data. Staging> <Creation. Flag>overwrite</Creation. Flag> <File. Name>stderr. txt</File. Name> <Source> <Creation. Flag>overwrite</Creation. Flag> <URI>@INPUT_FILE_URI@</URI> <Target> </Source> <URI>@STDERR_FILE_URI@</URI> @OPTIONAL_HPCFSP_CREDENTIAL@ </Target> </Data. Staging> @OPTIONAL_HPCFSP_CREDENTIAL@ <Data. Staging> </Data. Staging> <File. Name>output. txt</File. Name> </Job. Description> <Creation. Flag>overwrite</Creation. Flag> <Target> </Job. Definition> <URI>@OUTPUT_FILE_URI@</URI> </Target> @OPTIONAL_HPCFSP_CREDENTIAL@ </Data. Staging> JSDL Template Web: www. omii. ac. uk Email: info@omii. ac. uk
Endpoint Configuration # UNICORE interop config file endpoint_file=unicore. xml application_type=HPCProfile. Applicatio n application_type_namespace=http: //sch emas. ggf. org/jsdl/2006/07/jsdl-hpcpa working_dir= data_mode=ftp data_input_base=ftp: //zam 1161 v 01. za m. kfa-juelich. de: 8004/ogf 27/unicore data_output_base=ftp: //zam 1161 v 01. za m. kfa-juelich. de: 8004/ogf 27/unicore minem_install=/tmp/minem myproxy=no Web: www. omii. ac. uk hpcfsp=yes hpcfsp_username=interopdata hpcfsp_password=89 zukunft() auth_utoken=yes auth_x 509_credential=auth/client. pem auth_x 509_keypass=not_used auth_x 509_cert_dir=auth/certificates auth_utoken_username=ogf auth_utoken_password=ogf Email: info@omii. ac. uk
How it Fits Together… 1. Create Minem input files 2. Generate JSDLs from template 4 Minem 7 1 2 5 FTP mineminterop. pl 3. Upload input files UNICORE 4. Submit JSDLs across middlewares 5. Monitor jobs until completion BES++ Client 6. Download output files 7. Select best result 8. Generate/upload image to web server BES++ Minem 3 6 FTP My. Proxy Grid. SAM 8 Minem Grid. FTP Client Job Service Data Service Application Web: www. omii. ac. uk ARC Security Service Email: info@omii. ac. uk Minem
The Demo… Web: www. omii. ac. uk Email: info@omii. ac. uk
Future Work • Standards integration: o o Integrate GENESIS II and SMOA Computing Replacement of BES++ Client with SAGA • SAGA BES adapter currently in development! • Schedule across BES/non-BES endpoints (e. g. Globus) o GLUE 2 (e. g. using OMII-UK Grimoires software) • Service discovery (static) • Dynamic allocation (dynamic) o Integrate CREAM-BES? • Security: ‘Static’ trust set up of security, proper VO set up? • Middleware client ‘audit’ of interoperability? o Leads to ability to configure and use different middleware HPC-BP clients… • Use of HARC for advance reservation • Clean up the code, upload to OGF Forge within GIN-CG • Participation very much an open process – if you wish to donate an HPC-BP compliant endpoint, please let me know! Web: www. omii. ac. uk Email: info@omii. ac. uk
Future Direction o Workflow engine integration • To replace/provide alternative to the Perl script • Taverna 2 good candidate o Application abstraction • Use of endpoints: o o Utilise production-level deployments Utilise production-level security Web: www. omii. ac. uk Utilise production-level deployments • Interface: g in s ea ty cr ili /In ab d ie per rif ro Ve te In Now Abstraction level Email: info@omii. ac. uk Future
Dissemination • Thanks to the OMII-UK publicity machine: o o o o HPCWire: http: //www. hpcwire. com/offthewire/European-Grid. Interoperability-Goes-Global-79343767. html Super. Computing Online: http: //www. supercomputingonline. com/latest/european-interoperabilitygoes-global EGEE: http: //www. euegee. com/index. php? id=193&tx_ttnews[tt_news]=125&tx_ttnews[back. Pi d]=65&c. Hash=90 bb 3 f 97 cc http: //www. d 4 science. eu/aggregator/sources/2? page=1 http: //www. it-tude. com/grid_interoperability_eu. html http: //www. beliefproject. org/zero-in-fourth-issueemagazine/news + numerous OMII-UK website articles & UK NGS articles • Just type ‘European Interoperability Goes Global’ into Google… Web: www. omii. ac. uk Email: info@omii. ac. uk
Grid. SAM OMII-UK London e-Science Centre, Imperial College, London Institute of Computing Technology, Chinese Academy of Sciences (Beijing) Web: www. omii. ac. uk Email: info@omii. ac. uk
Grid. SAM Overview • What is Grid. SAM to the resource owners? o A web service to uniformly expose a computational resource • • • o Condor (via local or SSH submission) Portable Batch Scheduler (PBS) (via local or SSH submission) Globus Sun Grid. Engine Platform Load Sharing Facility (LSF) Single machine through Fork or SSH Acts as a client to these resources • What is Grid. SAM to end-users? o o A means to access computational resources in an open standards-based uniform way A set of end-user command-line tools and client-side APIs to interact with Grid. SAM Web Services • Submit and monitor compute jobs • Cross-protocol file transfer (gsiftp, sftp, Web. Dav, https, soon SRB, i. RODS) via Commons-VFS (http: //sourceforge. net/projects/commonsvfsgrid) Web: www. omii. ac. uk Email: info@omii. ac. uk
Supported OGF Standards • • • OGSA Basic Execution Service (BES) v 1. 0 JSDL v 1. 0 HPC Basic Profile v 1. 0 HPC Profile Application Extension v 1. 0 HPC File Staging Profile v 1. 0 HPC Common Case Profile: Activity Credential v 0. 1 • JSDL SPMD Application Extension v 1. 0 Web: www. omii. ac. uk Email: info@omii. ac. uk
Grid. SAM – Publications & Enabled Activities + in 2009/2010 – ICHEC Bioinformatics Portal, e. Sys. Bio, NAREGI/RENKEI Web: www. omii. ac. uk Email: info@omii. ac. uk
For Resource Owners… Persistence provided by one of: Hypersonic, Postgre. SQL, or existing My. SQL X 509 certificate DRM … Grid. SAM Service Computational Resource Manager Tomcat/ Axis Tomcat: 5. 0. 23, 5. 0. 28, 5. 5. 23 Axis: v 1. 2. 1 Linux + Java One of: PBS (Torque/Open. PBS/PBSPro) LSF, Condor, Sun Grid. Engine, Globus, Fork Linux Many flavours: RHEL 3, 4, 5, Fedora 7, 8, Scientific Linux 4 Java: JDK 1. 5. 0+ Web: www. omii. ac. uk Email: info@omii. ac. uk
For End-Users… My. Proxy (for Globus/ Grid. FTP) e yl t -s s Any/all of: Grid. SAM native interface, OGSABES v 1. 0, HPC Basic Profile v 1. 0 u ob xy ate l G ro ific P ert C Generic Grid. SAM BES/HPC Client Basic Profile Axis Client Windows/ Linux + Java … X 509 certificate Service + My. Proxy Interface JSDL credentials OSGA-BES HTTPS/HTTP WS-Security: X 509 User/Password HPC Basic Profile Many flavours: RHEL 3, 4, 5, Fedora 7, 8, Debian, Ubuntu, Scientific Linux 4, Windows XP, Windows Vista Java: JDK 1. 5. 0+ Web: www. omii. ac. uk Email: info@omii. ac. uk Grid. SAM Service
Open Community Development • Grid. SAM is Open Source, Open Community Development • Grid. SAM Source. Forge project: o o o 99. 03% activity, 1 release/month SVN source code repository Developer & discuss mailing lists http: //sourceforge. net /projects/gridsam/ Web: www. omii. ac. uk Email: info@omii. ac. uk
Grid. SAM e. g. with Condor • A staged event-driven architecture o o Submission pipeline is constructed as a network of stages connected by event queues Each stage performs a specific action upon incoming events Example Pipeline: Condor Web: www. omii. ac. uk Email: info@omii. ac. uk
Planned Future Developments • For end-users: o o o Full support for JSDL Resource selection across PBS, Globus, Condor & Fork DRMs JSDL Parameter Sweep Extension Support for SRB and i. RODS • For resource owners: o o LCAS/LCMAPS support Packaging option as a standalone, manually configurable web archive (WAR) file • Direct PBS deployment throughout NGS sites Web: www. omii. ac. uk Email: info@omii. ac. uk
The tutorial begins… all you need is to go to: http: //www. omii. ac. uk/wiki/HPCBPTutorial Web: www. omii. ac. uk Email: info@omii. ac. uk
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