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The Ibis e-Science Software Framework Henri Bal, Frank J. Seinstra, Jason Maassen, Niels Drost High Performance Distributed Computing Group Department.

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Presentation on theme: "The Ibis e-Science Software Framework Henri Bal, Frank J. Seinstra, Jason Maassen, Niels Drost High Performance Distributed Computing Group Department."— Presentation transcript:

1 The Ibis e-Science Software Framework Henri Bal, Frank J. Seinstra, Jason Maassen, Niels Drost High Performance Distributed Computing Group Department of Computer Science VU University, Amsterdam, The Netherlands

2 Introduction ● Distributed systems continue to change ● Clusters, grids, clouds, mobile devices ● Distributed applications continue to change ● e-Science, web, pervasive applications ● Distributed programming continues to be notoriously difficult

3 Distributed Systems: 1980s Multiple PCs on a (local) network ● Networks of Workstations (NOWs) ● Collections of Workstations (COWs) ● Processor pools ● Condor pools ● Clusters

4 Distributed Systems: 1990s Sharing wide-area resources ● Metacomputing (Smarr & Catlett, CACM) ● Flocking Condor (Epema) ● DAS (Distributed ASCI Supercomputer) ● Grid Blueprint (Foster & Kesselman) ● Desktop grids,

5 Distributed Systems: 2000s ● Cloud computing ● Pay-on-demand ● Virtualization ● Hardware diversity /heterogeneous computing ● Green IT ● The Networked World ● Sensor networks ● Smart phones

6 Our approach ● Study fundamental underlying problems ● … hand-in-hand with realistic applications ● … integrate solutions in one system: Ibis Distributed SystemsUser ! ●Funding from NWO (2002), VL-e ( ), EU (JavaGAT, XtreemOS, Contrail), VU, COMMIT

7 ● ‘Problem Solving’ vs. ‘System Fighting’ ● Jungle Computing ● Example applications: ● Computational Astrophysics ● Multimedia Content Analysis ● The Ibis Software Framework ● The 3 Common Uses of Ibis ● ‘Master Key’ + ‘Glue’ + ‘HPC’ ● Some current work: Green Clouds Outline

8 Ibis: ‘Problem Solving’ vs. ‘System Fighting’

9 ● DACH 2008, Japan ● Distributed multi-cluster system ● Heterogeneous ● Distributed database (image pairs) ● Large vs small databases/images ● Partial replication ● Image-pair comparison given (in C) ● Find all supernova candidates ● Task 1: As fast as possible ● Task 2: Idem, under system crashes A Random Example: Supernova Detection

10 ‘Problem Solving’ vs. ‘System Fighting’ ● All participating teams struggled (1 month) ● Middleware instabilities… ● Connectivity problems… ● Load balancing… ● But not the Ibis team ● Winner (by far) in both categories ● Note: many Japanese teams with years of experience ● Hardware, middleware, network, C-code, image data… ● Focus on ‘problem solving’, not ‘system fighting’ ● incl. ‘opening’ of black-box C-code

11 Ibis Results: Awards & Prizes 1 st Prize: SCALE st Prize: SCALE 2008 AAAI-VC 2007 Most Visionary Research Award 1 st Prize: DACH BS 1 st Prize: DACH BS 1 st Prize: DACH FT 1 st Prize: DACH FT WebPie: A Web-Scale Parallel Inference Engine J. Urbani, S. Kotoulas, J. Maassen, N. Drost, F.J. Seinstra, F. van Harmelen, and H.E. Bal 3 rd Prize: ISWC st Prize: SCALE 2010 ● Many domains; data/compute intensive, real-time... ● Winner Sustainability Award in the Enlighten Your Research (EYR) competition, 7 Dec (Frank Seinstra)

12 Ibis Users… …and many more

13 Jungle Computing

14 Jungle Computing (Frank Seinstra) ● ‘Worst case’ computing as required by end-users ● Distributed ● Heterogeneous ● Hierarchical (incl. multi-/many-cores)

15 Why Jungle Computing? ● Scientists often forced to use a wide variety of resources simultaneously to solve computational problems, e.g. due to: ● Desire for scalability ● Distributed nature of (input) data ● Software heterogeneity (e.g.: mix of C/MPI and CUDA) ● Ad hoc hardware availability ● Energy consumption (use most energy-efficient resource) ● … ● Note: most users do not need ‘worst case’ jungle ● Ibis aims to apply to any subset

16 Example Application Domains ● Computational Astrophysics (Leiden) ● AMUSE: multi-model / multi-kernel simulations ● “Simulating the Universe on an Intercontinental Grid” - Portegies Zwart et al (IEEE Computer, Aug 2010) ● Climate Modeling (Utrecht) ● CPL: multi-model / multi-kernel simulations ● Atmosphere, ocean, source rock formation, … - hardware: (potentially) very diverse - high resolution => speed & scalability - …

17 Domain Example #1: Computational Astrophysics

18 Domain Example #1: Computational Astrophysics Demonstrated live at SC’11, Nov 12-18, 2011, Seattle, USA (two week ago)

19 Domain Example #1: Computational Astrophysics AMUSE radiative transport gravitational dynamics hydro- dynamics stellar evolution ● The AMUSE system (Leiden University) ● Early Star Cluster Evolution, including gas ● Gravitational dynamics (N-body): GPU / GPU-cluster ● Stellar evolution: Beowulf cluster / Cloud ● Hydro-dynamics, Radiative transport: Supercomputer

20 Domain Example #1: Computational Astrophysics Demonstrated live at SC’11, Nov 12-18, 2011, Seattle, USA

21 Domain Example #2: Multimedia Content Analysis

22 Multimedia Content Analysis (MMCA) ● Aim: ● Automatic extraction of ‘semantic concepts’ from image sets and video streams ● Depending on specific problem & size of data set: ● May take hours, days, weeks, months, years…

23 ● Applications in (a.o): ● Remote Sensing ● Security / Surveillance ● Medical Imaging ● Document Analysis ● Multimedia Systems ● Astronomy ● Application types: ● Real-time vs. off-line ● Fine-grained vs. coarse-grained ● Data-intensive / compute-intensive / information-intensive Multimedia Content Analysis (MMCA)

24 Domain Example #2: Color-based Object Recognition by a Grid-connected Robot Dog Seinstra et al (IEEE Multimedia, Oct-Dec 2007) Seinstra et al (AAAI’07: Most Visionary Research Award)

25

26 Successful… ● …but many fundamental problems unsolved! ● Scaling up to very large systems ● Platform independence ● Middleware independence ● Connectivity (a.o. firewalls, …) ● Fault-tolerance ● … ● Software support tool(s) urgently needed! ● Jungle-aware + transparent + efficient ● No progress until ‘discovery’ of Ibis

27 The Ibis Software Framework

28 ● Offers all functionality to efficiently & transparently implement & run Jungle Computing applications ● Designed for dynamic / hostile environments ● Modular and flexible ● Allow replacement of Ibis components by external ones, including native code ● Open source ● Download:

29 Ibis Design ● Applications need functionality for ● Programming (as in programming languages) ● Deployment (as in operating systems) Programming Logical Likes math Deployment Practical Visual (GUI)

30 Ibis Software Stack

31 JavaGAT ● Java Grid Application Toolkit ● High-level API for developing (Grid) applications independently of the underlying (Grid) middleware ● Use (Grid) services; file cp, resource discovery, job submission, … ● Note: SAGA API standardized by OGF ● Simple API for Grid Applications (a.o. with LSU) ● SAGA on top of JavaGAT (and v.v.)

32 Zorilla ● A prototype P2P middleware ● A Zorilla system consists of a collection of nodes, connected by a P2P network ● Each node independent & implements all middleware functionality ● No central components ● Supports fault-tolerance and malleability ● Easily combines resources in multiple administrative domains

33 IbisDeploy

34 Ibis Portability Layer (IPL) ● Java-centric ‘run-anywhere’ communication library ● Sent along with your application ● “MPI for the Grid” ● Supports fault-tolerance and malleability ● Resource tracking (Join-Elect-Leave model) ● Open-world / Closed world ● Efficient ● Highly optimized object serialization ● Can use optimized native libraries (e.g. MPI, Infiniband)

35 SmartSockets ● Robust connection setup ● Always connection in 30 different scenarios Problems: Firewalls Network Address Translation (NAT) Non-routed networks Multi-homing …

36 Ibis Programming Models ● IPL-based programming models, a.o.: ● Satin: ● A divide-and-conquer model ● MPJ: ● The MPI binding for Java ● RMI: ● Object-Oriented remote Procedure Call ● Jorus: ● A ‘user transparent’ parallel model for multimedia applications

37 The 3 Common Uses of Ibis

38 Ibis as ‘Master Key’ (or ‘Passepartout’) ● Use JavaGAT to access ‘any’ system ● Develop/run applications independently of available middlewares ● JavaGAT ‘adaptors’ required for each middleware ● ‘Intelligent dispatching’ even allows for transparent use of multiple middlewares ● Example: file copy ● JavaGAT vs. Globus ● Simple, portable, … ● SAGA API standardized package org.gridlab.gat.io.cpi.rftgt4; import java.net.MalformedURLException; import java.net.URL; import java.rmi.RemoteException; import java.security.cert.X509Certificate; import java.util.Calendar; import java.util.HashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Vector; import javax.xml.namespace.QName; import javax.xml.rpc.ServiceException; import javax.xml.rpc.Stub; import javax.xml.soap.SOAPElement; import org.apache.axis.message.addressing.EndpointReferenceType; import org.apache.axis.types.URI.MalformedURIException; import org.globus.axis.util.Util; import org.globus.delegation.DelegationConstants; import org.globus.delegation.DelegationException; import org.globus.delegation.DelegationUtil; import org.globus.gsi.GlobusCredential; import org.globus.gsi.GlobusCredentialException; import org.globus.gsi.gssapi.GlobusGSSCredentialImpl; import org.globus.gsi.jaas.JaasGssUtil; import org.globus.rft.generated.BaseRequestType; import org.globus.rft.generated.CreateReliableFileTransferInputType; import org.globus.rft.generated.CreateReliableFileTransferOutputType; import org.globus.rft.generated.DeleteRequestType; import org.globus.rft.generated.DeleteType; import org.globus.rft.generated.OverallStatus; import org.globus.rft.generated.RFTFaultResourcePropertyType; import org.globus.rft.generated.RFTOptionsType; import org.globus.rft.generated.ReliableFileTransferFactoryPortType; import org.globus.rft.generated.ReliableFileTransferPortType; import org.globus.rft.generated.Start; import org.globus.rft.generated.TransferRequestType; import org.globus.rft.generated.TransferType; import org.globus.transfer.reliable.client.BaseRFTClient; import org.globus.transfer.reliable.service.RFTConstants; import org.globus.wsrf.NotificationConsumerManager; import org.globus.wsrf.NotifyCallback; import org.globus.wsrf.ResourceException; import org.globus.wsrf.WSNConstants; import org.globus.wsrf.container.ContainerException; import org.globus.wsrf.container.ServiceContainer; import org.globus.wsrf.core.notification.ResourcePropertyValueChangeNotificationElementType; import org.globus.wsrf.encoding.DeserializationException; import org.globus.wsrf.encoding.ObjectDeserializer; import org.globus.wsrf.impl.security.authentication.Constants; import org.globus.wsrf.impl.security.authorization.Authorization; import org.globus.wsrf.impl.security.authorization.HostAuthorization; import org.globus.wsrf.impl.security.authorization.IdentityAuthorization; import org.globus.wsrf.impl.security.authorization.SelfAuthorization; import org.globus.wsrf.impl.security.descriptor.ClientSecurityDescriptor; import org.globus.wsrf.impl.security.descriptor.ContainerSecurityDescriptor; import org.globus.wsrf.impl.security.descriptor.GSISecureMsgAuthMethod; import org.globus.wsrf.impl.security.descriptor.GSITransportAuthMethod; import org.globus.wsrf.impl.security.descriptor.ResourceSecurityDescriptor; import org.globus.wsrf.impl.security.descriptor.SecurityDescriptorException; import org.globus.wsrf.security.SecurityManager; import org.gridlab.gat.CouldNotInitializeCredentialException; import org.gridlab.gat.CredentialExpiredException; import org.gridlab.gat.GATContext; import org.gridlab.gat.GATInvocationException; import org.gridlab.gat.GATObjectCreationException; import org.gridlab.gat.Preferences; import org.gridlab.gat.URI; import org.gridlab.gat.io.cpi.FileCpi; import org.gridlab.gat.security.globus.GlobusSecurityUtils; import org.ietf.jgss.GSSCredential; import org.ietf.jgss.GSSException; import org.oasis.wsn.Subscribe; import org.oasis.wsn.TopicExpressionType; import org.oasis.wsrf.faults.BaseFaultType; import org.oasis.wsrf.lifetime.SetTerminationTime; import org.oasis.wsrf.properties.GetMultipleResourcePropertiesResponse; import org.oasis.wsrf.properties.GetMultipleResourceProperties_Element; import org.oasis.wsrf.properties.ResourcePropertyValueChangeNotificationType; class RFTGT4NotifyCallback implements NotifyCallback { RFTGT4FileAdaptor transfer; OverallStatus status; public RFTGT4NotifyCallback(RFTGT4FileAdaptor transfer) { super(); this.transfer = transfer; this.status = null; public void deliver(List topicPath, EndpointReferenceType producer, Object messageWrapper) { try { ResourcePropertyValueChangeNotificationType message = ((ResourcePropertyValueChangeNotificationElementType) messageWrapper).getResourcePropertyValueChangeNotification(); this.status = (OverallStatus) message.getNewValue().get_any()[0].getValueAsType(RFTConstants.OVERALL_STATUS_RESOURCE, OverallStatus.class); if (status.getFault() != null) { transfer.setFault(getFaultFromRP(status.getFault())); } // RunQueue.getInstance().add(this.resourceKey); } catch (Exception e) { } transfer.setStatus(status); } private BaseFaultType getFaultFromRP(RFTFaultResourcePropertyType fault) { if (fault == null) { return null; } if (fault.getDelegationEPRMissingFaultType() != null) { return fault.getDelegationEPRMissingFaultType(); } else if (fault.getRftAuthenticationFaultType() != null) { return fault.getRftAuthenticationFaultType(); } else if (fault.getRftAuthorizationFaultType() != null) { return fault.getRftAuthorizationFaultType(); } else if (fault.getRftDatabaseFaultType() != null) { return fault.getRftDatabaseFaultType(); } else if (fault.getRftRepeatedlyStartedFaultType() != null) { return fault.getRftRepeatedlyStartedFaultType(); } else if (fault.getTransferTransientFaultType() != null) { return fault.getTransferTransientFaultType(); } else if (fault.getRftTransferFaultType() != null) { return fault.getRftTransferFaultType(); } else { return null; public class RFTGT4FileAdaptor extends FileCpi { public static final Authorization DEFAULT_AUTHZ = HostAuthorization.getInstance(); Integer msgProtectionType = Constants.SIGNATURE; static final int TERM_TIME = 20; static final String PROTOCOL = "https"; private static final String BASE_SERVICE_PATH = "/wsrf/services/"; public static final int DEFAULT_DURATION_HOURS = 24; public static final Integer DEFAULT_MSG_PROTECTION = Constants.SIGNATURE; public static final String DEFAULT_FACTORY_PORT = "8443"; private static final int DEFAULT_GRIDFTP_PORT = 2811; NotificationConsumerManager notificationConsumerManager; EndpointReferenceType notificationConsumerEPR; EndpointReferenceType notificationProducerEPR; String securityType; String factoryUrl; GSSCredential proxy; Authorization authorization; String host; OverallStatus status; BaseFaultType fault; String locationStr; ReliableFileTransferFactoryPortType factoryPort; public RFTGT4FileAdaptor(GATContext gatContext, Preferences preferences, URI location) throws GATObjectCreationException { super(gatContext, preferences, location); if (!location.isCompatible("gsiftp") && !location.isCompatible("gridftp")) { throw new GATObjectCreationException("cannot handle this URI"); } String globusLocation = System.getenv("GLOBUS_LOCATION"); if (globusLocation == null) { throw new GATObjectCreationException("$GLOBUS_LOCATION is not set"); } System.setProperty("GLOBUS_LOCATION", globusLocation); System.setProperty("axis.ClientConfigFile", globusLocation + "/client-config.wsdd"); this.host = location.getHost(); this.securityType = Constants.GSI_SEC_MSG; this.authorization = null; this.proxy = null; try { proxy = GlobusSecurityUtils.getGlobusCredential(gatContext, preferences, "globus", location, DEFAULT_GRIDFTP_PORT); } catch (CouldNotInitializeCredentialException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (CredentialExpiredException e) { // TODO Auto-generated catch block e.printStackTrace(); } this.notificationConsumerManager = null; this.notificationConsumerEPR = null; this.notificationProducerEPR = null; this.status = null; this.fault = null; factoryPort = null; this.factoryUrl = PROTOCOL + "://" + host + ":" + DEFAULT_FACTORY_PORT + BASE_SERVICE_PATH + RFTConstants.FACTORY_NAME; locationStr = setLocationStr(location); } String setLocationStr(URI location) { if (location.getScheme().equals("any")) { return "gsiftp://" + location.getHost() + ":" + location.getPort() + "/" + location.getPath(); } else { return location.toString(); } protected boolean copy2(String destStr) throws GATInvocationException { EndpointReferenceType credentialEndpoint = getCredentialEPR(); TransferType[] transferArray = new TransferType[1]; transferArray[0] = new TransferType(); transferArray[0].setSourceUrl(locationStr); transferArray[0].setDestinationUrl(destStr); RFTOptionsType rftOptions = new RFTOptionsType(); rftOptions.setBinary(Boolean.TRUE); // rftOptions.setIgnoreFilePermErr(false); TransferRequestType request = new TransferRequestType(); request.setRftOptions(rftOptions); request.setTransfer(transferArray); request.setTransferCredentialEndpoint(credentialEndpoint); setRequest(request); while (!transfersDone()) { try { Thread.sleep(1000); } catch (InterruptedException e) { throw new GATInvocationException("RFTGT4FileAdaptor: " + e); } return transfersSucc(); } public void copy(URI dest) throws GATInvocationException { String destUrl = setLocationStr(dest); if (!copy2(destUrl)) { throw new GATInvocationException( "RFTGT4FileAdaptor: file copy failed"); } public void subscribe(ReliableFileTransferPortType rft) throws GATInvocationException { Map properties = new HashMap (); properties.put(ServiceContainer.CLASS, "org.globus.wsrf.container.GSIServiceContainer"); if (this.proxy != null) { ContainerSecurityDescriptor containerSecDesc = new ContainerSecurityDescriptor(); SecurityManager.getManager(); try { containerSecDesc.setSubject(JaasGssUtil.createSubject(this.proxy)); } catch (GSSException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: ContainerSecurityDescriptor failed, " + e); } properties.put(ServiceContainer.CONTAINER_DESCRIPTOR, containerSecDesc); } this.notificationConsumerManager = NotificationConsumerManager.getInstance(properties); try { this.notificationConsumerManager.startListening(); } catch (ContainerException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: NotificationConsumerManager failed, " + e); } List topicPath = new LinkedList (); topicPath.add(RFTConstants.OVERALL_STATUS_RESOURCE); ResourceSecurityDescriptor securityDescriptor = new ResourceSecurityDescriptor(); String authz = null; if (authorization == null) { authz = Authorization.AUTHZ_NONE; } else if (authorization instanceof HostAuthorization) { authz = Authorization.AUTHZ_NONE; } else if (authorization instanceof SelfAuthorization) { authz = Authorization.AUTHZ_SELF; } else if (authorization instanceof IdentityAuthorization) { // not supported throw new GATInvocationException( "RFTGT4FileAdaptor: identity authorization not supported"); } else { // throw an sg throw new GATInvocationException( "RFTGT4FileAdaptor: set authorization failed"); } securityDescriptor.setAuthz(authz); Vector authMethod = new Vector (); if (this.securityType.equals(Constants.GSI_SEC_MSG)) { authMethod.add(GSISecureMsgAuthMethod.BOTH); } else { authMethod.add(GSITransportAuthMethod.BOTH); } try { securityDescriptor.setAuthMethods(authMethod); } catch (SecurityDescriptorException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: setAuthMethods failed, " + e); } RFTGT4NotifyCallback notifyCallback = new RFTGT4NotifyCallback(this); try { notificationConsumerEPR = notificationConsumerManager.createNotificationConsumer(topicPath, notifyCallback, securityDescriptor); } catch (ResourceException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: createNotificationConsumer failed, " + e); } Subscribe subscriptionRequest = new Subscribe(); subscriptionRequest.setConsumerReference(notificationConsumerEPR); TopicExpressionType topicExpression = null; try { topicExpression = new TopicExpressionType( WSNConstants.SIMPLE_TOPIC_DIALECT, RFTConstants.OVERALL_STATUS_RESOURCE); } catch (MalformedURIException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: create TopicExpressionType failed, " + e); } subscriptionRequest.setTopicExpression(topicExpression); try { rft.subscribe(subscriptionRequest); } catch (RemoteException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: subscription failed, " + e); } protected EndpointReferenceType getCredentialEPR() throws GATInvocationException { this.status = null; URL factoryURL = null; try { factoryURL = new URL(factoryUrl); } catch (MalformedURLException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: set factoryURL failed, " + e); } try { factoryPort = BaseRFTClient.rftFactoryLocator.getReliableFileTransferFactoryPortTypePort(factoryURL); } catch (ServiceException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: set factoryPort failed, " + e); } setSecurityTypeFromURL(factoryURL); return populateRFTEndpoints(factoryPort); } protected void setRequest(BaseRequestType request) throws GATInvocationException { CreateReliableFileTransferInputType input = new CreateReliableFileTransferInputType(); if (request instanceof TransferRequestType) { input.setTransferRequest((TransferRequestType) request); } else { input.setDeleteRequest((DeleteRequestType) request); } Calendar termTimeDel = Calendar.getInstance(); termTimeDel.add(Calendar.MINUTE, TERM_TIME); input.setInitialTerminationTime(termTimeDel); CreateReliableFileTransferOutputType response = null; try { response = factoryPort.createReliableFileTransfer(input); } catch (RemoteException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: set createReliableFileTransfer failed, " + e); } EndpointReferenceType reliableRFTEndpoint = response.getReliableTransferEPR(); ReliableFileTransferPortType rft = null; try { rft = BaseRFTClient.rftLocator.getReliableFileTransferPortTypePort(reliableRFTEndpoint); } catch (ServiceException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: getReliableFileTransferPortTypePort failed, " + e); } setStubSecurityProperties((Stub) rft); subscribe(rft); Calendar termTime = Calendar.getInstance(); termTime.add(Calendar.MINUTE, TERM_TIME); SetTerminationTime reqTermTime = new SetTerminationTime(); reqTermTime.setRequestedTerminationTime(termTime); try { rft.setTerminationTime(reqTermTime); } catch (RemoteException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: setTerminationTime failed, " + e); } try { rft.start(new Start()); } catch (RemoteException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: start failed, " + e); } private void setSecurityTypeFromURL(URL url) { if (url.getProtocol().equals("http")) { securityType = Constants.GSI_SEC_MSG; } else { Util.registerTransport(); securityType = Constants.GSI_TRANSPORT; } private void setStubSecurityProperties(Stub stub) { ClientSecurityDescriptor secDesc = new ClientSecurityDescriptor(); if (this.securityType.equals(Constants.GSI_SEC_MSG)) { secDesc.setGSISecureMsg(this.getMessageProtectionType()); } else { secDesc.setGSITransport(this.getMessageProtectionType()); } secDesc.setAuthz(getAuthorization()); if (this.proxy != null) { // set proxy credential secDesc.setGSSCredential(this.proxy); } stub._setProperty(Constants.CLIENT_DESCRIPTOR, secDesc); } public Integer getMessageProtectionType() { return (this.msgProtectionType == null) ? RFTGT4FileAdaptor.DEFAULT_MSG_PROTECTION : this.msgProtectionType; } public Authorization getAuthorization() { return (authorization == null) ? DEFAULT_AUTHZ : this.authorization; } private EndpointReferenceType populateRFTEndpoints( ReliableFileTransferFactoryPortType factoryPort) throws GATInvocationException { EndpointReferenceType[] delegationFactoryEndpoints = fetchDelegationFactoryEndpoints(factoryPort); EndpointReferenceType delegationEndpoint = delegate(delegationFactoryEndpoints[0]); return delegationEndpoint; } private EndpointReferenceType delegate( EndpointReferenceType delegationFactoryEndpoint) throws GATInvocationException { GlobusCredential credential = null; if (this.proxy != null) { credential = ((GlobusGSSCredentialImpl) this.proxy).getGlobusCredential(); } else { try { credential = GlobusCredential.getDefaultCredential(); } catch (GlobusCredentialException e) { throw new GATInvocationException("RFTGT4FileAdaptor: " + e); } int lifetime = DEFAULT_DURATION_HOURS * 60 * 60; ClientSecurityDescriptor secDesc = new ClientSecurityDescriptor(); if (this.securityType.equals(Constants.GSI_SEC_MSG)) { secDesc.setGSISecureMsg(this.getMessageProtectionType()); } else { secDesc.setGSITransport(this.getMessageProtectionType()); } secDesc.setAuthz(getAuthorization()); if (this.proxy != null) { secDesc.setGSSCredential(this.proxy); } // Get the public key to delegate on. X509Certificate[] certsToDelegateOn = null; try { certsToDelegateOn = DelegationUtil.getCertificateChainRP( delegationFactoryEndpoint, secDesc); } catch (DelegationException e) { throw new GATInvocationException("RFTGT4FileAdaptor: " + e); } X509Certificate certToSign = certsToDelegateOn[0]; // FIXME remove when there is a DelegationUtil.delegate(EPR,...) String protocol = delegationFactoryEndpoint.getAddress().getScheme(); String host = delegationFactoryEndpoint.getAddress().getHost(); int port = delegationFactoryEndpoint.getAddress().getPort(); String factoryUrl = protocol + "://" + host + ":" + port + BASE_SERVICE_PATH + DelegationConstants.FACTORY_PATH; // send to delegation service and get epr. EndpointReferenceType credentialEndpoint = null; try { credentialEndpoint = DelegationUtil.delegate(factoryUrl, credential, certToSign, lifetime, false, secDesc); } catch (DelegationException e) { throw new GATInvocationException("RFTGT4FileAdaptor: " + e); } return credentialEndpoint; } public EndpointReferenceType[] fetchDelegationFactoryEndpoints( ReliableFileTransferFactoryPortType factoryPort) throws GATInvocationException { GetMultipleResourceProperties_Element request = new GetMultipleResourceProperties_Element(); request.setResourceProperty(new QName[] { RFTConstants.DELEGATION_ENDPOINT_FACTORY }); GetMultipleResourcePropertiesResponse response; try { response = factoryPort.getMultipleResourceProperties(request); } catch (RemoteException e) { e.printStackTrace(); throw new GATInvocationException( "RFTGT4FileAdaptor: getMultipleResourceProperties, " + e); } SOAPElement[] any = response.get_any(); EndpointReferenceType epr1 = null; try { epr1 = (EndpointReferenceType) ObjectDeserializer.toObject(any[0], EndpointReferenceType.class); } catch (DeserializationException e) { throw new GATInvocationException( "RFTGT4FileAdaptor: ObjectDeserializer, " + e); } EndpointReferenceType[] endpoints = new EndpointReferenceType[] { epr1 }; return endpoints; } synchronized void setStatus(OverallStatus status) { this.status = status; } public int transfersActive() { if (status == null) { return 1; } return status.getTransfersActive(); } public int transfersFinished() { if (status == null) { return 0; } return status.getTransfersFinished(); } public int transfersCancelled() { if (status == null) { return 0; } return status.getTransfersCancelled(); } public int transfersFailed() { if (status == null) { return 0; } return status.getTransfersFailed(); } public int transfersPending() { if (status == null) { return 1; } return status.getTransfersPending(); } public int transfersRestarted() { if (status == null) { return 0; } return status.getTransfersRestarted(); } public boolean transfersDone() { return (transfersActive() == 0 && transfersPending() == 0 && transfersRestarted() == 0); } public boolean transfersSucc() { return (transfersDone() && transfersFailed() == 0 && transfersCancelled() == 0); } /* * private BaseFaultType getFaultFromRP(RFTFaultResourcePropertyType fault) { * if (fault == null) { return null; } * * if (fault.getRftTransferFaultType() != null) { return * fault.getRftTransferFaultType(); } else if * (fault.getDelegationEPRMissingFaultType() != null) { return * fault.getDelegationEPRMissingFaultType(); } else if * (fault.getRftAuthenticationFaultType() != null) { return * fault.getRftAuthenticationFaultType(); } else if * (fault.getRftAuthorizationFaultType() != null) { return * fault.getRftAuthorizationFaultType(); } else if * (fault.getRftDatabaseFaultType() != null) { return * fault.getRftDatabaseFaultType(); } else if * (fault.getRftRepeatedlyStartedFaultType() != null) { return * fault.getRftRepeatedlyStartedFaultType(); } else if * (fault.getTransferTransientFaultType() != null) { return * fault.getTransferTransientFaultType(); } else { return null; } } */ /* * private BaseFaultType deserializeFaultRP(SOAPElement any) throws * Exception { return getFaultFromRP((RFTFaultResourcePropertyType) * ObjectDeserializer.toObject(any, RFTFaultResourcePropertyType.class)); } */ void setFault(BaseFaultType fault) { this.fault = fault; } } package tutorial; import org.gridlab.gat.GAT; import org.gridlab.gat.GATContext; import org.gridlab.gat.URI; import org.gridlab.gat.io.File; public class RemoteCopy { public static void main(String[] args) throws Exception { GATContext context = new GATContext(); URI src = new URI(args[0]); URI dest = new URI(args[1]); File file = GAT.createFile(context, src); file.copy(dest); GAT.end(); }

39 Ibis as ‘Glue’ ● Use IPL + SmartSockets, generally for wide-area communication ● Linking up separate ‘activities’ of an application ● Activities: often largely ‘independent’ tasks implemented in any popular language or model (e.g. C/MPI, CUDA, Fortran, Java…) ● Each typically running on a single GPU/node/Cluster/Cloud/… ● Automatically circumvent connectivity problems ● Example: With SmartSockets:No SmartSockets:

40 Ibis as ‘HPC Solution’ ● Use Ibis as replacement for e.g. C++/MPI code ● Benefits: ● (better) portability ● malleability (open world) ● fault-tolerance ● (run-time) task migration ● Downside: ● requires recoding ● Comparable speedups:

41 C++/MPI Sockets + SSH Tunneling SSH ● Code pre-installed at each cluster site ● Instable / faulty communication ● Connectivity problems ● Execution on each cluster ‘by hand’ MMCA: Situation in 2004/2005 Parallel Horus Client Parallel Horus Server Parallel Horus Client

42 C++/MPI Sockets + SSH Tunneling JavaGAT + IbisDeploy Phase 1: Ibis as ‘Master Key’ (2006) Parallel Horus Client Parallel Horus Server Parallel Horus Client ● Code pre-installed at each cluster site ● Instable / faulty communication ● Connectivity problems ● Execution on each cluster ‘by hand’

43 C++/MPI IPL + SmartSockets JavaGAT + IbisDeploy Phase 2: Ibis as ‘Glue’ (2006/2007) Parallel Horus Client Parallel Horus Server Parallel Horus Client ● Code pre-installed at each cluster site ● Instable / faulty communication ● Connectivity problems ● Execution on each cluster ‘by hand’

44 Ibis/Java IPL + SmartSockets JavaGAT + IbisDeploy Phase 3: Ibis as ‘HPC Solution’ (2008) Parallel Jorus Client Parallel Jorus Server Parallel Jorus Client ● Code pre-installed at each cluster site ● Instable / faulty communication ● Connectivity problems ● Execution on each cluster ‘by hand’

45 ‘Master Key’ + ‘Glue’ + ‘HPC’ ● Step-wise conversion to 100% Ibis / Java ● Phase 1: JavaGAT as ‘Master Key’ ● Phase 2: IPL + SmartSockets as ‘Glue’ ● Phase 3: Ibis as ‘HPC Solution’ ● After each phase a fully functional, working solution was available! ● Eventual result: ● ‘wall-socket computing from a memory stick’ ● Remember: the ‘Promise of the Grid’? ● Awards at AAAI 2007 and CCGrid 2008

46 100% Ibis Implementation (2008++) Seinstra, Maassen, Drost et al. (SCALE CCGrid 2008: First Prize Winner) Bal, Maassen, Drost, Seinstra et al. (IEEE Computer, Aug 2010)

47 Some current work

48 ● NWO Smart Energy Systems project with Univ. of Amsterdam (Cees de Laat) & SARA ● How to map high-performance applications onto hybrid distributed computing system, taking both performance & energy consumption into account ● System-level approach to reduce HPC energy consumption Green Clouds

49 DAS-4: infrastructure for Green IT Dual quad-core Xeon E5620 Various accelerators (GPUs, multicores, ….) Scientific Linux Built by ClusterVision VU (74) TU Delft (32)Leiden (16) UvA/MultimediaN (16/36) SURFnet6 10 Gb/s lambdas ASTRON (23)

50 ● Adapt resources to application needs dynamically, accounting for computational & energy efficiency ● Using Ibis malleability support ● Exploit hardware diversity ● Graphics Processing Units (GPUs) have much higher FLOPS/Watt for many applications ● Use optical and photonic networks ● Build a knowledge base & semantic infrastructure description Main ideas

51 Other current PhD projects using Ibis ● Distributed reasoning over semantic web data ● WebPIE: Parallel reasoner on Web scale ● Written in Java, uses Hadoop (MapReduce) ● Graph applications (HiPG) ● E.g. for bioinformatics applications ● ● Games & distributed model checking ● Deal with large state space ● Distributed smart phone applications ● Computation & communication offloading to a cloud

52 Conclusions ● Ibis enables problem solving (avoids system fighting) ● Successfully applied in many domains ● Astronomy, multimedia analysis, climate modeling, remote sensing, semantic web, medical imaging, … ● Data intensive, compute intensive, real-time… ● Open source, download: ●

53 Conclusions (2) ● Jungle Computing is hard ● High-Performance Jungle Computing even harder ● While research into efficient & green Jungle-aware programming models has only just begun… ● …Ibis provides the basic functionality to efficiently & transparently overcome most Jungle Computing complexities

54

55 Omitted

56 General Requirements ● Resource independence ● Transparent / easy deployment ● Middleware independence & interoperability ● Jungle-aware middleware ● Jungle-aware communication ● Robust connectivity ● System-support for malleability and fault-tolerance ● Globally unique naming ● Transparent parallelism & application-level fault-tolerance ● Easy integration with external software (legacy codes) ● MPI, CUDA, C++, Python, Java, Fortran, …

57 ● Need for user-friendly programming tools ● Shield domain-experts from all complexities of parallel, distributed, heterogeneous, and hierarchical computing ● Familiar (sequential) programming model(s) Solution: tool to make parallel & distributed computing transparent to user - familiar programming - easy execution Jungle Computing Systems User Multimedia Content Analysis (MMCA)

58 “The Future of Ibis” ● Ibis/Constellation: ● Generalized programming framework for ‘all’ Jungle Computing applications ● Automatically maps any application activity (task) onto any appropriate executor (HW) ● By way of ‘contexts’, for example: ● Activity's context: “I need a GPU” ● Executor’s context: “I represent a GPU” ● Note: ● Activities may represent any type of task: ● Also legacy codes, scripts, 3 rd party software, …


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