[kepler-users] Semantic Annotation, port bundling, and Suggest questions
Hello All: I'm want to make use of Kepler's (version 2.1) semantic annotation capability to help users a) quickly find compatible actors, and b) reduce wiring mistakes. For the later, I had intended to create port bundles, and then associate a unique tag with each unique bundle type as a way to support 'type mismatch' warning. The way I read the docs, this seems to be supported, but I'm having some difficulty figuring out the mechanics of making it work. I have used the tag manager to successfully create a well-structured domain ontology, which includes unique port tags. I have successfully applied tags to actors and individual ports. I have had difficulty making port bundling work, i.e. I can't see one once I have create it, and therefore haven't been able to associate a unique port tag with a bundle. I have applied the same tag to multiple actors and then tried Suggest-Similar Components, which reports no similar components in actor library. Similar results for Suggest-Compatible Input and Output. I would appreciate any suggestions or docs you might have. Thanks! Cheers, Frank White -- Frank White fwh...@optensity.com 781-771-2798 ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Kepler DOM timeout
Hello All: As of this morning, I am no longer able to build and run Kepler on my Windows machine. I also cannot execute workflows using the Kepler Webservice which is installed on a machine that has not been modified in weeks. I think I have traced my problem to not being able to access this file (http://ptolemy.eecs.berkeley.edu/xml/dtd/MoML_1.dtd) to validate my XML. When I try to get to the file in a browser, I time out. Is it possible that the URL has changed? The problem is mentioned in this thread [http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-July/002257.html]. The error message that I receive from using ant run from the Kepler build is pasted below. I am using kepler-2.1. I'd appreciate any help you can offer. Thanks much! Frank White ___ [run] java.net.ConnectException: Connection timed out: connect [run] at java.net.PlainSocketImpl. socketConnect(Native Method) [run] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [run] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [run] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [run] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [run] at java.net.Socket.connect(Socket.java:529) [run] at java.net.Socket.connect(Socket.java:478) [run] at sun.net.NetworkClient.doConnect(NetworkClient.java:163) [run] at sun.net.www.http.HttpClient.openServer(HttpClient.java:394) [run] at sun.net.www.http.HttpClient.openServer(HttpClient.java:529) [run] at sun.net.www.http.HttpClient.init(HttpClient.java:233) [run] at sun.net.www.http.HttpClient.New(HttpClient.java:306) [run] at sun.net.www.http.HttpClient.New(HttpClient.java:323) [run] at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:975) [run] at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:916) [run] at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:841) [run] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1177) [run] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source) [run] at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source) [run] at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source) [run] at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source) [run] at org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source) [run] at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) [run] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [run] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [run] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) [run] at org.apache.xerces.parsers.DOMParser.parse(Unknown Source) [run] at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source) [run] at org.kepler.moml.KeplerMetadataExtractor.extractActorMetadata(KeplerMetadataExtractor.java:112) [run] at org.kepler.objectmanager.cache.ActorCacheObject.init(ActorCacheObject.java:143) [run] at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.cache(ActorMetadataKAREntryHandler.java:170) [run] at org.kepler.kar.KARFile.cache(KARFile.java:917) [run] at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:631) [run] at org.kepler.kar.KARCacheManager.synchronizeKARCacheWithLocalRepositories(KARCacheManager.java:327) [run] at org.kepler.objectmanager.library.LibraryManager.buildLibrary(LibraryManager.java:335) [run] at org.kepler.moml.KARLibraryBuilder.buildLibrary(KARLibraryBuilder.java:78) [run] at ptolemy.actor.gui.UserActorLibrary.openLibrary(UserActorLibrary.java:202) [run] at ptolemy.actor.gui.UserActorLibrary.openUserLibrary(UserActorLibrary.java:140) [run] at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:330) [run] at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:347) [run] at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1128) [run] at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477) [run] at ptolemy.actor.gui.ConfigurationApplication.init(ConfigurationApplication.java:226) [run] at ptolemy.actor.gui.MoMLApplication.init(MoMLApplication.java:81) [run] at ptolemy.vergil.VergilApplication.init(VergilApplication.java:110) [run] at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219) [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java
[kepler-users] trouble moving kar files between kepler instances
Hello All: I'm having trouble moving actors (kar files) that I developed in one instance of Kepler in my development environment to run in another instance of Kepler in my 'production' environment. The dev instance was built from the latest kepler trunk, while the production instance was built from the Kepler 2.2 suite. Both instances load the 'reporting suite', and so should have identical modules. The most notable difference I'm seeing is in the dependencies list in the kar file manifests: kars built on the dev instance list just the dependent module names without version numbers, whereas kars built on 2.2 have the full module name and version number. Does anyone know a good way to transfer actor kar files between instances? Appreciate the help. Cheers! Frank White fwh...@optensity.com -- Frank White fwh...@optensity.com 781-771-2798 ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] dataflow using Kepler on Amazon EC2
Hello Lugman: I can speak to at least some of what you want to accomplish. My colleague and I have taken Jianwu Wang's and Jing Tao's fine work on the Kepler Workflow Run engine (see https://kepler-project.org/developers/interest-groups/distributed/technical-documentation/the-overview-of-the-workflow-run-engine-component) and built up an AMI that we regularly run on Amazon EC2. The AMI is built from base Amazon Fedora core 14 image, onto which we have installed Kepler 2.1, Tomcat6 and Axis2 - all of which are required to run the Kepler Web Service. This enables us to make SOAP/REST calls to execute Kepler .kar files that have been uploaded to a Kepler repository. There were a few difficulties along the way, but with Jing's and Jianwu's help, we were able to make it work quite reliably. On top of that, we have implemented several actors that call other Amazon services, actors that call just plain Java classes, and actors that call Java classes that wrap some fairly complex C++ libraries. Overall, we were able to find ample examples of how to do at least some of what you describe. We would be willing to share both the 'recipe' that we documented to build up our Kepler AMI, as well as the AMI itself as long as you understand that we are a small start-up, and have very limited resources to support it. Cheers, Frank White Optensity, Inc. Message: 1 Date: Tue, 22 Mar 2011 15:51:17 -0700 From: Jianwu Wangjia...@sdsc.edu To: Luqman Hodgkinsonluqman at berkeley.edu Cc:kepler-users at kepler-project.org Subject: Re: [kepler-users] dataflow using Kepler on Amazon EC2 Message-ID:4D8927E5.5030006 at sdsc.edu Content-Type: text/plain; charset=UTF-8; format=flowed Hi Luqman, Your target is still not clear to me. Please break it into sub tasks so that we can help more efficiently. Or you can try Kepler first before getting more specific questions to ask. About Kepler workflow execution on EC2, I did some experiments on it and don't think it is hard to execute Kepler workflows on EC2. Best wishes Sincerely yours Jianwu Wang jianwu at sdsc.edu http://users.sdsc.edu/~jianwu/ Assistant Project Scientist Scientific Workflow Automation Technologies (SWAT) Laboratory San Diego Supercomputer Center University of California, San Diego San Diego, CA, U.S.A. On 3/21/2011 5:10 PM, Luqman Hodgkinson wrote: Dear Kepler developers, I have a collection of Java classes linked by a custom dataflow architecture. All classes are in a single project but some of these classes call executables written in languages other than Java. I am investigating the possibility of transitioning to Kepler. Essentially my desires are to link these Java classes in a DAG representing the dataflow and to execute the dataflow in Amazon EC2. The data flowing along the edges are arbitrary custom Java classes. Additionally it is important to cache intermediate results. The data is acquired from a few web services: iRefIndex, IntAct, UniProt, and Gene Ontology. There are complex software dependencies so after setting up the dataflow I would like to save the entire system as an abstract machine image (AMI). How difficult would this transition be, and would it be worth the effort? I would appreciate your comments and advice. Sincerely, with best wishes, Luqman Hodgkinson, Ph.D. student, UC-Berkeley ___ Kepler-users mailing list Kepler-users at kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users -- ___ Kepler-users mailing list Kepler-users at kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users End of Kepler-users Digest, Vol 70, Issue 10 -- Frank White fwhite at optensity.com 781-771-2798
[kepler-users] Module Manager problems
Hello: I'm having a problem using the Kepler Module Manager. Here are the steps I've taken. The result is repeatable. 1) Downloaded Kepler-2.0-osx.jar - success 2) Ran installer - success 3) Launched Kepler 2.0 - success 4) Used Module Manager to install Kepler 2.1 - success 5) Relaunched Kepler 2.1 - success 6) Used Module Manager to install the Reporting-2.1 module - STALL Here's the output up to the stall. [null] Kepler Initializing... [null] INFO (org.kepler.objectmanager.library.LibraryManager:buildLibrary:328) Building Library... [null] INFO (org.kepler.objectmanager.cache.LocalRepositoryManager:scanReposForKarFiles:246) Scanning Local Repositories for KAR files .. [null] INFO (org.kepler.kar.KARCacheManager:synchronizeKARCacheWithLocalRepositories:374) The Cache is in sync with KAR files in Local Repositories. [null] Release: https://code.kepler-project.org/code/kepler/releases/released [null] ModuleDownloader downloadModules trying to download:reporting-2.1.0 Downloading module:reporting-2.1.0 ... [null] Spawning new Kepler process ** STALLS HERE ** At this point, I 'x' close the module manager window and menu quit Kepler. When I try to relaunch Kepler after that I get the following: bash-3.2$ ./kepler.sh [1] 5467 bash-3.2$ Exception in thread main java.lang.NullPointerException at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105) at org.kepler.build.runner.Kepler.main(Kepler.java:78) Caused by: java.lang.NullPointerException at org.kepler.build.Run.runSuite(Run.java:262) at org.kepler.build.Run.run(Run.java:202) at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101) ... 1 more --- Nested Exception --- java.lang.NullPointerException at org.kepler.build.Run.runSuite(Run.java:262) at org.kepler.build.Run.run(Run.java:202) at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101) at org.kepler.build.runner.Kepler.main(Kepler.java:78) The curious thing is I was able to use the Module Manager to successfully add Reporting-2.1 to a long running Kepler 2.1 installation just last Friday. Appreciate any help / insight you can provide. Cheers, Frank White -- Frank White fwhite at optensity.com 781-771-2798 -- next part -- An HTML attachment was scrubbed... URL: http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/attachments/20110131/67d8aad4/attachment-0001.html
[kepler-users] Module Manager problems
Hello Again: I think my problem may be that I've been selecting Reporting-2.1 /MODULE/ instead of the /SUITE/ in Module Manager. When I select the suite, it works fine. That makes some sense - by selecting only the reporting 2.1 module, several module dependencies were not met. It that's the case, then perhaps a dependency warning would be helpful. Otherwise, no further action. Thanks, Frank Frank White fwhite at optensity.com 781-771-2798 On 1/31/11 11:33 AM, Frank White wrote: Hello: I'm having a problem using the Kepler Module Manager. Here are the steps I've taken. The result is repeatable. 1) Downloaded Kepler-2.0-osx.jar - success 2) Ran installer - success 3) Launched Kepler 2.0 - success 4) Used Module Manager to install Kepler 2.1 - success 5) Relaunched Kepler 2.1 - success 6) Used Module Manager to install the Reporting-2.1 module - STALL Here's the output up to the stall. [null] Kepler Initializing... [null] INFO (org.kepler.objectmanager.library.LibraryManager:buildLibrary:328) Building Library... [null] INFO (org.kepler.objectmanager.cache.LocalRepositoryManager:scanReposForKarFiles:246) Scanning Local Repositories for KAR files .. [null] INFO (org.kepler.kar.KARCacheManager:synchronizeKARCacheWithLocalRepositories:374) The Cache is in sync with KAR files in Local Repositories. [null] Release: https://code.kepler-project.org/code/kepler/releases/released [null] ModuleDownloader downloadModules trying to download:reporting-2.1.0 Downloading module:reporting-2.1.0 ... [null] Spawning new Kepler process ** STALLS HERE ** At this point, I 'x' close the module manager window and menu quit Kepler. When I try to relaunch Kepler after that I get the following: bash-3.2$ ./kepler.sh [1] 5467 bash-3.2$ Exception in thread main java.lang.NullPointerException at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105) at org.kepler.build.runner.Kepler.main(Kepler.java:78) Caused by: java.lang.NullPointerException at org.kepler.build.Run.runSuite(Run.java:262) at org.kepler.build.Run.run(Run.java:202) at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101) ... 1 more --- Nested Exception --- java.lang.NullPointerException at org.kepler.build.Run.runSuite(Run.java:262) at org.kepler.build.Run.run(Run.java:202) at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101) at org.kepler.build.runner.Kepler.main(Kepler.java:78) The curious thing is I was able to use the Module Manager to successfully add Reporting-2.1 to a long running Kepler 2.1 installation just last Friday. Appreciate any help / insight you can provide. Cheers, Frank White -- Frank White fwhite at optensity.com 781-771-2798 -- next part -- An HTML attachment was scrubbed... URL: http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/attachments/20110131/84b66d95/attachment.html
[kepler-users] problem installing KeplerWebService
Hello All: I've been using Kepler / Ptolemy II for about a year, and I have found it to be a most elegant concept that has grown into a unique and very useful capability. I am particularly impressed with the number of very diverse communities of practice that are using and sharing their actors and workflows, and hope to contribute soon as well. Well done, all !! I am attempting to implement an instance of the Kepler Web Service, and I'm having some difficulty getting it to install correctly. I believe I have followed the instructions in 'the-overview-of-the-workflow-run-engine-component' faithfully. Axis2 installs into Tomcat5 and verifies correctly, and 'ant clean deployToTomcat' completes successfully. When I then immediately view the axis2 URL, KeplerWebService shows up under 'Faulty Services', and when I follow the link, it shows the exception below (taken from the catalina.out log file) which indicates that the axis2 deployment classloader can't find ptolemy.kernel.util.NamedObj. I verified that 'ant deployToTomcat' did in fact copy ptolemy.jar (and many many others) to $CATALINA_WEB/axis2/WEB-INF/lib, and that ptolemy/kernel/util/NamedObj.class is in fact included in ptolemy.jar. Has anyone seen this behavior before? Any thoughts how I might diagnose / remedy the problem would be greatly appreciated. Thanks, Frank [INFO] The KeplerWebService.aar service, which is not valid, caused java.lang.NoClassDefFoundError: ptolemy/kernel/util/NamedObj at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:265) at org.apache.axis2.description.java2wsdl.DefaultSchemaGenerator.init(DefaultSchemaGenerator.java:136) at org.apache.axis2.deployment.util.Utils.fillAxisService(Utils.java:499) at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:390) at org.apache.axis2.deployment.repository.util.ArchiveReader.buildServiceGroup(ArchiveReader.java:101) at org.apache.axis2.deployment.repository.util.ArchiveReader.processServiceGroup(ArchiveReader.java:143) at org.apache.axis2.deployment.ServiceDeployer.deploy(ServiceDeployer.java:81) at org.apache.axis2.deployment.repository.util.DeploymentFileData.deploy(DeploymentFileData.java:136) at org.apache.axis2.deployment.DeploymentEngine.doDeploy(DeploymentEngine.java:659) at org.apache.axis2.deployment.repository.util.WSInfoList.update(WSInfoList.java:144) at org.apache.axis2.deployment.RepositoryListener.update(RepositoryListener.java:337) at org.apache.axis2.deployment.RepositoryListener.checkServices(RepositoryListener.java:241) at org.apache.axis2.deployment.RepositoryListener.startListener(RepositoryListener.java:331) at org.apache.axis2.deployment.scheduler.SchedulerTask.checkRepository(SchedulerTask.java:64) at org.apache.axis2.deployment.scheduler.SchedulerTask.run(SchedulerTask.java:71) at org.apache.axis2.deployment.scheduler.Scheduler$SchedulerTimerTask.run(Scheduler.java:90) at java.util.TimerThread.mainLoop(Timer.java:544) at java.util.TimerThread.run(Timer.java:494) Caused by: java.lang.ClassNotFoundException: Class Not found : ptolemy.kernel.util.NamedObj at org.apache.axis2.deployment.DeploymentClassLoader.findClass(DeploymentClassLoader.java:86) at java.lang.ClassLoader.loadClass(ClassLoader.java:324) at java.lang.ClassLoader.loadClass(ClassLoader.java:269) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:337)
