Jeff, Basically you need to some setup work in your gateway as the gateway admin which includes creating and configuring a storage resource. From the error that I see it seems that the storage resource is not properly configured. More details on setting up storage resources and other configurations can be found here https://cwiki.apache.org/confluence/display/AIRAVATA/Tutorial+05+-+PHP+Reference+Gateway+for+Airavata+-+Gateway+Admin+Guide#Tutorial05-PHPReferenceGatewayforAiravata-GatewayAdminGuide-TutorialIV-RegisterandManageStorageResources
Can you try to setup it following this tutorial? If it still has issues we can set up a video call. On Mon, Jun 5, 2017 at 3:05 PM, Sale, Jeff <[email protected]> wrote: > OK, I made that change and tried again and it looks like I am making > progress. Still some errors with data staging. Here are the errors: > > DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql:// > localhost:3306/replica_catalog?autoReconnect=true, > Username=airavata,Password=airavata,validationQuery=SELECT 1 from > CONFIGURATION > > 1 replicacatalog_data INFO [pool-1-thread-1] openjpa.Runtime - > Starting OpenJPA 2.2.0 > > 10 replicacatalog_data INFO [pool-1-thread-1] openjpa.jdbc.JDBC - > Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" > (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java > mysql-connector-java-5.1.41 ( Revision: > 83c6dc41b96809df81444362933043b20a1d49d5 > )). > > [INFO] Message Received with message id > 'LAUNCH.EXP-3399a423-f598-4ef2-b33f-6c07b983ef2c' > and with message type 'EXPERIMENT' for experimentId: > Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 > > [INFO] Launching experiment with experimentId: Clone_of_Gaussian_Job_5_ > f7a276af-dec5-460e-a002-9c5de4d883e8 gateway Id: php_reference_gateway > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid user login > name, using gateway computer resource preference login name jsale > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid user login > name, using gateway computer resource preference login name jsale > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid user login > name, using gateway computer resource preference login name jsale > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid user login > name, using gateway computer resource preference login name jsale > > [WARN] Process compute resource scheduling doesn't have valid scratch > location, using gateway computer resource preference scratch > location/oasis/scratch/comet/jsale/temp_project/pga/ > > [WARN] Process compute resource scheduling doesn't have valid user login > name, using gateway computer resource preference login name jsale > > [INFO] Validation of > org.apache.airavata.orchestrator.core.validator.impl.BatchQueueValidator > is SUCCESSFUL > > [INFO] Validation of > org.apache.airavata.orchestrator.core.validator.impl.ExperimentStatusValidator > is SUCCESSFUL > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > Launched experiment > > [INFO] Message Received with message id > 'LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529 > and with message type:LAUNCHPROCESS, for > processId:PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, > expId:Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 > > [INFO] Message Received with message id LAUNCHPROCESS and with message > type: {}LAUNCH.PROCESS-aeeddab5-cd7b-466e-bbef-2bff4cc6a529 > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed event received for status STARTED > > [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 > :- Experiment status updated to EXECUTING > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, get process > cancel data from zookeeper node /experiments/Clone_of_ > Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8/ > PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c/cancelListener > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed STARTED -> CONFIGURING_WORKSPACE > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed event received for status CONFIGURING_WORKSPACE > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status > changed CREATED -> EXECUTING > > [INFO] Creating directory: comet.sdsc.edu:/oasis/scratch/ > comet/jsale/temp_project/pga/PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c > > [INFO] Session validation failed, key :jsale_comet.sdsc.edu_22_ > c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] Initialize a new SSH session for :jsale_comet.sdsc.edu_22_ > c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_4490424a-12a7-4d4f-95d2-1850b8cc5ce6, type: ENV_SETUP : Task status > changed EXECUTING -> COMPLETED > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed CONFIGURING_WORKSPACE -> INPUT_DATA_STAGING > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task > status changed CREATED -> EXECUTING > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed event received for status INPUT_DATA_STAGING > > [INFO] SSH Session validation succeeded, key :jsale_comet.sdsc.edu_22_ > c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] Channel creation test succeeded, key :jsale_comet.sdsc.edu_22_ > c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] Reuse SSH session for :jsale_comet.sdsc.edu_22_ > c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] Transferring from:/var/www/experimentData/ > jsale37/GaussianonComet/Clone_of_Gaussian_Job_51496689416/water_opt_8c.dat > To: /oasis/scratch/comet/jsale/temp_project/pga//PROCESS_ > e2a359f3-5caa-4ed7-b203-2fde6ce7962c/ > > [INFO] Session validation failed, key :jsale_Comet > Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [INFO] Initialize a new SSH session for :jsale_Comet > Storage_22_c7eb6c4d-d2b1-430b-9082-3f94a53d6115 > > [ERROR] JSch initialization error > > com.jcraft.jsch.JSchException: java.net.UnknownHostException: Comet Storage > > at com.jcraft.jsch.Util.createSocket(Util.java:349) > > at com.jcraft.jsch.Session.connect(Session.java:215) > > at com.jcraft.jsch.Session.connect(Session.java:183) > > at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession( > HPCRemoteCluster.java:137) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession( > HPCRemoteCluster.java:274) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty( > HPCRemoteCluster.java:173) > > at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging( > SCPDataStageTask.java:247) > > at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute( > SCPDataStageTask.java:158) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask( > GFacEngineImpl.java:814) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging( > GFacEngineImpl.java:604) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom( > GFacEngineImpl.java:347) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess( > GFacEngineImpl.java:286) > > at org.apache.airavata.gfac.impl.GFacWorker.executeProcess( > GFacWorker.java:227) > > at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86) > > at org.apache.airavata.common.logging.MDCUtil.lambda$ > wrapWithMDC$0(MDCUtil.java:40) > > at java.util.concurrent.ThreadPoolExecutor.runWorker( > ThreadPoolExecutor.java:1142) > > at java.util.concurrent.ThreadPoolExecutor$Worker.run( > ThreadPoolExecutor.java:617) > > at java.lang.Thread.run(Thread.java:745) > > Caused by: java.net.UnknownHostException: Comet Storage > > at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java: > 184) > > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) > > at java.net.Socket.connect(Socket.java:589) > > at java.net.Socket.connect(Socket.java:538) > > at java.net.Socket.<init>(Socket.java:434) > > at java.net.Socket.<init>(Socket.java:211) > > at com.jcraft.jsch.Util.createSocket(Util.java:343) > > ... 18 common frames omitted > > [ERROR] Data staging failed > > org.apache.airavata.gfac.core.GFacException: JSch initialization error > > at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession( > HPCRemoteCluster.java:137) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession( > HPCRemoteCluster.java:274) > > at org.apache.airavata.gfac.impl.HPCRemoteCluster.scpThirdParty( > HPCRemoteCluster.java:173) > > at org.apache.airavata.gfac.impl.task.SCPDataStageTask.inputDataStaging( > SCPDataStageTask.java:247) > > at org.apache.airavata.gfac.impl.task.SCPDataStageTask.execute( > SCPDataStageTask.java:158) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask( > GFacEngineImpl.java:814) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging( > GFacEngineImpl.java:604) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom( > GFacEngineImpl.java:347) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess( > GFacEngineImpl.java:286) > > at org.apache.airavata.gfac.impl.GFacWorker.executeProcess( > GFacWorker.java:227) > > at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86) > > at org.apache.airavata.common.logging.MDCUtil.lambda$ > wrapWithMDC$0(MDCUtil.java:40) > > at java.util.concurrent.ThreadPoolExecutor.runWorker( > ThreadPoolExecutor.java:1142) > > at java.util.concurrent.ThreadPoolExecutor$Worker.run( > ThreadPoolExecutor.java:617) > > at java.lang.Thread.run(Thread.java:745) > > Caused by: com.jcraft.jsch.JSchException: java.net.UnknownHostException: > Comet Storage > > at com.jcraft.jsch.Util.createSocket(Util.java:349) > > at com.jcraft.jsch.Session.connect(Session.java:215) > > at com.jcraft.jsch.Session.connect(Session.java:183) > > at org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542) > > ... 15 common frames omitted > > Caused by: java.net.UnknownHostException: Comet Storage > > at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java: > 184) > > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) > > at java.net.Socket.connect(Socket.java:589) > > at java.net.Socket.connect(Socket.java:538) > > at java.net.Socket.<init>(Socket.java:434) > > at java.net.Socket.<init>(Socket.java:211) > > at com.jcraft.jsch.Util.createSocket(Util.java:343) > > ... 18 common frames omitted > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING : Task > status changed EXECUTING -> FAILED > > [ERROR] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26 type: DATA_STAGING,:- > DATA_STAGING failed, reason: Data staging failed > > [ERROR] GFac Worker throws an exception > > org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg > :Error while executing DATA_STAGING task, actual msg :expId: > Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, processId: > PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c, taskId: > TASK_bd1d0984-ef2c-4f84-b327-ea5f09e10c26, type: DATA_STAGING :- > DATA_STAGING failed. Reason: Data staging failed > > at org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures( > GFacEngineImpl.java:628) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.inputDataStaging( > GFacEngineImpl.java:609) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom( > GFacEngineImpl.java:347) > > at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess( > GFacEngineImpl.java:286) > > at org.apache.airavata.gfac.impl.GFacWorker.executeProcess( > GFacWorker.java:227) > > at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86) > > at org.apache.airavata.common.logging.MDCUtil.lambda$ > wrapWithMDC$0(MDCUtil.java:40) > > at java.util.concurrent.ThreadPoolExecutor.runWorker( > ThreadPoolExecutor.java:1142) > > at java.util.concurrent.ThreadPoolExecutor$Worker.run( > ThreadPoolExecutor.java:617) > > at java.lang.Thread.run(Thread.java:745) > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed INPUT_DATA_STAGING -> FAILED > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Process status > changed event received for status FAILED > > [INFO] expId: Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8, > processId: PROCESS_e2a359f3-5caa-4ed7-b203-2fde6ce7962c :- Sent ack for > deliveryTag 1 > > [INFO] expId : Clone_of_Gaussian_Job_5_f7a276af-dec5-460e-a002-9c5de4d883e8 > :- Experiment status updated to FAILED > > > > -- Thank you Supun Nakandala Dept. Computer Science and Engineering University of Moratuwa
