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Posted to users@airavata.apache.org by "Sale, Jeff" <es...@ucsd.edu> on 2017/03/03 16:03:33 UTC
Java errors when starting Airavata server
I have installed Airavata and PGA but I am getting the following errors when I start the Airavata server. I was also getting an error related to the JAVA_HOME environment variable "Unable to locate an executable at "/usr/bin/java/bin/java" when I defined JAVA_HOME as /usr/bin/java. A search turned up some suggestions, one of which I tried, as you see in the first couple of lines below, before I started the server. It might be related to the changes I made to the airavata-server.properties file. I can share that outside of the list via email if it helps.
Jeffs-MacBook-Pro:bin jsale$ export JAVA_HOME=$(/System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java_home)
Jeffs-MacBook-Pro:bin jsale$ echo $JAVA_HOME
/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home
Jeffs-MacBook-Pro:bin jsale$ sh airavata-server-start.sh all
...._....................._..............._...._......................_.........
.../ \..._.__...__._..___| |__...___...../ \..(_)_.__.__.___...____._|.|_.__._..
../ _ \.| '_ \./ _` |/ __| '_ \./ _ \.../ _ \.| | '__/ _` \ \./ / _` | __/ _` |.
./ ___ \| |_) | (_| | (__| |.| | __/../ ___ \| | |.| (_| |\ V / (_| | || (_| |.
/_/...\_\ .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|\__\__,_|.
........|_|.....................................................................
................................................................................
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.........?????++??????..????????:.??????????I..????????..????????+????..........
........??.....???????....???????...???????+..+??????+.I.????????.....?,........
........????==????????..??..?????..=???????=..?????,.=+?.?????????===??=........
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..........I?..................+??.:?~.....=??????..................??...........
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............++?..............?.????...?....??????.+..............++I............
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..........................,..77..77......... .. ...7..........................
................................................................................
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-simple-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
[INFO] Settings loaded from file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/bin/airavata-server.properties
[INFO] Skipping Zookeeper embedded startup ...
[INFO] Airavata server instance starting...
[INFO] Server Arguments: --servers=all
[ERROR] Server Start Error:
org.apache.airavata.common.exception.ApplicationSettingsException: registry.jdbc.driver
at org.apache.airavata.common.utils.ApplicationSettings.getSettingImpl(ApplicationSettings.java:190)
at org.apache.airavata.common.utils.ApplicationSettings.getSetting(ApplicationSettings.java:321)
at org.apache.airavata.common.utils.ServerSettings.getCredentialStoreDBDriver(ServerSettings.java:150)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.<init>(CredentialStoreServerHandler.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServer.start(CredentialStoreServer.java:65)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
[INFO] Security module reached...
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[ERROR] Unable to read airavata server properties
[ERROR]
java.lang.NullPointerException
at org.apache.airavata.api.server.util.ExperimentCatalogInitUtil.getDBType(ExperimentCatalogInitUtil.java:143)
at org.apache.airavata.api.server.util.ExperimentCatalogInitUtil.initializeDB(ExperimentCatalogInitUtil.java:72)
at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:68)
at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
[ERROR] Server Start Error:
java.lang.NullPointerException
at org.apache.airavata.api.server.util.ExperimentCatalogInitUtil.initializeDB(ExperimentCatalogInitUtil.java:72)
at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:68)
at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for null
[INFO] setting basic.qos / prefetch count to 64 for null
[ERROR] registry.jdbc.driver
org.apache.airavata.common.exception.ApplicationSettingsException: registry.jdbc.driver
at org.apache.airavata.common.utils.ApplicationSettings.getSettingImpl(ApplicationSettings.java:190)
at org.apache.airavata.common.utils.ApplicationSettings.getSetting(ApplicationSettings.java:321)
at org.apache.airavata.registry.core.experiment.catalog.resources.Utils.getJDBCDriver(Utils.java:154)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:47)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
[ERROR] registry.jdbc.url
org.apache.airavata.common.exception.ApplicationSettingsException: registry.jdbc.url
at org.apache.airavata.common.utils.ApplicationSettings.getSettingImpl(ApplicationSettings.java:190)
at org.apache.airavata.common.utils.ApplicationSettings.getSetting(ApplicationSettings.java:321)
at org.apache.airavata.registry.core.experiment.catalog.resources.Utils.getJDBCURL(Utils.java:49)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:48)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
DriverClassName=null,Url=null?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
objc[87864]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
793 experiment_data INFO [main] openjpa.Runtime - OpenJPA dynamically loaded the class enhancer. Any classes that were not enhanced at build time will be enhanced when they are loaded by the JVM.
827 experiment_data INFO [main] openjpa.Runtime - Starting OpenJPA 2.2.0
[ERROR] Cannot load JDBC driver class 'null'
<openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:102)
at org.apache.openjpa.jdbc.conf.JDBCConfigurationImpl.getDBDictionaryInstance(JDBCConfigurationImpl.java:603)
at org.apache.openjpa.jdbc.meta.MappingRepository.endConfiguration(MappingRepository.java:1510)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:518)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:443)
at org.apache.openjpa.lib.conf.PluginValue.instantiate(PluginValue.java:104)
at org.apache.openjpa.conf.MetaDataRepositoryValue.instantiate(MetaDataRepositoryValue.java:68)
at org.apache.openjpa.lib.conf.ObjectValue.instantiate(ObjectValue.java:83)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.newMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:968)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.getMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:959)
at org.apache.openjpa.kernel.AbstractBrokerFactory.makeReadOnly(AbstractBrokerFactory.java:638)
at org.apache.openjpa.kernel.AbstractBrokerFactory.newBroker(AbstractBrokerFactory.java:203)
at org.apache.openjpa.kernel.DelegatingBrokerFactory.newBroker(DelegatingBrokerFactory.java:156)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:227)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:154)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:60)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:69)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot load JDBC driver class 'null'
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1429)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1371)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.apache.openjpa.lib.jdbc.DelegatingDataSource.getConnection(DelegatingDataSource.java:110)
at org.apache.openjpa.lib.jdbc.DecoratingDataSource.getConnection(DecoratingDataSource.java:87)
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:91)
... 24 more
Caused by: java.lang.ClassNotFoundException: null
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1420)
... 29 more
[ERROR] Unable to create experiment catalog instance
org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:232)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:102)
at org.apache.openjpa.jdbc.conf.JDBCConfigurationImpl.getDBDictionaryInstance(JDBCConfigurationImpl.java:603)
at org.apache.openjpa.jdbc.meta.MappingRepository.endConfiguration(MappingRepository.java:1510)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:518)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:443)
at org.apache.openjpa.lib.conf.PluginValue.instantiate(PluginValue.java:104)
at org.apache.openjpa.conf.MetaDataRepositoryValue.instantiate(MetaDataRepositoryValue.java:68)
at org.apache.openjpa.lib.conf.ObjectValue.instantiate(ObjectValue.java:83)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.newMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:968)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.getMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:959)
at org.apache.openjpa.kernel.AbstractBrokerFactory.makeReadOnly(AbstractBrokerFactory.java:638)
at org.apache.openjpa.kernel.AbstractBrokerFactory.newBroker(AbstractBrokerFactory.java:203)
at org.apache.openjpa.kernel.DelegatingBrokerFactory.newBroker(DelegatingBrokerFactory.java:156)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:227)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:154)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:60)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:69)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
... 7 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot load JDBC driver class 'null'
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1429)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1371)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.apache.openjpa.lib.jdbc.DelegatingDataSource.getConnection(DelegatingDataSource.java:110)
at org.apache.openjpa.lib.jdbc.DecoratingDataSource.getConnection(DecoratingDataSource.java:87)
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:91)
... 24 more
Caused by: java.lang.ClassNotFoundException: null
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1420)
... 29 more
[ERROR] org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
org.apache.airavata.registry.cpi.RegistryException: org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:86)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:232)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
... 5 more
Caused by: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:102)
at org.apache.openjpa.jdbc.conf.JDBCConfigurationImpl.getDBDictionaryInstance(JDBCConfigurationImpl.java:603)
at org.apache.openjpa.jdbc.meta.MappingRepository.endConfiguration(MappingRepository.java:1510)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:518)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:443)
at org.apache.openjpa.lib.conf.PluginValue.instantiate(PluginValue.java:104)
at org.apache.openjpa.conf.MetaDataRepositoryValue.instantiate(MetaDataRepositoryValue.java:68)
at org.apache.openjpa.lib.conf.ObjectValue.instantiate(ObjectValue.java:83)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.newMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:968)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.getMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:959)
at org.apache.openjpa.kernel.AbstractBrokerFactory.makeReadOnly(AbstractBrokerFactory.java:638)
at org.apache.openjpa.kernel.AbstractBrokerFactory.newBroker(AbstractBrokerFactory.java:203)
at org.apache.openjpa.kernel.DelegatingBrokerFactory.newBroker(DelegatingBrokerFactory.java:156)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:227)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:154)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:60)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:69)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
... 7 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot load JDBC driver class 'null'
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1429)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1371)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.apache.openjpa.lib.jdbc.DelegatingDataSource.getConnection(DelegatingDataSource.java:110)
at org.apache.openjpa.lib.jdbc.DecoratingDataSource.getConnection(DecoratingDataSource.java:87)
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:91)
... 24 more
Caused by: java.lang.ClassNotFoundException: null
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1420)
... 29 more
[ERROR] Server Start Error:
org.apache.airavata.orchestrator.core.exception.OrchestratorException: Error while initializing orchestrator service
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:120)
at org.apache.airavata.orchestrator.server.OrchestratorServer.start(OrchestratorServer.java:109)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: org.apache.airavata.registry.cpi.RegistryException: org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:86)
at org.apache.airavata.orchestrator.server.OrchestratorServerHandler.<init>(OrchestratorServerHandler.java:109)
... 4 more
Caused by: org.apache.airavata.registry.cpi.RegistryException: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:232)
at org.apache.airavata.registry.core.experiment.catalog.impl.ExperimentCatalogImpl.<init>(ExperimentCatalogImpl.java:65)
at org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory.getDefaultExpCatalog(RegistryFactory.java:82)
... 5 more
Caused by: <openjpa-2.2.0-r422266:1244990 fatal general error> org.apache.openjpa.persistence.PersistenceException: Cannot load JDBC driver class 'null'
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:102)
at org.apache.openjpa.jdbc.conf.JDBCConfigurationImpl.getDBDictionaryInstance(JDBCConfigurationImpl.java:603)
at org.apache.openjpa.jdbc.meta.MappingRepository.endConfiguration(MappingRepository.java:1510)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:518)
at org.apache.openjpa.lib.conf.Configurations.configureInstance(Configurations.java:443)
at org.apache.openjpa.lib.conf.PluginValue.instantiate(PluginValue.java:104)
at org.apache.openjpa.conf.MetaDataRepositoryValue.instantiate(MetaDataRepositoryValue.java:68)
at org.apache.openjpa.lib.conf.ObjectValue.instantiate(ObjectValue.java:83)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.newMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:968)
at org.apache.openjpa.conf.OpenJPAConfigurationImpl.getMetaDataRepositoryInstance(OpenJPAConfigurationImpl.java:959)
at org.apache.openjpa.kernel.AbstractBrokerFactory.makeReadOnly(AbstractBrokerFactory.java:638)
at org.apache.openjpa.kernel.AbstractBrokerFactory.newBroker(AbstractBrokerFactory.java:203)
at org.apache.openjpa.kernel.DelegatingBrokerFactory.newBroker(DelegatingBrokerFactory.java:156)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:227)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:154)
at org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:60)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.getEntityManager(ExpCatResourceUtils.java:69)
at org.apache.airavata.registry.core.experiment.catalog.ExpCatResourceUtils.isGatewayExist(ExpCatResourceUtils.java:221)
... 7 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot load JDBC driver class 'null'
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1429)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1371)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.apache.openjpa.lib.jdbc.DelegatingDataSource.getConnection(DelegatingDataSource.java:110)
at org.apache.openjpa.lib.jdbc.DecoratingDataSource.getConnection(DecoratingDataSource.java:87)
at org.apache.openjpa.jdbc.sql.DBDictionaryFactory.newDBDictionary(DBDictionaryFactory.java:91)
... 24 more
Caused by: java.lang.ClassNotFoundException: null
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.commons.dbcp.BasicDataSource.createConnectionFactory(BasicDataSource.java:1420)
... 29 more
[INFO] Starting
[INFO] State change: CONNECTED
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_task_launch_rabbitmq_exchange
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[INFO] Started Gfac Server on Port 8950 ...
Re: Java errors when starting Airavata server
Posted by "Christie, Marcus Aaron" <ma...@iu.edu>.
Jeff,
Glad to hear you are making progress! Replies inline below:
On Mar 3, 2017, at 1:54 PM, Sale, Jeff <es...@ucsd.edu>> wrote:
Thanks, Marcus. I guess I missed the instructions to uncomment those lines in the properties file. It is also a little unclear what lines related to derby db should be commented out. It might help to provide an example file. I found one on github but it doesn't look quite the same as the one which came with the installation.
I think the properties file documentation [1] gives a little more help. Comment out the *.jdbc.url and *.jdbc.driver properties that reference derby and uncomment the mysql equivalents.
Another problem I had pertained to using the SQL GRANT ALL command with a % rather than localhost. I am now able to connect to mysql with jdbc but I am still getting some errors. I noticed one issue related to the name of one of the databases. In the instructions it says to create a database named "credential_store" but one of the errors I was getting seemed to be looking for a database named "airavata_credentialstore”.
The jdbc.url you provide in airavata-server.properties needs to match whatever you name the database.
I created a database with that name and tried again and that seems to be resolved but I am still getting errors (see below):
… snip ...
[INFO] Database already created for Workflow Catalog!!!
[ERROR] Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) )
java.lang.Exception: Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) )
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:154)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQLScript(DatabaseCreator.java:299)
at org.apache.airavata.api.server.util.DatabaseCreator.createDatabase(DatabaseCreator.java:238)
at org.apache.airavata.api.server.util.DatabaseCreator.createRegistryDatabase(DatabaseCreator.java:66)
at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:70)
at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:74)
at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 767 bytes
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2497)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2455)
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839)
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:126)
... 9 more
This something we’ve fixed for the next release. As a workaround, go into your deployment directory and edit apache-airavata-server-0.17-SNAPSHOT/bin/database_scripts/credstore-mysql.sql and change the width of a few of the varchar columns:
CREATE TABLE COMMUNITY_USER (
GATEWAY_ID VARCHAR(100) NOT NULL,
COMMUNITY_USER_NAME VARCHAR(100) NOT NULL,
TOKEN_ID VARCHAR(100) NOT NULL,
…
CREATE TABLE CREDENTIALS (
GATEWAY_ID VARCHAR(100) NOT NULL,
TOKEN_ID VARCHAR(100) NOT NULL,
…
Thanks,
Marcus
[1] http://airavata.readthedocs.io/en/latest/airavata-properties/
RE: Java errors when starting Airavata server
Posted by "Sale, Jeff" <es...@ucsd.edu>.
Thanks, Marcus. I guess I missed the instructions to uncomment those lines in the properties file. It is also a little unclear what lines related to derby db should be commented out. It might help to provide an example file. I found one on github but it doesn't look quite the same as the one which came with the installation.
Another problem I had pertained to using the SQL GRANT ALL command with a % rather than localhost. I am now able to connect to mysql with jdbc but I am still getting some errors. I noticed one issue related to the name of one of the databases. In the instructions it says to create a database named "credential_store" but one of the errors I was getting seemed to be looking for a database named "airavata_credentialstore". I created a database with that name and tried again and that seems to be resolved but I am still getting errors (see below):
Jeffs-MacBook-Pro:bin jsale$ sh airavata-server-start.sh all
...._....................._..............._...._......................_.........
.../ \..._.__...__._..___| |__...___...../ \..(_)_.__.__.___...____._|.|_.__._..
../ _ \.| '_ \./ _` |/ __| '_ \./ _ \.../ _ \.| | '__/ _` \ \./ / _` | __/ _` |.
./ ___ \| |_) | (_| | (__| |.| | __/../ ___ \| | |.| (_| |\ V / (_| | || (_| |.
/_/...\_\ .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|\__\__,_|.
........|_|.....................................................................
................................................................................
................,+????++~..~~++..+????????+??++.++~...~+=???+++.................
..............:???????....:::...~??????????????.~..::...=????????...............
............????????..~~..?????..??????????????.?????..~~~.~???????.............
...........?????????I,~I~~??????.+????????????.~??????~=~..?????????~...........
.........?????++??????..????????:.??????????I..????????..????????+????..........
........??.....???????....???????...???????+..+??????+.I.????????.....?,........
........????==????????..??..?????..=???????=..?????,.=+?.?????????===??=........
......=??????????+????..+??=.???=.~??????????,.???=,???,.????=+??????????.......
....??????????+...+I++..???,=...:??????????????.....+??..++I?+..,??????????.....
....???????=??..........??..+??.:=:.???????......??..??=..........?=???????=....
....??????..?...........+?..???.....???????......???.??...........~=.??????=....
....~???~.~..............?..???.~=..,??????...7..???.?.:..............~????:....
...7....7 ...............?..????. ...??????... .????.?.?.............I ..:.:....
.....+7=,.+?................????:,I...?????..=.?????.?.............??~.=7+......
..........????..............??????~...~??..~~??????..?...........+???,..........
...........???............=.+???????,.?+:.?????????..+...........???+...........
............??............?,.??????.,??..??????????.,............???............
...........??,.............=.,????.?+....????????I.I..............=?............
..........I?..................+??.:?~.....=??????..................??...........
..........??...?...............??.:?=......??????..............?...??...........
............++?..............?.????...?....??????.+..............++I............
.............................?.??????~....???????.?.............................
............................~~.??????......??????...............................
.............................=???????......???????+.............................
..........................=I??++?+++?......?+++++++?+...........................
..........................,..77..77......... .. ...7..........................
................................................................................
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-simple-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
[INFO] Settings loaded from file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/bin/airavata-server.properties
[INFO] Skipping Zookeeper embedded startup ...
[INFO] Airavata server instance starting...
[INFO] Server Arguments: --servers=all
[INFO] Starting Credential store Server on Port 8960
[INFO] Listening to Credential store clients ....
[INFO] Security module reached...
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[INFO] Database already created for Experiment Catalog !!!
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/experiment_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
objc[90332]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
781 experiment_data INFO [main] openjpa.Runtime - OpenJPA dynamically loaded the class enhancer. Any classes that were not enhanced at build time will be enhanced when they are loaded by the JVM.
816 experiment_data INFO [main] openjpa.Runtime - Starting OpenJPA 2.2.0
913 experiment_data INFO [main] 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 )).
1567 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "NOTIFICATION_MESSAGE" on table "NOTIFICATION" is incompatible with the same column in the given schema definition. Existing column:
Full Name: NOTIFICATION.NOTIFICATION_MESSAGE
Type: varchar
Size: 4096
Default: null
Not Null: false
Given column:
Full Name: NOTIFICATION.NOTIFICATION_MESSAGE
Type: varchar
Size: 255
Default: null
Not Null: false
1568 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "EXPERIMENT_DATA_DIR" on table "PROCESS" is incompatible with the same column in the given schema definition. Existing column:
Full Name: PROCESS.EXPERIMENT_DATA_DIR
Type: varchar
Size: 512
Default: null
Not Null: false
Given column:
Full Name: PROCESS.EXPERIMENT_DATA_DIR
Type: varchar
Size: 255
Default: null
Not Null: false
1569 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "EXPERIMENT_DATA_DIR" on table "USER_CONFIGURATION_DATA" is incompatible with the same column in the given schema definition. Existing column:
Full Name: USER_CONFIGURATION_DATA.EXPERIMENT_DATA_DIR
Type: varchar
Size: 512
Default: null
Not Null: false
Given column:
Full Name: USER_CONFIGURATION_DATA.EXPERIMENT_DATA_DIR
Type: varchar
Size: 255
Default: null
Not Null: false
[INFO] Database already created for App Catalog !!!
DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/app_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION
1 appcatalog_data INFO [main] openjpa.Runtime - Starting OpenJPA 2.2.0
9 appcatalog_data INFO [main] 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 )).
518 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "APPLICATION_DESCRIPTION" on table "APPLICATION_INTERFACE" is incompatible with the same column in the given schema definition. Existing column:
Full Name: APPLICATION_INTERFACE.APPLICATION_DESCRIPTION
Type: varchar
Size: 500
Default: null
Not Null: false
Given column:
Full Name: APPLICATION_INTERFACE.APPLICATION_DESCRIPTION
Type: varchar
Size: 255
Default: null
Not Null: false
518 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "MODULE_DESC" on table "APPLICATION_MODULE" is incompatible with the same column in the given schema definition. Existing column:
Full Name: APPLICATION_MODULE.MODULE_DESC
Type: varchar
Size: 500
Default: null
Not Null: false
Given column:
Full Name: APPLICATION_MODULE.MODULE_DESC
Type: varchar
Size: 255
Default: null
Not Null: false
519 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "GATEWAY_USAGE_MODULE_LOAD_CMD" on table "COMPUTE_RESOURCE" is incompatible with the same column in the given schema definition. Existing column:
Full Name: COMPUTE_RESOURCE.GATEWAY_USAGE_MODULE_LOAD_CMD
Type: varchar
Size: 500
Default: null
Not Null: false
Given column:
Full Name: COMPUTE_RESOURCE.GATEWAY_USAGE_MODULE_LOAD_CMD
Type: varchar
Size: 255
Default: null
Not Null: false
[INFO] Database already created for Workflow Catalog!!!
[ERROR] Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) )
java.lang.Exception: Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) )
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:154)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQLScript(DatabaseCreator.java:299)
at org.apache.airavata.api.server.util.DatabaseCreator.createDatabase(DatabaseCreator.java:238)
at org.apache.airavata.api.server.util.DatabaseCreator.createRegistryDatabase(DatabaseCreator.java:66)
at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:70)
at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:74)
at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 767 bytes
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2497)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2455)
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839)
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:126)
... 9 more
[ERROR] Server Start Error:
java.lang.RuntimeException: Database failure
at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:77)
at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:74)
at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Caused by: java.lang.Exception: Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) )
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:154)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQLScript(DatabaseCreator.java:299)
at org.apache.airavata.api.server.util.DatabaseCreator.createDatabase(DatabaseCreator.java:238)
at org.apache.airavata.api.server.util.DatabaseCreator.createRegistryDatabase(DatabaseCreator.java:66)
at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:70)
... 5 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 767 bytes
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2497)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2455)
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839)
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739)
at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:126)
... 9 more
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for null
[INFO] setting basic.qos / prefetch count to 64 for null
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] Starting
[INFO] Started Orchestrator Server on Port 8940 ...
[INFO] State change: CONNECTED
[INFO] Starting
[INFO] State change: CONNECTED
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_task_launch_rabbitmq_exchange
[INFO] connected to rabbitmq: amqp://guest@127.0.0.1:5672/ for airavata_rabbitmq_exchange
[INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange
[INFO] Started Gfac Server on Port 8950 ...
Re: Java errors when starting Airavata server
Posted by "Christie, Marcus Aaron" <ma...@iu.edu>.
On Mar 3, 2017, at 11:03 AM, Sale, Jeff <es...@ucsd.edu>> wrote:
[INFO] Settings loaded from file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/bin/airavata-server.properties
[INFO] Skipping Zookeeper embedded startup ...
[INFO] Airavata server instance starting...
[INFO] Server Arguments: --servers=all
[ERROR] Server Start Error:
org.apache.airavata.common.exception.ApplicationSettingsException: registry.jdbc.driver
at org.apache.airavata.common.utils.ApplicationSettings.getSettingImpl(ApplicationSettings.java:190)
at org.apache.airavata.common.utils.ApplicationSettings.getSetting(ApplicationSettings.java:321)
at org.apache.airavata.common.utils.ServerSettings.getCredentialStoreDBDriver(ServerSettings.java:150)
at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.<init>(CredentialStoreServerHandler.java:64)
at org.apache.airavata.credential.store.server.CredentialStoreServer.start(CredentialStoreServer.java:65)
at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320)
at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169)
at org.apache.airavata.server.ServerMain.main(ServerMain.java:152)
Jeff,
Make sure you have defined the ‘registry.jdbc.driver’ and other registry.jdbc properties in airavata-server.properties. This error means that this setting is missing from the airavata-server.properties file.
See also Step 10 under *Airavata Installation* in the documentation [1].
Thanks,
Marcus
[1] http://airavata.readthedocs.io/en/latest/Airavata-Installation/