[rhall]

After a reboot, make sure that the port is still open:

netstat -an | grep 8080 | grep LISTEN

[coldturkey]

I am a little embarrassed to say that a reboot worked. Thanks again.

[rhall]

For anyone still having issues with SMRT Analysis installations, I'm experimenting with a simpler, somewhat limited, install method using Vagrant and VirtualBox.

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/SMRT-Analysis-2.0.1-Virtual-Machine-Install-(Experimental)

[frcop]

WARN org.hibernate.cfg.SettingsFactory - Could not obtain connection to query metada

I've got a similar problem. I can create the db, but dbdata.sh crashes with the error message below. Any ideas on what's wrong?

Sep 18, 2013 9:59:54 AM com.pacbio.secondary.smrtportal.dbupdate.InitDbData <init>
INFO: Inserting required smrtportal data...
Sep 18, 2013 9:59:54 AM com.pacbio.secondary.smrtportal.common.entities.EntityUtil getEntityManager
INFO: Initializing EntityManagerFactory: smrtportal
2 [main] INFO org.hibernate.cfg.annotations.Version - Hibernate Annotations 3.5.5-Final
28 [main] INFO org.hibernate.cfg.Environment - Hibernate 3.5.5-Final
31 [main] INFO org.hibernate.cfg.Environment - hibernate.properties not found
37 [main] INFO org.hibernate.cfg.Environment - Bytecode provider name : javassist
43 [main] INFO org.hibernate.cfg.Environment - using JDK 1.4 java.sql.Timestamp handling
195 [main] INFO org.hibernate.annotations.common.Version - Hibernate Commons Annotations 3.2.0.Final
203 [main] INFO org.hibernate.ejb.Version - Hibernate EntityManager 3.5.5-Final
703 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.CustomField
736 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.CustomField on table CustomField
812 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.InputGroup
813 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.InputGroup on table InputGroup
820 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobInput
820 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobInput on table JobInput
826 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobGroup
827 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobGroup on table JobGroup
834 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.Job
834 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.Job on table Job
862 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.Input
863 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.Input on table Input
904 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.SmrtGroup
905 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.SmrtGroup on table SmrtGroup
910 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.User
911 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.User on table User
925 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.UserGroup
926 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.UserGroup on table UserGroup
932 [main] INFO org.hibernate.cfg.AnnotationBinder - Binding entity from annotated class: com.pacbio.secondary.smrtportal.common.models.JobStatus
933 [main] INFO org.hibernate.cfg.annotations.EntityBinder - Bind entity com.pacbio.secondary.smrtportal.common.models.JobStatus on table JobStatus
947 [main] INFO org.hibernate.cfg.AnnotationConfiguration - Hibernate Validator not found: ignoring
1021 [main] INFO org.hibernate.cfg.search.HibernateSearchEventListenerRegister - Unable to find org.hibernate.search.event.FullTextIndexEventListener on the classpath. Hibernate Search is not enabled.
1078 [main] INFO org.hibernate.connection.ConnectionProviderFactory - Initializing connection provider: org.hibernate.connection.C3P0ConnectionProvider
1081 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - C3P0 using driver: com.mysql.jdbc.Driver at URL: jdbc:mysql://localhost:3306/smrtportal?zeroDateTimeBehavior=convertToNull&useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&
1081 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - Connection properties: {user=smrtportal, password=****, autocommit=true, release_mode=auto}
1081 [main] INFO org.hibernate.connection.C3P0ConnectionProvider - autocommit mode: true
Sep 18, 2013 9:59:56 AM com.mchange.v2.log.MLog <clinit>
INFO: MLog clients using java 1.4+ standard logging.
Sep 18, 2013 9:59:56 AM com.mchange.v2.c3p0.C3P0Registry banner
INFO: Initializing c3p0-0.9.1 [built 16-January-2007 14:46:42; debug? true; trace: 10]
Sep 18, 2013 9:59:56 AM com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource getPoolManager
INFO: Initializing c3p0 pool... com.mchange.v2.c3p0.PoolBackedDataSource@dfc1a7a [ connectionPoolDataSource -> com.mchange.v2.c3p0.WrapperConnectionPoolDataSource@5a820451 [ acquireIncrement -> 3, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> automaticTestTable, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, debugUnreturnedConnectionStackTraces -> false, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> z8kfsx8xdca9431vgwip1|4c345833, idleConnectionTestPeriod -> 3600, initialPoolSize -> 3, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 15, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 3, nestedDataSource -> com.mchange.v2.c3p0.DriverManagerDataSource@a312f49e [ description -> null, driverClass -> null, factoryClassLocation -> null, identityToken -> z8kfsx8xdca9431vgwip1|3397a6b5, jdbcUrl -> jdbc:mysql://localhost:3306/smrtportal?zeroDateTimeBehavior=convertToNull&useUnicode=true&characterEncoding=UTF-8&autoReconnect=true&, properties -> {user=******, password=******, autocommit=true, release_mode=auto} ], preferredTestQuery -> null, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false; userOverrides: {} ], dataSourceName -> null, factoryClassLocation -> null, identityToken -> z8kfsx8xdca9431vgwip1|5aa3626f, numHelperThreads -> 3 ]
5563 [main] WARN org.hibernate.cfg.SettingsFactory - Could not obtain connection to query metadata
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.Util.getInstance(Util.java:382)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1013)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2239)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2168)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:794)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:378)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:120)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:143)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:132)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPoolManager.initializeAutomaticTestTable(C3P0PooledConnectionPoolManager.java:772)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPoolManager.createPooledConnectionPool(C3P0PooledConnectionPoolManager.java:696)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPoolManager.getPool(C3P0PooledConnectionPoolManager.java:257)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPoolManager.getPool(C3P0PooledConnectionPoolManager.java:271)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getConnection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:78)
at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:114)
at org.hibernate.cfg.Configuration.buildSettingsInternal(Configuration.java:2163)
at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2159)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1383)
at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:954)
at org.hibernate.ejb.Ejb3Configuration.buildEntityManagerFactory(Ejb3Configuration.java:891)
at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:57)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:48)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:32)
at com.pacbio.secondary.smrtportal.common.entities.EntityUtil.getEntityManager(EntityUtil.java:107)
at com.pacbio.secondary.smrtportal.common.entities.EntityHelper.getEntityManager(EntityHelper.java:321)
at com.pacbio.secondary.smrtportal.common.entities.PagedSearch.list(PagedSearch.java:176)
at com.pacbio.secondary.smrtportal.common.entities.EntityHelper.list(EntityHelper.java:120)
at com.pacbio.secondary.smrtportal.common.helpers.GroupHelper.list(GroupHelper.java:120)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.getGroupAll(InitDbData.java:302)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.<init>(InitDbData.java:57)
at com.pacbio.secondary.smrtportal.dbupdate.InitDbData.main(InitDbData.java:364)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

[rhall]

Are you using a local mysql instance, or did you create the database on a remote server? It looks like you are having problems connecting to the mysql server, which shouldn't be an issue if you have previously managed to setup the database. The following link may be some help

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Installation-assumes-local-mysql-instance

[frcop]

Thanks for the reply.

I'm using a local mysql server. I agree that it's a problem with the connection to the mysql server, but the strange thing is that I can run the createDB script and that sets up the (empty) db correctly, the database and tables are present as described in the sql file.

Next I run dbdata.sh, which (deduced from the log I showed) tries to connect with the mysql with user smrtportal. This user exists and has smrtportal as password, so that also looks ok. As this step happens in a java class, I can't verify the code to see where things exactly go wrong.

We've set this up on a VM with Ubuntu 12.04. I don't see how, but could this version cause the problem? We've tried to setup your "experimental" VM, but IT told me that gave an error in the untar step. [update] I was able to install the VM on my Mac, but I'm not sure if this will be an sustainable option... (4CPU, 8GB). Can I connect to NFS storage?

Any help would be appreciated.

[phenotype]

Hi,

The createdb.sh script is written in mysql:
mysql -u someUser [-pSomePasswd] < SMRTPortalSchema.sql

But the dbdata.sh script looks up settings from the persistence.xml file.
source /opt/smrtanalysis/etc/setup.sh
/opt/smrtanalysis/etc/scripts/dbdata.sh


Check your bind address:
grep bind /etc/mysql/my.cnf

If you had changed the bind address to something other than the default 127.0.0.1, then you need to replace localhost in the $SEYMOUR_HOME/redist/tomcat/webapps/smrtportal/WEB-INF/classes/META-INF/persistence.xml file with the actual IP address, or hostname of the server running mysql.

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Cannot-create-a-mysql-database

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Installation-assumes-local-mysql-instance

[frcop]

Thanks for the reply, but I had already verified that and the bind is indeed to localhost

bind-address = 127.0.0.1

[Loddi]

Hey I had the same problem and this link helped me to fix it:

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/Cannot-import-new-SMRT-Cells