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From: Luca C. <lcl...@uc...> - 2009-06-18 18:08:49
|
Anthony Bretaudeau wrote: > Hi, > I've got a problem when reloading opal2 app from tomcat manager. After > doing so, registered webservices stop working and the only solution is > to restart tomcat (which is quite uncomfortable as we have other apps in > production on the same tomcat server). > Looking at the log, I see some db related errors when reloading: see below. > Can you help me? > Thanks! Anthony, we already saw this problem. It is caused by a a race condition of HSQL during the reload of the webapp, basically HSQL is restarted before the old HSQL is completely destroyed. It doesn't always happen, sometime the reload works well. If you use external database this problem won't appear. My suggestion is to stop the webapp, wait some seconds and then start the webapp again, this should avoid this race condition. Sincerely, Luca > > Jun 18, 2009 3:18:48 PM org.apache.catalina.core.StandardContext reload > INFO: Reloading this Context has started > Exception in thread "HSQLDB Timer @5d802746" java.lang.NullPointerException > at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source) > at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source) > at java.lang.Thread.run(Thread.java:595) > [http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate - could not get > database metadata > java.sql.SQLException: The database is already in use by another > process: org.hsqldb.NIOLockFile@f6fbb688[file > =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false, > fl =null]: java.lang.Exception: checkHeartbeat(): lock file > [/index/www-tmp/opal/opaldb.lck] is presumably locked by another process. > at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source) > at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) > at org.hsqldb.jdbcDriver.getConnection(Unknown Source) > at org.hsqldb.jdbcDriver.connect(Unknown Source) > at java.sql.DriverManager.getConnection(DriverManager.java:525) > at java.sql.DriverManager.getConnection(DriverManager.java:140) > at > org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) > at > org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51) > at > org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168) > at > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346) > at > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327) > at > edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48) > at > edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79) > at > edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) > at > org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) > at > org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) > at > org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) > at > org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) > at > org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) > at > org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) > at > org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) > at > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) > at > org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) > at > org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Thread.java:595) > [http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate - could not complete > schema update > java.sql.SQLException: The database is already in use by another > process: org.hsqldb.NIOLockFile@f6fbb688[file > =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false, > fl =null]: java.lang.Exception: checkHeartbeat(): lock file > [/index/www-tmp/opal/opaldb.lck] is presumably locked by another process. > at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source) > at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) > at org.hsqldb.jdbcDriver.getConnection(Unknown Source) > at org.hsqldb.jdbcDriver.connect(Unknown Source) > at java.sql.DriverManager.getConnection(DriverManager.java:525) > at java.sql.DriverManager.getConnection(DriverManager.java:140) > at > org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) > at > org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51) > at > org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168) > at > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346) > at > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327) > at > edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48) > at > edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79) > at > edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) > at > org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) > at > org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) > at > org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) > at > org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) > at > org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) > at > org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) > at > org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) > at > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) > at > org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) > at > org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Thread.java:595) > [http-8383-Processor19] ERROR util.JDBCExceptionReporter - The database > is already in use by another process: > org.hsqldb.NIOLockFile@f6fbb688[file =/index/www-tmp/opal/opaldb.lck, > exists=true, locked=false, valid=false, fl =null]: java.lang.Exception: > checkHeartbeat(): lock file [/index/www-tmp/opal/opaldb.lck] is > presumably locked by another process. > org.hibernate.exception.JDBCConnectionException: Cannot open connection > at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:97) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52) > at > org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449) > at > org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167) > at > org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:74) > at $Proxy3.getMetaData(Unknown Source) > at > edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:85) > at > edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103) > at > org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) > at > org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) > at > org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) > at > org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025) > at > org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904) > at > org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495) > at > org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) > at > org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525) > at > org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276) > at > org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Thread.java:595) > Caused by: java.sql.SQLException: The database is already in use by > another process: org.hsqldb.NIOLockFile@f6fbb688[file > =/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false, > fl =null]: java.lang.Exception: checkHeartbeat(): lock file > [/index/www-tmp/opal/opaldb.lck] is presumably locked by another process. > at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source) > at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) > at org.hsqldb.jdbcDriver.getConnection(Unknown Source) > at org.hsqldb.jdbcDriver.connect(Unknown Source) > at java.sql.DriverManager.getConnection(DriverManager.java:525) > at java.sql.DriverManager.getConnection(DriverManager.java:140) > at > org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133) > at > org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446) > ... 32 more > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
|
From: Anthony B. <ant...@ir...> - 2009-06-18 15:22:52
|
Hi,
I've got a problem when reloading opal2 app from tomcat manager. After
doing so, registered webservices stop working and the only solution is
to restart tomcat (which is quite uncomfortable as we have other apps in
production on the same tomcat server).
Looking at the log, I see some db related errors when reloading: see below.
Can you help me?
Thanks!
Jun 18, 2009 3:18:48 PM org.apache.catalina.core.StandardContext reload
INFO: Reloading this Context has started
Exception in thread "HSQLDB Timer @5d802746" java.lang.NullPointerException
at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
at java.lang.Thread.run(Thread.java:595)
[http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate - could not get
database metadata
java.sql.SQLException: The database is already in use by another
process: org.hsqldb.NIOLockFile@f6fbb688[file
=/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
fl =null]: java.lang.Exception: checkHeartbeat(): lock file
[/index/www-tmp/opal/opaldb.lck] is presumably locked by another process.
at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
at org.hsqldb.jdbcDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:525)
at java.sql.DriverManager.getConnection(DriverManager.java:140)
at
org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133)
at
org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51)
at
org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168)
at
org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346)
at
org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327)
at
edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48)
at
edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79)
at
edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
at
org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025)
at
org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904)
at
org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495)
at
org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
at
org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276)
at
org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:595)
[http-8383-Processor19] ERROR hbm2ddl.SchemaUpdate - could not complete
schema update
java.sql.SQLException: The database is already in use by another
process: org.hsqldb.NIOLockFile@f6fbb688[file
=/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
fl =null]: java.lang.Exception: checkHeartbeat(): lock file
[/index/www-tmp/opal/opaldb.lck] is presumably locked by another process.
at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
at org.hsqldb.jdbcDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:525)
at java.sql.DriverManager.getConnection(DriverManager.java:140)
at
org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133)
at
org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51)
at
org.hibernate.tool.hbm2ddl.SchemaUpdate.execute(SchemaUpdate.java:168)
at
org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:346)
at
org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1327)
at
edu.sdsc.nbcr.opal.state.HibernateUtil.<clinit>(HibernateUtil.java:48)
at
edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:79)
at
edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
at
org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025)
at
org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904)
at
org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495)
at
org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
at
org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276)
at
org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:595)
[http-8383-Processor19] ERROR util.JDBCExceptionReporter - The database
is already in use by another process:
org.hsqldb.NIOLockFile@f6fbb688[file =/index/www-tmp/opal/opaldb.lck,
exists=true, locked=false, valid=false, fl =null]: java.lang.Exception:
checkHeartbeat(): lock file [/index/www-tmp/opal/opaldb.lck] is
presumably locked by another process.
org.hibernate.exception.JDBCConnectionException: Cannot open connection
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:97)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52)
at
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449)
at
org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
at
org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:74)
at $Proxy3.getMetaData(Unknown Source)
at
edu.sdsc.nbcr.opal.dashboard.persistence.DBManager.<init>(DBManager.java:85)
at
edu.sdsc.nbcr.opal.dashboard.servlet.OpalInfoServlet.init(OpalInfoServlet.java:103)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
at
org.apache.catalina.core.StandardContext.reload(StandardContext.java:3025)
at
org.apache.catalina.manager.ManagerServlet.reload(ManagerServlet.java:904)
at
org.apache.catalina.manager.HTMLManagerServlet.reload(HTMLManagerServlet.java:495)
at
org.apache.catalina.manager.HTMLManagerServlet.doGet(HTMLManagerServlet.java:99)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
at
org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:276)
at
org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:81)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.sql.SQLException: The database is already in use by
another process: org.hsqldb.NIOLockFile@f6fbb688[file
=/index/www-tmp/opal/opaldb.lck, exists=true, locked=false, valid=false,
fl =null]: java.lang.Exception: checkHeartbeat(): lock file
[/index/www-tmp/opal/opaldb.lck] is presumably locked by another process.
at org.hsqldb.jdbc.jdbcUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
at org.hsqldb.jdbcDriver.connect(Unknown Source)
at java.sql.DriverManager.getConnection(DriverManager.java:525)
at java.sql.DriverManager.getConnection(DriverManager.java:140)
at
org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133)
at
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446)
... 32 more
|
|
From: Anthony B. <ant...@ir...> - 2009-06-17 07:30:33
|
Hi, I'll give you the code soon, but for now you can view an example there: The original WSDL generated by Opal: http://genoweb3.irisa.fr:8383/opal2/services/TuiuiuServicePort?wsdl And the specific WSDL generated by our code: http://genoweb3.irisa.fr:8383/typedservices/TuiuiuServicePort.wsdl We use the 'type' tag to create it. In fact it's basically an xslt stylesheet applied to the original WSDL and which uses types defined in the config file. Then we have a servlet filter that do the conversion from the corresponding SOAP request (with specific fields) to a SOAP request in the format expected by Opal: this is done with another xslt stylesheet which uses the types from config file to reconstruct the command line args. Regards, Anthony Luca Clementi wrote: > osallou wrote: >> Hi, >> a few comments about mail. >> About drmaa, the case: >> >> opal2/ -> using DRMAA version X >> someotherapp/ -> using DRMAA version Y >> >> is not a good case. This is true for most of libraries, but not for >> DRMAA. drmaa library requires that you init it only once as a thread >> safe library. It should not be loaded multiple times on the same >> container (see drmaa doc). To manage this, it needs to be put in >> common/shared libs so that it is loaded only once for all web apps. > > Dear Olivier, > Thanks for the info. In the next release we will consider moving DRMAA > in common/lib as you suggest. >> About the code we developped, it is just a servlet filter, it does >> not modify the Opal code. It is placed as a filter in front of the >> webapp in the web container. This way, the basic WSDL generated by >> Opal is still valid (and generic). We provide in fact an additional >> WSDL per application which is specific (defines each parameters) and >> more useful for end-user when used via tools like Taverna which loads >> the WSDL to present it as a component inthe GUI. >> So, this is only an add-on which can be added (or not) in the web >> container to provide additional functionality. Anthony will provide >> you the code to have a look. If basic WSDL is used, the filter >> transparently send the message to Opal. If specific WSDL is used, >> then it modify it (from specific to generic) and send the transformed >> message to Opal. > > That sounds very interesting. > > So far our approach is based on creating customized opal node for the > various Workflow systems (at the moment we have one for Kepler and one > for Vision) that read the application metadata (the 'type' tag in our > appConfig > http://www.nbcr.net/software/opal/docs/2.0/opalgui-advancedsub.html) > and create their input and output accordingly. > > > Just a question, how do you describe the input and output of your > application? Do you use our 'type' tag or you have defined you own > language? > > Sincerely, > Luca |
|
From: Luca C. <lcl...@uc...> - 2009-06-16 23:59:04
|
osallou wrote: > Hi, > a few comments about mail. > About drmaa, the case: > > opal2/ -> using DRMAA version X > someotherapp/ -> using DRMAA version Y > > is not a good case. This is true for most of libraries, but not for > DRMAA. drmaa library requires that you init it only once as a thread > safe library. It should not be loaded multiple times on the same > container (see drmaa doc). To manage this, it needs to be put in > common/shared libs so that it is loaded only once for all web apps. Dear Olivier, Thanks for the info. In the next release we will consider moving DRMAA in common/lib as you suggest. > About the code we developped, it is just a servlet filter, it does not > modify the Opal code. It is placed as a filter in front of the webapp in > the web container. This way, the basic WSDL generated by Opal is still > valid (and generic). We provide in fact an additional WSDL per > application which is specific (defines each parameters) and more useful > for end-user when used via tools like Taverna which loads the WSDL to > present it as a component inthe GUI. > So, this is only an add-on which can be added (or not) in the web > container to provide additional functionality. Anthony will provide you > the code to have a look. If basic WSDL is used, the filter transparently > send the message to Opal. If specific WSDL is used, then it modify it > (from specific to generic) and send the transformed message to Opal. That sounds very interesting. So far our approach is based on creating customized opal node for the various Workflow systems (at the moment we have one for Kepler and one for Vision) that read the application metadata (the 'type' tag in our appConfig http://www.nbcr.net/software/opal/docs/2.0/opalgui-advancedsub.html) and create their input and output accordingly. Just a question, how do you describe the input and output of your application? Do you use our 'type' tag or you have defined you own language? Sincerely, Luca |
|
From: Luca C. <lcl...@uc...> - 2009-06-15 18:34:37
|
Anthony Bretaudeau wrote: > Hello, > Here at GenOuest (a french bioinformatics platform, see www.genouest.org > <http://www.genouest.org>), we're using Opal Toolkit 2.0 to deploy our > web services. > While installing and testing it, we have found some bugs/limitations and > we've reported them on the bug tracker: > http://sourceforge.net/tracker/?func=detail&aid=2800992&group_id=211778&atid=1019127 > <http://sourceforge.net/tracker/?func=detail&aid=2800992&group_id=211778&atid=1019127> > http://sourceforge.net/tracker/?func=detail&aid=2799937&group_id=211778&atid=1019127 > <http://sourceforge.net/tracker/?func=detail&aid=2799937&group_id=211778&atid=1019127> Dear Anthony, We should definitely upgrade DRMAA jar, next release well be using the new version. I don't think that bundling DRMAA in the common/lib/ would make any difference in this case. You would have the conflict you mentioned in the tracker anyway. AFAIK if you always bundle inside the webapp you library, you should also be able to use two different version of a lib with two different webapp. opal2/ -> using DRMAA version X someotherapp/ -> using DRMAA version Y > I'm a bit disappointed as I haven't seen much activity lately in this > bug tracker... > So I'm wondering if there's a better way to communicate with main > developers? Our mailing list (CCed) is the best way to reach Opal developers. > We've developed a bit of code around Opal to fit our needs. If you're > interested, we could share it (basically, using each app configuration > file, we generate a modified WSDL with detailed and typed input data for > each app parameter). If you want to send us the code, we will take a look at it. Since we just released Opal 2, it might take a while before we modify the WSDL again, but we'd like to check out your work. Opal applications are untyped because we wanted to have the same WSDL hence the same client stubs (simplicity was one of our main concern). > Anyway, working with Opal has been quite enjoyable, and I thank you for > this. We are very glad to hear that other people are using it!! Regards, Luca > Bye. > > Anthony Bretaudeau > GenOuest Platform |
|
From: NBCR <nbc...@nb...> - 2009-05-29 03:06:16
|
Dear Opal Users, Opal-py 2.0.0 includes support for the new Opal-core 2.0 features (e.g. input file with SOAP attachment and getJobStatistics client call) and extended documentation with developer guide. Opal Toolkit team |
|
From: NBCR <nbc...@nb...> - 2009-04-23 01:51:11
|
Opal 2.0.0 is released!
We are pleased to announce the availability of the official release of
Opal Version 2.0. Opal2 is a complete redesign of Opal 1.x with many new
features:
* New resource managers can now easily be added using a plug-in
based model
* The status database has now better performances with the new
database schema
* The dashboard will work out of the box using the in-memory HSQL
database
* WSDL improvements include support for unlimited input file size
(SOAP with Attachment), URLs for application inputs, and retrieval
of job statistics
For more info please refer to Opal web site http://opal.nbcr.net (updated!)
|
|
From: Jerome <je...@ib...> - 2009-04-03 17:27:05
|
Hi Luca That is! Thank's a lot. Luca Clementi wrote: > Jerome wrote: >> Hi all >> I'm just running a new fresh version of the opal2 beta version on a >> tomcat 5.5.27 version. The instalation of opal and the deployment of >> my first application (DateService) run without problem. Afterward, the >> submit job (Fork on loca server for now) run too , and put the results >> in the $CATALIA_HOME/webapps/opal-jobs/appxxxxxx/ directory. I put too >> the opal.xml file in the Catalina/localhost directory. >> The problem is that can "enter" with the navigator in this directory. >> It is not disponible appalication. I can't remember me out what is >> wrong with this? How to sda that tomcat act as a "simple" apache server? >> >> Best regards. >> > > > Dear Jerome, > I think the problem you have can be fixed modifying the file > $CATALIA_HOME/conf/web.xml as explained below. > > Change: > <servlet> > <servlet-name>default</servlet-name> > > <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class> > <init-param> > <param-name>debug</param-name> > <param-value>0</param-value> > </init-param> > <init-param> > <param-name>listings</param-name> > <param-value>false</param-value> > </init-param> > <load-on-startup>1</load-on-startup> > </servlet> > > into > > > <init-param> > <param-name>listings</param-name> > <param-value>true</param-value> > </init-param> > > You just have to turn into true the parameter listing. > > > I hope this solve your problem, > Luca > > -- -- Jérôme L'ignorant affirme, le savant doute, le sage réfléchit. (Aristote) |
|
From: Luca C. <lcl...@uc...> - 2009-04-03 01:24:50
|
Jerome wrote:
> Hi all
> I'm just running a new fresh version of the opal2 beta version on a
> tomcat 5.5.27 version. The instalation of opal and the deployment of my
> first application (DateService) run without problem. Afterward, the
> submit job (Fork on loca server for now) run too , and put the results
> in the $CATALIA_HOME/webapps/opal-jobs/appxxxxxx/ directory. I put too
> the opal.xml file in the Catalina/localhost directory.
> The problem is that can "enter" with the navigator in this directory.
> It is not disponible appalication. I can't remember me out what is wrong
> with this? How to sda that tomcat act as a "simple" apache server?
>
> Best regards.
>
Dear Jerome,
I think the problem you have can be fixed modifying the file
$CATALIA_HOME/conf/web.xml as explained below.
Change:
<servlet>
<servlet-name>default</servlet-name>
<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
<init-param>
<param-name>debug</param-name>
<param-value>0</param-value>
</init-param>
<init-param>
<param-name>listings</param-name>
<param-value>false</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
into
<init-param>
<param-name>listings</param-name>
<param-value>true</param-value>
</init-param>
You just have to turn into true the parameter listing.
I hope this solve your problem,
Luca
|
|
From: Jerome <je...@ib...> - 2009-04-03 00:57:24
|
Hi all I'm just running a new fresh version of the opal2 beta version on a tomcat 5.5.27 version. The instalation of opal and the deployment of my first application (DateService) run without problem. Afterward, the submit job (Fork on loca server for now) run too , and put the results in the $CATALIA_HOME/webapps/opal-jobs/appxxxxxx/ directory. I put too the opal.xml file in the Catalina/localhost directory. The problem is that can "enter" with the navigator in this directory. It is not disponible appalication. I can't remember me out what is wrong with this? How to sda that tomcat act as a "simple" apache server? Best regards. -- -- Jérôme D'ailleurs, la plupart des gens préfèrent glisser leur peau sous les draps que de la risquer sous les drapeaux. (Raymond Devos) |
|
From: Luca C. <lcl...@uc...> - 2009-03-30 23:04:38
|
Jerome wrote:
> Hi Luca
>
> You are rigth.I'm running a 5.5.27 tomcat version. So i will wait, don't
> worry.
>
> But if you could explain me what was the issue cause for?
>
In tomcat 5.5.27 they changed the default behavior of the JSP compiler
(from 5.5.26 and below), the new default is much more picky regarding
how you quote (") string inside a JSP page.
It was a very simple fix, I uploaded a patch version at:
http://nbcr.net/software/opal/opal-ws-2.0beta.tar.gz
Let me know if you have any problem.
Sincerely,
Luca
> Luca Clementi wrote:
>> Jerome wrote:
>>> Hi all
>>> I've just install the opal version 2 on a tomcat 5.5.27. The
>>> instalation process "ant install" run correct. To do the first try,
>>> i've decide to install the cat service. the deployment process run
>>> well to, and the list of application in my server show me the Cat .
>>> But when i click on the link, i get back a error:
>>>
>>> javax.servlet.ServletException:
>>> /opalGUI-jsp/DisplaySimpleForm.jsp(88,64) Attribute value "files[" +
>>> index + "]" is quoted with " which must be escaped when used within
>>> the value
>>> org.apache.struts.chain.ComposableRequestProcessor.process(ComposableRequestProcessor.java:286)
>>>
>>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>
>>>
>>> .../...
>>>
>>>
>>> Have i do something wrong?
>>>
>> He Jerome,
>> are you running tomcat version greater than 5.5.26?
>>
>> I know what the problem is. I will do a fix on Monday for that. For the
>> moment either you move to a tomcat version lower or equal 5.5.26, or
>> later on Monday I can provide you with a bug fix for that problem.
>>
>> Sincerely,
>> Luca
>>
>> PS that's the problem you are seeing:
>> http://www.nabble.com/TC-5.5.27-upgrade-JSP-tag-attribute-quoting-td19986031.html
>>
>
>
--
----------------------------------------------------------------
Luca Clementi UC, San Diego
cl...@sd... \|||/ 9500 Gilman Dr. # 0446
Tel: +1-858-246-0336 (o o) La Jolla, CA 92093-0446
--------------------------ooO-(_)-Ooo---------------------------
|
|
From: Luca C. <lcl...@uc...> - 2009-03-28 18:01:37
|
Jerome wrote: > Hi all > I've just install the opal version 2 on a tomcat 5.5.27. The instalation > process "ant install" run correct. To do the first try, i've decide to > install the cat service. the deployment process run well to, and the > list of application in my server show me the Cat . But when i click on > the link, i get back a error: > > javax.servlet.ServletException: > /opalGUI-jsp/DisplaySimpleForm.jsp(88,64) Attribute value "files[" + > index + "]" is quoted with " which must be escaped when used within the > value > org.apache.struts.chain.ComposableRequestProcessor.process(ComposableRequestProcessor.java:286) > org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913) > > .../... > > > Have i do something wrong? > He Jerome, are you running tomcat version greater than 5.5.26? I know what the problem is. I will do a fix on Monday for that. For the moment either you move to a tomcat version lower or equal 5.5.26, or later on Monday I can provide you with a bug fix for that problem. Sincerely, Luca PS that's the problem you are seeing: http://www.nabble.com/TC-5.5.27-upgrade-JSP-tag-attribute-quoting-td19986031.html |
|
From: Jerome <je...@ib...> - 2009-03-28 00:54:42
|
Hi all I've just install the opal version 2 on a tomcat 5.5.27. The instalation process "ant install" run correct. To do the first try, i've decide to install the cat service. the deployment process run well to, and the list of application in my server show me the Cat . But when i click on the link, i get back a error: javax.servlet.ServletException: /opalGUI-jsp/DisplaySimpleForm.jsp(88,64) Attribute value "files[" + index + "]" is quoted with " which must be escaped when used within the value org.apache.struts.chain.ComposableRequestProcessor.process(ComposableRequestProcessor.java:286) org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913) .../... Have i do something wrong? Regards. -- -- Jérôme - Maraud, faquin, butor de pied plat ridicule ! - Ah ?.. Et moi, Cyrano Savinien-Hercule De Bergerac. (Edmond Rostand, Cyrano de Bergerac) |
|
From: Sriram K. <sr...@sd...> - 2009-03-14 00:43:10
|
We are pleased to announce the availability of the 2.0-RC (release candidate) for Opal. Opal2 is a complete redesign of Opal 1.x to support a plug-in based model where resource providers can be added easily at the back-end. State management is now provided via Hibernate, which means that the dashboard will work out of the box using the in-memory HSQL database. WSDL improvements include support for MIME attachments, URLs for application inputs, and retrieval of job statistics. This release improves upon the 2.0alpha1 release with various bug fixes, updated documentation, including the availability of a developers guide for the creation of Opal job managers. A technical paper on Opal2 that was recently submitted to ICWS 2009, the IEEE International Conference on Web Services, is available at: http://nbcr.net/software/opal/publications/opal2_icws.pdf . Opal2.0-RC can be downloaded from: https://sourceforge.net/project/showfiles.php?group_id=211778&package_id=297015 Sincerely, The Opal Team |
|
From: Clementi, L. <lcl...@uc...> - 2008-12-09 17:15:17
|
Hi Doug, We use Globus job status code. After a quick googling I found this page: https://lists.cs.wisc.edu/archive/condor-users/2006-June/msg00096.shtml It is not official but it does the work. Sincerely, Luca ________________________________________ From: Jennewein, Douglas M [Dou...@us...] Sent: Tuesday, December 09, 2008 7:28 AM To: opa...@li... Subject: [Opaltoolkit-users] Output codes Is there a document that lists the different opal output status codes, eg 8 for Execution Complete, and describes what they mean? Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us...<mailto:Dou...@us...> |
|
From: Jennewein, D. M <Dou...@us...> - 2008-12-09 15:28:35
|
Is there a document that lists the different opal output status codes, eg 8 for Execution Complete, and describes what they mean? Doug Jennewein Research Analyst Department of Computer Science University of South Dakota Vermillion, SD 57069 (605) 677-5388 (605) 677-6662 (fax) Dou...@us... <mailto:Dou...@us...> |
|
From: Sriram K. <sr...@sd...> - 2008-10-28 23:49:54
|
We are pleased to release the 2.0alpha1 version of Opal for testing purposes. Opal2 is a complete redesign of Opal 1.x to support a plug- in based model where resource providers can be added in easily at the back-end. State management is now provided via Hibernate, which means that the dashboard will work out of the box using the in-memory HSQL database. WSDL improvements include support for MIME attachments and URLs for application inputs. Opal 2.0 is not backwards compatible with Opal 1.x due to the modifications required to the WSDL. We anticipate a few more changes to the WSDL before the stable release. This release is mostly to provide the users a feel for the upcoming changes. Opal2.0alpha1 can be downloaded from here: http://sourceforge.net/project/showfiles.php?group_id=211778&package_id=297015 Sincerely, Opal Team |
|
From: Luca C. <lcl...@uc...> - 2008-10-20 17:25:57
|
banafshe bamdad wrote:
> Hi,
>
> Opal could not find map files during autodock running. So, I exchanged
> "autodock_special_config.xml" and added some param tag to get map
> files instead take map files url. Is it true?
>
> thanks
>
Dear Banafshe,
these files are samples you are free to change them as you prefer.
Autodock accept a URL because instead of asking to the user to input all
the gridmap files, we ask him a URL of a Autogrid output directory. Then
as a binary location we use the configs/run_autodock.py instead of
pointing directly to autodock4 binary (that script uses wget to download
all the mapfiles from autogrid). One last thing you have to remember is
to change the tomcat default file listing, to do so you have to change
the web.xml:
<init-param>
<param-name>listings</param-name>
<param-value>true</param-value>
</init-param>
<init-param>
<param-name>globalXsltFile</param-name>
<param-value><path to the attached file></param-value>
</init-param>
so that it points to the attached xslt file.
But again this is not required, this is only how we set up our Autodock
service.
Sincerely,
Luca
|
|
From: banafshe b. <ban...@gm...> - 2008-10-19 14:57:45
|
Hi, Opal could not find map files during autodock running. So, I exchanged "autodock_special_config.xml" and added some param tag to get map files instead take map files url. Is it true? thanks |
|
From: Reynoldson, J. <Joe...@us...> - 2008-10-16 20:07:03
|
Sriram, This worked for me. Thanks! J -----Original Message----- From: Sriram Krishnan [mailto:sr...@sd...] Sent: Monday, October 13, 2008 7:16 PM To: Reynoldson, Joe Cc: opa...@li...; Luca Clementi Subject: Re: [Opaltoolkit-users] specifying numprocs via opal-perl-1.9.2 Joe, An updated OpalTypes.pm is available here: http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/trunk/opal/opa l-perl/OpalTypes.pm?revision=288 . The JobInputType now has getter and setter methods for "numProcs". Please let us know if that does the trick for you. This update will be available in the future as a new opal-perl release (1.9.3). Cheers, Sriram On Oct 9, 2008, at 11:22 AM, Luca Clementi wrote: > Reynoldson, Joe wrote: >> I am using opal-perl-1.9.2, and I need to specify the number of >> processors for a job. I cannot find a method of the JobInputType >> class >> to set number of processors. How can I specify numprocs? >> >> >> >> Thanks, >> >> >> >> Joe Reynoldson >> > > Dear Joe, > we currently do not support that feature in the perl client library. > > We can add it, it shouldn't be too difficult. > > Sincerely, > Luca > > ------------------------------------------------------------------------ - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
|
From: Jennewein, D. M <Dou...@us...> - 2008-10-15 18:10:58
|
Thanks, Sriram. It looks like that did the trick. -----Original Message----- From: Sriram Krishnan [mailto:sr...@sd...] Sent: Monday, October 13, 2008 6:48 PM To: Jennewein, Douglas M Cc: opa...@li... Subject: Re: [Opaltoolkit-users] Accessing opal over https Hi Doug, I added a patch to do this into SVN. You can get the latest Java source here: http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/trunk/opal/opa l-core/src/edu/sdsc/nbcr/opal/GenericServiceClient.java?revision=287 . You can use this file to replace your src/edu/sdsc/nbcr/opal/ GenericServiceClient.java. To get the https to work, you will have to do the following: * keytool -import -alias testx -trustcacerts -file rio.usd.edu I am also attaching the rio.usd.edu file, which is the public key for your server. Now you can recompile Opal, and access your https service using another additional flag "-m" as follows: * ant jar * java -Djavax.net.ssl.trustStore=$HOME/.keystore edu.sdsc.nbcr.opal.GenericServiceClient -l https://rio.usd.edu/opal/services/GeneSeqer -r getAppMetadata -m Let me know if you have any problem with this. The next release version of Opal will contain this patch, along with the required documentation. Cheers, Sriram |
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From: Sriram K. <sr...@sd...> - 2008-10-14 00:16:08
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Joe, An updated OpalTypes.pm is available here: http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/trunk/opal/opal-perl/OpalTypes.pm?revision=288 . The JobInputType now has getter and setter methods for "numProcs". Please let us know if that does the trick for you. This update will be available in the future as a new opal-perl release (1.9.3). Cheers, Sriram On Oct 9, 2008, at 11:22 AM, Luca Clementi wrote: > Reynoldson, Joe wrote: >> I am using opal-perl-1.9.2, and I need to specify the number of >> processors for a job. I cannot find a method of the JobInputType >> class >> to set number of processors. How can I specify numprocs? >> >> >> >> Thanks, >> >> >> >> Joe Reynoldson >> > > Dear Joe, > we currently do not support that feature in the perl client library. > > We can add it, it shouldn't be too difficult. > > Sincerely, > Luca > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Sriram K. <sr...@sd...> - 2008-10-13 23:48:45
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Hi Doug, I added a patch to do this into SVN. You can get the latest Java source here: http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/trunk/opal/opal-core/src/edu/sdsc/nbcr/opal/GenericServiceClient.java?revision=287 . You can use this file to replace your src/edu/sdsc/nbcr/opal/ GenericServiceClient.java. To get the https to work, you will have to do the following: * keytool -import -alias testx -trustcacerts -file rio.usd.edu I am also attaching the rio.usd.edu file, which is the public key for your server. Now you can recompile Opal, and access your https service using another additional flag "-m" as follows: * ant jar * java -Djavax.net.ssl.trustStore=$HOME/.keystore edu.sdsc.nbcr.opal.GenericServiceClient -l https://rio.usd.edu/opal/services/GeneSeqer -r getAppMetadata -m Let me know if you have any problem with this. The next release version of Opal will contain this patch, along with the required documentation. Cheers, Sriram |
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From: Sriram K. <sr...@sd...> - 2008-10-10 00:59:38
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Hi Doug, If you know how to set up your Java keystore, then it is fairly easy for us to provide a patch. This basically involves getting your server's certificate and adding it on the client's keystore as a trusted certificate. If you don't, we will have to write up something to this effect. This might take a bit longer. Let us know. Thanks, Sriram On Oct 9, 2008, at 11:18 AM, Luca Clementi wrote: > Jennewein, Douglas M wrote: >> I need to access our opal services over https, but am unable to do >> so. >> I’ve tried this with the sample java client and the perl client. >> Here >> is the output I get when trying to invoke a service with the generic >> service client: >> >> >> >> [root@rio opal]# java edu.sdsc.nbcr.opal.GenericServiceClient -l >> https://rio.usd.edu/opal/services/GeneSeqer -r getAppMetadata >> >> >> >> Reading command line arguments >> >> Service URL: https://rio.usd.edu/opal/services/GeneSeqer >> >> Invoking operation: getAppMetadata >> >> >> >> HTTPS protocol handler registered >> >> >> >> Required property X509_USER_PROXY not set >> >> >> >> The sample clients connect fine over http, but http is not available >> from the location that needs access to the services – only https >> is. Is >> it possible to configure opal to respond to requests over https? >> >> >> > Dear Doug, > we support GSI security which is https with also client side > authentication. > You can find a guide here: > http://nbcr.net/software/opal/docs/1.9/security.html > > Sincerely, > Luca > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Reynoldson, J. <Joe...@us...> - 2008-10-09 19:36:25
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Adding that feature would be very helpful to me. Thanks Luca, J -----Original Message----- From: Luca Clementi [mailto:lcl...@uc...] Sent: Thursday, October 09, 2008 1:23 PM To: Reynoldson, Joe Cc: opa...@li... Subject: Re: [Opaltoolkit-users] specifying numprocs via opal-perl-1.9.2 Reynoldson, Joe wrote: > I am using opal-perl-1.9.2, and I need to specify the number of > processors for a job. I cannot find a method of the JobInputType class > to set number of processors. How can I specify numprocs? > > > > Thanks, > > > > Joe Reynoldson > Dear Joe, we currently do not support that feature in the perl client library. We can add it, it shouldn't be too difficult. Sincerely, Luca |
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