[dhis 2.26, pg 9.3, Ubuntu] Continued errors in starting tomcat 8.5

Hi,

Due to a out-of-memory crash, we are trying to get our hosted instance back on track using the same dhis.conf and other configuration that was working before the crash. However, we are against the wall with the following error not allowing tomcat to deploy the war. The longer version of the output log is placed at https://pastebin.com/kwF7Lj0b

The final termination error is pasted below.

···
  • INFO 2018-07-09 14:32:49,364 Executing startup routine [2 of 15, runlevel 2]: PeriodTypePopulator (DefaultStartupRoutineExecutor.java [localhost-s

tartStop-1])

  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,369 parse S_3: ROLLBACK (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 StartTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 bind to S_3 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 ProcessUtility (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])

  • WARN 2018-07-09 14:32:49,370 CommitTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])

  • ERROR 2018-07-09 14:32:49,372 org.hibernate.WrongClassException: Object [id=678182] was not of the specified subclass [org.hisp.dhis.period.PeriodType] : Discriminator: BiWeekly

at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1816)

at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1627)

at org.hibernate.loader.Loader.getRow(Loader.java:1556)

at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:740)

at org.hibernate.loader.Loader.processResultSet(Loader.java:985)

at org.hibernate.loader.Loader.doQuery(Loader.java:943)

at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)

at org.hibernate.loader.Loader.doList(Loader.java:2615)

at org.hibernate.loader.Loader.listUsingQueryCache(Loader.java:2460)

at org.hibernate.loader.Loader.list(Loader.java:2422)

at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:109)

at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1896)

at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:366)

at org.hisp.dhis.period.hibernate.HibernatePeriodStore.getAllPeriodTypes(HibernatePeriodStore.java:228)

at org.hisp.dhis.period.PeriodTypePopulator.executeInTransaction(PeriodTypePopulator.java:66)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine$1.doInTransaction(TransactionContextStartupRoutine.java:57)

at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine.execute(TransactionContextStartupRoutine.java:52)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:113)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:70)

at org.hisp.dhis.system.startup.StartupListener.contextInitialized(StartupListener.java:71)

at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)

:

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:748)

(StartupListener.java [localhost-startStop-1])

  • INFO 2018-07-09 14:32:49,422 De-registering jdbc driver: org.postgresql.Driver@25a564f1 (StartupListener.java [localhost-startStop-1])

What could we be doing wrong? We have tried to also use the db by making a clean setup but the problem persists. Is there any corruption with the db? Thanks in advance.

  • Gautam

Dear gautam,
It seems you tried to upgrade the database with newest version of dhis2.29 which insert bi weekly in periodtype table.

So to resolve it just go to database and delete that row with id=678182 which is bi weekly in periodtype table.

After that start the tomcat as usual.

Thanks

···

On Mon, Jul 9, 2018 at 1:27 PM Gautam Morey gautam@lifeplot.in wrote:

Hi,

Due to a out-of-memory crash, we are trying to get our hosted instance back on track using the same dhis.conf and other configuration that was working before the crash. However, we are against the wall with the following error not allowing tomcat to deploy the war. The longer version of the output log is placed at https://pastebin.com/kwF7Lj0b

The final termination error is pasted below.

  • INFO 2018-07-09 14:32:49,364 Executing startup routine [2 of 15, runlevel 2]: PeriodTypePopulator (DefaultStartupRoutineExecutor.java [localhost-s

tartStop-1])

  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,369 parse S_3: ROLLBACK (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 StartTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 bind to S_3 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 ProcessUtility (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 CommitTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])
  • ERROR 2018-07-09 14:32:49,372 org.hibernate.WrongClassException: Object [id=678182] was not of the specified subclass [org.hisp.dhis.period.PeriodType] : Discriminator: BiWeekly

at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1816)

at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1627)

at org.hibernate.loader.Loader.getRow(Loader.java:1556)

at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:740)

at org.hibernate.loader.Loader.processResultSet(Loader.java:985)

at org.hibernate.loader.Loader.doQuery(Loader.java:943)

at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)

at org.hibernate.loader.Loader.doList(Loader.java:2615)

at org.hibernate.loader.Loader.listUsingQueryCache(Loader.java:2460)

at org.hibernate.loader.Loader.list(Loader.java:2422)

at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:109)

at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1896)

at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:366)

at org.hisp.dhis.period.hibernate.HibernatePeriodStore.getAllPeriodTypes(HibernatePeriodStore.java:228)

at org.hisp.dhis.period.PeriodTypePopulator.executeInTransaction(PeriodTypePopulator.java:66)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine$1.doInTransaction(TransactionContextStartupRoutine.java:57)

at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine.execute(TransactionContextStartupRoutine.java:52)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:113)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:70)

at org.hisp.dhis.system.startup.StartupListener.contextInitialized(StartupListener.java:71)

at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)

:

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:748)

(StartupListener.java [localhost-startStop-1])

  • INFO 2018-07-09 14:32:49,422 De-registering jdbc driver: org.postgresql.Driver@25a564f1 (StartupListener.java [localhost-startStop-1])

What could we be doing wrong? We have tried to also use the db by making a clean setup but the problem persists. Is there any corruption with the db? Thanks in advance.

  • Gautam

Mailing list: https://launchpad.net/~dhis2-users

Post to : dhis2-users@lists.launchpad.net

Unsubscribe : https://launchpad.net/~dhis2-users

More help : https://help.launchpad.net/ListHelp

Dear Tuzo,

Thank you very much. This has worked very well.

In a bid to revive the server, multiple tries were made with varying versions of the war file. This kept adding rows to the periodtype table that older versions could not work with.

···

On Tue, Jul 10, 2018 at 10:06 AM, tuzo engelbert tuzoengelbert@gmail.com wrote:

Dear gautam,
It seems you tried to upgrade the database with newest version of dhis2.29 which insert bi weekly in periodtype table.

So to resolve it just go to database and delete that row with id=678182 which is bi weekly in periodtype table.

After that start the tomcat as usual.

Thanks

On Mon, Jul 9, 2018 at 1:27 PM Gautam Morey gautam@lifeplot.in wrote:

Hi,

Due to a out-of-memory crash, we are trying to get our hosted instance back on track using the same dhis.conf and other configuration that was working before the crash. However, we are against the wall with the following error not allowing tomcat to deploy the war. The longer version of the output log is placed at https://pastebin.com/kwF7Lj0b

The final termination error is pasted below.

  • INFO 2018-07-09 14:32:49,364 Executing startup routine [2 of 15, runlevel 2]: PeriodTypePopulator (DefaultStartupRoutineExecutor.java [localhost-s

tartStop-1])

  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,369 parse S_3: ROLLBACK (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,369 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 StartTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 bind to S_3 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 ProcessUtility (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 SQL Warning Code: 0, SQLState: 00000 (SqlExceptionHelper.java [localhost-startStop-1])
  • WARN 2018-07-09 14:32:49,370 CommitTransactionCommand (SqlExceptionHelper.java [localhost-startStop-1])
  • ERROR 2018-07-09 14:32:49,372 org.hibernate.WrongClassException: Object [id=678182] was not of the specified subclass [org.hisp.dhis.period.PeriodType] : Discriminator: BiWeekly

at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1816)

at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1627)

at org.hibernate.loader.Loader.getRow(Loader.java:1556)

at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:740)

at org.hibernate.loader.Loader.processResultSet(Loader.java:985)

at org.hibernate.loader.Loader.doQuery(Loader.java:943)

at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)

at org.hibernate.loader.Loader.doList(Loader.java:2615)

at org.hibernate.loader.Loader.listUsingQueryCache(Loader.java:2460)

at org.hibernate.loader.Loader.list(Loader.java:2422)

at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:109)

at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1896)

at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:366)

at org.hisp.dhis.period.hibernate.HibernatePeriodStore.getAllPeriodTypes(HibernatePeriodStore.java:228)

at org.hisp.dhis.period.PeriodTypePopulator.executeInTransaction(PeriodTypePopulator.java:66)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine$1.doInTransaction(TransactionContextStartupRoutine.java:57)

at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)

at org.hisp.dhis.system.startup.TransactionContextStartupRoutine.execute(TransactionContextStartupRoutine.java:52)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:113)

at org.hisp.dhis.system.startup.DefaultStartupRoutineExecutor.execute(DefaultStartupRoutineExecutor.java:70)

at org.hisp.dhis.system.startup.StartupListener.contextInitialized(StartupListener.java:71)

at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792)

at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)

at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)

:

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:985)

at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:748)

(StartupListener.java [localhost-startStop-1])

  • INFO 2018-07-09 14:32:49,422 De-registering jdbc driver: org.postgresql.Driver@25a564f1 (StartupListener.java [localhost-startStop-1])

What could we be doing wrong? We have tried to also use the db by making a clean setup but the problem persists. Is there any corruption with the db? Thanks in advance.

  • Gautam

Mailing list: https://launchpad.net/~dhis2-users

Post to : dhis2-users@lists.launchpad.net

Unsubscribe : https://launchpad.net/~dhis2-users

More help : https://help.launchpad.net/ListHelp

Warm regards,

Gautam Morey

Founder & CEO

Sofomo Embedded Solutions Pvt Ltd

www.lifeplot.in

Mobile : +91-9890118767