A frequent error

User 511751460d

03-04-2012 08:21:12

Dears:


My ijc5.9 always show this error.


 


java.util.NoSuchElementException: Timeout waiting for idle object


at org.apache.commons.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1144)


at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:106)


Caused: org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object


at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:114)


at com.im.commons.db.datasource.BaseDataSource.doGetConnection(BaseDataSource.java:361)


at com.im.commons.db.datasource.BaseDataSource.getConnectionFromDriverManager(BaseDataSource.java:475)


at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriver(DriverManagerDataSource.java:164)


at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnectionFromDriver(AbstractDriverBasedDataSource.java:149)


at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnection(AbstractDriverBasedDataSource.java:119)


at org.springframework.jdbc.datasource.DataSourceUtils.doGetConnection(DataSourceUtils.java:111)


at org.springframework.jdbc.datasource.DataSourceUtils.getConnection(DataSourceUtils.java:77)


Caused: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object


at org.springframework.jdbc.datasource.DataSourceUtils.getConnection(DataSourceUtils.java:80)


at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:572)


at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:614)


at com.im.df.impl.db.dao.DerbyDataRetrievingWorker.computeTask(DerbyDataRetrievingWorker.java:107)


at com.im.df.impl.db.dao.ResultsBuilder.execute(ResultsBuilder.java:144)


at com.im.df.impl.db.dao.DFDaoSupport.getData(DFDaoSupport.java:121)


at com.im.df.impl.db.dao.DFDaoWrapper.getData(DFDaoWrapper.java:89)


at com.im.df.impl.db.EDPCache.getData(EDPCache.java:178)


at com.im.df.impl.db.EDPCache._fetchValues(EDPCache.java:135)


at com.im.df.impl.db.EDPCache.fetchValues(EDPCache.java:78)


at com.im.df.impl.db.DBEntityDataProviderImpl.getData(DBEntityDataProviderImpl.java:227)


at com.im.df.impl.db.ResultSetImpl$VS.getData(ResultSetImpl.java:766)


at com.im.ijc.widgets.abstractwidget.FieldHelper.getCurrentValue(FieldHelper.java:79)


at com.im.ijc.widgets.abstractwidget.AbstractSingleFieldWidget.getCurrentValue(AbstractSingleFieldWidget.java:325)


[catch] at com.im.ijc.widgets.abstractwidget.AbstractSingleFieldWidget$3.run(AbstractSingleFieldWidget.java:344)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEventImpl(Unknown Source)


at java.awt.EventQueue.access$000(Unknown Source)


at java.awt.EventQueue$1.run(Unknown Source)


at java.awt.EventQueue$1.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:137)


at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)

ChemAxon 2bdd02d1e5

03-04-2012 08:30:42

This is known problem and is fixed in IJC 5.9.1 which is going to be released very soon (this week). We are sorry for this difficulty.


Thanks for reporting this.







User 511751460d

03-04-2012 08:56:54

Thanks very much。

User 511751460d

02-06-2012 02:01:47

Dears:


When I import a sdf , another err occured.


 



java.lang.OutOfMemoryError: Java heap space


at javax.swing.text.GapContent.allocateArray(Unknown Source)


at javax.swing.text.GapVector.resize(Unknown Source)


at javax.swing.text.GapVector.shiftEnd(Unknown Source)


at javax.swing.text.GapContent.shiftEnd(Unknown Source)


at javax.swing.text.GapVector.open(Unknown Source)


at javax.swing.text.GapVector.replace(Unknown Source)


at javax.swing.text.GapContent.insertString(Unknown Source)


at javax.swing.text.AbstractDocument.handleInsertString(Unknown Source)


at javax.swing.text.AbstractDocument.insertString(Unknown Source)


at javax.swing.text.PlainDocument.insertString(Unknown Source)


at javax.swing.JTextArea.append(Unknown Source)


at com.im.ijc.core.api.util.ProgressPanelEnvironmentRO.addMessage(ProgressPanelEnvironmentRO.java:84)


at com.im.ijc.io.quickimport.QuickImportWizardIterator.processError(QuickImportWizardIterator.java:1002)


at com.im.ijc.io.quickimport.QuickImportWizardIterator.loadData(QuickImportWizardIterator.java:892)


at com.im.ijc.io.quickimport.QuickImportWizardIterator.access$200(QuickImportWizardIterator.java:95)


at com.im.ijc.io.quickimport.QuickImportWizardIterator$2.run(QuickImportWizardIterator.java:555)


at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1418)


at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1957)



thanks very much。

ChemAxon 2bdd02d1e5

04-06-2012 10:09:44

Hi Li,


you probably try to import quite big file, isn't it?


Could you please try to increase maximum memory allocation. It can be done in instantjchem.conf file, it is located in etc directory under IJC home directory. There is line saying something like this:


default_options="--branding instantjchem -J-Xms48m -J-Xmx512m


Now if you change -J-Xmx512m to -J-Xmx1024m it should make the import working. IJC must be restarted after change or better do it when IJC is not running. Does it really work for you?


Have a nice day!

User 511751460d

04-06-2012 14:15:49

Thanks very much.


Yes, I try to import a 3G file.


I have split it and imported those .


BEST REGARDS,