error importing large smiles file

Hi ,


I am using Instant JChem 2.1 on Windows Vista. In importing PubChem on localdb as smiles string, it imported abt 30% and gave this error. Duplicate checking and default standardizer was on


INFO [com.im.ijc.core.io.quickimport.QuickImportWizardPanel3]: Import task finished


SEVERE [org.openide.util.RequestProcessor]


java.lang.OutOfMemoryError: Java heap space


at chemaxon.formats.MolImporter.incNextRecordIndex(MolImporter.java:1115)


at chemaxon.formats.MolImporter.read(MolImporter.java:838)


at com.im.ijc.io.formats.StructureFileParser$Parser.parseRow(StructureFileParser.java:180)


at com.im.ijc.core.io.quickimport.QuickImportWizardIterator.loadData(QuickImportWizardIterator.java:665)


at com.im.ijc.core.io.quickimport.QuickImportWizardIterator.access$100(QuickImportWizardIterator.java:90)


at com.im.ijc.core.io.quickimport.QuickImportWizardIterator$2.run(QuickImportWizardIterator.java:522)


at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:539)


[catch] at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:964)


SEVERE [org.openide.util.RequestProcessor]


java.lang.OutOfMemoryError: Java heap space


at java.util.Arrays.copyOf(Unknown Source)


at java.util.Arrays.copyOf(Unknown Source)


at java.util.ArrayList.ensureCapacity(Unknown Source)


at java.util.ArrayList.add(Unknown Source)


at org.springframework.jdbc.core.RowMapperResultSetExtractor.extractData(RowMapperResultSetExtractor.java:92)


at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:599)


at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:537)


at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:587)


at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:612)


at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:644)


at org.springframework.jdbc.object.SqlQuery.execute(SqlQuery.java:112)


at org.springframework.jdbc.object.SqlQuery.execute(SqlQuery.java:122)


at org.springframework.jdbc.object.SqlQuery.execute(SqlQuery.java:137)


at com.im.df.impl.db.dao.DFDaoSupport.fetchAllIds(DFDaoSupport.java:323)


at com.im.df.impl.db.DBSchemaManager.fetchAllIds(DBSchemaManager.java:795)


at com.im.df.impl.db.DBEntityDataProviderImpl.queryForIds(DBEntityDataProviderImpl.java:124)


at com.im.df.impl.db.ResultSetImpl.applyQueryInternal(ResultSetImpl.java:129)


at com.im.df.impl.db.ResultSetImpl.applyQuery(ResultSetImpl.java:115)


at com.im.ijc.core.query.exec.QueryBR.phase1InRequestProcessor(QueryBR.java:62)


at com.im.df.util.BackgroundRunner.processTheTask(BackgroundRunner.java:112)


at com.im.df.util.BackgroundRunner$1.run(BackgroundRunner.java:79)


at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:539)


[catch] at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:964)

When working with large data sets you may need to increase the amount of memory available to IJC.





You can do this using Tools -> Options and then selecting the Miscellaneous category and looking at the Startup options tab.





See here for more info:


http://www.chemaxon.com/instantjchem/ijc_2_0/docs/user/help/htmlfiles/tips_and_tricks/memory_usage.html





Tim