User 173254b396
09-11-2010 12:58:01
Hi,
We have been trying to create a Markush library in mysql 5.1.5. We create the Markush structure from the scaffold file(mrv) and fragments file(s)(mrv) with molconvert. The import (jcman 5.3.8) the created Markush structure to the database works if we have only several structures in the fragment file. However, our fragment files can go up to 10^5 order of magnitude. When we try to import a Markush which has 2-3000 structures the import crashes with java.langOutOfMemoryError no matter how much memory is allocated to java (1.5.0_06).
Any help is appreciated.
Regards, Péter
Error log:
/home/kemipv/software/jchem538/bin/jcman0 a all_markush CVGI0779c_markush.mrv --connect "name=NAME" --driver com.mysql.jdbc.Driver --dburl jdbc:mysql://semldx00021:3306/vl
Collecting file information ...
Done.
Importing structures from CVGI0779c_markush.mrv ...
CVGI0779c_markush.mrv CVGI0779c_markush.mrv.allError in molecule 1
java.util.concurrent.ExecutionException: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.OutOfMemoryError: Java heap space
at chemaxon.util.concurrent.processors.WorkUnitData.getResult(Unknown Source)
at chemaxon.util.concurrent.processors.ScheduledWorkUnitData.getResult(Unknown Source)
at chemaxon.util.concurrent.processors.WorkUnitDataIterator.getNext(Unknown Source)
at chemaxon.jchem.db.ParallelStructTableUpdater.importFile(ParallelStructTableUpdater.java:369)
at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:129)
at chemaxon.jchem.db.Importer.importMols(Importer.java:469)
at chemaxon.jchem.Command.importFromFile(Command.java:1191)
at chemaxon.jchem.Command.run(Command.java:655)
at chemaxon.jchem.Command.main(Command.java:216)
Caused by: chemaxon.util.concurrent.processors.WorkUnitException: java.lang.OutOfMemoryError: Java heap space
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(Unknown Source)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(Unknown Source)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(Unknown Source)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work(Unknown Source)
at chemaxon.util.concurrent.worker.Worker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
at java.util.concurrent.FutureTask.run(FutureTask.java:123)
at chemaxon.util.concurrent.worker.Worker.run(Unknown Source)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
at java.util.concurrent.FutureTask.run(FutureTask.java:123)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.OutOfMemoryError: Java heap space