DB2 Database creation - ChemAxon Forum Archive

User 98d11041ad

08-06-2009 19:54:09

To whom it may concern,

Upon attempting to create initial tables for JCHEMBASE using the command line jcman tool the following exception is presented at the command below:

$ /usr/ChemAxon/JChem/bin/jcman c ctcols --coldefs ", logp n umeric(18,9), rotbl_bnd_cnt numeric(1,0)" --ctcolcfg "logp=logp();rotbl_bnd_cnt
=rotatableBondCount()>4"
sun.io.MalformedInputException
        at sun.io.ByteToCharUTF8.convert(ByteToCharUTF8.java:262)
        at sun.nio.cs.StreamDecoder$ConverterSD.convertInto(StreamDecoder.java:3
14)
        at sun.nio.cs.StreamDecoder$ConverterSD.implRead(StreamDecoder.java:364)

        at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:250)
        at java.io.InputStreamReader.read(InputStreamReader.java:212)
        at java.io.BufferedReader.fill(BufferedReader.java:157)
        at java.io.BufferedReader.readLine(BufferedReader.java:320)
        at java.io.BufferedReader.readLine(BufferedReader.java:383)
        at chemaxon.struc.PeriodicSystem.readElements(PeriodicSystem.java:110)
        at chemaxon.struc.PeriodicSystem.<clinit>(PeriodicSystem.java:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
java.lang.ExceptionInInitializerError
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:205)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
Caused by: java.lang.NullPointerException
        at chemaxon.struc.PeriodicSystem.getElementCount(PeriodicSystem.java:293
)
        at chemaxon.struc.PeriodicSystem.readIsotopes(PeriodicSystem.java:203)
        at chemaxon.struc.PeriodicSystem.indexOfIsotope(PeriodicSystem.java:276)

        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        ... 25 more
Descriptor table cleanup failed for table ctcols .

java.lang.RuntimeException: java.lang.ExceptionInInitializerError
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1021)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
Caused by: java.lang.ExceptionInInitializerError
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:205)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        ... 5 more
Caused by: java.lang.NullPointerException
        at chemaxon.struc.PeriodicSystem.getElementCount(PeriodicSystem.java:293
)
        at chemaxon.struc.PeriodicSystem.readIsotopes(PeriodicSystem.java:203)
        at chemaxon.struc.PeriodicSystem.indexOfIsotope(PeriodicSystem.java:276)

        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        ... 25 more

I am running SUN JDK 1.5 per the instructions:

$$JAVA_HOME/bin/java -version

java version "1.5.0_09"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)
Java HotSpot(TM) Server VM (build 1.5.0_09-b03, mixed mode)

ChemAxon 9c0afc9aaf

08-06-2009 20:09:35

Hi,

According to the stack trace you are udin IBM J9 Java:

at java.lang.J9VMInternals.initializeImpl(Native Method)

$$JAVA_HOME/bin/java -version

Probably your PATH environment variable is not set correctly.

Please put $JAVA_HOME at the front of PATH.

Please test with this command:

$ java -version

Best regards,

Szilard

User 98d11041ad

08-06-2009 20:23:02

Szilard,

I am sorry for the confusion, I must have pasted the wrong stack, since I have been switching JVMs to see if the bahavior changes,

$ export CLASSPATH=/localdata/simple/lib/db2jcc.jar:/localda
ta/simple/lib/db2jcc_javax.jar:/localdata/simple/lib/db2jcc_license_cu.jar
$ export JAVA_HOME=/opt/sun/jdk
$ /usr/ChemAxon/JChem/bin/jcman c ctcols --coldefs ", logp n
umeric(18,9), rotbl_bnd_cnt numeric(1,0)" --ctcolcfg "logp=logp();rotbl_bnd_cnt
=rotatableBondCount()>4"
sun.io.MalformedInputException
        at sun.io.ByteToCharUTF8.convert(ByteToCharUTF8.java:262)
        at sun.nio.cs.StreamDecoder$ConverterSD.convertInto(StreamDecoder.java:3
14)
        at sun.nio.cs.StreamDecoder$ConverterSD.implRead(StreamDecoder.java:364)

        at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:250)
        at java.io.InputStreamReader.read(InputStreamReader.java:212)
        at java.io.BufferedReader.fill(BufferedReader.java:157)
        at java.io.BufferedReader.readLine(BufferedReader.java:320)
        at java.io.BufferedReader.readLine(BufferedReader.java:383)
        at chemaxon.struc.PeriodicSystem.readElements(PeriodicSystem.java:110)
        at chemaxon.struc.PeriodicSystem.<clinit>(PeriodicSystem.java:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
java.lang.ExceptionInInitializerError
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:205)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
Caused by: java.lang.NullPointerException
        at chemaxon.struc.PeriodicSystem.getElementCount(PeriodicSystem.java:293
)
        at chemaxon.struc.PeriodicSystem.readIsotopes(PeriodicSystem.java:203)
        at chemaxon.struc.PeriodicSystem.indexOfIsotope(PeriodicSystem.java:276)

        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        ... 25 more
Descriptor table cleanup failed for table ctcols .

java.lang.RuntimeException: java.lang.ExceptionInInitializerError
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1021)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:936)
        at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.ja
va:2692)
        at chemaxon.jchem.Command.createTable(Command.java:772)
        at chemaxon.jchem.Command.run(Command.java:583)
        at chemaxon.jchem.Command.main(Command.java:204)
Caused by: java.lang.ExceptionInInitializerError
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:205)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.marvin.io.formats.smiles.SmilesExport.<clinit>(SmilesExport.
java:311)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        at java.lang.Class.forNameImpl(Native Method)
        at java.lang.Class.forName(Class.java:127)
        at chemaxon.formats.MFileFormat.createExportModule(MFileFormat.java:918)

        at chemaxon.formats.MFileFormatUtil.createExportModule(MFileFormatUtil.j
ava:989)
        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1442)
        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1305)
        at chemaxon.struc.Molecule.toFormat(Molecule.java:1283)
        at chemaxon.jep.Evaluator.loadNamedMols(Evaluator.java:530)
        at chemaxon.jep.Evaluator.loadDefaultNamedMols(Evaluator.java:452)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:304)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:279)
        at chemaxon.jep.Evaluator.<init>(Evaluator.java:231)
        at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.ja
va:858)
        at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:831
)
        at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1014)
        ... 5 more
Caused by: java.lang.NullPointerException
        at chemaxon.struc.PeriodicSystem.getElementCount(PeriodicSystem.java:293
)
        at chemaxon.struc.PeriodicSystem.readIsotopes(PeriodicSystem.java:203)
        at chemaxon.struc.PeriodicSystem.indexOfIsotope(PeriodicSystem.java:276)

        at chemaxon.struc.MolAtom.isotopeType(MolAtom.java:4486)
        at chemaxon.marvin.modules.GraphInvariants.<clinit>(GraphInvariants.java
:86)
        at java.lang.J9VMInternals.initializeImpl(Native Method)
        at java.lang.J9VMInternals.initialize(J9VMInternals.java:187)
        ... 25 more

Here is th stack generated with the SUN JVM:

$ $JAVA_HOME/bin/java -version
java version "1.5.0_09"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)
Java HotSpot(TM) Server VM (build 1.5.0_09-b03, mixed mode)

ChemAxon 9c0afc9aaf

08-06-2009 20:27:48

I'm sorry, you have posted a stack trace with IBM Java again (see J9VMInternals in the stack).

Please note how to check the JVM in the classpath:

java -version

Thank you,

Szilard

User 98d11041ad

08-06-2009 20:37:57

Please note the version at the end of the message:

$ $JAVA_HOME/bin/java -version

java version "1.5.0_09"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)

Java HotSpot(TM) Server VM (build 1.5.0_09-b03, mixed mode)

Which happens to be the same as

$ /opt/sun/jdk/bin/java -version

java version "1.5.0_09"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)

Java HotSpot(TM) Server VM (build 1.5.0_09-b03, mixed mode)

as well as

$ java -version

java version "1.5.0_09"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)

Java HotSpot(TM) Server VM (build 1.5.0_09-b03, mixed mode)

User 98d11041ad

08-06-2009 20:41:22

I have since my last message upgraded to SUN Java 1.6 and that seems to solve the problem.

Thank you for your valuable help.