JChem Base and InChI

User 3d3f3767a2

06-10-2009 21:08:17

Hi All,


First of all, let me just say thanks for the awesome UGM conference - you guys do an excellent job.


Secondly, I am having some issues using inchi with JChem.  I have tried to setup my structure database using the following command (on my laptop which is running OSX 10.5.8):


./jcman c structures --coldefs ", mol_text mediumtext, pdb_text mediumtext, structure_thumb blob, structure_full blob, inchi text, average_mass numeric(18,6), mono_mass numeric(18,6), iupac varchar(3000), logp numeric(18,4), pka numeric(18,4)" --ctcolcfg "mol_text=molFormat(\"mol\");pdb_text=molFormat(\"pdb\");structure_thumb=molImage(\"png:w100,h100,#ffffff\");structure_full=molImage(\"png:w300,h300,#ffffff\");inchi=molFormat(\"inchi:AuxNone\");average_mass=mass();mono_mass=exactMass();iupac=name();logp=logp();pka=pka(\"acidic\", \"2\")"  --driver com.mysql.jdbc.Driver --dburl jdbc:mysql:///molecules_structure_search_development --login root

Unfortunately, I get the following error:


 


java.lang.UnsatisfiedLinkError: /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib:  no suitable image found.  Did find:  /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib: mach-o, but wrong architecture

at java.lang.ClassLoader$NativeLibrary.load(Native Method)

at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1881)

at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1761)

at java.lang.Runtime.load0(Runtime.java:770)

at java.lang.System.load(System.java:1020)

at chemaxon.marvin.io.formats.inchi.Inchi.install(Inchi.java:88)

at chemaxon.marvin.io.formats.inchi.Inchi.<clinit>(Inchi.java:157)

at chemaxon.marvin.io.formats.inchi.InchiExport.convert(InchiExport.java:148)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1493)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1458)

at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1307)

at chemaxon.struc.Molecule.toFormat(Molecule.java:1285)

at chemaxon.jep.function.MolString.run(MolString.java:81)

at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.java:910)

at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:853)

at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1036)

at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:958)

at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.java:2735)

at chemaxon.jchem.Command.createTable(Command.java:777)

at chemaxon.jchem.Command.run(Command.java:590)

at chemaxon.jchem.Command.main(Command.java:207)

Descriptor table cleanup failed for table structures .




java.lang.RuntimeException: java.lang.UnsatisfiedLinkError: /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib:  no suitable image found.  Did find:  /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib: mach-o, but wrong architecture

at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1043)

at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:958)

at chemaxon.jchem.db.UpdateHandler.createStructureTable(UpdateHandler.java:2735)

at chemaxon.jchem.Command.createTable(Command.java:777)

at chemaxon.jchem.Command.run(Command.java:590)

at chemaxon.jchem.Command.main(Command.java:207)

Caused by: java.lang.UnsatisfiedLinkError: /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib:  no suitable image found.  Did find:  /Users/knox/.chemaxon/lib/inchi-1_2/libinchi.jnilib: mach-o, but wrong architecture

at java.lang.ClassLoader$NativeLibrary.load(Native Method)

at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1881)

at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1761)

at java.lang.Runtime.load0(Runtime.java:770)

at java.lang.System.load(System.java:1020)

at chemaxon.marvin.io.formats.inchi.Inchi.install(Inchi.java:88)

at chemaxon.marvin.io.formats.inchi.Inchi.<clinit>(Inchi.java:157)

at chemaxon.marvin.io.formats.inchi.InchiExport.convert(InchiExport.java:148)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1493)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1458)

at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1307)

at chemaxon.struc.Molecule.toFormat(Molecule.java:1285)

at chemaxon.jep.function.MolString.run(MolString.java:81)

at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)

at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)

at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)

at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)

at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)

at chemaxon.jchem.db.TableInfo.saveChemTermColNamesAndExprs(TableInfo.java:910)

at chemaxon.jchem.db.TableInfo.saveCreationProperties(TableInfo.java:853)

at chemaxon.jchem.db.TableInfo.createTable(TableInfo.java:1036)

... 5 more


 


I have tried deleting everything from .chemaxon (which is where it seems to be trying to load libinchi) to no avail.  I am running JChem 5.2.4 (I am downloading the latest JChem now, I'll let you know how it goes).  


java -version outputs:


 


java version "1.6.0_15"

Java(TM) SE Runtime Environment (build 1.6.0_15-b03-226)

Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02-92, mixed mode)

If I remove the "inchi=molFormat(\"inchi:AuxNone\")" part, the database table is built with no errors.


Any suggestions or ideas what I might be doing wrong?


Thanks,

Craig Knox

 

User 3d3f3767a2

06-10-2009 21:42:00

Same issue with the latest version (5.2.5.1).


Thanks,
Craig Knox 

ChemAxon 9c0afc9aaf

06-10-2009 22:38:46

Hi,


We are glad you have enjoyed our UGM and looking forward to see you again in the future.


The issue seems to be file format (inchi) specific, so I have moved it to this forum where the experts of this area will answer your question soon.


(I assume you cannot convert to InChi with either "molconvert" or "msketch" either ?)


 


Best regards,


 


Szilard


 

ChemAxon 7c2d26e5cf

07-10-2009 12:50:13

Please give detail description of your machine where this error invoked?


- CPU type / architecture


- Operating system type/version


- Java version

User 3d3f3767a2

11-01-2010 22:01:55

Hi,


Sorry, I had sort of given up on this issue and I just noticed I had received a response.


I am still having this problem, but now only when I actually try to add a structure to the database.


I am using JChem 5.2.6.


- CPU is Intel Core 2 Duo (64-bit)


- OS is Mac OSX 10.5 (I get the same errors on Mac OSX 10.6 and Fedora release 9)


- Java version on Mac OSX 10.5 is 1.6.0_17, on Fedora is 1.6.0_07-b06


I am running JChem in JRuby, and here is the trace (that is relevant to JChem):



Error in molecule 1
java.util.concurrent.ExecutionException: java.lang.UnsatisfiedLinkError: /Users/knox/.chemaxon/lib/inchi-1_2r/libinchi.jnilib: no suitable image found. Did find: /Users/knox/.chemaxon/lib/inchi-1_2r/libinchi.jnilib: mach-o, but wrong architecture
at chemaxon.util.concurrent.processors.WorkUnitData.getResult(WorkUnitData.java:65)
at chemaxon.util.concurrent.processors.ScheduledWorkUnitData.getResult(ScheduledWorkUnitData.java:53)
at chemaxon.util.concurrent.processors.WorkUnitDataIterator.getNext(WorkUnitDataIterator.java:74)
at chemaxon.jchem.db.ParallelStructTableUpdater.importFile(ParallelStructTableUpdater.java:361)
at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:129)
at chemaxon.jchem.db.Importer.importMols(Importer.java:469)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)


Thanks,
Craig 

User 3d3f3767a2

11-01-2010 22:07:05

It almost seems like the InChI library being included only works with a 32 bit version of java?  I think the inchi runtime has been released only in a 32-bit version, correct?

User 3d3f3767a2

11-01-2010 22:08:33

There is actually a bit more stuff relevant to JChem in the stack trace:


	at java.lang.Thread.run(Thread.java:637)
Caused by: java.lang.UnsatisfiedLinkError: /Users/knox/.chemaxon/lib/inchi-1_2r/libinchi.jnilib: no suitable image found. Did find: /Users/knox/.chemaxon/lib/inchi-1_2r/libinchi.jnilib: mach-o, but wrong architecture
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1861)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1741)
at java.lang.Runtime.load0(Runtime.java:770)
at java.lang.System.load(System.java:1020)
at chemaxon.marvin.io.formats.inchi.Inchi.install(Inchi.java:88)
at chemaxon.marvin.io.formats.inchi.Inchi.<clinit>(Inchi.java:157)
at chemaxon.marvin.io.formats.inchi.InchiExport.convert(InchiExport.java:148)
at chemaxon.struc.Molecule.exportToObject(Molecule.java:1493)
at chemaxon.struc.Molecule.exportToObject(Molecule.java:1458)
at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1307)
at chemaxon.struc.Molecule.toFormat(Molecule.java:1285)
at chemaxon.jep.function.MolString.run(MolString.java:103)
at chemaxon.nfunk.jep.EvaluatorVisitor.visit(EvaluatorVisitor.java:290)
at chemaxon.nfunk.jep.ASTFunNode.jjtAccept(ASTFunNode.java:53)
at chemaxon.nfunk.jep.EvaluatorVisitor.getValue(EvaluatorVisitor.java:155)
at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:477)
at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)
at chemaxon.jchem.db.UpdateHandler.calcChemTermColValues(UpdateHandler.java:1512)
at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:1201)
at chemaxon.jchem.db.UpdateHandler.createRowData(UpdateHandler.java:3173)
at chemaxon.jchem.db.UpdateHandler.createRowData(UpdateHandler.java:3153)
at chemaxon.jchem.db.ParallelStructTableUpdater$UpdateHandlerAdapter.process(ParallelStructTableUpdater.java:119)
at chemaxon.util.concurrent.util.AbstractWorkUnit.call(AbstractWorkUnit.java:32)
at chemaxon.util.concurrent.processors.WorkUnitProcessorBase.process(WorkUnitProcessorBase.java:200)
at chemaxon.util.concurrent.processors.WorkUnitProcessorBase$Worker.call(WorkUnitProcessorBase.java:403)

ChemAxon 0a9e2a55e1

12-01-2010 09:53:17

Hi,


We have 4 types of inchi dynamic libraries. Windows, Mac, Linux 32 bit, and Linux 64 bit. We are going to make 2 windows and 2 mac libraries (for 32 and 64 bit seperately), because in some cases (64 bit machine, 64 bit java, windows or mac) the old (32 bit) libraries do not work. This is a top priority task now, because recently mac and windows users are changing 32 bit to 64 bit, so we are gong to solve this soon.


Until then in many cases using 32 bit java on a 64 bit operating system can load the 32 bit inchi library.


Best regards,


Peter

User 3d3f3767a2

20-01-2010 16:33:45

Hi Peter,



Thanks for your reply.  Unfortunately, I am using GlassFish v3 which requires JDK 1.6 or higher, and the 32-bit version of the JDK topped out at 1.5 on OSX.  Anyways, I am testing in a Linux VM and everything is working fine in terms of loading the correct library.


 


However, I am now having a new issue on our production server AND on OSX involving the InChI library.  When I try to add new structures or to regenerate my chemical terms using jcman I get the following error:



Error for column INCHI with structure cd_id=6756: Error while evaluating expression:
molFormat("inchi:AuxNone")
The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file '/tmp/temp_java_inchi1103957287004931162log'
Opened input file '/tmp/temp_java_inchi4105934872081090776sdf'
Opened output file '/tmp/temp_java_inchi4315926920627405773in'
Opened problem file '/tmp/temp_java_inchi4439730041582366666prb'
, expression: molFormat("inchi:AuxNone")


Seemingly at random.  This happens every 2-3 compounds and then finally the whole thing crashes with the following error report:


 



#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0xb41ea863Error for column INCHI with structure cd_id=6786: Error while evaluating expression:
molFormat("inchi:AuxNone")
The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file '/tmp/temp_java_inchi8195051325373022575log'
Opened input file '/tmp/temp_java_inchi3142459267159966325sdf'
Opened output file '/tmp/temp_java_inchi4196914164367407338in'
Opened problem file '/tmp/temp_java_inchi2798450800472605875prb'
, expression: molFormat("inchi:AuxNone")
, pid=7925, tid=3028224912
#
# JRE version: 6.0_18-b07
# Java VM: Java HotSpot(TM) Client VM (16.0-b13 mixed mode, sharing linux-x86 )
# Problematic frame:
# C [libinchi.so+0x22863] TranspositionGetMcrAndFixSetAndUnorderedPartition+0x183
#
# An error report file with more information is saved as:
# /home/knox/development/moldb/vendor/jchem/bin/hs_err_pid7925.log
#
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
./jcman: line 116: 7925 Aborted java $javaopts chemaxon.jchem.Command "$@"


 


finally, if I view this error report file it looks like this:


 


#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0xb41ea863, pid=7925, tid=3028224912
#
# JRE version: 6.0_18-b07
# Java VM: Java HotSpot(TM) Client VM (16.0-b13 mixed mode, sharing linux-x86 )
# Problematic frame:
# C [libinchi.so+0x22863] TranspositionGetMcrAndFixSetAndUnorderedPartition+0x183
#
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

--------------- T H R E A D ---------------

Current thread (0x0a038400): JavaThread "Thread-3" [_thread_in_native, id=7944, stack(0xb47a0000,0xb47f1000)]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x00000000

Registers:
EAX=0x00000000, EBX=0x00000000, ECX=0x0a166f1e, EDX=0x00000000
ESP=0xb47edbe0, EBP=0xb47edc18, ESI=0x0a64b080, EDI=0x00000000
EIP=0xb41ea863, CR2=0x00000000, EFLAGS=0x00010246

Top of Stack: (sp=0xb47edbe0)
0xb47edbe0: 0a166f1e 00000000 00000006 0000002d
0xb47edbf0: 00000000 00000000 00000010 00000000
0xb47edc00: 0a2085f6 0a166f1e 0a648418 00000001
0xb47edc10: b47ee394 00000002 b47ee048 b41ef556
0xb47edc20: b47ee028 b47ee01c b47ee010 0000002d
0xb47edc30: 00000002 b47ee02c 00000000 00000000
0xb47edc40: 00000002 00000000 b47edd38 b422ddd6
0xb47edc50: 0a29be90 00c40d71 0a69af60 09be9768

Instructions: (pc=0xb41ea863)
0xb41ea853: fa 1f f7 7d e0 8d 14 51 8b 4d ec 01 c0 89 55 dc
0xb41ea863: 0f b7 12 66 09 14 08 8b 4d dc 0f b7 11 8b 4d e8

Stack: [0xb47a0000,0xb47f1000], sp=0xb47edbe0, free space=136b47ed570k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libinchi.so+0x22863] TranspositionGetMcrAndFixSetAndUnorderedPartition+0x183
C [libinchi.so+0x27556] CanonGraph+0x2fc6
C [libinchi.so+0x29167] GetBaseCanonRanking+0x1027
C [libinchi.so+0x57ba4] Create_INChI+0x8b4
C [libinchi.so+0x8830b] CreateOneComponentINChI+0x16b
C [libinchi.so+0x88d41] CreateOneStructureINChI+0x551
C [libinchi.so+0x891d1] ProcessOneStructure+0x1d1
C [libinchi.so+0xee358] main+0x3e8
C [libinchi.so+0xeec6a] Java_chemaxon_marvin_io_formats_inchi_Inchi_callInchiC+0x9a
j chemaxon.marvin.io.formats.inchi.Inchi.callInchiC([Ljava/lang/String;)V+0
j chemaxon.marvin.io.formats.inchi.Inchi.main([Ljava/lang/String;)V+76
J chemaxon.marvin.io.formats.inchi.InchiExport.convert(Lchemaxon/struc/Molecule;)Ljava/lang/Object;
j chemaxon.marvin.io.formats.inchi.InchikeyExport.convert(Lchemaxon/struc/Molecule;)Ljava/lang/Object;+12
J chemaxon.struc.Molecule.exportToObject([Lchemaxon/struc/Molecule;Ljava/lang/String;Lchemaxon/marvin/io/MolExportModule;Lchemaxon/struc/MPropertyContainer;)Ljava/lang/Object;
J chemaxon.struc.Molecule.exportToObject(Ljava/lang/String;)Ljava/lang/Object;
J chemaxon.struc.Molecule.exportToFormat(Ljava/lang/String;)Ljava/lang/String;
J chemaxon.jep.function.MolString.run(Ljava/util/Stack;)V
J chemaxon.nfunk.jep.EvaluatorVisitor.visit(Lchemaxon/nfunk/jep/ASTFunNode;Ljava/lang/Object;)Ljava/lang/Object;
J chemaxon.nfunk.jep.ASTFunNode.jjtAccept(Lchemaxon/nfunk/jep/ParserVisitor;Ljava/lang/Object;)Ljava/lang/Object;
J chemaxon.nfunk.jep.EvaluatorVisitor.getValue(Lchemaxon/nfunk/jep/Node;Ljava/util/Vector;Lchemaxon/nfunk/jep/SymbolTable;)Ljava/lang/Object;
J chemaxon.nfunk.jep.JEP.getValueAsObject()Ljava/lang/Object;
J chemaxon.jchem.db.UpdateHandler.calcChemTermColValues()V
j chemaxon.jchem.db.UpdateHandler.init()V+704
j chemaxon.jchem.db.UpdateHandler.execute(Z)I+59
j chemaxon.jchem.db.UpdateHandler.execute()V+2
j chemaxon.jchem.db.Regenerator$RegenThread.run()V+242
v ~StubRoutines::call_stub
V [libjvm.so+0x2189e0]
V [libjvm.so+0x33dee8]
V [libjvm.so+0x2181e7]
V [libjvm.so+0x21829a]
V [libjvm.so+0x298cc5]
V [libjvm.so+0x3e4e8e]
V [libjvm.so+0x33f3de]
C [libpthread.so.0+0x632f]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j chemaxon.marvin.io.formats.inchi.Inchi.callInchiC([Ljava/lang/String;)V+0
j chemaxon.marvin.io.formats.inchi.Inchi.main([Ljava/lang/String;)V+76
J chemaxon.marvin.io.formats.inchi.InchiExport.convert(Lchemaxon/struc/Molecule;)Ljava/lang/Object;
j chemaxon.marvin.io.formats.inchi.InchikeyExport.convert(Lchemaxon/struc/Molecule;)Ljava/lang/Object;+12
J chemaxon.struc.Molecule.exportToObject([Lchemaxon/struc/Molecule;Ljava/lang/String;Lchemaxon/marvin/io/MolExportModule;Lchemaxon/struc/MPropertyContainer;)Ljava/lang/Object;
J chemaxon.struc.Molecule.exportToObject(Ljava/lang/String;)Ljava/lang/Object;
J chemaxon.struc.Molecule.exportToFormat(Ljava/lang/String;)Ljava/lang/String;
J chemaxon.jep.function.MolString.run(Ljava/util/Stack;)V
J chemaxon.nfunk.jep.EvaluatorVisitor.visit(Lchemaxon/nfunk/jep/ASTFunNode;Ljava/lang/Object;)Ljava/lang/Object;
J chemaxon.nfunk.jep.ASTFunNode.jjtAccept(Lchemaxon/nfunk/jep/ParserVisitor;Ljava/lang/Object;)Ljava/lang/Object;
J chemaxon.nfunk.jep.EvaluatorVisitor.getValue(Lchemaxon/nfunk/jep/Node;Ljava/util/Vector;Lchemaxon/nfunk/jep/SymbolTable;)Ljava/lang/Object;
J chemaxon.nfunk.jep.JEP.getValueAsObject()Ljava/lang/Object;
J chemaxon.jchem.db.UpdateHandler.calcChemTermColValues()V
j chemaxon.jchem.db.UpdateHandler.init()V+704
j chemaxon.jchem.db.UpdateHandler.execute(Z)I+59
j chemaxon.jchem.db.UpdateHandler.execute()V+2
j chemaxon.jchem.db.Regenerator$RegenThread.run()V+242
v ~StubRoutines::call_stub

--------------- P R O C E S S ---------------

Java Threads: ( => current thread )
0xb44fe800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7945, stack(0xb4500000,0xb4551000)]
=>0x0a038400 JavaThread "Thread-3" [_thread_in_native, id=7944, stack(0xb47a0000,0xb47f1000)]
0x0a060c00 JavaThread "Thread-2" [_thread_in_vm, id=7943, stack(0xb47f1000,0xb4842000)]
0x0a019000 JavaThread "MySQL Statement Cancellation Timer" daemon [_thread_blocked, id=7935, stack(0xb4856000,0xb48a7000)]
0xb4d02800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=7932, stack(0xb4caf000,0xb4d00000)]
0xb4d00800 JavaThread "CompilerThread0" daemon [_thread_blocked, id=7931, stack(0xb4e2b000,0xb4eac000)]
0x09bde800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=7930, stack(0xb4eac000,0xb4efd000)]
0x09bd9800 JavaThread "Finalizer" daemon [_thread_blocked, id=7929, stack(0xb51e1000,0xb5232000)]
0x09bd4c00 JavaThread "Reference Handler" daemon [_thread_blocked, id=7928, stack(0xb5232000,0xb5283000)]
0x09bb0800 JavaThread "main" [_thread_blocked, id=7926, stack(0xb75d4000,0xb7625000)]

Other Threads:
0x09bd3400 VMThread [stack: 0xb5283000,0xb5304000] [id=7927]
0x09be1800 WatcherThread [stack: 0xb4c2e000,0xb4caf000] [id=7933]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
def new generation total 27200K, used 1812K [0x703e0000, 0x72160000, 0x7aa80000)
eden space 24192K, 3% used [0x703e0000, 0x704b1720, 0x71b80000)
from space 3008K, 32% used [0x71e70000, 0x71f63990, 0x72160000)
to space 3008K, 0% used [0x71b80000, 0x71b80000, 0x71e70000)
tenured generation total 60280K, used 18491K [0x7aa80000, 0x7e55e000, 0x8f7e0000)
the space 60280K, 30% used [0x7aa80000, 0x7bc8edd0, 0x7bc8ee00, 0x7e55e000)
compacting perm gen total 12288K, used 9742K [0x8f7e0000, 0x903e0000, 0x937e0000)
the space 12288K, 79% used [0x8f7e0000, 0x90163a28, 0x90163c00, 0x903e0000)
ro space 10240K, 61% used [0x937e0000, 0x93e03068, 0x93e03200, 0x941e0000)
rw space 12288K, 60% used [0x941e0000, 0x949146d0, 0x94914800, 0x94de0000)

Dynamic libraries:
0037a000-00390000 r-xp 00000000 fd:00 10273006 /lib/libnsl-2.8.so
00390000-00391000 r-xp 00015000 fd:00 10273006 /lib/libnsl-2.8.so
00391000-00392000 rwxp 00016000 fd:00 10273006 /lib/libnsl-2.8.so
00392000-00394000 rwxp 00392000 00:00 0
00bb1000-00bcd000 r-xp 00000000 fd:00 10272938 /lib/ld-2.8.so
00bcd000-00bce000 r-xp 0001c000 fd:00 10272938 /lib/ld-2.8.so
00bce000-00bcf000 rwxp 0001d000 fd:00 10272938 /lib/ld-2.8.so
00bd1000-00d34000 r-xp 00000000 fd:00 10272940 /lib/libc-2.8.so
00d34000-00d36000 r-xp 00163000 fd:00 10272940 /lib/libc-2.8.so
00d36000-00d37000 rwxp 00165000 fd:00 10272940 /lib/libc-2.8.so
00d37000-00d3a000 rwxp 00d37000 00:00 0
00d3c000-00d63000 r-xp 00000000 fd:00 10273010 /lib/libm-2.8.so
00d63000-00d64000 r-xp 00026000 fd:00 10273010 /lib/libm-2.8.so
00d64000-00d65000 rwxp 00027000 fd:00 10273010 /lib/libm-2.8.so
00d67000-00d6a000 r-xp 00000000 fd:00 10272946 /lib/libdl-2.8.so
00d6a000-00d6b000 r-xp 00002000 fd:00 10272946 /lib/libdl-2.8.so
00d6b000-00d6c000 rwxp 00003000 fd:00 10272946 /lib/libdl-2.8.so
00d8c000-00da1000 r-xp 00000000 fd:00 10273013 /lib/libpthread-2.8.so
00da1000-00da2000 r-xp 00014000 fd:00 10273013 /lib/libpthread-2.8.so
00da2000-00da3000 rwxp 00015000 fd:00 10273013 /lib/libpthread-2.8.so
00da3000-00da5000 rwxp 00da3000 00:00 0
00dbd000-00dc5000 r-xp 00000000 fd:00 10273014 /lib/librt-2.8.so
00dc5000-00dc6000 r-xp 00007000 fd:00 10273014 /lib/librt-2.8.so
00dc6000-00dc7000 rwxp 00008000 fd:00 10273014 /lib/librt-2.8.so
08048000-08052000 r-xp 00000000 fd:00 4482003 /usr/java/jdk1.6.0_18/bin/java
08052000-08053000 rwxp 00009000 fd:00 4482003 /usr/java/jdk1.6.0_18/bin/java
09bab000-0a831000 rwxp 09bab000 00:00 0 [heap]
703e0000-72160000 rwxp 703e0000 00:00 0
72160000-7aa80000 rwxp 72160000 00:00 0
7aa80000-7e55e000 rwxp 7aa80000 00:00 0
7e55e000-7eafe000 ---p 7e55e000 00:00 0
7eafe000-8f7e0000 rwxp 7eafe000 00:00 0
8f7e0000-903e0000 rwxp 8f7e0000 00:00 0
903e0000-937e0000 rwxp 903e0000 00:00 0
937e0000-93e04000 r-xs 00001000 fd:00 4614392 /usr/java/jdk1.6.0_18/jre/lib/i386/client/classes.jsa
93e04000-941e0000 rwxp 93e04000 00:00 0
941e0000-94915000 rwxp 00625000 fd:00 4614392 /usr/java/jdk1.6.0_18/jre/lib/i386/client/classes.jsa
94915000-94de0000 rwxp 94915000 00:00 0
94de0000-94ec0000 rwxp 00d5a000 fd:00 4614392 /usr/java/jdk1.6.0_18/jre/lib/i386/client/classes.jsa
94ec0000-951e0000 rwxp 94ec0000 00:00 0
951e0000-951e8000 r-xs 00e3a000 fd:00 4614392 /usr/java/jdk1.6.0_18/jre/lib/i386/client/classes.jsa
951e8000-955e0000 rwxp 951e8000 00:00 0
b3e00000-b3e41000 rwxp b3e00000 00:00 0
b3e41000-b3f00000 ---p b3e41000 00:00 0
b4000000-b40f1000 rwxp b4000000 00:00 0
b40f1000-b4100000 ---p b40f1000 00:00 0
b411f000-b4122000 ---p b411f000 00:00 0
b4122000-b4170000 rwxp b4122000 00:00 0
b4170000-b4173000 ---p b4170000 00:00 0
b4173000-b41c1000 rwxp b4173000 00:00 0
b41c1000-b41c8000 r-xs 00000000 fd:00 4426014 /usr/lib/gconv/gconv-modules.cache
b41c8000-b42c6000 r-xp 00000000 fd:00 5065054 /home/knox/.chemaxon/lib/inchi-1_2r/libinchi.so
b42c6000-b42d7000 rwxp 000fd000 fd:00 5065054 /home/knox/.chemaxon/lib/inchi-1_2r/libinchi.so
b42d7000-b42d8000 rwxp b42d7000 00:00 0
b42d8000-b42ed000 r-xp 00000000 fd:00 4614420 /usr/java/jdk1.6.0_18/jre/lib/i386/libdcpr.so
b42ed000-b4300000 rwxp 00014000 fd:00 4614420 /usr/java/jdk1.6.0_18/jre/lib/i386/libdcpr.so
b4300000-b4400000 rwxp b4300000 00:00 0
b4400000-b44ff000 rwxp b4400000 00:00 0
b44ff000-b4500000 ---p b44ff000 00:00 0
b4500000-b4503000 ---p b4500000 00:00 0
b4503000-b4551000 rwxp b4503000 00:00 0
b4551000-b45d5000 r-xp 00000000 fd:00 4614418 /usr/java/jdk1.6.0_18/jre/lib/i386/libawt.so
b45d5000-b45dc000 rwxp 00084000 fd:00 4614418 /usr/java/jdk1.6.0_18/jre/lib/i386/libawt.so
b45dc000-b4600000 rwxp b45dc000 00:00 0
b4600000-b4700000 rwxp b4600000 00:00 0
b4701000-b4703000 rwxp b4701000 00:00 0
b4704000-b470b000 r-xp 00000000 fd:00 4614447 /usr/java/jdk1.6.0_18/jre/lib/i386/libnio.so
b470b000-b470c000 rwxp 00006000 fd:00 4614447 /usr/java/jdk1.6.0_18/jre/lib/i386/libnio.so
b470c000-b478b000 r-xp 00000000 fd:00 4614423 /usr/java/jdk1.6.0_18/jre/lib/i386/libfontmanager.so
b478b000-b4796000 rwxp 0007e000 fd:00 4614423 /usr/java/jdk1.6.0_18/jre/lib/i386/libfontmanager.so
b4796000-b479a000 rwxp b4796000 00:00 0
b479a000-b479f000 r-xp 00000000 fd:00 4614412 /usr/java/jdk1.6.0_18/jre/lib/i386/headless/libmawt.so
b479f000-b47a0000 rwxp 00004000 fd:00 4614412 /usr/java/jdk1.6.0_18/jre/lib/i386/headless/libmawt.so
b47a0000-b47a3000 ---p b47a0000 00:00 0
b47a3000-b47f1000 rwxp b47a3000 00:00 0
b47f1000-b47f4000 ---p b47f1000 00:00 0
b47f4000-b4842000 rwxp b47f4000 00:00 0
b4842000-b4855000 r-xp 00000000 fd:00 4614446 /usr/java/jdk1.6.0_18/jre/lib/i386/libnet.so
b4855000-b4856000 rwxp 00013000 fd:00 4614446 /usr/java/jdk1.6.0_18/jre/lib/i386/libnet.so
b4856000-b4859000 ---p b4856000 00:00 0
b4859000-b48a7000 rwxp b4859000 00:00 0
b48a7000-b48ad000 r-xp 00000000 fd:00 4614442 /usr/java/jdk1.6.0_18/jre/lib/i386/libmanagement.so
b48ad000-b48ae000 rwxp 00005000 fd:00 4614442 /usr/java/jdk1.6.0_18/jre/lib/i386/libmanagement.so
b48ae000-b48b5000 r-xs 000a5000 fd:00 5096916 /home/knox/development/hmdb_structure_search/java/lib/mysql-connector-java-5.1.6-bin.jar
b48b5000-b48b9000 r-xs 0008b000 fd:00 6504962 /home/knox/development/moldb/vendor/jchem/lib/jdbc/sqljdbc.jar
b48b9000-b48ca000 r-xs 001bd000 fd:00 6504959 /home/knox/development/moldb/vendor/jchem/lib/jdbc/ojdbc5.jar
b48ca000-b48d1000 r-xs 00111000 fd:00 4606353 /usr/java/jdk1.6.0_18/jre/lib/resources.jar
b48d1000-b48d7000 r-xs 000ab000 fd:00 6504963 /home/knox/development/moldb/vendor/jchem/lib/jdbc/mysql-connector-java-5.1.10-bin.jar
b48d7000-b48e0000 r-xs 000a4000 fd:00 6504961 /home/knox/development/moldb/vendor/jchem/lib/jdbc/hsqldb.jar
b48e0000-b4906000 r-xs 00240000 fd:00 6504958 /home/knox/development/moldb/vendor/jchem/lib/jdbc/derby.jar
b4906000-b491b000 r-xs 0029f000 fd:00 6504960 /home/knox/development/moldb/vendor/jchem/lib/jdbc/db2jcc.jar
b491b000-b4925000 r-xs 0007d000 fd:00 6505352 /home/knox/development/moldb/vendor/jchem/lib/dom4j.jar
b4925000-b4926000 r-xs 0000c000 fd:00 6505409 /home/knox/development/moldb/vendor/jchem/lib/commons-logging-1.1.jar
b4926000-b4935000 r-xs 001ac000 fd:00 6505431 /home/knox/development/moldb/vendor/jchem/lib/xerces.jar
b4935000-b4949000 r-xs 00133000 fd:00 6505423 /home/knox/development/moldb/vendor/jchem/lib/castor-1.0.1-xml.jar
b4949000-b494d000 r-xs 0005f000 fd:00 6505363 /home/knox/development/moldb/vendor/jchem/lib/jchem-sss.jar
b494d000-b494f000 r-xs 0000a000 fd:00 6505437 /home/knox/development/moldb/vendor/jchem/lib/jchem-regsys.jar
b494f000-b4952000 r-xs 0002a000 fd:00 6505391 /home/knox/development/moldb/vendor/jchem/lib/jchem-reaction.jar
b4952000-b4954000 r-xs 0000a000 fd:00 6505415 /home/knox/development/moldb/vendor/jchem/lib/jchem-metabolizer.jar
b4954000-b4955000 r-xs 00000000 fd:00 6505351 /home/knox/development/moldb/vendor/jchem/lib/jchem-logging.jar
b4955000-b4956000 r-xs 00002000 fd:00 6505438 /home/knox/development/moldb/vendor/jchem/lib/jchem-jep.jar
b4956000-b4989000 rwxp b4956000 00:00 0
b4989000-b4b1f000 r-xs 02fc6000 fd:00 4606356 /usr/java/jdk1.6.0_18/jre/lib/rt.jar
b4b1f000-b4b23000 r-xs 00049000 fd:00 6505377 /home/knox/development/moldb/vendor/jchem/lib/jchem-jcman.jar
b4b23000-b4b25000 r-xs 0000a000 fd:00 6505416 /home/knox/development/moldb/vendor/jchem/lib/jchem-interop.jar
b4b25000-b4b26000 r-xs 0000e000 fd:00 6505381 /home/knox/development/moldb/vendor/jchem/lib/jchem-fragmenter.jar
b4b26000-b4b28000 r-xs 0000c000 fd:00 6505383 /home/knox/development/moldb/vendor/jchem/lib/jchem-drugdesign.jar
b4b28000-b4b2c000 r-xs 00058000 fd:00 6505388 /home/knox/development/moldb/vendor/jchem/lib/jchem-descriptors.jar
b4b2c000-b4b2f000 r-xs 0003f000 fd:00 6505419 /home/knox/development/moldb/vendor/jchem/lib/jchem-db.jar
b4b2f000-b4b3a000 r-xs 000f8000 fd:00 6505370 /home/knox/development/moldb/vendor/jchem/lib/jchem-clustering.jar
b4b3a000-b4b3c000 r-xs 00006000 fd:00 6505372 /home/knox/development/moldb/vendor/jchem/lib/jchem-cluster.jar
b4b3c000-b4b46000 r-xs 0009e000 fd:00 6505427 /home/knox/development/moldb/vendor/jchem/lib/jchem-cartridge.jar
b4b46000-b4b5f000 r-xs 00137000 fd:00 6505365 /home/knox/development/moldb/vendor/jchem/lib/jchem-alchemist.jar
b4b5f000-b4b62000 r-xs 00011000 fd:00 6505355 /home/knox/development/moldb/vendor/jchem/lib/servlet.jar
b4b62000-b4b6c000 r-xs 0005e000 fd:00 6505389 /home/knox/development/moldb/vendor/jchem/lib/looks-2.1.4.jar
b4b6c000-b4b78000 r-xs 000f9000 fd:00 6505407 /home/knox/development/moldb/vendor/jchem/lib/jogl.jar
b4b78000-b4b79000 r-xs 00000000 fd:00 6505360 /home/knox/development/moldb/vendor/jchem/lib/jnbtools.jar
b4b79000-b4b83000 r-xs 00075000 fd:00 6505412 /home/knox/development/moldb/vendor/jchem/lib/jh.jar
b4b83000-b4b84000 r-xs 00007000 fd:00 6505390 /home/knox/development/moldb/vendor/jchem/lib/jextexp.jar
b4b84000-b4b88000 r-xs 00021000 fd:00 6505411 /home/knox/development/moldb/vendor/jchem/lib/izmcomtlb.jar
b4b88000-b4b90000 r-xs 0003f000 fd:00 6505367 /home/knox/development/moldb/vendor/jchem/lib/izmcomjni.jar
b4b90000-b4b91000 r-xs 00004000 fd:00 6505418 /home/knox/development/moldb/vendor/jchem/lib/gluegen-rt.jar
b4b91000-b4b93000 r-xs 0000b000 fd:00 6505426 /home/knox/development/moldb/vendor/jchem/lib/freehep-util-2.0.2.jar
b4b93000-b4b96000 r-xs 0000e000 fd:00 6505386 /home/knox/development/moldb/vendor/jchem/lib/freehep-io-2.0.2.jar
b4b96000-b4b98000 r-xs 00011000 fd:00 6505375 /home/knox/development/moldb/vendor/jchem/lib/freehep-graphicsio-pdf-2.1.1.jar
b4b98000-b4b9d000 r-xs 00027000 fd:00 6505349 /home/knox/development/moldb/vendor/jchem/lib/freehep-graphicsio-emf-2.1.1.jar
b4b9d000-b4ba2000 r-xs 0002b000 fd:00 6505369 /home/knox/development/moldb/vendor/jchem/lib/freehep-graphicsio-2.1.1.jar
b4ba2000-b4ba4000 r-xs 0001d000 fd:00 6505435 /home/knox/development/moldb/vendor/jchem/lib/freehep-graphics2d-2.1.1.jar
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b4bd7000-b4bdd000 r-xs 000b3000 fd:00 6505368 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-plugin.jar
b4bdd000-b4bdf000 r-xs 00000000 fd:00 6505436 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-mprop.jar
b4bdf000-b4bea000 r-xs 000b1000 fd:00 6505421 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-modelling.jar
b4bea000-b4beb000 r-xs 00000000 fd:00 6505408 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-math.jar
b4beb000-b4bed000 r-xs 00010000 fd:00 6505425 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-license.jar
b4bed000-b4bef000 r-xs 00000000 fd:00 6505399 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-jnbadapter.jar
b4bef000-b4bf2000 r-xs 00023000 fd:00 6505354 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-jep.jar
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b4c29000-b4c2b000 r-xs 0000c000 fd:00 6505359 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.mdl.jar
b4c2b000-b4c2e000 r-xs 00010000 fd:00 6505382 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.jar
b4c2e000-b4c2f000 ---p b4c2e000 00:00 0
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b4caf000-b4cb2000 ---p b4caf000 00:00 0
b4cb2000-b4d00000 rwxp b4cb2000 00:00 0
b4d00000-b4dff000 rwxp b4d00000 00:00 0
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b4e01000-b4e03000 r-xs 00007000 fd:00 6505410 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.image.jar
b4e03000-b4e04000 r-xs 00002000 fd:00 6505358 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.gaussian.jar
b4e04000-b4e05000 r-xs 0000e000 fd:00 6505392 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.cml.jar
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b4e09000-b4e0a000 r-xs 00004000 fd:00 6505378 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-vmn.jar
b4e0a000-b4e0b000 r-xs 00003000 fd:00 6505364 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-tripos.jar
b4e0b000-b4e0d000 r-xs 0000d000 fd:00 6505374 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-smiles.jar
b4e0d000-b4e0e000 r-xs 00003000 fd:00 6505348 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-peptide.jar
b4e0e000-b4e0f000 r-xs 00000000 fd:00 6505434 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-jtf.jar
b4e0f000-b4e12000 r-xs 00015000 fd:00 6505404 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-enumeration.jar
b4e12000-b4e15000 r-xs 00042000 fd:00 6505376 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-diverse-modules.jar
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b4e1c000-b4e20000 r-xs 00018000 fd:00 6505393 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-checkers.jar
b4e20000-b4e23000 r-xs 0003e000 fd:00 6505406 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-beans.jar
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b4e2b000-b4e2e000 ---p b4e2b000 00:00 0
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b4eaf000-b4efd000 rwxp b4eaf000 00:00 0
b4efd000-b4fe1000 r-xp 0019a000 fd:00 4397268 /usr/lib/locale/locale-archive
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b51e1000-b51e4000 ---p b51e1000 00:00 0
b51e4000-b5232000 rwxp b51e4000 00:00 0
b5232000-b5235000 ---p b5232000 00:00 0
b5235000-b5283000 rwxp b5235000 00:00 0
b5283000-b5284000 ---p b5283000 00:00 0
b5284000-b5312000 rwxp b5284000 00:00 0
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b532c000-b534a000 rwxp b532c000 00:00 0
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b5426000-b5444000 rwxp b5426000 00:00 0
b5444000-b5447000 ---p b5444000 00:00 0
b5447000-b54cd000 rwxp b5447000 00:00 0
b54cd000-b54d3000 rwxp b54cd000 00:00 0
b54d3000-b54ed000 rwxp b54d3000 00:00 0
b54ed000-b5521000 rwxp b54ed000 00:00 0
b5521000-b5579000 rwxp b5521000 00:00 0
b5579000-b5f41000 rwxp b5579000 00:00 0
b5f41000-b7579000 rwxp b5f41000 00:00 0
b7579000-b7588000 r-xp 00000000 fd:00 4614455 /usr/java/jdk1.6.0_18/jre/lib/i386/libzip.so
b7588000-b758a000 rwxp 0000e000 fd:00 4614455 /usr/java/jdk1.6.0_18/jre/lib/i386/libzip.so
b758a000-b7594000 r-xp 00000000 fd:00 10272888 /lib/libnss_files-2.8.so
b7594000-b7595000 r-xp 0000a000 fd:00 10272888 /lib/libnss_files-2.8.so
b7595000-b7596000 rwxp 0000b000 fd:00 10272888 /lib/libnss_files-2.8.so
b7596000-b759a000 r-xs 00020000 fd:00 6505387 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-alignment.jar
b759a000-b75a0000 rwxp b759a000 00:00 0
b75a0000-b75a8000 rwxs 00000000 fd:00 10690588 /tmp/hsperfdata_knox/7925
b75a8000-b75ae000 r-xp 00000000 fd:00 4614459 /usr/java/jdk1.6.0_18/jre/lib/i386/native_threads/libhpi.so
b75ae000-b75af000 rwxp 00006000 fd:00 4614459 /usr/java/jdk1.6.0_18/jre/lib/i386/native_threads/libhpi.so
b75af000-b75d2000 r-xp 00000000 fd:00 4614431 /usr/java/jdk1.6.0_18/jre/lib/i386/libjava.so
b75d2000-b75d4000 rwxp 00023000 fd:00 4614431 /usr/java/jdk1.6.0_18/jre/lib/i386/libjava.so
b75d4000-b75d7000 ---p b75d4000 00:00 0
b75d7000-b7625000 rwxp b75d7000 00:00 0
b7625000-b7aa7000 r-xp 00000000 fd:00 4614410 /usr/java/jdk1.6.0_18/jre/lib/i386/client/libjvm.so
b7aa7000-b7ac8000 rwxp 00482000 fd:00 4614410 /usr/java/jdk1.6.0_18/jre/lib/i386/client/libjvm.so
b7ac8000-b7ee6000 rwxp b7ac8000 00:00 0
b7ee6000-b7eed000 r-xp 00000000 fd:00 4614414 /usr/java/jdk1.6.0_18/jre/lib/i386/jli/libjli.so
b7eed000-b7eef000 rwxp 00006000 fd:00 4614414 /usr/java/jdk1.6.0_18/jre/lib/i386/jli/libjli.so
b7eef000-b7ef0000 r-xs 00002000 fd:00 6505397 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-inchi.jar
b7ef0000-b7ef2000 r-xs 0001d000 fd:00 6505356 /home/knox/development/moldb/vendor/jchem/lib/jchem.jar
b7ef2000-b7ef3000 r-xp 00cb0000 fd:00 4397268 /usr/lib/locale/locale-archive
b7ef3000-b7ef4000 rwxp b7ef3000 00:00 0
b7ef4000-b7ef5000 r-xp b7ef4000 00:00 0
b7ef5000-b7f00000 r-xp 00000000 fd:00 4614454 /usr/java/jdk1.6.0_18/jre/lib/i386/libverify.so
b7f00000-b7f01000 rwxp 0000b000 fd:00 4614454 /usr/java/jdk1.6.0_18/jre/lib/i386/libverify.so
b7f01000-b7f02000 rwxp b7f01000 00:00 0
b7f02000-b7f03000 r-xp b7f02000 00:00 0 [vdso]
bfced000-bfd02000 rwxp bffeb000 00:00 0 [stack]

VM Arguments:
jvm_args: -Xmx500M
java_command: chemaxon.jchem.Command u
Launcher Type: SUN_STANDARD

Environment Variables:
JAVA_HOME=/usr/java/jdk1.6.0_18
CLASSPATH=/home/knox/development/moldb/vendor/jchem/bin/./../lib/jchem.jar:/home/knox/development/hmdb_structure_search/java/lib/mysql-connector-java-5.1.6-bin.jar:
PATH=/usr/local/jruby/bin:/usr/java/java/bin/:/usr/lib/qt-3.3/bin:/usr/kerberos/bin:/usr/java/jdk1.6.0_18/bin:/usr/lib/ccache:/usr/local/bin:/bin:/usr/bin:/home/knox/bin
LD_LIBRARY_PATH=/usr/java/jdk1.6.0_18/jre/lib/i386/client:/usr/java/jdk1.6.0_18/jre/lib/i386:/usr/java/jdk1.6.0_18/jre/../lib/i386
SHELL=/bin/bash

Signal Handlers:
SIGSEGV: [libjvm.so+0x417270], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x417270], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x33ccc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x33ccc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x33ccc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x33ccc0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x33f900], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x33f630], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x33f630], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x33f630], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x33f630], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004


--------------- S Y S T E M ---------------

OS:Fedora release 9 (Sulphur)

uname:Linux 2.6.27.5-41.fc9.i686 #1 SMP Thu Nov 13 20:52:14 EST 2008 i686
libc:glibc 2.8 NPTL 2.8
rlimit: STACK 10240k, CORE 0k, NPROC 1024, NOFILE 1024, AS infinity
load average:2.03 1.47 0.73

CPU:total 2 (1 cores per cpu, 2 threads per core) family 15 model 4 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ht

Memory: 4k page, physical 3103396k(99444k free), swap 2031608k(2031520k free)

vm_info: Java HotSpot(TM) Client VM (16.0-b13) for linux-x86 JRE (1.6.0_18-b07), built on Dec 17 2009 13:58:25 by "java_re" with gcc 3.2.1-7a (J2SE release)

time: Tue Jan 19 18:24:27 2010
elapsed time: 360 seconds


 


Like I said this same error occurs on OSX and Fedora 9.  It seems like the VM I am using to test doesn't suffer from the same issue.  I should note the VM (where I get NO errors) is using Ubuntu 9 (running a 64-bit version of Java).


Also, this is using the latest version of JChem (3.0).


Any ideas?


Thanks,


Craig

User 3d3f3767a2

20-01-2010 18:18:07

Scratch that, I get the same error in Ubuntu when I try to import structures into a clean database using an SDF file.


Thanks,
Craig 

ChemAxon 0a9e2a55e1

27-01-2010 10:27:04

Dear Craig,


Sorry for the late answer. We have found a bug in chemical terms using inchi. I think these errors are related to that bug too. We are wokring on it.


 


Best Regards,


Peter

User 3d3f3767a2

28-01-2010 19:20:46

Sorry to bug you, but is there any ETA on a bug fix?  It's kind of a show stopper right now.  Or do you know when this bug popped up?  Maybe I can revert to an old version of JChem for now.


 


Thanks!


Craig

ChemAxon 0a9e2a55e1

01-02-2010 11:10:11

Dear Craig,


We are planning to fix this in the next minor release (5.3.1) in March. We have checked the older versions, and it seems that this problem is generated by the rebuilding of the InChI dynamic libraries (1_2r version) because of some critical bugs, so reverting to an older version do not work in this case.


Best regards,


Peter

ChemAxon 990acf0dec

25-02-2010 18:39:05

Dear Craig,

I would like to inform you that we had to make an urgent patch release that was named 5.3.1; the fix promised in this topic is still targeted to be included in the patch release coming at the end of March, but it will probably be named 5.3.2.

Best regards,

Akos

User 3d3f3767a2

02-03-2010 16:41:00

Thanks for the update Akos, looking forward to the fix!


 


Craig

User 3d3f3767a2

31-03-2010 19:55:04

Hi Akos,


Just wondering if this plan for 5.3.2 is still a go?  Otherwise I will need to make alternate plans to get the inchi/inchikey into our databases.


Thanks,


Craig

ChemAxon 0a9e2a55e1

01-04-2010 09:33:03

Dear Craig,


The fix for the crash of IJC and jcman when using inchi is in 5.3.2 - with the inchi windows 64 bit support also.


The relese was a bit postponed because of a critical bug in JChem, but we will publish 5.3.2 in a few days.


Best Regards,


Peter

User 3d3f3767a2

19-04-2010 19:00:32

I just tried regenerating my database using ./jcman r with 5.3.2 and I get the same errors...


A bunch of these:


    The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file '/tmp/temp_java_inchi1542442969675947949log'
Opened input file '/tmp/temp_java_inchi4066676129092404284sdf'
Opened output file '/tmp/temp_java_inchi9096635107571806927in'
Opened problem file '/tmp/temp_java_inchi8006270305307308665prb'
, expression: molFormat("inchi:AuxNone")
Error for column INCHIKEY with structure cd_id=8008: Error while evaluating expression:
molFormat('inchikey')
The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file '/tmp/temp_java_inchi2161965035610579176log'
Opened input file '/tmp/temp_java_inchi6493329457724118394sdf'
Opened output file '/tmp/temp_java_inchi7125885545080635761in'
Opened problem file '/tmp/temp_java_inchi8308090731010948391prb'
, expression: molFormat('inchikey')
Error for column INCHI with structure cd_id=8008: Error while evaluating expression:
molFormat("inchi:AuxNone")


followed by this:


#
# An unexpected error has been detected by Java Runtime Environment:
#
# SIGBUS (0x7) at pc=0x00007f895c1390d8, pid=11333, tid=1090754896
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.2-b01 mixed mode linux-amd64)
# Problematic frame:
# ./jcman: line 116: 11333 Segmentation fault java $javaopts chemaxon.jchem.Command "$@"

Did the fix not make it in?  Running Debian 64-bit.


Thanks,
Craig 

ChemAxon 0a9e2a55e1

21-04-2010 21:52:59

Dear Craig,


We have added the fix into the new release. In out tests neither jcman, nor IJC crashed after adding an inchi or inchikey chemical terms column to the database.


Is this problem only occures when You regenerate the table, or the new version of jcman crashes also when creating a new database?


Can You send us a sample data, so we can check this crash?


Best Regards,


Peter

User 3d3f3767a2

27-04-2010 22:55:32

Hi peter,


It seems there are 2 issues here.  One is the program crashing, which seems to be because of a corrupt glibc library on my debian machine, which I have fixed.


The issue with the inchi, however, still persists.  From what I can tell, this issue only seems to occur with structures containing an aromatic ring with a nitrogen in the ring.


An example to try is the PubChem structure 91443 (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=91443)


The following was all done after building a new database for JChem 5.3.2, and was repeated on a Debian and Ubuntu machine (both 64-bit) with the same results.


This will work fine in molconvert:


./molconvert inchi CID_91443.sdf


But if you have a JChem table with a calculated column for inchi/inchikey, then the error occurs, for example:


./jcman a structures CID_921443.sdf


produces:



: Error while evaluating expression:
molFormat("inchi:AuxNone")
    The following error occured in the IUPAC software:
InChI version 1, Software version 1.02 release 01/10/2009
Opened log file '/tmp/temp_java_inchi4413724228011745105log'
Opened input file '/tmp/temp_java_inchi1614615637080167939sdf'
Opened output file '/tmp/temp_java_inchi704703169511626486in'
Opened problem file '/tmp/temp_java_inchi758479656869677103prb'
, expression: molFormat("inchi:AuxNone")


The structures table definition contains a column like this:


inchi text


which is defined with: 


molFormat("inchi:AuxNone")


I'm not sure what is going on, but I am curious as to what structure field is passed into the inchi library/application to get the inchi/inchikey?  I have found that for molconvert, I can get it to crash inchi if I don't dearomatize the structure beforehand (when there is a nitrogen in the ring).


Thanks,


Craig


 


 











pvadasz wrote:

Dear Craig,


We have added the fix into the new release. In out tests neither jcman, nor IJC crashed after adding an inchi or inchikey chemical terms column to the database.


Is this problem only occures when You regenerate the table, or the new version of jcman crashes also when creating a new database?


Can You send us a sample data, so we can check this crash?


Best Regards,


Peter


ChemAxon 0a9e2a55e1

28-04-2010 09:40:17

Dear Craig,


So if I understand it right: the jcman no longer crashes on Your computer. I have double-checked on our test machines and it do no crash in 5.3.2 - so my fix in the threads and Your in the glibc library solved the problem.


Checking the other issue, there are two things:


- Marvin only gives the beginning of the error message.


- In the molecule You have sent - thanks for the example - molconvert and jcman/IJC molFormat("inchi:AuxNone") gives different  output - that's really strange, because both simply calls the inchi export modules...


We are checking these, and will fix them.


Best regards,


Peter

User 3d3f3767a2

28-04-2010 18:32:39

Hi Peter,


Thanks for your quick reply.  Yes, you have it right, jcman no longer crashes.  Just to confirm, have you been able to reproduce this (new) problem with the example I provided?


Thanks,


Craig

ChemAxon 0a9e2a55e1

04-05-2010 14:05:34

Dear Craig,


We are investigating this issue. Yes there is an error in if I convert the structure You have mentioned. The problem always occures when there is a ring with 2 nitrogenes that is  aromatized. For example a 5 atom ring with 3 carbons and 2 nitrogenes: c1c[nH]cn1 . With only one nitrogene (and 4 carbons), or without carbons it can be converted to inchi, and also the molecule with 2 nitrogenes can be converted if we dearomatize it first. My chemist colleges said it is about the place of an implicit hidrogene in the problematic molecule. We have checked the generated inchi outputs, and it seems inchi can not store this information, and gives an error message. The error message is:


Error -9986 (Cannot process aromatic bonds)


(This is the missing error message I have mentioned in my last post.)


So we can generate cases when inchi surely fails because of this, but, we do not know all such cases.


If You use jcman or IJC and put molecules in the jchem table, it is standardized, and all chemical terms expressions are calculated based on the standardized format. The default standardization contains aromatization - it is necessary for the search, and duplication checking, so even if You add the molecule non-aromatic form, the 


molFormat("inchi:AuxNone")


chemical terms expression gives an error.


I don't really know what would be a good solution, a hotfix can be that You use the


molFormat("inchi:-a,AuxNone")


instead, but in this case the inchi is calculated from the dearomatized format for all structures.


During the tests we have found a bug in using the basic export options in inchi, so maybe the -a option do not work in the latest release, but it is good in the next release coming very soon.


Is the -a option a possible solution for You?


 


Best Regards,


Peter

User 3d3f3767a2

10-05-2010 16:45:22

Hi Peter,


Thanks for your detailed reply.


From what I can tell from reading up on this issue, this seems to be a much bigger problem then I thought.  From what I can tell, JChem is exporting standardized structures in SDF/MOL format with "type 4 bonds" which are not supposed to be used to represent the actual structure, but for searching only.  


I was reading this forum, where they specifically refer to ChemAxon-generated SDF files generating type 4 bonds. Further down they mention this:


 


Bonds type 4 are NOT aromatic bonds. They are query bonds for database
searches. This is clearly defined in the MDL format specification. These
MUST NOT be used to encode normal structure data files. File a bug report
with the suppliers of whatever tool you used to write you file.


I think this might be where the problem is coming from.  Is there anyway to fix this?  


I guess, for now I could dearomatize everything (to maintain consistency), but this is not an ideal work around.  And right now, like you mention, inchi:-a does not work in the current version.


Thanks,


Craig

ChemAxon 0a9e2a55e1

14-05-2010 08:27:43

Dear Craig,


We have checked again this issue with a chemist, and it seems, that in molecules containing no nitrogenes the same output is generated in aromarized, and dearomatized form. If the molecule contains at least one aromatic nitrogene than not only the output seems different if it works, but the conversion crashes - when there are at least two nitrogenes always as You have mentioned in Your bug report, whene there is only one it also crashes in some cases. So we have decided to dearomatize the molecule automatically, so You do not have to use the -a option. It will make no difference in the currently converted molecules, but these problematic molecules will also be converted.


I have sent the forum link You have mentioned to the JChem developers to check it.


Best Regards,


Peter

User 3d3f3767a2

29-05-2010 17:29:50

Hi Peter,


Thanks for the release, it has solved most of my problems.


I still have a case where the inchi/inchikey fails to generate in Jchem, but still works fine on the command line with molconvert, with similar error output:


CC1=CC=CC2=C1C(=CC=N2)C1=C(NN=C1)C1=NC=CC=C1 


Currently, my chemical terms for inchi/inchikey are:


molFormat("inchi:-a,AuxNone")


molFormat("inchikey:-a")


 


Thanks!
Craig 

ChemAxon 0a9e2a55e1

07-06-2010 14:05:59

Dear Craig,


Sorry for the late answer. I have checked Yout smiles on my current version and can not reproduce it. I have also tried to convert it with the sdf:-a option in a table and convert it with the original IUPAC software (the inchi export currently does the same process), but it was converted without any problem, giving the following output:


InChI=1S/C18H14N4/c1-12-5-4-7-15-17(12)13(8-10-20-15)14-11-21-22-18(14)16-6-2-3-9-19-16/h2-11H,1H3,(H,21,22)
AuxInfo=1/1/N:1,21,20,4,3,22,5,9,19,10,16,2,8,12,6,17,7,13,18,11,15,14/rA:22nCCCCCCCCCCNCCNNCCNCCCC/rB:s1;d2;s3;d4;s5;s2d6;s7;d8;s9;s6d10;s8;d12;s13;s14;s12d15;s13;d17;s18;d19;s20;s17d21;/rC:;;;;;;;;;;;;;;;;;;;;;;


Is there any other molecule You that is problematic on Your computer? (Maybe I can reproduce this with that molecule.) Which operating system do You use when this problem occures? I will try to check it on a machine similar to Yours.


Best Regards,


Peter