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
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b4ba4000-b4ba7000 r-xs 00014000 fd:00 6505422 /home/knox/development/moldb/vendor/jchem/lib/forms-1.1.0.jar
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b4ba8000-b4ba9000 r-xs 00000000 fd:00 6505394 /home/knox/development/moldb/vendor/jchem/lib/chemaxon-inchi.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
b4bf2000-b4bf3000 r-xs 00002000 fd:00 6505402 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-jcw.jar
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b4c21000-b4c29000 r-xs 00119000 fd:00 6505433 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.name.jar
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
b4c2f000-b4caf000 rwxp b4c2f000 00:00 0
b4caf000-b4cb2000 ---p b4caf000 00:00 0
b4cb2000-b4d00000 rwxp b4cb2000 00:00 0
b4d00000-b4dff000 rwxp b4d00000 00:00 0
b4dff000-b4e00000 ---p b4dff000 00:00 0
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
b4e05000-b4e06000 r-xs 0000a000 fd:00 6505361 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.cdx.jar
b4e06000-b4e08000 r-xs 00000000 fd:00 6505362 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats.abbrevgroup.jar
b4e08000-b4e09000 r-xs 00001000 fd:00 6505396 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-formats-xyz.jar
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
b4e15000-b4e18000 r-xs 0000d000 fd:00 6505401 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-concurrent.jar
b4e18000-b4e1c000 r-xs 00018000 fd:00 6505347 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans-codeassist.jar
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
b4e23000-b4e2b000 r-xs 000a3000 fd:00 6505371 /home/knox/development/moldb/vendor/jchem/lib/MarvinBeans.jar
b4e2b000-b4e2e000 ---p b4e2b000 00:00 0
b4e2e000-b4eac000 rwxp b4e2e000 00:00 0
b4eac000-b4eaf000 ---p b4eac000 00:00 0
b4eaf000-b4efd000 rwxp b4eaf000 00:00 0
b4efd000-b4fe1000 r-xp 0019a000 fd:00 4397268 /usr/lib/locale/locale-archive
b4fe1000-b51e1000 r-xp 00000000 fd:00 4397268 /usr/lib/locale/locale-archive
b51e1000-b51e4000 ---p b51e1000 00:00 0
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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
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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