User 2f67f74af0
23-09-2008 20:35:27
Attached is the error report file I get when trying to use cxcalc from command line to calculate pka from an SDF file.
Any help will be appreciated.
Regards.
Saif
#
# An unexpected error has been detected by Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00002b720e9981d1, pid=12826, tid=1095575872
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (10.0-b22 mixed mode linux-amd64)
# Problematic frame:
# V [libjvm.so+0x4ac1d1]
#
# 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 (0x000000004c914400): JavaThread "CompilerThread1" daemon [_thread_in_native, id=12841, stack(0x00000000413d2000,0x00000000414d3000)]
siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x0000000000000008
Registers:
RAX=0x00002aaac8000b50, RBX=0x00000000414ce6e0, RCX=0x0000000000000000, RDX=0x00002aaac4a89960
RSP=0x00000000414cc460, RBP=0x00000000414cc4a0, RSI=0x00002aaac4143830, RDI=0x0000000000000000
R8 =0x00002aaac4a89960, R9 =0x0000000000000000, R10=0x00000000000001f5, R11=0x00000000000001f5
R12=0x00002aaac472b878, R13=0x00002aaac92ed678, R14=0x00002aaac4143830, R15=0x00000000414ce6c0
RIP=0x00002b720e9981d1, EFL=0x0000000000010287, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00000000414cc460)
0x00000000414cc460: 00002b720ed14590 00002aaac806fba1
0x00000000414cc470: 00002aaac9911388 00002aaac9911388
0x00000000414cc480: 00000000414cc760 00002aaac4143830
0x00000000414cc490: 00000000414cc780 0000000000000003
0x00000000414cc4a0: 00000000414cc510 00002b720e997e96
0x00000000414cc4b0: 00002aaac92d79e8 000000004cb3c340
0x00000000414cc4c0: 0000000300000004 0000000000000000
0x00000000414cc4d0: 00000000414cc740 00000000414cc780
0x00000000414cc4e0: 00000000414ce6c0 00002aaac88c2ba0
0x00000000414cc4f0: 00002aaac806fc10 00000000414ce6c0
0x00000000414cc500: 00000000414cc740 0000000000000001
0x00000000414cc510: 00000000414cc7d0 00002b720e9953c1
0x00000000414cc520: 00000000414cc570 00000000414cc760
0x00000000414cc530: 00000000414cc570 00002b720e9e2e88
0x00000000414cc540: 00000000414cc780 000000004c914740
0x00000000414cc550: 00000000414cf048 00002b720ea1fb16
0x00000000414cc560: 0000000000000000 00000000414cfb20
0x00000000414cc570: 00000000414cc5e0 00002b720ea22453
0x00000000414cc580: 00002aaac9a56ad0 0000000000001362
0x00000000414cc590: 000000604c8f07f0 00002aaac9a5b260
0x00000000414cc5a0: 00002aaac9a5b260 00002aaac9a5b190
0x00000000414cc5b0: 00000000414cfb20 0000000000000001
0x00000000414cc5c0: 00002aaac9905060 00002aaac9a5b1d0
0x00000000414cc5d0: 00002aaac9a5b248 00000000414d04d8
0x00000000414cc5e0: 00000000414cc5f0 00002b720eb1d548
0x00000000414cc5f0: 00000000414cc640 00002b720e7868d8
0x00000000414cc600: 00002aaa00018002 00002aaac9205810
0x00000000414cc610: 00002aaac9205810 00000000414d11c0
0x00000000414cc620: 00002aaac9205810 00002b720ed424e0
0x00000000414cc630: 00002aaac8347dd0 00000000414cfb58
0x00000000414cc640: 00002aaac8881390 00002b720eb204e6
0x00000000414cc650: 00000000414d11c0 000000004c8f0650
Instructions: (pc=0x00002b720e9981d1)
0x00002b720e9981c1: 8b 97 c8 09 00 00 44 89 c7 48 8b 0c fa 49 89 d0
0x00002b720e9981d1: 4c 8b 49 08 49 83 39 00 75 2b 8b 73 08 66 90 8b
Stack: [0x00000000413d2000,0x00000000414d3000], sp=0x00000000414cc460, free space=1001k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0x4ac1d1]
V [libjvm.so+0x4abe96]
V [libjvm.so+0x4a93c1]
V [libjvm.so+0x243b2b]
V [libjvm.so+0x2410a4]
V [libjvm.so+0x1e05f7]
V [libjvm.so+0x248f88]
V [libjvm.so+0x248926]
V [libjvm.so+0x62a7a9]
V [libjvm.so+0x624a51]
V [libjvm.so+0x50628a]
Current CompileTask:
C2:909 chemaxon.marvin.io.formats.smiles.SmilesExport.setupDB(IZ)V (1121 bytes)
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x000000004cb50400 JavaThread "pool-1-thread-8" daemon [_thread_blocked, id=12851, stack(0x00000000419d8000,0x0000000041ad9000)]
0x000000004c947800 JavaThread "pool-1-thread-7" daemon [_thread_in_Java, id=12850, stack(0x00000000418d7000,0x00000000419d8000)]
0x000000004cda5800 JavaThread "pool-1-thread-6" daemon [_thread_in_Java, id=12849, stack(0x00000000417d6000,0x00000000418d7000)]
0x000000004cda5000 JavaThread "pool-1-thread-5" daemon [_thread_in_Java, id=12848, stack(0x00000000416d5000,0x00000000417d6000)]
0x000000004c949400 JavaThread "pool-1-thread-4" daemon [_thread_in_Java, id=12847, stack(0x000000004105c000,0x000000004115d000)]
0x000000004cd79400 JavaThread "pool-1-thread-3" daemon [_thread_in_Java, id=12846, stack(0x0000000040f5b000,0x000000004105c000)]
0x000000004ca22000 JavaThread "pool-1-thread-2" daemon [_thread_blocked, id=12845, stack(0x0000000040396000,0x0000000040497000)]
0x000000004ca21800 JavaThread "pool-1-thread-1" daemon [_thread_blocked, id=12844, stack(0x0000000040186000,0x0000000040287000)]
0x000000004c916800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=12842, stack(0x00000000414d3000,0x00000000415d4000)]
=>0x000000004c914400 JavaThread "CompilerThread1" daemon [_thread_in_native, id=12841, stack(0x00000000413d2000,0x00000000414d3000)]
0x000000004c910800 JavaThread "CompilerThread0" daemon [_thread_in_native, id=12840, stack(0x00000000412d1000,0x00000000413d2000)]
0x000000004c90f400 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=12839, stack(0x00000000411d0000,0x00000000412d1000)]
0x000000004c8e3c00 JavaThread "Finalizer" daemon [_thread_blocked, id=12838, stack(0x0000000040e5a000,0x0000000040f5b000)]
0x000000004c8e2800 JavaThread "Reference Handler" daemon [_thread_blocked, id=12837, stack(0x0000000040d59000,0x0000000040e5a000)]
0x000000004c875c00 JavaThread "main" [_thread_blocked, id=12827, stack(0x0000000040bb0000,0x0000000040cb1000)]
Other Threads:
0x000000004c8dd400 VMThread [stack: 0x0000000040295000,0x0000000040396000] [id=12836]
0x000000004c918400 WatcherThread [stack: 0x00000000415d4000,0x00000000416d5000] [id=12843]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap
PSYoungGen total 47232K, used 36561K [0x00002aaabbb90000, 0x00002aaabfe30000, 0x00002aaabfe30000)
eden space 27712K, 86% used [0x00002aaabbb90000,0x00002aaabd2f4558,0x00002aaabd6a0000)
from space 19520K, 64% used [0x00002aaabd6a0000,0x00002aaabe2f0000,0x00002aaabe9b0000)
to space 20224K, 0% used [0x00002aaabea70000,0x00002aaabea70000,0x00002aaabfe30000)
PSOldGen total 136576K, used 113181K [0x00002aaab3630000, 0x00002aaabbb90000, 0x00002aaabbb90000)
object space 136576K, 82% used [0x00002aaab3630000,0x00002aaaba4b7798,0x00002aaabbb90000)
PSPermGen total 21504K, used 10872K [0x00002aaaae230000, 0x00002aaaaf730000, 0x00002aaab3630000)
object space 21504K, 50% used [0x00002aaaae230000,0x00002aaaaecce1a8,0x00002aaaaf730000)
Dynamic libraries:
40000000-40009000 r-xp 00000000 08:03 21083535 /usr/local/jdk1.6.0_06/bin/java
40108000-4010a000 rwxp 00008000 08:03 21083535 /usr/local/jdk1.6.0_06/bin/java
40186000-40189000 ---p 40186000 00:00 0
40189000-40287000 rwxp 40189000 00:00 0
40295000-40296000 ---p 40295000 00:00 0
40296000-40396000 rwxp 40296000 00:00 0
40396000-40399000 ---p 40396000 00:00 0
40399000-40497000 rwxp 40399000 00:00 0
40bb0000-40bb3000 ---p 40bb0000 00:00 0
40bb3000-40cb1000 rwxp 40bb3000 00:00 0
40d59000-40d5c000 ---p 40d59000 00:00 0
40d5c000-40e5a000 rwxp 40d5c000 00:00 0
40e5a000-40e5d000 ---p 40e5a000 00:00 0
40e5d000-40f5b000 rwxp 40e5d000 00:00 0
40f5b000-40f5e000 ---p 40f5b000 00:00 0
40f5e000-4105c000 rwxp 40f5e000 00:00 0
4105c000-4105f000 ---p 4105c000 00:00 0
4105f000-4115d000 rwxp 4105f000 00:00 0
411d0000-411d3000 ---p 411d0000 00:00 0
411d3000-412d1000 rwxp 411d3000 00:00 0
412d1000-412d4000 ---p 412d1000 00:00 0
412d4000-413d2000 rwxp 412d4000 00:00 0
413d2000-413d5000 ---p 413d2000 00:00 0
413d5000-414d3000 rwxp 413d5000 00:00 0
414d3000-414d6000 ---p 414d3000 00:00 0
414d6000-415d4000 rwxp 414d6000 00:00 0
415d4000-415d5000 ---p 415d4000 00:00 0
415d5000-416d5000 rwxp 415d5000 00:00 0
416d5000-416d8000 ---p 416d5000 00:00 0
416d8000-417d6000 rwxp 416d8000 00:00 0
417d6000-417d9000 ---p 417d6000 00:00 0
417d9000-418d7000 rwxp 417d9000 00:00 0
418d7000-418da000 ---p 418d7000 00:00 0
418da000-419d8000 rwxp 418da000 00:00 0
419d8000-419db000 ---p 419d8000 00:00 0
419db000-41ad9000 rwxp 419db000 00:00 0
41cf4000-41cf5000 ---p 41cf4000 00:00 0
41cf5000-41df5000 rwxp 41cf5000 00:00 0
41df5000-41df6000 ---p 41df5000 00:00 0
41df6000-41ef6000 rwxp 41df6000 00:00 0
41ef6000-41ef7000 ---p 41ef6000 00:00 0
41ef7000-41ff7000 rwxp 41ef7000 00:00 0
41ff7000-41ff8000 ---p 41ff7000 00:00 0
41ff8000-420f8000 rwxp 41ff8000 00:00 0
420f8000-420f9000 ---p 420f8000 00:00 0
420f9000-421f9000 rwxp 420f9000 00:00 0
421f9000-421fa000 ---p 421f9000 00:00 0
421fa000-422fa000 rwxp 421fa000 00:00 0
422fa000-422fb000 ---p 422fa000 00:00 0
422fb000-423fb000 rwxp 422fb000 00:00 0
423fb000-423fc000 ---p 423fb000 00:00 0
423fc000-424fc000 rwxp 423fc000 00:00 0
4c86e000-4d016000 rwxp 4c86e000 00:00 0
3c16c00000-3c16c1a000 r-xp 00000000 08:02 197378 /lib64/ld-2.5.so
3c16e1a000-3c16e1b000 r-xp 0001a000 08:02 197378 /lib64/ld-2.5.so
3c16e1b000-3c16e1c000 rwxp 0001b000 08:02 197378 /lib64/ld-2.5.so
3c17c00000-3c17d4a000 r-xp 00000000 08:02 197380 /lib64/libc-2.5.so
3c17d4a000-3c17f49000 ---p 0014a000 08:02 197380 /lib64/libc-2.5.so
3c17f49000-3c17f4d000 r-xp 00149000 08:02 197380 /lib64/libc-2.5.so
3c17f4d000-3c17f4e000 rwxp 0014d000 08:02 197380 /lib64/libc-2.5.so
3c17f4e000-3c17f53000 rwxp 3c17f4e000 00:00 0
3c18000000-3c18082000 r-xp 00000000 08:02 197390 /lib64/libm-2.5.so
3c18082000-3c18281000 ---p 00082000 08:02 197390 /lib64/libm-2.5.so
3c18281000-3c18282000 r-xp 00081000 08:02 197390 /lib64/libm-2.5.so
3c18282000-3c18283000 rwxp 00082000 08:02 197390 /lib64/libm-2.5.so
3c18400000-3c18402000 r-xp 00000000 08:02 197381 /lib64/libdl-2.5.so
3c18402000-3c18602000 ---p 00002000 08:02 197381 /lib64/libdl-2.5.so
3c18602000-3c18603000 r-xp 00002000 08:02 197381 /lib64/libdl-2.5.so
3c18603000-3c18604000 rwxp 00003000 08:02 197381 /lib64/libdl-2.5.so
3c18800000-3c18815000 r-xp 00000000 08:02 197382 /lib64/libpthread-2.5.so
3c18815000-3c18a14000 ---p 00015000 08:02 197382 /lib64/libpthread-2.5.so
3c18a14000-3c18a15000 r-xp 00014000 08:02 197382 /lib64/libpthread-2.5.so
3c18a15000-3c18a16000 rwxp 00015000 08:02 197382 /lib64/libpthread-2.5.so
3c18a16000-3c18a1a000 rwxp 3c18a16000 00:00 0
3c1b800000-3c1b807000 r-xp 00000000 08:02 197385 /lib64/librt-2.5.so
3c1b807000-3c1ba07000 ---p 00007000 08:02 197385 /lib64/librt-2.5.so
3c1ba07000-3c1ba08000 r-xp 00007000 08:02 197385 /lib64/librt-2.5.so
3c1ba08000-3c1ba09000 rwxp 00008000 08:02 197385 /lib64/librt-2.5.so
3c1e400000-3c1e415000 r-xp 00000000 08:02 197403 /lib64/libnsl-2.5.so
3c1e415000-3c1e614000 ---p 00015000 08:02 197403 /lib64/libnsl-2.5.so
3c1e614000-3c1e615000 r-xp 00014000 08:02 197403 /lib64/libnsl-2.5.so
3c1e615000-3c1e616000 rwxp 00015000 08:02 197403 /lib64/libnsl-2.5.so
3c1e616000-3c1e618000 rwxp 3c1e616000 00:00 0
2aaaaaaab000-2aaaaaad3000 rwxp 2aaaaaaab000 00:00 0
2aaaaaad8000-2aaaaaad9000 r-xp 2aaaaaad8000 00:00 0
2aaaaaad9000-2aaaaaada000 rwxp 2aaaaaad9000 00:00 0
2aaaaaada000-2aaaaaae1000 r-xp 00000000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaaae1000-2aaaaabe2000 ---p 00007000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaabe2000-2aaaaabe4000 rwxp 00008000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaabe4000-2aaaaabe5000 rwxp 2aaaaabe4000 00:00 0
2aaaaabe5000-2aaaaabed000 rwxs 00000000 08:02 850405 /tmp/hsperfdata_root/12826
2aaaaac0f000-2aaaaac19000 r-xp 00000000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaac19000-2aaaaae18000 ---p 0000a000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae18000-2aaaaae19000 r-xp 00009000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae19000-2aaaaae1a000 rwxp 0000a000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae1a000-2aaaaae27000 r-xp 00000000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaae27000-2aaaaaf26000 ---p 0000d000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaaf26000-2aaaaaf29000 rwxp 0000c000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaaf29000-2aaaaaf51000 r-xp 00000000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaaaf51000-2aaaab051000 ---p 00028000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaab051000-2aaaab058000 rwxp 00028000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaab058000-2aaaab066000 r-xp 00000000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab066000-2aaaab168000 ---p 0000e000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab168000-2aaaab16b000 rwxp 00010000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab16b000-2aaaab75c000 rwxp 2aaaab16b000 00:00 0
2aaaab75c000-2aaaae16c000 rwxp 2aaaab75c000 00:00 0
2aaaae16c000-2aaaae184000 rwxp 2aaaae16c000 00:00 0
2aaaae184000-2aaaae22c000 rwxp 2aaaae184000 00:00 0
2aaaae230000-2aaaaf730000 rwxp 2aaaae230000 00:00 0
2aaaaf730000-2aaab3630000 rwxp 2aaaaf730000 00:00 0
2aaab3630000-2aaabbb90000 rwxp 2aaab3630000 00:00 0
2aaabbb90000-2aaabfe30000 rwxp 2aaabbb90000 00:00 0
2aaabfe30000-2aaabfe3b000 rwxp 2aaabfe30000 00:00 0
2aaabfe3b000-2aaabfe5a000 rwxp 2aaabfe3b000 00:00 0
2aaabfe5a000-2aaabfe9d000 rwxp 2aaabfe5a000 00:00 0
2aaabfe9d000-2aaabfebe000 rwxp 2aaabfe9d000 00:00 0
2aaabfebe000-2aaabff02000 rwxp 2aaabfebe000 00:00 0
2aaabff02000-2aaabff0d000 rwxp 2aaabff02000 00:00 0
2aaabff0d000-2aaabff2c000 rwxp 2aaabff0d000 00:00 0
2aaabff2c000-2aaac00b7000 r-xs 02df0000 08:03 21084096 /usr/local/jdk1.6.0_06/jre/lib/rt.jar
2aaac00b7000-2aaac0212000 rwxp 2aaac00b7000 00:00 0
2aaac0212000-2aaac37eb000 r-xp 00000000 08:02 6708309 /usr/lib/locale/locale-archive
2aaac37eb000-2aaac3879000 r-xs 00f05000 08:03 2619435 /usr/local/ChemAxon/JChem/lib/jchem.jar
2aaac3879000-2aaac387b000 r-xs 00004000 08:03 2619434 /usr/local/ChemAxon/JChem/lib/aloe.jar
2aaac387b000-2aaac3884000 r-xs 0004a000 08:03 2619416 /usr/local/ChemAxon/JChem/lib/backport-util-concurrent.jar
2aaac3884000-2aaac388a000 r-xs 0002e000 08:03 2619414 /usr/local/ChemAxon/JChem/lib/batik-core.jar
2aaac388a000-2aaac389e000 r-xs 00133000 08:03 2619421 /usr/local/ChemAxon/JChem/lib/castor-1.0.1-xml.jar
2aaac389e000-2aaac38ad000 r-xs 001ac000 08:03 2619425 /usr/local/ChemAxon/JChem/lib/xerces.jar
2aaac38ad000-2aaac38ae000 r-xs 0000c000 08:03 2619442 /usr/local/ChemAxon/JChem/lib/commons-logging-1.1.jar
2aaac38ae000-2aaac38af000 r-xs 00015000 08:03 2619429 /usr/local/ChemAxon/JChem/lib/chart.jar
2aaac38af000-2aaac38b7000 r-xs 00068000 08:03 2619426 /usr/local/ChemAxon/JChem/lib/dom4j.jar
2aaac38b7000-2aaac38ba000 r-xs 00014000 08:03 2619415 /usr/local/ChemAxon/JChem/lib/forms-1.1.0.jar
2aaac38ba000-2aaac38bc000 r-xs 00004000 08:03 2619430 /usr/local/ChemAxon/JChem/lib/freehep-export-2.1.1.jar
2aaac38bc000-2aaac38be000 r-xs 0001d000 08:03 2619420 /usr/local/ChemAxon/JChem/lib/freehep-graphics2d-2.1.1.jar
2aaac38be000-2aaac38c3000 r-xs 0002b000 08:03 2619423 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-2.1.1.jar
2aaac38c3000-2aaac38c8000 r-xs 00027000 08:03 2619409 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-emf-2.1.1.jar
2aaac38c8000-2aaac38ca000 r-xs 00011000 08:03 2619424 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-pdf-2.1.1.jar
2aaac38ca000-2aaac38cd000 r-xs 0000e000 08:03 2619417 /usr/local/ChemAxon/JChem/lib/freehep-io-2.0.2.jar
2aaac38cd000-2aaac38d3000 r-xs 00031000 08:03 2619428 /usr/local/ChemAxon/JChem/lib/freehep-swing-2.0.3.jar
2aaac38d3000-2aaac38d5000 r-xs 0000b000 08:03 2619427 /usr/local/ChemAxon/JChem/lib/freehep-util-2.0.2.jar
2aaac38d5000-2aaac38d6000 r-xs 00004000 08:03 2619412 /usr/local/ChemAxon/JChem/lib/gluegen-rt.jar
2aaac38d6000-2aaac38de000 r-xs 0003f000 08:03 2619439 /usr/local/ChemAxon/JChem/lib/izmcomjni.jar
2aaac38de000-2aaac38e2000 r-xs 00021000 08:03 2619438 /usr/local/ChemAxon/JChem/lib/izmcomtlb.jar
2aaac38e2000-2aaac38e3000 r-xs 00007000 08:03 2619432 /usr/local/ChemAxon/JChem/lib/jextexp.jar
2aaac38e3000-2aaac38ed000 r-xs 00075000 08:03 2619422 /usr/local/ChemAxon/JChem/lib/jh.jar
2aaac38ed000-2aaac38ee000 r-xs 00000000 08:03 2619433 /usr/local/ChemAxon/JChem/lib/jnbtools.jar
2aaac38ee000-2aaac38fa000 r-xs 000f9000 08:03 2619413 /usr/local/ChemAxon/JChem/lib/jogl.jar
2aaac38fa000-2aaac3904000 r-xs 0005e000 08:03 2619410 /usr/local/ChemAxon/JChem/lib/looks-2.1.4.jar
2aaac3904000-2aaac3907000 r-xs 0000e000 08:03 2619411 /usr/local/ChemAxon/JChem/lib/openide-lookup-1.9-patched-1.0.jar
2aaac3907000-2aaac3908000 r-xs 00000000 08:03 2619389 /usr/local/ChemAxon/JChem/plugins/extensions.jar
2aaac3908000-2aaac390f000 r-xs 000a5000 08:03 15385926 /usr/local/mysql-connector-java-5.1.6/mysql-connector-java-5.1.6-bin.jar
2aaac4000000-2aaac6644000 rwxp 2aaac4000000 00:00 0
2aaac6644000-2aaac8000000 ---p 2aaac6644000 00:00 0
2aaac8000000-2aaacace1000 rwxp 2aaac8000000 00:00 0
2aaacace1000-2aaacc000000 ---p 2aaacace1000 00:00 0
2b720e3b4000-2b720e3b5000 rwxp 2b720e3b4000 00:00 0
2b720e3df000-2b720e3e0000 rwxp 2b720e3df000 00:00 0
2b720e3e0000-2b720e3e7000 r-xp 00000000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e3e7000-2b720e4e8000 ---p 00007000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e4e8000-2b720e4ea000 rwxp 00008000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e4ea000-2b720e4ec000 rwxp 2b720e4ea000 00:00 0
2b720e4ec000-2b720ebe1000 r-xp 00000000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ebe1000-2b720ece0000 ---p 006f5000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ece0000-2b720ee2a000 rwxp 006f4000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ee2a000-2b720ee67000 rwxp 2b720ee2a000 00:00 0
7fff9c6e0000-7fff9c6f6000 rwxp 7fff9c6e0000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
VM Arguments:
jvm_args: -Xmx200M
java_command: chemaxon.marvin.Calculator -S -t myLOGP logp -a 0.15 -k 0.05 DrugLike_usual_2184729Cpd.sdf
Launcher Type: SUN_STANDARD
Environment Variables:
JAVA_HOME=/usr/local/jdk1.6
CLASSPATH=/usr/local/ChemAxon/JChem/bin/../lib/jchem.jar:/usr/local/connector/mysql-connector-java-5.1.6-bin.jar:
PATH=/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/jdk1.6/bin:/usr/local/tomcat6/bin:/usr/local/mysql/bin:/usr/local/mysql/support-files:/usr/sbin:/root/bin
LD_LIBRARY_PATH=/usr/local/jdk1.6.0_06/jre/lib/amd64/server:/usr/local/jdk1.6.0_06/jre/lib/amd64:/usr/local/jdk1.6.0_06/jre/../lib/amd64
SHELL=/bin/bash
Signal Handlers:
SIGSEGV: [libjvm.so+0x6616e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x6616e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x506740], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
--------------- S Y S T E M ---------------
OS:Red Hat Enterprise Linux Server release 5.2 (Tikanga)
uname:Linux 2.6.18-92.el5xen #1 SMP Tue Apr 29 13:31:30 EDT 2008 x86_64
libc:glibc 2.5 NPTL 2.5
rlimit: STACK 10240k, CORE 0k, NPROC 63499, NOFILE 1024, AS infinity
load average:4.74 2.78 2.34
CPU:total 8 (4 cores per cpu, 1 threads per core) family 6 model 15 stepping 7, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3
Memory: 4k page, physical 8120320k(17928k free), swap 16386260k(16386060k free)
vm_info: Java HotSpot(TM) 64-Bit Server VM (10.0-b22) for linux-amd64 JRE (1.6.0_06-b02), built on Mar 25 2008 01:03:02 by "java_re" with gcc 3.2.2 (SuSE Linux)
time: Mon Sep 22 11:29:53 2008
elapsed time: 36 seconds
Any help will be appreciated.
Regards.
Saif
#
# An unexpected error has been detected by Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00002b720e9981d1, pid=12826, tid=1095575872
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (10.0-b22 mixed mode linux-amd64)
# Problematic frame:
# V [libjvm.so+0x4ac1d1]
#
# 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 (0x000000004c914400): JavaThread "CompilerThread1" daemon [_thread_in_native, id=12841, stack(0x00000000413d2000,0x00000000414d3000)]
siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x0000000000000008
Registers:
RAX=0x00002aaac8000b50, RBX=0x00000000414ce6e0, RCX=0x0000000000000000, RDX=0x00002aaac4a89960
RSP=0x00000000414cc460, RBP=0x00000000414cc4a0, RSI=0x00002aaac4143830, RDI=0x0000000000000000
R8 =0x00002aaac4a89960, R9 =0x0000000000000000, R10=0x00000000000001f5, R11=0x00000000000001f5
R12=0x00002aaac472b878, R13=0x00002aaac92ed678, R14=0x00002aaac4143830, R15=0x00000000414ce6c0
RIP=0x00002b720e9981d1, EFL=0x0000000000010287, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x00000000414cc460)
0x00000000414cc460: 00002b720ed14590 00002aaac806fba1
0x00000000414cc470: 00002aaac9911388 00002aaac9911388
0x00000000414cc480: 00000000414cc760 00002aaac4143830
0x00000000414cc490: 00000000414cc780 0000000000000003
0x00000000414cc4a0: 00000000414cc510 00002b720e997e96
0x00000000414cc4b0: 00002aaac92d79e8 000000004cb3c340
0x00000000414cc4c0: 0000000300000004 0000000000000000
0x00000000414cc4d0: 00000000414cc740 00000000414cc780
0x00000000414cc4e0: 00000000414ce6c0 00002aaac88c2ba0
0x00000000414cc4f0: 00002aaac806fc10 00000000414ce6c0
0x00000000414cc500: 00000000414cc740 0000000000000001
0x00000000414cc510: 00000000414cc7d0 00002b720e9953c1
0x00000000414cc520: 00000000414cc570 00000000414cc760
0x00000000414cc530: 00000000414cc570 00002b720e9e2e88
0x00000000414cc540: 00000000414cc780 000000004c914740
0x00000000414cc550: 00000000414cf048 00002b720ea1fb16
0x00000000414cc560: 0000000000000000 00000000414cfb20
0x00000000414cc570: 00000000414cc5e0 00002b720ea22453
0x00000000414cc580: 00002aaac9a56ad0 0000000000001362
0x00000000414cc590: 000000604c8f07f0 00002aaac9a5b260
0x00000000414cc5a0: 00002aaac9a5b260 00002aaac9a5b190
0x00000000414cc5b0: 00000000414cfb20 0000000000000001
0x00000000414cc5c0: 00002aaac9905060 00002aaac9a5b1d0
0x00000000414cc5d0: 00002aaac9a5b248 00000000414d04d8
0x00000000414cc5e0: 00000000414cc5f0 00002b720eb1d548
0x00000000414cc5f0: 00000000414cc640 00002b720e7868d8
0x00000000414cc600: 00002aaa00018002 00002aaac9205810
0x00000000414cc610: 00002aaac9205810 00000000414d11c0
0x00000000414cc620: 00002aaac9205810 00002b720ed424e0
0x00000000414cc630: 00002aaac8347dd0 00000000414cfb58
0x00000000414cc640: 00002aaac8881390 00002b720eb204e6
0x00000000414cc650: 00000000414d11c0 000000004c8f0650
Instructions: (pc=0x00002b720e9981d1)
0x00002b720e9981c1: 8b 97 c8 09 00 00 44 89 c7 48 8b 0c fa 49 89 d0
0x00002b720e9981d1: 4c 8b 49 08 49 83 39 00 75 2b 8b 73 08 66 90 8b
Stack: [0x00000000413d2000,0x00000000414d3000], sp=0x00000000414cc460, free space=1001k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.so+0x4ac1d1]
V [libjvm.so+0x4abe96]
V [libjvm.so+0x4a93c1]
V [libjvm.so+0x243b2b]
V [libjvm.so+0x2410a4]
V [libjvm.so+0x1e05f7]
V [libjvm.so+0x248f88]
V [libjvm.so+0x248926]
V [libjvm.so+0x62a7a9]
V [libjvm.so+0x624a51]
V [libjvm.so+0x50628a]
Current CompileTask:
C2:909 chemaxon.marvin.io.formats.smiles.SmilesExport.setupDB(IZ)V (1121 bytes)
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x000000004cb50400 JavaThread "pool-1-thread-8" daemon [_thread_blocked, id=12851, stack(0x00000000419d8000,0x0000000041ad9000)]
0x000000004c947800 JavaThread "pool-1-thread-7" daemon [_thread_in_Java, id=12850, stack(0x00000000418d7000,0x00000000419d8000)]
0x000000004cda5800 JavaThread "pool-1-thread-6" daemon [_thread_in_Java, id=12849, stack(0x00000000417d6000,0x00000000418d7000)]
0x000000004cda5000 JavaThread "pool-1-thread-5" daemon [_thread_in_Java, id=12848, stack(0x00000000416d5000,0x00000000417d6000)]
0x000000004c949400 JavaThread "pool-1-thread-4" daemon [_thread_in_Java, id=12847, stack(0x000000004105c000,0x000000004115d000)]
0x000000004cd79400 JavaThread "pool-1-thread-3" daemon [_thread_in_Java, id=12846, stack(0x0000000040f5b000,0x000000004105c000)]
0x000000004ca22000 JavaThread "pool-1-thread-2" daemon [_thread_blocked, id=12845, stack(0x0000000040396000,0x0000000040497000)]
0x000000004ca21800 JavaThread "pool-1-thread-1" daemon [_thread_blocked, id=12844, stack(0x0000000040186000,0x0000000040287000)]
0x000000004c916800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=12842, stack(0x00000000414d3000,0x00000000415d4000)]
=>0x000000004c914400 JavaThread "CompilerThread1" daemon [_thread_in_native, id=12841, stack(0x00000000413d2000,0x00000000414d3000)]
0x000000004c910800 JavaThread "CompilerThread0" daemon [_thread_in_native, id=12840, stack(0x00000000412d1000,0x00000000413d2000)]
0x000000004c90f400 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=12839, stack(0x00000000411d0000,0x00000000412d1000)]
0x000000004c8e3c00 JavaThread "Finalizer" daemon [_thread_blocked, id=12838, stack(0x0000000040e5a000,0x0000000040f5b000)]
0x000000004c8e2800 JavaThread "Reference Handler" daemon [_thread_blocked, id=12837, stack(0x0000000040d59000,0x0000000040e5a000)]
0x000000004c875c00 JavaThread "main" [_thread_blocked, id=12827, stack(0x0000000040bb0000,0x0000000040cb1000)]
Other Threads:
0x000000004c8dd400 VMThread [stack: 0x0000000040295000,0x0000000040396000] [id=12836]
0x000000004c918400 WatcherThread [stack: 0x00000000415d4000,0x00000000416d5000] [id=12843]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap
PSYoungGen total 47232K, used 36561K [0x00002aaabbb90000, 0x00002aaabfe30000, 0x00002aaabfe30000)
eden space 27712K, 86% used [0x00002aaabbb90000,0x00002aaabd2f4558,0x00002aaabd6a0000)
from space 19520K, 64% used [0x00002aaabd6a0000,0x00002aaabe2f0000,0x00002aaabe9b0000)
to space 20224K, 0% used [0x00002aaabea70000,0x00002aaabea70000,0x00002aaabfe30000)
PSOldGen total 136576K, used 113181K [0x00002aaab3630000, 0x00002aaabbb90000, 0x00002aaabbb90000)
object space 136576K, 82% used [0x00002aaab3630000,0x00002aaaba4b7798,0x00002aaabbb90000)
PSPermGen total 21504K, used 10872K [0x00002aaaae230000, 0x00002aaaaf730000, 0x00002aaab3630000)
object space 21504K, 50% used [0x00002aaaae230000,0x00002aaaaecce1a8,0x00002aaaaf730000)
Dynamic libraries:
40000000-40009000 r-xp 00000000 08:03 21083535 /usr/local/jdk1.6.0_06/bin/java
40108000-4010a000 rwxp 00008000 08:03 21083535 /usr/local/jdk1.6.0_06/bin/java
40186000-40189000 ---p 40186000 00:00 0
40189000-40287000 rwxp 40189000 00:00 0
40295000-40296000 ---p 40295000 00:00 0
40296000-40396000 rwxp 40296000 00:00 0
40396000-40399000 ---p 40396000 00:00 0
40399000-40497000 rwxp 40399000 00:00 0
40bb0000-40bb3000 ---p 40bb0000 00:00 0
40bb3000-40cb1000 rwxp 40bb3000 00:00 0
40d59000-40d5c000 ---p 40d59000 00:00 0
40d5c000-40e5a000 rwxp 40d5c000 00:00 0
40e5a000-40e5d000 ---p 40e5a000 00:00 0
40e5d000-40f5b000 rwxp 40e5d000 00:00 0
40f5b000-40f5e000 ---p 40f5b000 00:00 0
40f5e000-4105c000 rwxp 40f5e000 00:00 0
4105c000-4105f000 ---p 4105c000 00:00 0
4105f000-4115d000 rwxp 4105f000 00:00 0
411d0000-411d3000 ---p 411d0000 00:00 0
411d3000-412d1000 rwxp 411d3000 00:00 0
412d1000-412d4000 ---p 412d1000 00:00 0
412d4000-413d2000 rwxp 412d4000 00:00 0
413d2000-413d5000 ---p 413d2000 00:00 0
413d5000-414d3000 rwxp 413d5000 00:00 0
414d3000-414d6000 ---p 414d3000 00:00 0
414d6000-415d4000 rwxp 414d6000 00:00 0
415d4000-415d5000 ---p 415d4000 00:00 0
415d5000-416d5000 rwxp 415d5000 00:00 0
416d5000-416d8000 ---p 416d5000 00:00 0
416d8000-417d6000 rwxp 416d8000 00:00 0
417d6000-417d9000 ---p 417d6000 00:00 0
417d9000-418d7000 rwxp 417d9000 00:00 0
418d7000-418da000 ---p 418d7000 00:00 0
418da000-419d8000 rwxp 418da000 00:00 0
419d8000-419db000 ---p 419d8000 00:00 0
419db000-41ad9000 rwxp 419db000 00:00 0
41cf4000-41cf5000 ---p 41cf4000 00:00 0
41cf5000-41df5000 rwxp 41cf5000 00:00 0
41df5000-41df6000 ---p 41df5000 00:00 0
41df6000-41ef6000 rwxp 41df6000 00:00 0
41ef6000-41ef7000 ---p 41ef6000 00:00 0
41ef7000-41ff7000 rwxp 41ef7000 00:00 0
41ff7000-41ff8000 ---p 41ff7000 00:00 0
41ff8000-420f8000 rwxp 41ff8000 00:00 0
420f8000-420f9000 ---p 420f8000 00:00 0
420f9000-421f9000 rwxp 420f9000 00:00 0
421f9000-421fa000 ---p 421f9000 00:00 0
421fa000-422fa000 rwxp 421fa000 00:00 0
422fa000-422fb000 ---p 422fa000 00:00 0
422fb000-423fb000 rwxp 422fb000 00:00 0
423fb000-423fc000 ---p 423fb000 00:00 0
423fc000-424fc000 rwxp 423fc000 00:00 0
4c86e000-4d016000 rwxp 4c86e000 00:00 0
3c16c00000-3c16c1a000 r-xp 00000000 08:02 197378 /lib64/ld-2.5.so
3c16e1a000-3c16e1b000 r-xp 0001a000 08:02 197378 /lib64/ld-2.5.so
3c16e1b000-3c16e1c000 rwxp 0001b000 08:02 197378 /lib64/ld-2.5.so
3c17c00000-3c17d4a000 r-xp 00000000 08:02 197380 /lib64/libc-2.5.so
3c17d4a000-3c17f49000 ---p 0014a000 08:02 197380 /lib64/libc-2.5.so
3c17f49000-3c17f4d000 r-xp 00149000 08:02 197380 /lib64/libc-2.5.so
3c17f4d000-3c17f4e000 rwxp 0014d000 08:02 197380 /lib64/libc-2.5.so
3c17f4e000-3c17f53000 rwxp 3c17f4e000 00:00 0
3c18000000-3c18082000 r-xp 00000000 08:02 197390 /lib64/libm-2.5.so
3c18082000-3c18281000 ---p 00082000 08:02 197390 /lib64/libm-2.5.so
3c18281000-3c18282000 r-xp 00081000 08:02 197390 /lib64/libm-2.5.so
3c18282000-3c18283000 rwxp 00082000 08:02 197390 /lib64/libm-2.5.so
3c18400000-3c18402000 r-xp 00000000 08:02 197381 /lib64/libdl-2.5.so
3c18402000-3c18602000 ---p 00002000 08:02 197381 /lib64/libdl-2.5.so
3c18602000-3c18603000 r-xp 00002000 08:02 197381 /lib64/libdl-2.5.so
3c18603000-3c18604000 rwxp 00003000 08:02 197381 /lib64/libdl-2.5.so
3c18800000-3c18815000 r-xp 00000000 08:02 197382 /lib64/libpthread-2.5.so
3c18815000-3c18a14000 ---p 00015000 08:02 197382 /lib64/libpthread-2.5.so
3c18a14000-3c18a15000 r-xp 00014000 08:02 197382 /lib64/libpthread-2.5.so
3c18a15000-3c18a16000 rwxp 00015000 08:02 197382 /lib64/libpthread-2.5.so
3c18a16000-3c18a1a000 rwxp 3c18a16000 00:00 0
3c1b800000-3c1b807000 r-xp 00000000 08:02 197385 /lib64/librt-2.5.so
3c1b807000-3c1ba07000 ---p 00007000 08:02 197385 /lib64/librt-2.5.so
3c1ba07000-3c1ba08000 r-xp 00007000 08:02 197385 /lib64/librt-2.5.so
3c1ba08000-3c1ba09000 rwxp 00008000 08:02 197385 /lib64/librt-2.5.so
3c1e400000-3c1e415000 r-xp 00000000 08:02 197403 /lib64/libnsl-2.5.so
3c1e415000-3c1e614000 ---p 00015000 08:02 197403 /lib64/libnsl-2.5.so
3c1e614000-3c1e615000 r-xp 00014000 08:02 197403 /lib64/libnsl-2.5.so
3c1e615000-3c1e616000 rwxp 00015000 08:02 197403 /lib64/libnsl-2.5.so
3c1e616000-3c1e618000 rwxp 3c1e616000 00:00 0
2aaaaaaab000-2aaaaaad3000 rwxp 2aaaaaaab000 00:00 0
2aaaaaad8000-2aaaaaad9000 r-xp 2aaaaaad8000 00:00 0
2aaaaaad9000-2aaaaaada000 rwxp 2aaaaaad9000 00:00 0
2aaaaaada000-2aaaaaae1000 r-xp 00000000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaaae1000-2aaaaabe2000 ---p 00007000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaabe2000-2aaaaabe4000 rwxp 00008000 08:03 21114746 /usr/local/jdk1.6.0_06/jre/lib/amd64/native_threads/libhpi.so
2aaaaabe4000-2aaaaabe5000 rwxp 2aaaaabe4000 00:00 0
2aaaaabe5000-2aaaaabed000 rwxs 00000000 08:02 850405 /tmp/hsperfdata_root/12826
2aaaaac0f000-2aaaaac19000 r-xp 00000000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaac19000-2aaaaae18000 ---p 0000a000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae18000-2aaaaae19000 r-xp 00009000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae19000-2aaaaae1a000 rwxp 0000a000 08:02 196252 /lib64/libnss_files-2.5.so
2aaaaae1a000-2aaaaae27000 r-xp 00000000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaae27000-2aaaaaf26000 ---p 0000d000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaaf26000-2aaaaaf29000 rwxp 0000c000 08:03 21114739 /usr/local/jdk1.6.0_06/jre/lib/amd64/libverify.so
2aaaaaf29000-2aaaaaf51000 r-xp 00000000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaaaf51000-2aaaab051000 ---p 00028000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaab051000-2aaaab058000 rwxp 00028000 08:03 21114757 /usr/local/jdk1.6.0_06/jre/lib/amd64/libjava.so
2aaaab058000-2aaaab066000 r-xp 00000000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab066000-2aaaab168000 ---p 0000e000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab168000-2aaaab16b000 rwxp 00010000 08:03 21114744 /usr/local/jdk1.6.0_06/jre/lib/amd64/libzip.so
2aaaab16b000-2aaaab75c000 rwxp 2aaaab16b000 00:00 0
2aaaab75c000-2aaaae16c000 rwxp 2aaaab75c000 00:00 0
2aaaae16c000-2aaaae184000 rwxp 2aaaae16c000 00:00 0
2aaaae184000-2aaaae22c000 rwxp 2aaaae184000 00:00 0
2aaaae230000-2aaaaf730000 rwxp 2aaaae230000 00:00 0
2aaaaf730000-2aaab3630000 rwxp 2aaaaf730000 00:00 0
2aaab3630000-2aaabbb90000 rwxp 2aaab3630000 00:00 0
2aaabbb90000-2aaabfe30000 rwxp 2aaabbb90000 00:00 0
2aaabfe30000-2aaabfe3b000 rwxp 2aaabfe30000 00:00 0
2aaabfe3b000-2aaabfe5a000 rwxp 2aaabfe3b000 00:00 0
2aaabfe5a000-2aaabfe9d000 rwxp 2aaabfe5a000 00:00 0
2aaabfe9d000-2aaabfebe000 rwxp 2aaabfe9d000 00:00 0
2aaabfebe000-2aaabff02000 rwxp 2aaabfebe000 00:00 0
2aaabff02000-2aaabff0d000 rwxp 2aaabff02000 00:00 0
2aaabff0d000-2aaabff2c000 rwxp 2aaabff0d000 00:00 0
2aaabff2c000-2aaac00b7000 r-xs 02df0000 08:03 21084096 /usr/local/jdk1.6.0_06/jre/lib/rt.jar
2aaac00b7000-2aaac0212000 rwxp 2aaac00b7000 00:00 0
2aaac0212000-2aaac37eb000 r-xp 00000000 08:02 6708309 /usr/lib/locale/locale-archive
2aaac37eb000-2aaac3879000 r-xs 00f05000 08:03 2619435 /usr/local/ChemAxon/JChem/lib/jchem.jar
2aaac3879000-2aaac387b000 r-xs 00004000 08:03 2619434 /usr/local/ChemAxon/JChem/lib/aloe.jar
2aaac387b000-2aaac3884000 r-xs 0004a000 08:03 2619416 /usr/local/ChemAxon/JChem/lib/backport-util-concurrent.jar
2aaac3884000-2aaac388a000 r-xs 0002e000 08:03 2619414 /usr/local/ChemAxon/JChem/lib/batik-core.jar
2aaac388a000-2aaac389e000 r-xs 00133000 08:03 2619421 /usr/local/ChemAxon/JChem/lib/castor-1.0.1-xml.jar
2aaac389e000-2aaac38ad000 r-xs 001ac000 08:03 2619425 /usr/local/ChemAxon/JChem/lib/xerces.jar
2aaac38ad000-2aaac38ae000 r-xs 0000c000 08:03 2619442 /usr/local/ChemAxon/JChem/lib/commons-logging-1.1.jar
2aaac38ae000-2aaac38af000 r-xs 00015000 08:03 2619429 /usr/local/ChemAxon/JChem/lib/chart.jar
2aaac38af000-2aaac38b7000 r-xs 00068000 08:03 2619426 /usr/local/ChemAxon/JChem/lib/dom4j.jar
2aaac38b7000-2aaac38ba000 r-xs 00014000 08:03 2619415 /usr/local/ChemAxon/JChem/lib/forms-1.1.0.jar
2aaac38ba000-2aaac38bc000 r-xs 00004000 08:03 2619430 /usr/local/ChemAxon/JChem/lib/freehep-export-2.1.1.jar
2aaac38bc000-2aaac38be000 r-xs 0001d000 08:03 2619420 /usr/local/ChemAxon/JChem/lib/freehep-graphics2d-2.1.1.jar
2aaac38be000-2aaac38c3000 r-xs 0002b000 08:03 2619423 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-2.1.1.jar
2aaac38c3000-2aaac38c8000 r-xs 00027000 08:03 2619409 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-emf-2.1.1.jar
2aaac38c8000-2aaac38ca000 r-xs 00011000 08:03 2619424 /usr/local/ChemAxon/JChem/lib/freehep-graphicsio-pdf-2.1.1.jar
2aaac38ca000-2aaac38cd000 r-xs 0000e000 08:03 2619417 /usr/local/ChemAxon/JChem/lib/freehep-io-2.0.2.jar
2aaac38cd000-2aaac38d3000 r-xs 00031000 08:03 2619428 /usr/local/ChemAxon/JChem/lib/freehep-swing-2.0.3.jar
2aaac38d3000-2aaac38d5000 r-xs 0000b000 08:03 2619427 /usr/local/ChemAxon/JChem/lib/freehep-util-2.0.2.jar
2aaac38d5000-2aaac38d6000 r-xs 00004000 08:03 2619412 /usr/local/ChemAxon/JChem/lib/gluegen-rt.jar
2aaac38d6000-2aaac38de000 r-xs 0003f000 08:03 2619439 /usr/local/ChemAxon/JChem/lib/izmcomjni.jar
2aaac38de000-2aaac38e2000 r-xs 00021000 08:03 2619438 /usr/local/ChemAxon/JChem/lib/izmcomtlb.jar
2aaac38e2000-2aaac38e3000 r-xs 00007000 08:03 2619432 /usr/local/ChemAxon/JChem/lib/jextexp.jar
2aaac38e3000-2aaac38ed000 r-xs 00075000 08:03 2619422 /usr/local/ChemAxon/JChem/lib/jh.jar
2aaac38ed000-2aaac38ee000 r-xs 00000000 08:03 2619433 /usr/local/ChemAxon/JChem/lib/jnbtools.jar
2aaac38ee000-2aaac38fa000 r-xs 000f9000 08:03 2619413 /usr/local/ChemAxon/JChem/lib/jogl.jar
2aaac38fa000-2aaac3904000 r-xs 0005e000 08:03 2619410 /usr/local/ChemAxon/JChem/lib/looks-2.1.4.jar
2aaac3904000-2aaac3907000 r-xs 0000e000 08:03 2619411 /usr/local/ChemAxon/JChem/lib/openide-lookup-1.9-patched-1.0.jar
2aaac3907000-2aaac3908000 r-xs 00000000 08:03 2619389 /usr/local/ChemAxon/JChem/plugins/extensions.jar
2aaac3908000-2aaac390f000 r-xs 000a5000 08:03 15385926 /usr/local/mysql-connector-java-5.1.6/mysql-connector-java-5.1.6-bin.jar
2aaac4000000-2aaac6644000 rwxp 2aaac4000000 00:00 0
2aaac6644000-2aaac8000000 ---p 2aaac6644000 00:00 0
2aaac8000000-2aaacace1000 rwxp 2aaac8000000 00:00 0
2aaacace1000-2aaacc000000 ---p 2aaacace1000 00:00 0
2b720e3b4000-2b720e3b5000 rwxp 2b720e3b4000 00:00 0
2b720e3df000-2b720e3e0000 rwxp 2b720e3df000 00:00 0
2b720e3e0000-2b720e3e7000 r-xp 00000000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e3e7000-2b720e4e8000 ---p 00007000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e4e8000-2b720e4ea000 rwxp 00008000 08:03 21114729 /usr/local/jdk1.6.0_06/jre/lib/amd64/jli/libjli.so
2b720e4ea000-2b720e4ec000 rwxp 2b720e4ea000 00:00 0
2b720e4ec000-2b720ebe1000 r-xp 00000000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ebe1000-2b720ece0000 ---p 006f5000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ece0000-2b720ee2a000 rwxp 006f4000 08:03 21114763 /usr/local/jdk1.6.0_06/jre/lib/amd64/server/libjvm.so
2b720ee2a000-2b720ee67000 rwxp 2b720ee2a000 00:00 0
7fff9c6e0000-7fff9c6f6000 rwxp 7fff9c6e0000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
VM Arguments:
jvm_args: -Xmx200M
java_command: chemaxon.marvin.Calculator -S -t myLOGP logp -a 0.15 -k 0.05 DrugLike_usual_2184729Cpd.sdf
Launcher Type: SUN_STANDARD
Environment Variables:
JAVA_HOME=/usr/local/jdk1.6
CLASSPATH=/usr/local/ChemAxon/JChem/bin/../lib/jchem.jar:/usr/local/connector/mysql-connector-java-5.1.6-bin.jar:
PATH=/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/jdk1.6/bin:/usr/local/tomcat6/bin:/usr/local/mysql/bin:/usr/local/mysql/support-files:/usr/sbin:/root/bin
LD_LIBRARY_PATH=/usr/local/jdk1.6.0_06/jre/lib/amd64/server:/usr/local/jdk1.6.0_06/jre/lib/amd64:/usr/local/jdk1.6.0_06/jre/../lib/amd64
SHELL=/bin/bash
Signal Handlers:
SIGSEGV: [libjvm.so+0x6616e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x6616e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x5044d0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x506740], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x5064a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
--------------- S Y S T E M ---------------
OS:Red Hat Enterprise Linux Server release 5.2 (Tikanga)
uname:Linux 2.6.18-92.el5xen #1 SMP Tue Apr 29 13:31:30 EDT 2008 x86_64
libc:glibc 2.5 NPTL 2.5
rlimit: STACK 10240k, CORE 0k, NPROC 63499, NOFILE 1024, AS infinity
load average:4.74 2.78 2.34
CPU:total 8 (4 cores per cpu, 1 threads per core) family 6 model 15 stepping 7, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3
Memory: 4k page, physical 8120320k(17928k free), swap 16386260k(16386060k free)
vm_info: Java HotSpot(TM) 64-Bit Server VM (10.0-b22) for linux-amd64 JRE (1.6.0_06-b02), built on Mar 25 2008 01:03:02 by "java_re" with gcc 3.2.2 (SuSE Linux)
time: Mon Sep 22 11:29:53 2008
elapsed time: 36 seconds