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[Joelib-help] Re: [Joelib-devel] corrected LibGhemical JNI interface
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From: Gert S. <Ger...@re...> - 2003-09-10 13:19:04
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> the package path in the LibGhemical JNI interface was corrected.
>
> Now the precompiled shared libraries should work correctly !;-)
>
> Regards, Joerg
I can't seem to get LibGhemical to work properly under Linux. At the
bottom of the mail I will attach the error message I'm constantly
receiving. I tried upgrading from RedHat 7.2 to RedHat 9.0, but to no
avail. Trying to compile the interface-source (in libghemical/src/jni)
didn't help either.
I'm no hero when it comes to C++ and I'm quite stuck in the further
investigation of this error, so hints would be most welcome.
-------------------------Error Message-------------------------------
[gert@leffe linux]$ joetest.sh joelib/test/WekaTest LR N L O
Adding /home/gert/.//dev/src/joelib_test to CLASSPATH.
...(snip)...
21:10:10 [INFO ] joelib.data.JOEElementTable - Using element
table: joelib/data/plain/element.txt
21:10:10 [INFO ] joelib.io.IOTypeHolder - 14
input/output types loaded.
21:10:10 [INFO ] joelib.data.JOEAtomTyper - Using atom
type model: joelib/data/plain/atomtype.txt
21:10:10 [INFO ] joelib.data.JOEAromaticTyper - Using
aromaticity model: joelib/data/plain/aromatic.txt
21:10:13 [INFO ] joelib.io.SimpleReader - ... 96
molecules successful loaded in 2806 ms.
reading file "param_mm/default/atomtypes.txt": found 23 atomtypes.
reading file "param_mm/default/parameters1.txt": found 86 bs-terms.
reading file "param_mm/default/parameters2.txt": found 186 ab-terms.
reading file "param_mm/default/parameters3.txt": found 70 tr-terms.
reading file "param_mm/default/parameters4.txt": found 3 op-terms.
reading file "param_mm/default/parameters5.txt": found 24 lj-datasets.
reading file "param_mm/default/parameters6.txt": found 19 ci-datasets.
An unexpected exception has been detected in native code outside the VM.
Unexpected Signal : 11 occurred at PC=0x0
Function=[Unknown.]
Library=(N/A)
NOTE: We are unable to locate the function name symbol for the error
just occurred. Please refer to release documentation for possible
reason and solutions.
Current Java thread:
at joelib.util.ghemical.GhemicalInterface.addAtom(Native Method)
at
joelib.util.ghemical.GhemicalInterface.createGhemicalModel(GhemicalInterface.java:317)
at
joelib.util.ghemical.GhemicalInterface.doGeometryOptimization(GhemicalInterface.java:371)
at joelib.test.WekaTest.optimizeMolecules(WekaTest.java:273)
at joelib.test.WekaTest.main(WekaTest.java:77)
Dynamic libraries:
08048000-0804e000 r-xp 00000000 08:02 2633593
/usr/java/j2sdk1.4.1_02/bin/java
0804e000-0804f000 rw-p 00005000 08:02 2633593
/usr/java/j2sdk1.4.1_02/bin/java
40000000-40015000 r-xp 00000000 08:02 2534563 /lib/ld-2.3.2.so
40015000-40016000 rw-p 00014000 08:02 2534563 /lib/ld-2.3.2.so
40017000-40020000 r-xp 00000000 08:02 2339520
/usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
40020000-40021000 rw-p 00008000 08:02 2339520
/usr/java/j2sdk1.4.1_02/jre/lib/i386/native_threads/libhpi.so
40022000-40023000 r--p 0092f000 08:02 457938
/usr/lib/locale/locale-archive
40023000-4002e000 r-xp 00000000 08:02 2534598
/lib/libnss_files-2.3.2.so
4002e000-4002f000 rw-p 0000a000 08:02 2534598
/lib/libnss_files-2.3.2.so
4002f000-40031000 r--s 00000000 08:02 180933
/home/gert/dev/src/joelib/lib/cdk-libio.jar
40031000-4003b000 r-xp 00000000 08:02 589445
/lib/tls/libpthread-0.29.so
4003b000-4003c000 rw-p 0000a000 08:02 589445
/lib/tls/libpthread-0.29.so
4003e000-40040000 r-xp 00000000 08:02 2534584 /lib/libdl-2.3.2.so
40040000-40041000 rw-p 00002000 08:02 2534584 /lib/libdl-2.3.2.so
40042000-4035a000 r-xp 00000000 08:02 1521284
/usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
4035a000-4053e000 rw-p 00317000 08:02 1521284
/usr/java/j2sdk1.4.1_02/jre/lib/i386/client/libjvm.so
4054f000-40561000 r-xp 00000000 08:02 2534591 /lib/libnsl-2.3.2.so
40561000-40562000 rw-p 00011000 08:02 2534591 /lib/libnsl-2.3.2.so
40564000-40585000 r-xp 00000000 08:02 589443 /lib/tls/libm-2.3.2.so
40585000-40586000 rw-p 00020000 08:02 589443 /lib/tls/libm-2.3.2.so
40586000-40596000 r-xp 00000000 08:02 2339526
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
40596000-40598000 rw-p 0000f000 08:02 2339526
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libverify.so
40598000-405b9000 r-xp 00000000 08:02 2339527
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
405b9000-405bb000 rw-p 00020000 08:02 2339527
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libjava.so
405bb000-405d0000 r-xp 00000000 08:02 2339529
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
405d0000-405d2000 rw-p 00014000 08:02 2339529
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libzip.so
405d2000-41ca1000 r--s 00000000 08:02 2339771
/usr/java/j2sdk1.4.1_02/jre/lib/rt.jar
41ce4000-41cfb000 r--s 00000000 08:02 2339751
/usr/java/j2sdk1.4.1_02/jre/lib/sunrsasign.jar
41cfb000-41d6c000 r--s 00000000 08:02 2339753
/usr/java/j2sdk1.4.1_02/jre/lib/jsse.jar
41d6c000-41d7f000 r--s 00000000 08:02 2339752
/usr/java/j2sdk1.4.1_02/jre/lib/jce.jar
41fa7000-41fd9000 r--p 008e1000 08:02 457938
/usr/lib/locale/locale-archive
41fd9000-41ff6000 r--s 00000000 08:02 1587110
/usr/java/j2sdk1.4.1_02/jre/lib/ext/sunjce_provider.jar
41ff6000-41ff9000 r--s 00000000 08:02 1587111
/usr/java/j2sdk1.4.1_02/jre/lib/ext/dnsns.jar
41ff9000-42000000 r--s 00000000 08:02 180922
/home/gert/dev/src/joelib/lib/aelfred-1.2.jar
42000000-4212e000 r-xp 00000000 08:02 589441 /lib/tls/libc-2.3.2.so
4212e000-42131000 rw-p 0012e000 08:02 589441 /lib/tls/libc-2.3.2.so
42133000-423ef000 r--s 00000000 08:02 2339769
/usr/java/j2sdk1.4.1_02/jre/lib/charsets.jar
443ef000-443f0000 r--s 00000000 08:02 1832792
/home/gert/dev/src/joelib/lib/database.jar
4c470000-4c670000 r--p 00000000 08:02 457938
/usr/lib/locale/locale-archive
4c870000-4c90f000 r--s 00000000 08:02 1587112
/usr/java/j2sdk1.4.1_02/jre/lib/ext/localedata.jar
4c90f000-4c91d000 r--s 00000000 08:02 1587113
/usr/java/j2sdk1.4.1_02/jre/lib/ext/ldapsec.jar
4c91d000-4c964000 r--s 00000000 08:02 1587618
/usr/java/j2sdk1.4.1_02/jre/lib/ext/vecmath.jar
4c964000-4cbca000 r--s 00000000 08:02 1587619
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dcore.jar
4cbca000-4cd13000 r--s 00000000 08:02 1587620
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3dutils.jar
4cd13000-4ce66000 r--s 00000000 08:02 1587621
/usr/java/j2sdk1.4.1_02/jre/lib/ext/j3daudio.jar
4ce66000-4d31a000 r--s 00000000 08:02 1521290
/usr/java/j2sdk1.4.1_02/lib/tools.jar
4d31a000-4d3ca000 r--s 00000000 08:02 180916
/home/gert/dev/src/joelib/lib/ant.jar
4d3ca000-4d46a000 r--s 00000000 08:02 180924
/home/gert/dev/src/joelib/lib/optional.jar
4d46a000-4d4bc000 r--s 00000000 08:02 180938
/home/gert/dev/src/joelib/lib/ccl.jar
4d4bc000-4d4c1000 r--s 00000000 08:02 180929
/home/gert/dev/src/joelib/lib/cdk-apps.jar
4d4c1000-4d4cb000 r--s 00000000 08:02 180930
/home/gert/dev/src/joelib/lib/cdk-core.jar
4d4cb000-4d50b000 r--s 00000000 08:02 180931
/home/gert/dev/src/joelib/lib/cdk-extra.jar
4d50b000-4d532000 r--s 00000000 08:02 179889
/home/gert/dev/src/joelib/lib/log4j.jar
4d532000-4d550000 r--s 00000000 08:02 180932
/home/gert/dev/src/joelib/lib/cdk-io.jar
4d550000-4d564000 r--s 00000000 08:02 180934
/home/gert/dev/src/joelib/lib/cdk-render.jar
4d564000-4d56f000 r--s 00000000 08:02 180935
/home/gert/dev/src/joelib/lib/cdk-standard.jar
4d56f000-4d59f000 r--s 00000000 08:02 180918
/home/gert/dev/src/joelib/lib/crimson.jar
4d59f000-4d5a8000 r--s 00000000 08:02 180919
/home/gert/dev/src/joelib/lib/jaxp.jar
4d5a8000-4d686000 r--s 00000000 08:02 180939
/home/gert/dev/src/joelib/lib/jalopy-1.0b10.jar
4d686000-4d68a000 r--s 00000000 08:02 180957
/home/gert/dev/src/joelib/lib/jalopy-ant-0.6.1.jar
4d68a000-4d6a0000 r--s 00000000 08:02 180961
/home/gert/dev/src/joelib/lib/jdom-1.0b8.jar
4d6a0000-4d6f6000 r--s 00000000 08:02 180962
/home/gert/dev/src/joelib/lib/log4j-1.2.6.jar
4d6f6000-4d706000 r--s 00000000 08:02 180963
/home/gert/dev/src/joelib/lib/oro-2.0.6.jar
4d706000-4d720000 r--s 00000000 08:02 180958
/home/gert/dev/src/joelib/lib/javancss.jar
4d720000-4d748000 r--s 00000000 08:02 180959
/home/gert/dev/src/joelib/lib/jaxen-core-1.0-fcs.jar
4d748000-4d74f000 r--s 00000000 08:02 180960
/home/gert/dev/src/joelib/lib/jaxp-1.2.jar
4d74f000-4d76f000 r--s 00000000 08:02 180920
/home/gert/dev/src/joelib/lib/jdom.jar
4d76f000-4d786000 r--s 00000000 08:02 180928
/home/gert/dev/src/joelib/lib/JSX1.0.7.4.jar
4d786000-4d79e000 r--s 00000000 08:02 180921
/home/gert/dev/src/joelib/lib/junit-3.2.jar
4d79e000-4d7bd000 r--s 00000000 08:02 180923
/home/gert/dev/src/joelib/lib/mm.mysql-2.0.14-bin.jar
4d7bd000-4d7d6000 r--s 00000000 08:02 180971
/home/gert/dev/src/joelib/lib/mysql.jar
4d7d6000-4d8f6000 r--s 00000000 08:02 180936
/home/gert/dev/src/joelib/lib/plucker-build-1.2.jar
4d8f6000-4d967000 r--s 00000000 08:02 180964
/home/gert/dev/src/joelib/lib/pmd-1.2.jar
4d967000-4d96e000 r--s 00000000 08:02 180965
/home/gert/dev/src/joelib/lib/sax-2.0.1.jar
4d96e000-4d974000 r--s 00000000 08:02 180966
/home/gert/dev/src/joelib/lib/saxpath-1.0-fcs.jar
4d974000-4da3f000 r--s 00000000 08:02 180925
/home/gert/dev/src/joelib/lib/sgt.jar
4da3f000-4ddf8000 r--s 00000000 08:02 180927
/home/gert/dev/src/joelib/lib/weka.jar
4ddf8000-4df80000 r--s 00000000 08:02 180926
/home/gert/dev/src/joelib/lib/xerces.jar
4df80000-4e248000 r-xp 00000000 08:02 2339537
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
4e248000-4e25d000 rw-p 002c7000 08:02 2339537
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libawt.so
4e283000-4e2d6000 r-xp 00000000 08:02 2339536
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
4e2d6000-4e2d7000 rw-p 00052000 08:02 2339536
/usr/java/j2sdk1.4.1_02/jre/lib/i386/libmlib_image.so
4e2f1000-4e2f8000 r-xp 00000000 08:02 768661
/usr/X11R6/lib/libXp.so.6.2
4e2f8000-4e2f9000 rw-p 00006000 08:02 768661
/usr/X11R6/lib/libXp.so.6.2
4e2f9000-4e347000 r-xp 00000000 08:02 768669
/usr/X11R6/lib/libXt.so.6.0
4e347000-4e34b000 rw-p 0004d000 08:02 768669
/usr/X11R6/lib/libXt.so.6.0
4e34b000-4e358000 r-xp 00000000 08:02 768647
/usr/X11R6/lib/libXext.so.6.4
4e358000-4e359000 rw-p 0000c000 08:02 768647
/usr/X11R6/lib/libXext.so.6.4
4e359000-4e35d000 r-xp 00000000 08:02 768671
/usr/X11R6/lib/libXtst.so.6.1
4e35d000-4e35e000 rw-p 00004000 08:02 768671
/usr/X11R6/lib/libXtst.so.6.1
4e35e000-4e43a000 r-xp 00000000 08:02 768637
/usr/X11R6/lib/libX11.so.6.2
4e43a000-4e43d000 rw-p 000db000 08:02 768637
/usr/X11R6/lib/libX11.so.6.2
4e43d000-4e445000 r-xp 00000000 08:02 768635
/usr/X11R6/lib/libSM.so.6.0
4e445000-4e446000 rw-p 00007000 08:02 768635
/usr/X11R6/lib/libSM.so.6.0
4e446000-4e45a000 r-xp 00000000 08:02 768631
/usr/X11R6/lib/libICE.so.6.3
4e45a000-4e45b000 rw-p 00013000 08:02 768631
/usr/X11R6/lib/libICE.so.6.3
4e45d000-4e66e000 r-xp 00000000 08:02 2013189
/home/gert/dev/src/joelib/lib/linux/libghemical.so
4e66e000-4e85c000 rw-p 00210000 08:02 2013189
/home/gert/dev/src/joelib/lib/linux/libghemical.so
51a93000-51aca000 r-xp 00000000 08:02 344420
/usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
51aca000-51ad3000 rw-p 00037000 08:02 344420
/usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
51ad5000-51adc000 r-xp 00000000 08:02 2536295
/lib/libgcc_s-3.2.2-20030225.so.1
51adc000-51add000 rw-p 00007000 08:02 2536295
/lib/libgcc_s-3.2.2-20030225.so.1
Local Time = Wed Sep 10 15:10:13 2003
Elapsed Time = 4
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (1.4.1_02-b06 mixed mode)
#
# An error report file has been saved as hs_err_pid1713.log.
# Please refer to the file for further information.
#
/home/gert/.//bin/joetest.sh: line 72: 1713 Aborted (core
dumped) ${JAVA_HOME}/bin/java -classpath ${CLASSPATH} "$@"
----------------------End Error Message---------------------------
Thank you,
Gert Sclep
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