Re: [Joelib-help] Re: [Joelib-devel] corrected LibGhemical JNI interface

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Hi Gert,

are you using IBM's JDK ?

The interface works only under the IBM JDK under Linux ... SUN's JDK 
seems to have an JNI bug.

Regards, Joerg

>>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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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                          E. Hemingway