Bugs item #2978796, was opened at 2010-03-29 19:50 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2978796&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Library Functions Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: https://www.google.com/accounts () Assigned to: Nobody/Anonymous (nobody) Summary: Open Babel Crash over JNI Initial Comment: To whom it may concern My name is Alfredo Alba ( alba.alfr...@gmail.com) Operating on Linux CentOS 5.4 and Fedora core 11, and 12. Have been using Open Babel over the JNI interface for a while and recently I found that when running in a concurrent environment it causes carashes. I have tried SUN JVM 1.6 and IBM JVM 1.6 as well they both present the issue. Essentially I am running a Web App with the LD_PRELOAD=/usr/loca/lib/libopenbabeljni.so option. In this scenario when 2 Smile to InChI conversion calls execute simultaneously Sometimes Open babel produces the following Stack: terminate called after throwing an instance of 'std::ios_base::failure' what(): basic_ios::clear JVMDUMP006I Processing dump event "abort", detail "" - please wait. JVMDUMP032I JVM requested System dump using '/localdata/tomcat55/bin/core.20100328.223821.420.0001.dmp' in response to an event Unhandled exception Type=Segmentation error vmState=0x00020002 J9Generic_Signal_Number=00000004 Signal_Number=0000000b Error_Value=00000000 Signal_Code=00000001 Handler1=00002AAAAACE7310 Handler2=00002AAAAB06F720 InaccessibleAddress=0000000000000010 RDI=000000000000000C RSI=00000000000001B0 RAX=00000000000001B1 RBX=00002AACCC1EA730 RCX=000000000000000C RDX=0000000000000000 R8=00002AACCC000128 R9=0101010101010101 R10=0000000000000006 R11=0000000000200206 R12=00002AACCC000078 R13=00002AACCC000020 R14=0000000000000001 R15=0000000000000880 RIP=0000003F6F872B31 GS=0000 FS=0000 RSP=0000000041C86F30 EFlags=0000000000210202 CS=0033 RBP=0000000000000000 ERR=0000000000000006 TRAPNO=000000000000000E OLDMASK=0000000000000000 CR2=0000000000000010 xmm0 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm1 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm2 00002aacbc083b58 (f: 3154656000.000000, d: 2.318224e-310) xmm3 00002aacbc083ba5 (f: 3154656256.000000, d: 2.318224e-310) xmm4 00002aaaaae4a100 (f: 2867110144.000000, d: 2.317785e-310) xmm5 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm6 0000000042799c10 (f: 1115266048.000000, d: 5.510146e-315) xmm7 000000000a175ac0 (f: 169302720.000000, d: 8.364666e-316) xmm8 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm9 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm10 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm11 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm12 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm13 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm14 0000000000000000 (f: 0.000000, d: 0.000000e+00) xmm15 0000000000000000 (f: 0.000000, d: 0.000000e+00) Module=/lib64/libc.so.6 Module_base_address=0000003F6F800000 Target=2_40_20090519_035743_LHdSMr (Linux 2.6.18-164.11.1.el5) CPU=amd64 (16 logical CPUs) (0xfbb2e1000 RAM) ----------- Stack Backtrace ----------- /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab067d33] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaace7cad] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaace7b5f] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab06ee21] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaace728b] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaace7319] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab06f891] /lib64/libc.so.6 [0x3f6f8302d0] /lib64/libc.so.6 [0x3f6f872b31] /lib64/libc.so.6(__libc_malloc+0x6e) [0x3f6f874bee] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab06488c] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab06568e] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaad319ac] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaad20ac4] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaad206cb] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9vm24.so [0x2aaaaad1fc75] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf7550de] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf716b61] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf716a40] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf717a50] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf72d1c3] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf72d2b0] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf732aa5] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf7654f1] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf765427] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9prt24.so [0x2aaaab06ee21] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9gc24.so [0x2aaaaf76546b] /opt/ibm/ibm-java-x86_64-60/jre/lib/amd64/default/libj9thr24.so [0x2aaaaae4efd6] /lib64/libpthread.so.0 [0x3f70006617] /lib64/libc.so.6(clone+0x6d) [0x3f6f8d3c2d] --------------------------------------- JVMDUMP006I Processing dump event "gpf", detail "" - please wait. JVMDUMP010I System dump written to /localdata/tomcat55/bin/core.20100328.223821.420.0001.dmp JVMDUMP032I JVM requested Snap dump using '/localdata/tomcat55/bin/Snap.20100328.223821.420.0003.trc' in response to an event JVMDUMP010I Snap dump written to /localdata/tomcat55/bin/Snap.20100328.223821.420.0003.trc JVMDUMP032I JVM requested Java dump using '/localdata/tomcat55/bin/javacore.20100328.223821.420.0004.txt' in response to an event JVMDUMP032I JVM requested System dump using '/localdata/tomcat55/bin/core.20100328.223821.420.0002.dmp' in response to an event JVMDUMP010I Java dump written to /localdata/tomcat55/bin/javacore.20100328.223821.420.0004.txt JVMDUMP013I Processed dump event "abort", detail "". The following smiles are instances where concurrent execution causes the issue: [ Sun Mar 28 22:38:20 PDT 2010 ] Attempting to convert: O1CCOCC1 From smi to inchi [ Sun Mar 28 22:38:20 PDT 2010 ] Attempting to convert: OS(=O)O From smi to inchi [ Sun Mar 28 22:38:20 PDT 2010 ] Attempting to convert: C([C@@H](N)CCCCN)(=O)O From smi to inchi ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2978796&group_id=40728 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. 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