Dear all, Sending this again since -alas- the problem is still occuring!
Best regards, Stuart. -----Original Message----- From: Rison, Stuart Sent: 22 January 2003 18:06 To: '[EMAIL PROTECTED]'; '[EMAIL PROTECTED]' Subject: Artemis and ACT hugely unstable... Hi, I've been having real problems of the late with both Artemis and ACT; both very soon after having started. Sometimes whilst a sequence is being loaded in, other time soon after. I suspect it have something to do with the fact that my motherboard blew recently and, although it was replaced with a supposedly identical model, my system has not been the same since. Before I go and try and reinstall Linux, I thought I'd check if anybody can come up with an alternative explanation. Attached are copies of the message sent to the terminal by each program (.txt) and a copy of the actual crash log file (.log). System is a Pentium IV; RedHat 8.0; Linux 2.4.18-14; 1Gb RAM As mentioned on the Artemis web pages, I use the blackdown.org jre1.4.1beta. Any help much appreciated. Cheers, Stuart. ---------------------------------------------------------------------------- Dr. Stuart C. G. Rison Department of Pathology and Infectious Diseases Royal Veterinary College Royal College Street London, NW1 0TU United Kingdom. email: [EMAIL PROTECTED] Tel: 020 7468 5054 Fax: 020 7468 5306 "That's bioinformatics... and we don't want to be doing bioinformatics, we want to do real science.", Sydney Brenner, UCL Pfizer Lecture, 8 May 2001 ----------------------------------------------------------------------------
act_crash.log
Description: Binary data
[rison@cmws2349 rison]$ act
[rison@cmws2349 rison]$
An unexpected exception has been detected in native code outside the VM.
Unexpected Signal : 11 occurred at PC=0x400332E0
Function=(null)+0x400332E0
Library=/lib/i686/libpthread.so.0
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.
Dynamic libraries:
08048000-0804d000 r-xp 00000000 03:41 489622 /usr/local/j2re1.4.1/bin/java
0804d000-0804e000 rw-p 00004000 03:41 489622 /usr/local/j2re1.4.1/bin/java
40000000-40012000 r-xp 00000000 03:03 617730 /lib/ld-2.2.93.so
40012000-40013000 rw-p 00012000 03:03 617730 /lib/ld-2.2.93.so
40013000-4001c000 r-xp 00000000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001c000-4001d000 ---p 00009000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001d000-4001e000 rw-p 00009000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001e000-4002d000 r-xp 00000000 03:41 489645
/usr/local/j2re1.4.1/lib/i386/libverify.so
4002d000-4002f000 rw-p 0000e000 03:41 489645
/usr/local/j2re1.4.1/lib/i386/libverify.so
4002f000-4003c000 r-xp 00000000 03:03 959110 /lib/i686/libpthread-0.10.so
4003c000-4003f000 rw-p 0000d000 03:03 959110 /lib/i686/libpthread-0.10.so
40060000-40062000 r-xp 00000000 03:03 617743 /lib/libdl-2.2.93.so
40062000-40063000 rw-p 00001000 03:03 617743 /lib/libdl-2.2.93.so
40063000-404c7000 r-xp 00000000 03:41 1174102
/usr/local/j2re1.4.1/lib/i386/client/libjvm.so
404c7000-404e4000 rw-p 00463000 03:41 1174102
/usr/local/j2re1.4.1/lib/i386/client/libjvm.so
404f4000-40506000 r-xp 00000000 03:03 617747 /lib/libnsl-2.2.93.so
40506000-40507000 rw-p 00012000 03:03 617747 /lib/libnsl-2.2.93.so
40509000-4052a000 r-xp 00000000 03:03 959108 /lib/i686/libm-2.2.93.so
4052a000-4052b000 rw-p 00021000 03:03 959108 /lib/i686/libm-2.2.93.so
4052b000-4054a000 r-xp 00000000 03:41 489646
/usr/local/j2re1.4.1/lib/i386/libjava.so
4054a000-4054c000 rw-p 0001e000 03:41 489646
/usr/local/j2re1.4.1/lib/i386/libjava.so
4054c000-40561000 r-xp 00000000 03:41 489648
/usr/local/j2re1.4.1/lib/i386/libzip.so
40561000-40564000 rw-p 00014000 03:41 489648
/usr/local/j2re1.4.1/lib/i386/libzip.so
40564000-41c31000 r--s 00000000 03:41 489689 /usr/local/j2re1.4.1/lib/rt.jar
41c74000-41c8b000 r--s 00000000 03:41 489669
/usr/local/j2re1.4.1/lib/sunrsasign.jar
41c8b000-41cfc000 r--s 00000000 03:41 489671 /usr/local/j2re1.4.1/lib/jsse.jar
41cfc000-41d0f000 r--s 00000000 03:41 489670 /usr/local/j2re1.4.1/lib/jce.jar
41d0f000-41fcb000 r--s 00000000 03:41 489687 /usr/local/j2re1.4.1/lib/charsets.jar
41ff3000-41ffc000 r-xp 00000000 03:03 617763 /lib/libnss_files-2.2.93.so
41ffc000-41ffd000 rw-p 00008000 03:03 617763 /lib/libnss_files-2.2.93.so
41ffd000-42000000 r--s 00000000 03:41 1597589 /usr/local/j2re1.4.1/lib/ext/dnsns.jar
42000000-42126000 r-xp 00000000 03:03 959106 /lib/i686/libc-2.2.93.so
42126000-4212b000 rw-p 00126000 03:03 959106 /lib/i686/libc-2.2.93.so
4c3b3000-4c572000 r--p 00000000 03:41 195465 /usr/lib/locale/locale-archive
4c776000-4c793000 r--s 00000000 03:41 1597588
/usr/local/j2re1.4.1/lib/ext/sunjce_provider.jar
4c793000-4c832000 r--s 00000000 03:41 1597590
/usr/local/j2re1.4.1/lib/ext/localedata.jar
4c832000-4c840000 r--s 00000000 03:41 1597591
/usr/local/j2re1.4.1/lib/ext/ldapsec.jar
4c840000-4ca82000 r-xp 00000000 03:41 489656
/usr/local/j2re1.4.1/lib/i386/libawt.so
4ca82000-4ca97000 rw-p 00241000 03:41 489656
/usr/local/j2re1.4.1/lib/i386/libawt.so
4cabc000-4cb2e000 r-xp 00000000 03:41 489655
/usr/local/j2re1.4.1/lib/i386/libmlib_image.so
4cb2e000-4cb2f000 rw-p 00071000 03:41 489655
/usr/local/j2re1.4.1/lib/i386/libmlib_image.so
4cb2f000-4cb35000 r--s 00000000 03:41 1531264 /usr/lib/gconv/gconv-modules.cache
4cb35000-4cb36000 r-xp 00000000 03:41 423510
/usr/X11R6/lib/X11/locale/common/xlcUTF8Load.so.2
4cb36000-4cb37000 rw-p 00000000 03:41 423510
/usr/X11R6/lib/X11/locale/common/xlcUTF8Load.so.2
4cb37000-4cb40000 r-xp 00000000 03:41 423513
/usr/X11R6/lib/X11/locale/common/xomGeneric.so.2
4cb40000-4cb41000 rw-p 00008000 03:41 423513
/usr/X11R6/lib/X11/locale/common/xomGeneric.so.2
4cb46000-4cb4b000 rw-s 00000000 00:04 1245191 /SYSV00000000 (deleted)
4cb4b000-4cb52000 r-xp 00000000 03:41 684149 /usr/X11R6/lib/libXp.so.6.2
4cb52000-4cb53000 rw-p 00006000 03:41 684149 /usr/X11R6/lib/libXp.so.6.2
4cb53000-4cba1000 r-xp 00000000 03:41 684157 /usr/X11R6/lib/libXt.so.6.0
4cba1000-4cba5000 rw-p 0004d000 03:41 684157 /usr/X11R6/lib/libXt.so.6.0
4cba5000-4cbad000 r-xp 00000000 03:41 684127 /usr/X11R6/lib/libSM.so.6.0
4cbad000-4cbae000 rw-p 00007000 03:41 684127 /usr/X11R6/lib/libSM.so.6.0
4cbae000-4cbc2000 r-xp 00000000 03:41 684123 /usr/X11R6/lib/libICE.so.6.3
4cbc2000-4cbc3000 rw-p 00013000 03:41 684123 /usr/X11R6/lib/libICE.so.6.3
4cbc5000-4cbd2000 r-xp 00000000 03:41 684137 /usr/X11R6/lib/libXext.so.6.4
4cbd2000-4cbd3000 rw-p 0000c000 03:41 684137 /usr/X11R6/lib/libXext.so.6.4
4cbd3000-4cbd7000 r-xp 00000000 03:41 684159 /usr/X11R6/lib/libXtst.so.6.1
4cbd7000-4cbd8000 rw-p 00004000 03:41 684159 /usr/X11R6/lib/libXtst.so.6.1
4cbd8000-4ccb3000 r-xp 00000000 03:41 684129 /usr/X11R6/lib/libX11.so.6.2
4ccb3000-4ccb6000 rw-p 000da000 03:41 684129 /usr/X11R6/lib/libX11.so.6.2
4ccb6000-4cd76000 r-xp 00000000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4cd76000-4cd77000 ---p 000c0000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4cd77000-4cd9e000 rw-p 000c0000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4ce1f000-4ce3b000 r-xp 00000000 03:41 423508
/usr/X11R6/lib/X11/locale/common/ximcp.so.2
4ce3b000-4ce3d000 rw-p 0001b000 03:41 423508
/usr/X11R6/lib/X11/locale/common/ximcp.so.2
4d041000-4d05e000 r--s 00000000 00:04 1409030 /SYSV00000000 (deleted)
4d1c4000-4d1c8000 rw-s 00000000 00:04 1343496 /SYSV00000000 (deleted)
4d1c8000-4d1cc000 rw-s 00000000 00:04 1376265 /SYSV00000000 (deleted)
Local Time = Wed Jan 22 17:53:02 2003
Elapsed Time = 113
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (Blackdown-1.4.1-beta mixed mode)
#
# An error report file has been saved as /tmp/hs_err_pid1576.log.
# Please refer to the file for further information.
#
art_crash.log
Description: Binary data
[rison@cmws2349 rison]$ reading options from "options"
warning: could not auto save to: #M_tuberculosis_R5_007.tab#
warning: could not auto save to: #M_tuberculosis_R5.nt#
An unexpected exception has been detected in native code outside the VM.
Unexpected Signal : 11 occurred at PC=0x400332E0
Function=(null)+0x400332E0
Library=/lib/i686/libpthread.so.0
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.
Dynamic libraries:
08048000-0804d000 r-xp 00000000 03:41 489622 /usr/local/j2re1.4.1/bin/java
0804d000-0804e000 rw-p 00004000 03:41 489622 /usr/local/j2re1.4.1/bin/java
40000000-40012000 r-xp 00000000 03:03 617730 /lib/ld-2.2.93.so
40012000-40013000 rw-p 00012000 03:03 617730 /lib/ld-2.2.93.so
40013000-4001c000 r-xp 00000000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001c000-4001d000 ---p 00009000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001d000-4001e000 rw-p 00009000 03:41 489639
/usr/local/j2re1.4.1/lib/i386/native_threads/libhpi.so
4001e000-4002d000 r-xp 00000000 03:41 489645
/usr/local/j2re1.4.1/lib/i386/libverify.so
4002d000-4002f000 rw-p 0000e000 03:41 489645
/usr/local/j2re1.4.1/lib/i386/libverify.so
4002f000-4003c000 r-xp 00000000 03:03 959110 /lib/i686/libpthread-0.10.so
4003c000-4003f000 rw-p 0000d000 03:03 959110 /lib/i686/libpthread-0.10.so
40060000-40062000 r-xp 00000000 03:03 617743 /lib/libdl-2.2.93.so
40062000-40063000 rw-p 00001000 03:03 617743 /lib/libdl-2.2.93.so
40063000-404c7000 r-xp 00000000 03:41 1174102
/usr/local/j2re1.4.1/lib/i386/client/libjvm.so
404c7000-404e4000 rw-p 00463000 03:41 1174102
/usr/local/j2re1.4.1/lib/i386/client/libjvm.so
404f4000-40506000 r-xp 00000000 03:03 617747 /lib/libnsl-2.2.93.so
40506000-40507000 rw-p 00012000 03:03 617747 /lib/libnsl-2.2.93.so
40509000-4052a000 r-xp 00000000 03:03 959108 /lib/i686/libm-2.2.93.so
4052a000-4052b000 rw-p 00021000 03:03 959108 /lib/i686/libm-2.2.93.so
4052b000-4054a000 r-xp 00000000 03:41 489646
/usr/local/j2re1.4.1/lib/i386/libjava.so
4054a000-4054c000 rw-p 0001e000 03:41 489646
/usr/local/j2re1.4.1/lib/i386/libjava.so
4054c000-40561000 r-xp 00000000 03:41 489648
/usr/local/j2re1.4.1/lib/i386/libzip.so
40561000-40564000 rw-p 00014000 03:41 489648
/usr/local/j2re1.4.1/lib/i386/libzip.so
40564000-41c31000 r--s 00000000 03:41 489689 /usr/local/j2re1.4.1/lib/rt.jar
41c74000-41c8b000 r--s 00000000 03:41 489669
/usr/local/j2re1.4.1/lib/sunrsasign.jar
41c8b000-41cfc000 r--s 00000000 03:41 489671 /usr/local/j2re1.4.1/lib/jsse.jar
41cfc000-41d0f000 r--s 00000000 03:41 489670 /usr/local/j2re1.4.1/lib/jce.jar
41d0f000-41fcb000 r--s 00000000 03:41 489687 /usr/local/j2re1.4.1/lib/charsets.jar
41ff3000-41ffc000 r-xp 00000000 03:03 617763 /lib/libnss_files-2.2.93.so
41ffc000-41ffd000 rw-p 00008000 03:03 617763 /lib/libnss_files-2.2.93.so
41ffd000-42000000 r--s 00000000 03:41 1597589 /usr/local/j2re1.4.1/lib/ext/dnsns.jar
42000000-42126000 r-xp 00000000 03:03 959106 /lib/i686/libc-2.2.93.so
42126000-4212b000 rw-p 00126000 03:03 959106 /lib/i686/libc-2.2.93.so
4c3b3000-4c572000 r--p 00000000 03:41 195465 /usr/lib/locale/locale-archive
4c776000-4c793000 r--s 00000000 03:41 1597588
/usr/local/j2re1.4.1/lib/ext/sunjce_provider.jar
4c793000-4c832000 r--s 00000000 03:41 1597590
/usr/local/j2re1.4.1/lib/ext/localedata.jar
4c832000-4c840000 r--s 00000000 03:41 1597591
/usr/local/j2re1.4.1/lib/ext/ldapsec.jar
4c840000-4ca82000 r-xp 00000000 03:41 489656
/usr/local/j2re1.4.1/lib/i386/libawt.so
4ca82000-4ca97000 rw-p 00241000 03:41 489656
/usr/local/j2re1.4.1/lib/i386/libawt.so
4cabc000-4cb2e000 r-xp 00000000 03:41 489655
/usr/local/j2re1.4.1/lib/i386/libmlib_image.so
4cb2e000-4cb2f000 rw-p 00071000 03:41 489655
/usr/local/j2re1.4.1/lib/i386/libmlib_image.so
4cb2f000-4cb35000 r--s 00000000 03:41 1531264 /usr/lib/gconv/gconv-modules.cache
4cb35000-4cb36000 r-xp 00000000 03:41 423510
/usr/X11R6/lib/X11/locale/common/xlcUTF8Load.so.2
4cb36000-4cb37000 rw-p 00000000 03:41 423510
/usr/X11R6/lib/X11/locale/common/xlcUTF8Load.so.2
4cb37000-4cb40000 r-xp 00000000 03:41 423513
/usr/X11R6/lib/X11/locale/common/xomGeneric.so.2
4cb40000-4cb41000 rw-p 00008000 03:41 423513
/usr/X11R6/lib/X11/locale/common/xomGeneric.so.2
4cb46000-4cb4b000 rw-s 00000000 00:04 983047 /SYSV00000000 (deleted)
4cb4b000-4cb52000 r-xp 00000000 03:41 684149 /usr/X11R6/lib/libXp.so.6.2
4cb52000-4cb53000 rw-p 00006000 03:41 684149 /usr/X11R6/lib/libXp.so.6.2
4cb53000-4cba1000 r-xp 00000000 03:41 684157 /usr/X11R6/lib/libXt.so.6.0
4cba1000-4cba5000 rw-p 0004d000 03:41 684157 /usr/X11R6/lib/libXt.so.6.0
4cba5000-4cbad000 r-xp 00000000 03:41 684127 /usr/X11R6/lib/libSM.so.6.0
4cbad000-4cbae000 rw-p 00007000 03:41 684127 /usr/X11R6/lib/libSM.so.6.0
4cbae000-4cbc2000 r-xp 00000000 03:41 684123 /usr/X11R6/lib/libICE.so.6.3
4cbc2000-4cbc3000 rw-p 00013000 03:41 684123 /usr/X11R6/lib/libICE.so.6.3
4cbc5000-4cbd2000 r-xp 00000000 03:41 684137 /usr/X11R6/lib/libXext.so.6.4
4cbd2000-4cbd3000 rw-p 0000c000 03:41 684137 /usr/X11R6/lib/libXext.so.6.4
4cbd3000-4cbd7000 r-xp 00000000 03:41 684159 /usr/X11R6/lib/libXtst.so.6.1
4cbd7000-4cbd8000 rw-p 00004000 03:41 684159 /usr/X11R6/lib/libXtst.so.6.1
4cbd8000-4ccb3000 r-xp 00000000 03:41 684129 /usr/X11R6/lib/libX11.so.6.2
4ccb3000-4ccb6000 rw-p 000da000 03:41 684129 /usr/X11R6/lib/libX11.so.6.2
4ccb6000-4cd76000 r-xp 00000000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4cd76000-4cd77000 ---p 000c0000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4cd77000-4cd9e000 rw-p 000c0000 03:41 489658
/usr/local/j2re1.4.1/lib/i386/libfontmanager.so
4ce1f000-4ce3b000 r-xp 00000000 03:41 423508
/usr/X11R6/lib/X11/locale/common/ximcp.so.2
4ce3b000-4ce3d000 rw-p 0001b000 03:41 423508
/usr/X11R6/lib/X11/locale/common/ximcp.so.2
4d143000-4d147000 rw-s 00000000 00:04 1081350 /SYSV00000000 (deleted)
4d147000-4d14b000 rw-s 00000000 00:04 1114120 /SYSV00000000 (deleted)
4d14b000-4d168000 r--s 00000000 00:04 1146889 /SYSV00000000 (deleted)
Local Time = Wed Jan 22 17:49:43 2003
Elapsed Time = 61
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (Blackdown-1.4.1-beta mixed mode)
#
# An error report file has been saved as /tmp/hs_err_pid1517.log.
# Please refer to the file for further information.
#
