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Ticket Resolution Summary Owner Reporter
#541 invalid IZ2640: execd core dump andreas
Description

[Imported from gridengine issuezilla http://gridengine.sunsource.net/issues/show_bug.cgi?id=2640]

        Issue #:      2640             Platform:     PC                  Reporter: andreas (andreas)
       Component:     gridengine          OS:        Linux
     Subcomponent:    execution        Version:      6.1AR_snapshot3_8      CC:
                                                                                   [_] bbarth
                                                                                   [_] Remove selected CCs
        Status:       STARTED          Priority:     P2
      Resolution:                     Issue type:    DEFECT
                                   Target milestone: ---
      Assigned to:    pollinger (pollinger)
      QA Contact:     pollinger
          URL:
       * Summary:     execd core dump
   Status whiteboard:
      Attachments:

     Issue 2640 blocks:
   Votes for issue 2640:


   Opened: Fri Jul 4 07:49:00 -0700 2008 
------------------------


Two core dumps

$ LD_PRELOAD=/opt/sge/lib/lx24-amd64/libcore.so gdb
/opt/sge/bin/lx24-amd64/sge_execd execd.core.7420
GNU gdb Red Hat Linux (6.3.0.0-1.143.el4rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...(no debugging symbols found)
Using host libthread_db library "/lib64/tls/libthread_db.so.1".

Core was generated by `/opt/sge/bin/lx24-amd64/sge_execd'.
Program terminated with signal 11, Segmentation fault.

warning: .dynamic section for "/lib64/libdl.so.2" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libm.so.6" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libpthread.so.0" is not at the
expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libc.so.6" is not at the expected address

warning: .dynamic section for "/lib64/ld-linux-x86-64.so.2" is not at the
expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/libresolv.so.2" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations
Reading symbols from /opt/sge/lib/lx24-amd64/libcore.so...(no debugging symbols
found)...done.
Loaded symbols for /opt/sge/lib/lx24-amd64/libcore.so
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/tls/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libm.so.6
Reading symbols from /lib64/tls/libpthread.so.0...(no debugging symbols
found)...done.
Loaded symbols for /lib64/tls/libpthread.so.0
Reading symbols from /lib64/tls/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...
(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /lib64/libnss_files.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_files.so.2
Reading symbols from /lib64/libnss_dns.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_dns.so.2
Reading symbols from /lib64/libresolv.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libresolv.so.2

#0  0x00000000004d97de in cl_raw_list_lock ()
(gdb) where
#0  0x00000000004d97de in cl_raw_list_lock ()
#1  0x00000000004d4bd9 in cl_commlib_app_message_queue_cleanup ()
#2  0x00000000004d3124 in cl_com_handle_service_thread ()
#3  0x00000039f7806137 in start_thread () from /lib64/tls/libpthread.so.0
#4  0x0000000000000000 in ?? ()

$ LD_PRELOAD=/opt/sge/lib/lx24-amd64/libcore.so gdb
/opt/sge/bin/lx24-amd64/sge_execd execd.core.7451
GNU gdb Red Hat Linux (6.3.0.0-1.143.el4rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...(no debugging symbols found)
Using host libthread_db library "/lib64/tls/libthread_db.so.1".

Core was generated by `/opt/sge/bin/lx24-amd64/sge_execd'.
Program terminated with signal 11, Segmentation fault.

warning: .dynamic section for "/lib64/libdl.so.2" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libm.so.6" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libpthread.so.0" is not at the
expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/tls/libc.so.6" is not at the expected address

warning: .dynamic section for "/lib64/ld-linux-x86-64.so.2" is not at the
expected address

warning: difference appears to be caused by prelink, adjusting expectations

warning: .dynamic section for "/lib64/libresolv.so.2" is not at the expected address

warning: difference appears to be caused by prelink, adjusting expectations
Reading symbols from /opt/sge/lib/lx24-amd64/libcore.so...(no debugging symbols
found)...done.
Loaded symbols for /opt/sge/lib/lx24-amd64/libcore.so
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/tls/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libm.so.6
Reading symbols from /lib64/tls/libpthread.so.0...(no debugging symbols
found)...done.
Loaded symbols for /lib64/tls/libpthread.so.0
Reading symbols from /lib64/tls/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...
(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /lib64/libnss_files.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_files.so.2
Reading symbols from /lib64/libnss_dns.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_dns.so.2
Reading symbols from /lib64/libresolv.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libresolv.so.2

#0  0x00000000004d97de in cl_raw_list_lock ()
(gdb) where
#0  0x00000000004d97de in cl_raw_list_lock ()
#1  0x00000000004d4bd9 in cl_commlib_app_message_queue_cleanup ()
#2  0x00000000004d3124 in cl_com_handle_service_thread ()
#3  0x000000386bd06137 in start_thread () from /lib64/tls/libpthread.so.0
#4  0x0000000000000000 in ?? ()

   ------- Additional comments from andreas Fri Jul 4 08:54:02 -0700 2008 -------
Need to clarify if these stack traces are really authentic.

   ------- Additional comments from andreas Thu Jul 10 09:07:41 -0700 2008 -------
Got a slightly better stack trace:

env LD_PRELOAD=/opt/sge/lib/lx24-amd64/libcore.so gdb
/opt/sge/bin/lx24-amd64/sge_execd /share/sge/execd_spool//i155-301/core.7451
GNU gdb Red Hat Linux (6.3.0.0-1.153.el4_6.2rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...(no debugging symbols found)
Using host libthread_db library "/lib64/tls/libthread_db.so.1".

Core was generated by `/opt/sge/bin/lx24-amd64/sge_execd'.
Program terminated with signal 11, Segmentation fault.
Reading symbols from /opt/sge/lib/lx24-amd64/libcore.so...(no debugging symbols
found)...done.
Loaded symbols for /opt/sge/lib/lx24-amd64/libcore.so
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/tls/libm.so.6...
(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libm.so.6
Reading symbols from /lib64/tls/libpthread.so.0...(no debugging symbols
found)...done.
Loaded symbols for /lib64/tls/libpthread.so.0
Reading symbols from /lib64/tls/libc.so.6...
(no debugging symbols found)...done.
Loaded symbols for /lib64/tls/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /lib64/libnss_files.so.2...
(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_files.so.2
Reading symbols from /lib64/libnss_dns.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_dns.so.2
Reading symbols from /lib64/libresolv.so.2...
(no debugging symbols found)...done.
Loaded symbols for /lib64/libresolv.so.2
#0  0x00000000004d97de in cl_raw_list_lock ()
(gdb) where
#0  0x00000000004d97de in cl_raw_list_lock ()
#1  0x00000000004d4bd9 in cl_commlib_app_message_queue_cleanup ()
#2  0x00000000004d3124 in cl_com_handle_service_thread ()
#3  0x000000386bd06137 in start_thread () from /lib64/tls/libpthread.so.0
#4  0x000000386b0c7113 in clone () from /lib64/tls/libc.so.6
#546 fixed IZ2656: Fix to support JAVA_HOME discovery on alternatives-based systems paulmillar
Description

[Imported from gridengine issuezilla http://gridengine.sunsource.net/issues/show_bug.cgi?id=2656]

        Issue #:      2656             Platform:     All       Reporter: paulmillar (paulmillar)
       Component:     gridengine          OS:        All
     Subcomponent:    build            Version:      current      CC:    None defined
        Status:       NEW              Priority:     P3
      Resolution:                     Issue type:    PATCH
                                   Target milestone: ---
      Assigned to:    andreas (andreas)
      QA Contact:     andreas
          URL:
       * Summary:     Fix to support JAVA_HOME discovery on alternatives-based systems
   Status whiteboard:
      Attachments:
                      Date/filename:                                        Description:                                                                                      Submitted by:
                      Mon Jul 14 16:05:00 -0700 2008: fix-alternatives.diff Proposed patch to fix JAVA_HOME discovery on alternatives- (sym-link-) based systems (text/plain) paulmillar

     Issue 2656 blocks:
   Votes for issue 2656:


   Opened: Mon Jul 14 16:02:00 -0700 2008 
------------------------


Alternatives is a system that allows fine-grain control over which of different
(competing) applications to use for some particular activity.  This is achieved
by casting the command (typically /usr/bin/<cmd>) as a sym-link into a suitably
named file in /etc/alternatives/ directory, which is (itself) a sym-link to the
specific application; for example, /usr/bin/java is a sym-link to
/etc/alternatives/java, which might be a sym-link to
/usr/lib/jvm/java-6-sun/jre/bin/java.

When guessing a value for JAVA_HOME on alternatives-based systems, the current
aimk.site doesn't fare well.  It assumes a JAVA_HOME of /usr, which leads to
interesting build failures (as -I/usr/include/linux becomes appended to the
compilation flags).

The proposed patch fixes this by testing whether the java binary in the user's
path is a sym-link.  If so, following the sym-link to discover the actual
location of the JDK.

Cheers,

Paul.

Index: aimk.site
===================================================================
RCS file: /cvs/gridengine/source/aimk.site,v
retrieving revision 1.66
diff -u -r1.66 aimk.site
--- aimk.site   3 Jul 2008 15:14:14 -0000       1.66
+++ aimk.site   14 Jul 2008 23:01:49 -0000
@@ -157,6 +157,11 @@
 if ( ! $?JAVA_HOME ) then
    set JAVA_BIN = `which \java`

+   # Resolve any symbolic links to find true absolute path to the executable.
+   if ( -l "$JAVA_BIN" ) then
+       set JAVA_BIN = `readlink -f /usr/bin/java`
+   endif
+
    if ( -e "$JAVA_BIN" ) then
       set JAVAV = `$JAVA_BIN -version |& head -1`
       set JAVAV = `expr "$JAVAV" : 'java version "1\.\([0-9]\).*"'`

   ------- Additional comments from paulmillar Mon Jul 14 16:05:15 -0700 2008 -------
Created an attachment (id=179)
Proposed patch to fix JAVA_HOME discovery on alternatives- (sym-link-) based systems
#552 fixed IZ2668: Adding admin and submit hosts: seperated => separated Dave Love <d.love@…> templedf
Description

[Imported from gridengine issuezilla http://gridengine.sunsource.net/issues/show_bug.cgi?id=2668]

        Issue #:      2668             Platform:     All      Reporter: templedf (templedf)
       Component:     gridengine          OS:        All
     Subcomponent:    install          Version:      6.2         CC:    None defined
        Status:       NEW              Priority:     P5
      Resolution:                     Issue type:    DEFECT
                                   Target milestone: ---
      Assigned to:    dom (dom)
      QA Contact:     dom
          URL:
       * Summary:     Adding admin and submit hosts: seperated => separated
   Status whiteboard:
      Attachments:

     Issue 2668 blocks:
   Votes for issue 2668:


   Opened: Mon Jul 21 15:28:00 -0700 2008 
------------------------


In the "Adding admin and submit hosts" section of the installation, "separated"
is misspelled as "seperated".
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