[GE users] critical error: !!!!!!!!!! Nameindex = 137101 not found in element !!!!!!!!!!

j_polasek j-polasek at tamu.edu
Thu Nov 12 15:57:42 GMT 2009


Thanks Lubos!!  That did the trick.  The clone update ran perfectly.  Now to test the environments.

Jeff

On Nov 12, 2009, at 9:04 AM, petrik wrote:

> Ok, then you had in your environment the DYLD_LIBRARY_PATH pointing to 
> the old libraries and it was used when upgrading. Unset this variable 
> before starting the upgrade process and of course revert back to your 
> inst_qmaster.sh file.
> 
> Let us know, if you succeeded.
> 
> Lubos.
> 
> j_polasek wrote:
>> Hi Lubos,
>> 
>> Thanks for the help.  I wasn't clear, neither spooling method will 
>> work, both give the same type error (i don't remember if the element 
>> number is the same or not).
>> 
>> Unfortunately the change didn't help.  I get the following error when 
>> running the modified script.
>> 
>> Initializing spooling database
>> critical error: !!!!!!!!!! Nameindex = 137101 not found in element 
>> !!!!!!!!!!
>> ./util/install_modules/inst_qmaster.sh: line 774: 57403 Abort trap     
>>         $SPOOLINIT $SPOOLING_METHOD $SPOOLING_LIB "$SPOOLING_ARGS" init
>> 
>> Hit <RETURN> to continue >> 
>> 
>> but it lets me continue.  I answer yes to importing the interactive 
>> run info, and then i get the following error
>> 
>> dyld: Symbol not found: _AH_fields
>>  Referenced from: /common/sge6.2/./utilbin/darwin-x86/spooldefaults
>>  Expected in: /common/sge/lib/darwin-x86/libspoolc.dylib
>> 
>> ./util/install_modules/inst_common.sh: line 243: 13716 Trace/BPT trap 
>>         $SGE_UTILBIN/adminrun $ADMINUSER "$@"
>> 
>> Command failed: ./utilbin/darwin-x86/spooldefaults configuration 
>> /tmp/configuration_2009-11-12_08:07:02.17608
>> 
>> Probably a permission problem. Please check file access permissions.
>> Check read/write permission. Check if SGE daemons are running.
>> 
>> Any idea why it is looking in the original sge (6.1 version) directory 
>> rather than the sge6.2 (6.2 version) directory for libspoolc.dylib?
>> 
>> Thanks
>> 
>> Jeff
>> 
>> 
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>> On Nov 11, 2009, at 4:49 PM, petrik wrote:
>> 
>>> Hi Jeff,
>>> I remember seeing this once, but not during an upgrade (during an
>>> installation). I don't know what is causing it but I think following
>>> should solve it for you.
>>> 
>>> Change the InitSpoolingDatabase() in
>>> ./util/install_modules/inst_qmaster.sh so that it doesn't call
>>> ExecuteAsAdmin and instead it calls spoolinit as root and sets relevant
>>> file permissions after that.
>>> e.g.: ExecuteAsAdmin $SPOOLINIT $SPOOLING_METHOD $SPOOLING_LIB
>>> "$SPOOLING_ARGS" init
>>> to
>>> $SPOOLINIT $SPOOLING_METHOD $SPOOLING_LIB "$SPOOLING_ARGS" init
>>> chown -R $ADMINUSER:<admin_user's_group> /common/sge6.2/default/common
>>> chown -R $ADMINUSER:<admin_user's_group>
>>> /common/sge6.2/default/spool/qmaster
>>> 
>>> Let me know if this worked for you.
>>> 
>>> Regards,
>>>  Lubos.
>>> 
>>> PS: My suggestion will not work if root cannot write to
>>> /common/sge6.2/default.
>>> PPS: Just to be clear you are saying that with bdb it works, but not
>>> when you choose classic, right?
>>> 
>>> 
>>> j_polasek wrote:
>>>> Howdy all,
>>>> 
>>>> I am in the process of attempting to update an SGE  6.1u6 OS X 10.5 
>>>> cluster (that I didn't instal)  to 6.2U4.  I am using the "cloned 
>>>> cluster configuration"method as listed in 
>>>> http://wikis.sun.com/display/GridEngine/Upgrading+Sun+Grid+Engine+Software#UpgradingSunGridEngineSoftware-dobackup
>>>> 
>>>> Everything works like it should up until I choose the "classic" 
>>>> spooling method (not BDB).  I get the following error:
>>>> 
>>>> Initializing spooling database
>>>> critical error: !!!!!!!!!! Nameindex = 137101 not found in element 
>>>> !!!!!!!!!!
>>>> ./util/install_modules/inst_common.sh: line 243: 52505 Abort trap 
>>>>             $SGE_UTILBIN/adminrun $ADMINUSER "$@"
>>>> 
>>>> Command failed: ./utilbin/darwin-x86/spoolinit classic libspoolc 
>>>> /common/sge6.2/default/common;/common/sge6.2/default/spool/qmaster init
>>>> 
>>>> Probably a permission problem. Please check file access permissions.
>>>> Check read/write permission. Check if SGE daemons are running.
>>>> 
>>>> The SGE daemons are not running and I let the script reset the 
>>>> permissions earlier in the install script.  
>>>> 
>>>> The admin user is sge and owns the directories and has full rw 
>>>> permissions.
>>>> 
>>>> I have not been able to find anything about this in the archives.
>>>> 
>>>> Anyone have any hints to get me over this hump??
>>>> 
>>>> Thanks
>>>> 
>>>> Jeff
>>>> 
>>>> Jeff Polasek
>>>> systems manager
>>>> Chemical Engineering
>>>> TAMU
>>>> 
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