[GE globus] Re: VDT modifications to Globus 2 SEG

Jeff Porter rjporter at lbl.gov
Fri Jul 11 21:54:17 BST 2008


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So I just did the same and, after a couple of definition changes, also 
had success.  It looks like this script from Graham/Vladimir is 
minimally changed from the one currently on the LeSC web while the VDT 
version differs quite a bit.  I don't know when these two scripts 
diverged but I had been told that the VDT one had been modified to work 
correctly with GT2 - perhaps the LeSC version changed as well but more 
intelligently ;-) .  I think Graham had forwarded me this script earlier 
but I hadn't made the comparison before.

In the end, it looks like Graham/Vladimir version is a good candidate 
for replacing what's currently in the VDT - it removes the ".real" hack 
and does a better test for job-state.   It does need a patch for an OSG 
definition and I'd like to run some tests using some currently working 
production scripts, but after that I'll check with Alain about updating 
the VDT.

thanks,
Jeff


On 7/11/08 7:41 AM, John Sanabria wrote:
> Hi,
>
> I have copied Vladimir's sge.pm file to
>
> -> /opt/vdt/./globus/lib/perl/Globus/GRAM/JobManager/sge.pm
> -> /opt/vdt/./globus/setup/globus/sge.pm
>
> Previous to this change I had this situation. When I submitted jobs 
> using globus-job-submit and check for its status I always got a 
> PENDING message although the job was running.
>
> Now, when I submit a job and check for its status I got the correct 
> answer "ACTIVE".
>
> Thanks Vladimir for your always useful support and Blair let me know 
> how your issue goes.
>
> Regards and happy weekend ;-)
>
> Vladimir Mencl wrote:
>> On 07/11/2008 11:35 AM, Jeff Porter wrote:
>>>
>>> Hi Vladimir,
>>>
>>> Could you or Graham forward me your sge.pm file?    I remember 
>>> thinking the exact same thing as you (that this bug is obsolete) and 
>>> had tried just removing ".real" part. That ended up not working 
>>> correctly.  I think the problem was that the globus job manager's 
>>> stdout/err would overwrite the job's stdout/err (this is from my 
>>> memory - I've not had the chance to look at this today).  I think 
>>> this problem is a GT2-SGE mismatch and doesn't come into play with 
>>> GT4.  So if you're only running GT4, then that additional code is 
>>> irrelevant and I also skip it in the VDT's sge.pm.
>>> I do agree that your "-c" suggestion would be a good additional test.
>>
>> Hi Jeff,
>>
>> Please find attached my current sge.pm.  It's based on the one I got 
>> from Graham Jenkins, and differs only in minor customizations to the 
>> local environment.
>>
>> However, I am only running GT4 (and I expect so does Graham), so the 
>> file may be irrelevant for a discussion on whether a problem with GT2 
>> has been resolved....
>>
>> Cheers,
>> Vladimir
>>
>>>
>>> thanks,
>>> Jeff
>>>
>>>
>>> On 7/10/08 3:19 PM, Vladimir Mencl wrote:
>>>> On 07/11/2008 02:06 AM, Blair Bethwaite wrote:
>>>>> On Thu, Jul 10, 2008 at 11:45 PM, Yoshio Tanaka
>>>>> <yoshio.tanaka at aist.go.jp> wrote:
>>>>>> Which version of the LeSC Globus-SGE adapter is included in VDT?
>>>>>
>>>>> Good point Yoshio, I should have looked at that to begin with! The
>>>>> headers in sge.pm on Komolongma say:
>>>>> # Marko Krznaric
>>>>> # London eScience Centre
>>>>> # June 2003
>>>>> #
>>>>> # Contributions by David McBride
>>>>> # London eScience Centre
>>>>> # Oct 2003
>>>>> #
>>>>> # Contributions by Jeff Porter
>>>>> # Lawrence Berkeley National Laboratory
>>>>> # Sept 2007
>>>>
>>>> Hi,
>>>>
>>>> I'm also running an SGE cluster with GT4, and I don't get this 
>>>> problem. I'm using a sge.pm I got from Graham Jenkins, and it does 
>>>> not have the code fragment which appends ".real" to whatever 
>>>> standard output and standard error are (lines 372-373).
>>>>
>>>> The comment just above these lines refers to a streaming issue in 
>>>> Globus: bug #1288, 
>>>> http://bugzilla.globus.org/bugzilla/show_bug.cgi?id=1288
>>>> The bug is _ancient_ - dates from 2003, and is marked as resolved.
>>>> I would expect it's safe to commented these lines out.
>>>>
>>>> Looking at the code itself, the code does not take into account 
>>>> that stdout and stderr could be /dev/null, and should not change 
>>>> the file name in that case.
>>>>
>>>> In the "if" condition at the end of the line, it does check for a 
>>>> block special file (-b), but it should also check for a character 
>>>> special file with -c:
>>>>
>>>>  print (....) if (! -b $description->stdout() && ! -c 
>>>> $description->stdout() );
>>>>                                               
>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>> and similarly for stderr.
>>>>
>>>>
>>>> I would thus recommend either fixing the code to also check for 
>>>> character special files, or commenting these lines out completely.
>>>>
>>>>
>>>> Cheers,
>>>> Vladimir
>>>>
>>>>
>>
>>
>

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