[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.


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 thinking the exact same thing as you (that this bug is obsolete) and 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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