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

Jeff Porter rjporter at lbl.gov
Fri Jul 11 00:35:59 BST 2008

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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the exact same thing as you (that this bug is obsolete) and had tried 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.


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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