[MOBY-dev] XML parsing takes forever

[Edward Kawas]

Now I can confirm that it is slow parsing and not an infinite loop! The XML
file took over an hour on my virtual machine to parse. I will see what I can
do with other SAX parsers for Perl.

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of José María
Fernández González
Sent: October-30-08 12:55 PM
To: Core developer announcements
Subject: Re: [MOBY-dev] XML parsing takes forever

Hi everybody,
	I'm using the XML::LibXML SAX parser for other projects and tasks,
and it can
be really, really slow. You don't realize that until you are parsing a large
file from a pipe, and you see that most of the time the program which is
parsing is CPU (and not I/O) bounded.

	Best Regards,
		José María

Edward Kawas wrote:
> I think that you are right about the parser not going into an infinite
loop.
> For some reason, the SAX parser seems to be really slow (although, I don't
> want to say that until I know for sure).
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau
> Sent: October-30-08 11:56 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] XML parsing takes forever
> 
> Hi,
> 
> thx for helping to investigate the problem!
> 
> I'm pretty sure the parser gets out of it's mess. When you truncate the 
> XML file by removing all but a few ElementContainers, it takes awhile, but

> it actually returns without error.
> 
> And memory consuption doesn't seem to be a problem either, as mostly 'top'

> reveals that the invoked webservice script uses a steady amount of memory.
> 
> thx,
> Kenny
> 
> On Thu, 30 Oct 2008, Edward Kawas wrote:
> 
>> So this one might take some time... from what I can see, our parser goes
>> into an infinite loop (although, I am not certain about that ...).
>>
>> I will play around with this XML file and get back to you.
>>
>> Thanks,
>>
>> Eddie
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau
>> Sent: October-30-08 8:03 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] XML parsing takes forever
>>
>> Hi,
>>
>> here you go,
>>
>> Kenny
>>
>> On Thu, 30 Oct 2008, Edward Kawas wrote:
>>
>>> Hi,
>>>
>>> This is the right list! Could you send me the XML for your second
> service?
>>> Thanks,
>>>
>>> Eddie
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

José María Fernández González
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinformática
Biología Estructural y Biocomputación	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncológicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fernández Almagro, 3	Madrid (Spain)

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