[DAS2] DAS/2 Code Sprint, August 14-18

[Helt,Gregg]

Hmm...  those queries really shouldn't stretch memory requirements too
much -- the mrna objects are already in memory, so for the most part any
extra memory is taken up by the output streaming through the server.
Steve, can you send me the log file for the server when it was hitting
these out-of-memory errors?

	Thanks,
	Gregg

> -----Original Message-----
> From: Chervitz, Steve
> Sent: Thursday, August 10, 2006 1:15 PM
> To: Helt,Gregg; Brian Gilman
> Cc: DAS/2
> Subject: Re: [DAS2] DAS/2 Code Sprint, August 14-18
> 
> The netaffxdas das/2 server is back up now. Turned out to be a memory
> trouble. The server got some whomping queries thrown at it, such as
these:
> 
>
M_musculus_Aug_2005/features?overlaps=chr1/0:194923535;type=mrna;format=
bp
> s
> 
>
H_sapiens_Mar_2006/features?overlaps=chr20/0:62435964;type=mrna;format=b
ps
> 
> Which it could not complete due to out of memory errors. But it could
> handle
> this sizeable query even after the above failed:
> 
>
H_sapiens_May_2004/features?overlaps=chr20/0:62435964;type=refseq;format
=b
> rs
> 
> Eventually, Jetty just decided it had enough and shut down it's
connection,
> shouting: WARN!! Stopping Acceptor ServerSocket
> 
> My fix was to restart the das/2 server giving the java process another
> 200M
> of maximal heap. However, both das/1 and das/2 servers can now
potentially
> claim 89% of physical ram on that box, which could become unhealthy.
> 
> Ed notes that we might want to prevent such big queries in the first
place.
> There is an error code in the das spec for this (HTTP error 413
"Request
> Entity Too Large"). But how do we determine the what's a reasonable
> maximum
> allowable query result? It will depend on the feature density on a
> particular assembly. This could be a good action item for the code
sprint.
> 
> Steve
> 
> 
> 
> > From: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> > Date: Thu, 10 Aug 2006 09:39:12 -0700
> > To: Brian Gilman <gilmanb at pantherinformatics.com>
> > Cc: DAS/2 <das2 at lists.open-bio.org>, "Chervitz, Steve"
> > <Steve_Chervitz at affymetrix.com>
> > Conversation: [DAS2] DAS/2 Code Sprint, August 14-18
> > Subject: RE: [DAS2] DAS/2 Code Sprint, August 14-18
> >
> > Apologies, it looks like we're currently having some problem with
proxy
> > redirection on the Affy DAS/2 server.  Steve, can you check on this?
> > When I request anything but the top level ~/sequence, I'm getting
back
> > HTTP error 502 "Bad Gateway" with the message:
> > "The proxy server received an invalid response from an upstream
server."
> >
> > However, I just tried the biopackages server and it is working,
though
> > response times are slower than usual (unless the response has
already
> > been cached).  Here's a feature query I recently ran, so it will be
> > returned quickly from the server cache:
> >
> >
http://das.biopackages.net/das/genome/human/17/feature?overlaps=chr21/26
> > 027736:26068042;type=SO:mRNA
> >
> > hope that helps,
> > gregg
> >
> >> -----Original Message-----
> >> From: Brian Gilman [mailto:gilmanb at pantherinformatics.com]
> >> Sent: Thursday, August 10, 2006 8:10 AM
> >> To: Helt,Gregg
> >> Cc: DAS/2
> >> Subject: Re: [DAS2] DAS/2 Code Sprint, August 14-18
> >>
> >> Trying to get a features document?
> >>
> >>     Hello Greg et al. I'm desperately trying to get a features
> > document
> >> out of one of the DAS 2 servers and have not been able to do it
yet.
> > Can
> >> someone help me out!?
> >>
> >>                                            Thanks!
> >>
> >>                                               -B
> >>
> >> Helt,Gregg wrote:
> >>
> >>> Affymetrix is hosting a DAS/2 code sprint on August 14-18, to
> > coincide
> >>> with the CSB conference at Stanford.  The sprint will be held at
> > Affy's
> >>> Santa Clara location, which is about a 20 minute drive from the
> > Stanford
> >>> campus.  For those attending CSB, the proximity should make it
easy
> > to
> >>> join in, even if it's just for a morning or afternoon.  We can
> > provide
> >>> transportation to and from CSB if needed.  If you are interested
in
> >>> attending please email me, and specify whether you'll need a
> > workstation
> >>> or will be bringing your own laptop.
> >>>
> >>> This is a code sprint, so the focus will be on DAS/2 client and
> > server
> >>> implementations.  As with previous sprints I'd like to start each
day
> >>> with a teleconference at 9 AM Pacific time.  If you can't be there
> >>> physically but still want to participate, please join in!
> >>>
> >>>            Gregg
> >>>
> >>>
> >>> _______________________________________________
> >>> DAS2 mailing list
> >>> DAS2 at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/das2
> >>>
> >>>
> >>>
> >>>
> >