[InterMine Dev] Fwd: web app restarts

Josh Heimbach josh at intermine.org
Fri May 8 15:57:47 BST 2015

Hi Joe,

While adding web service documentation in intermine 1.3.1, the endpoint 
/service/regions/sequence was retired for the reason that it was 
duplicating information found elsewhere. Much of the codebase has been 
refactored and improved since 1.3, so perhaps using a different servlet 
might solve the memory issue.

Could you send me an example request that you would make to 
/service/regions/sequence along with its parameters? I'll look for a 
suitable alternative web service that returns the same information.


> -------- Forwarded Message --------
> Subject: [InterMine Dev] web app restarts
> Date: Thu, 07 May 2015 17:28:06 -0700
> From: Joe Carlson <jwcarlson at lbl.gov>
> To: dev at intermine.org <dev at intermine.org>, David M. Goodstein 
> <dmgoodstein at lbl.gov>
> Hi Julie and gang
> We have just deployed our latest phytozome build based on intermine 1.4.
> This is our first public release using Hikari.
> Our hopes were that going to hikari would solve some of the problem
> we've been seeing about tomcat restarts. We've traded emails about this
> in the past where we see that we have to restart every couple of hours
> when under load. (We run a 'are you alive' cron job every 3 minuts and
> force a restart if we don't get a response.)
> At the time I think we had attributed it to the postgres connection and
> we looking forward to the hikari pooling. It behaved well in internal
> use, but now that we're public we continue to see the restarts.
> I'm trying to do a little forensics to see what might be causing them.
> I'm seeing "OutOfMemoryError: Java heap space", typically after a call
> to retrieving the genomic sequence of a region
> (service/regions/sequence). I had noticed that you had removed this
> service in 1.4. I restored it since we're making use of it to deliver
> sequence to our main web portal. Did you remove this because you had
> seen it as being problematic?
> At this point, I'm not absolutely sure this is the source of the
> restarts but I'm very suspicious of
> org.intermine.bio.web.export.GenomicRegionSequenceExporter. There is a
> static map of entire chromosomes that is being stored. The substring is
> retrieved by calling substring on elements of this map. This may work
> for smaller mines but we have enough sequence in our database that I
> suspect this is part of our problem.
> Was this web service removed deliberately? Is there something to replace
> it? As I recall, the other sequence retrieval services I found only
> retrieved the sequence for specific features and not chromosome slices.
> Thanks,
> Joe Carlson
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