Re: [Treebase-devel] treebase-error

[William P. <wil...@ya...>]

Okay, I think I figured out the source of the problem -- and it's not related to any settings changes (etc) that happened at the Tomcat / Postgres end.

Turns out that when the original submitter had uploaded his 800,000 character dataset, he didn't have any "character sets" exposed -- i.e. the notation that indicates the beginning and end of each gene. Later, this notation was introduced in subsequent uploads (that then failed). And then when I've been testing smaller uploads (e.g. 80,000 characters) I also used charsets, and it was getting hung up. Just now I uploaded the same 80,000 character dataset but without the charset, and boom -- right away it uploaded fine. 

A charset only has a small effect on the database. For example, my 80,000-character file with a charset only required that three records be created (one in the table charset, another in the table charset_colrange, and a third in the table columnrange). However, for Mesquite (the program that parses all incoming data), it probably means building up a lot of data in memory. My guess, then, is that our version of Mesquite is choking on large files that have charsets. 

The file with charsets is still choking up treebasedev (see here), so feel free to kill the current request that's hung there.

thanks,

bp

On Nov 28, 2011, at 12:28 PM, Mattison Ward wrote:

> Ok - pushed.
> 
> On Mon, Nov 28, 2011 at 11:56 AM, William Piel <wil...@ya...> wrote:
> 
> On Nov 28, 2011, at 11:52 AM, Mattison Ward wrote:
> 
>> Hi Bill and Harry.
>> 
>> A little before 10:55 AM the load went very high on treebase production.  A little before 11:44 the tomcat service stopped responding.  I restarted it.  The tomcat error logs are attached.
>> 
>> -- 
>> Mattison Ward
> 
> Thanks. 
> 
> Maybe it is time to do a push to production so that we can monitor activity with JavaMelody, and seeing as some bugs have been addressed. 
> 
> bp