[Gmod-help] Re: [Gmod-gbrowse] Running GBrowse under FastCGI

[Scott Cain]

Hi Dong,

Searching in Chado can be slow.  By default, the Chado adaptor
searches first feature.name (which has an index and searching it
should be plenty fast), then will fall back on a view called
all_feature_names, which is a union of feature.name,
feature.uniquename, synonym.name (and sometimes dbxref.access and
featureprop.value).  This can be quite slow.  I'm working on (and
nearly finished with) a new version of the Chado adaptor that uses
PostgreSQL's full text searching engine on a materialized version of
that all_feature_names view which speeds it up considerably.  I expect
to release that in the next few weeks.

In the mean time, it certainly couldn't hurt looking at

  http://gmod.org/wiki/PostgreSQL_Performance_Tips

for hints on tuning your postgres server.

Scott


On Thu, Jul 22, 2010 at 1:36 AM,  <donghe at caltech.edu> wrote:
> Hi Dave,
>
> I re-installed everything in my developing box, now, FCGI works, however
> the Gbrowse2 still responses slowly, FCGI only saves scripts loading time,
> the searching time is still too long because thousands of scaffolds are
> stored in  Chado. I am trying to reduce the searching time. Do you have
> any suggestions?
>
> Thanks
>
> Dong
>
>
>> Hello all,
>>
>> I don't have FCGI experience (yet, it's on my todo list), and I couldn't
>> find the answer at fastcgi.com..  Dong's question has been out there for a
>> week without a response.
>>
>> Does anyone have an idea?  Dong, have you resolved this problem on your
>> own?
>>
>> Thanks,
>>
>> Dave C.
>>
>> On Wed, Jul 14, 2010 at 10:16 AM, <donghe at caltech.edu> wrote:
>>
>>> Hi Scott,
>>>
>>> I fellow your instruction to install mod_fcgid and fcgi-perl modules in
>>> my
>>> box, and copy that configuration stanza into my main Apache
>>> configuration
>>> file, then restart httpd, the process looks fine, only got this warning
>>> message:
>>>
>>> ---------------------------------------------------------------------
>>> Starting httpd: [Wed Jul 14 10:08:37 2010] [warn] module fcgid_module is
>>> already loaded, skipping
>>>
>>> -------------------------------------------------------------------
>>>
>>> but, GBrowse's performance is same as before, and I did not find any
>>> fcgi
>>> running by using 'ps -ef | grep fcgi'.
>>>
>>> How to know if fastcgi is being using instead of cgi?
>>>
>>> Thanks
>>>
>>> Dong
>>>
>>>
>>>
>>>
>>>
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>>
>>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research