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

[donghe at caltech.edu]

Hi Scott,

Thank you, I am looking forward to your new release

Dong


> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Sprint
>>>> What will you do first with EVO, the first 4G phone?
>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> Gmod-gbrowse at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> ===> PLEASE KEEP RESPONSES ON THE LIST <===
>>> http://gmod.org/wiki/GMOD_News
>>> http://gmod.org/wiki/Calendar
>>> http://gmod.org/wiki/Help_Desk_Feedback
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>