Again: function create_point(integer, integer) does not exist

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Again: function create_point(integer, integer) does not exist

Sofia Robb
Hello,

I know that I have emailed about this before, and I tried what fixed my issue last time, but it does not seem to be helping this time.

I see this error in my postgres logs:
ERROR:  function create_point(integer, integer) does not exist at character 13
HINT:  No function matches the given name and argument types. You might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
        automatic analyze of table "drupal.chado.featureloc"

I log into psql drupal and run this code:
drupal=# SET search_path = frange,chado,pg_catalog;
SET
drupal=# CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);
CREATE INDEX

An index is created, but I still see the errors in my logs. 

Also I am having issues with some pages taking a while to load, for example, the search features page (modified to not browse features and to search with name or unique name or synonyms list). Could this create_point error be the cause of my slowness?

Thanks,
Sofia

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Re: Again: function create_point(integer, integer) does not exist

Stephen Ficklin-2
HI Sofia,

What type of activity are you doing that gives you that create_point error?  

This error usually occurs when features are inserted/updated/deleted that have records in the featureloc table of Chado.    It wouldn't occur on a select (that I'm aware of) so it shouldn't slow your search pages.  Slowness on search pages usually occurs because the inner joins that the database performs are too slow with the the amount of data.   The devel module (https://www.drupal.org/project/devel) has a feature that will print to the page all the SQL queries that are used to generate a page and the time each one takes.  You could use that to pinpoint where the slowness is occurring and then explore a solution.

Stephen


On 2/2/2016 12:56 PM, Sofia Robb wrote:
Hello,

I know that I have emailed about this before, and I tried what fixed my issue last time, but it does not seem to be helping this time.

I see this error in my postgres logs:
ERROR:  function create_point(integer, integer) does not exist at character 13
HINT:  No function matches the given name and argument types. You might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
        automatic analyze of table "drupal.chado.featureloc"

I log into psql drupal and run this code:
drupal=# SET search_path = frange,chado,pg_catalog;
SET
drupal=# CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);
CREATE INDEX

An index is created, but I still see the errors in my logs. 

Also I am having issues with some pages taking a while to load, for example, the search features page (modified to not browse features and to search with name or unique name or synonyms list). Could this create_point error be the cause of my slowness?

Thanks,
Sofia


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Re: Again: function create_point(integer, integer) does not exist

Sofia Robb
Hi Stephen,

Thanks, I will try the devel module.  

I am not doing any of those. I am the only user right now. I am trying to work on my Blast Homology Search View (trying to create links to feature pages from the results) and sometimes the search preview loads, and other times the indicator just spins and spins. I check `top`, and I will have lots of postgres processes and I have these boxrange errors printing to my postgres log. I don't know what is going on.

 19179 postgres  20   0  237532  15660   9444 R  49.8  0.3  18:44.54 postgres
 19184 postgres  20   0  237420  15828   9704 R  49.8  0.3  18:32.88 postgres
 19190 postgres  20   0  237420  16092   9968 R  49.8  0.3  18:22.46 postgres
 19193 postgres  20   0  237420  16364  10244 R  49.8  0.3  18:17.16 postgres
 20568 postgres  20   0 1957168 1.012g  38112 R  49.8 17.9   6:40.45 postgres
 19197 postgres  20   0  238112  17408  10868 R  49.5  0.3  18:16.89 postgres


Thanks,
Sofia


On Tue, Feb 2, 2016 at 4:23 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

What type of activity are you doing that gives you that create_point error?  

This error usually occurs when features are inserted/updated/deleted that have records in the featureloc table of Chado.    It wouldn't occur on a select (that I'm aware of) so it shouldn't slow your search pages.  Slowness on search pages usually occurs because the inner joins that the database performs are too slow with the the amount of data.   The devel module (https://www.drupal.org/project/devel) has a feature that will print to the page all the SQL queries that are used to generate a page and the time each one takes.  You could use that to pinpoint where the slowness is occurring and then explore a solution.

Stephen



On 2/2/2016 12:56 PM, Sofia Robb wrote:
Hello,

I know that I have emailed about this before, and I tried what fixed my issue last time, but it does not seem to be helping this time.

I see this error in my postgres logs:
ERROR:  function create_point(integer, integer) does not exist at character 13
HINT:  No function matches the given name and argument types. You might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
        automatic analyze of table "drupal.chado.featureloc"

I log into psql drupal and run this code:
drupal=# SET search_path = frange,chado,pg_catalog;
SET
drupal=# CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);
CREATE INDEX

An index is created, but I still see the errors in my logs. 

Also I am having issues with some pages taking a while to load, for example, the search features page (modified to not browse features and to search with name or unique name or synonyms list). Could this create_point error be the cause of my slowness?

Thanks,
Sofia


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Re: Again: function create_point(integer, integer) does not exist

Stephen Ficklin-2
Hi Sofia,

Any luck with the devel module to find the bottleneck? 
 

Stephen

On 2/2/2016 3:45 PM, Sofia Robb wrote:
Hi Stephen,

Thanks, I will try the devel module.  

I am not doing any of those. I am the only user right now. I am trying to work on my Blast Homology Search View (trying to create links to feature pages from the results) and sometimes the search preview loads, and other times the indicator just spins and spins. I check `top`, and I will have lots of postgres processes and I have these boxrange errors printing to my postgres log. I don't know what is going on.

 19179 postgres  20   0  237532  15660   9444 R  49.8  0.3  18:44.54 postgres
 19184 postgres  20   0  237420  15828   9704 R  49.8  0.3  18:32.88 postgres
 19190 postgres  20   0  237420  16092   9968 R  49.8  0.3  18:22.46 postgres
 19193 postgres  20   0  237420  16364  10244 R  49.8  0.3  18:17.16 postgres
 20568 postgres  20   0 1957168 1.012g  38112 R  49.8 17.9   6:40.45 postgres
 19197 postgres  20   0  238112  17408  10868 R  49.5  0.3  18:16.89 postgres


Thanks,
Sofia


On Tue, Feb 2, 2016 at 4:23 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

What type of activity are you doing that gives you that create_point error?  

This error usually occurs when features are inserted/updated/deleted that have records in the featureloc table of Chado.    It wouldn't occur on a select (that I'm aware of) so it shouldn't slow your search pages.  Slowness on search pages usually occurs because the inner joins that the database performs are too slow with the the amount of data.   The devel module (https://www.drupal.org/project/devel) has a feature that will print to the page all the SQL queries that are used to generate a page and the time each one takes.  You could use that to pinpoint where the slowness is occurring and then explore a solution.

Stephen



On 2/2/2016 12:56 PM, Sofia Robb wrote:
Hello,

I know that I have emailed about this before, and I tried what fixed my issue last time, but it does not seem to be helping this time.

I see this error in my postgres logs:
ERROR:  function create_point(integer, integer) does not exist at character 13
HINT:  No function matches the given name and argument types. You might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
        automatic analyze of table "drupal.chado.featureloc"

I log into psql drupal and run this code:
drupal=# SET search_path = frange,chado,pg_catalog;
SET
drupal=# CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);
CREATE INDEX

An index is created, but I still see the errors in my logs. 

Also I am having issues with some pages taking a while to load, for example, the search features page (modified to not browse features and to search with name or unique name or synonyms list). Could this create_point error be the cause of my slowness?

Thanks,
Sofia


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Re: Again: function create_point(integer, integer) does not exist

Sofia Robb
Yes, some of the queries are taking a really long time. I am trying to get elasticsearch working. Any idea how to make elastic search see the chado schema? Also Doreen Main's lab shared their homology and domain gene search module with me. It creates a materialized view. It is working really really well. I love it. It is much faster and I have my interpro and GO search capabilities. 

I have not figured out why I am getting the create_point error though. I think in the past on other machines when I installed bioseg it went away, but I am not 100% sure. I need to try it. (I am running postgres 9.2 on CentOS7)

I am attaching a screen shot of the query info that the devel module prints to the screen. These are the two queries that routinely take the most time.

Thanks for checking in on me!
Sofia



On Wed, Feb 10, 2016 at 11:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Sofia,

Any luck with the devel module to find the bottleneck? 
 

Stephen


On 2/2/2016 3:45 PM, Sofia Robb wrote:
Hi Stephen,

Thanks, I will try the devel module.  

I am not doing any of those. I am the only user right now. I am trying to work on my Blast Homology Search View (trying to create links to feature pages from the results) and sometimes the search preview loads, and other times the indicator just spins and spins. I check `top`, and I will have lots of postgres processes and I have these boxrange errors printing to my postgres log. I don't know what is going on.

 19179 postgres  20   0  237532  15660   9444 R  49.8  0.3  18:44.54 postgres
 19184 postgres  20   0  237420  15828   9704 R  49.8  0.3  18:32.88 postgres
 19190 postgres  20   0  237420  16092   9968 R  49.8  0.3  18:22.46 postgres
 19193 postgres  20   0  237420  16364  10244 R  49.8  0.3  18:17.16 postgres
 20568 postgres  20   0 1957168 1.012g  38112 R  49.8 17.9   6:40.45 postgres
 19197 postgres  20   0  238112  17408  10868 R  49.5  0.3  18:16.89 postgres


Thanks,
Sofia


On Tue, Feb 2, 2016 at 4:23 PM, Stephen Ficklin <[hidden email]> wrote:
HI Sofia,

What type of activity are you doing that gives you that create_point error?  

This error usually occurs when features are inserted/updated/deleted that have records in the featureloc table of Chado.    It wouldn't occur on a select (that I'm aware of) so it shouldn't slow your search pages.  Slowness on search pages usually occurs because the inner joins that the database performs are too slow with the the amount of data.   The devel module (https://www.drupal.org/project/devel) has a feature that will print to the page all the SQL queries that are used to generate a page and the time each one takes.  You could use that to pinpoint where the slowness is occurring and then explore a solution.

Stephen



On 2/2/2016 12:56 PM, Sofia Robb wrote:
Hello,

I know that I have emailed about this before, and I tried what fixed my issue last time, but it does not seem to be helping this time.

I see this error in my postgres logs:
ERROR:  function create_point(integer, integer) does not exist at character 13
HINT:  No function matches the given name and argument types. You might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
        automatic analyze of table "drupal.chado.featureloc"

I log into psql drupal and run this code:
drupal=# SET search_path = frange,chado,pg_catalog;
SET
drupal=# CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);
CREATE INDEX

An index is created, but I still see the errors in my logs. 

Also I am having issues with some pages taking a while to load, for example, the search features page (modified to not browse features and to search with name or unique name or synonyms list). Could this create_point error be the cause of my slowness?

Thanks,
Sofia


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