Re: [sqlite] How to optimize a multi-condition query

[Kees Nuyt]

On Mon, 18 Oct 2010 15:07:35 +0200, Hilmar Berger
 wrote:

>  Hi,
>
>thanks to everybody that answered. I tried your suggestions but there 
>was no measurable improvement. Possibly this is the best what I can get 
>out of Sqlite.
>However, I tried a similar query on a larger table using both SQlite and 
>Postgresql (same machine, same table structure + indices, same data).
>Postrgresql took 25secs for this query while it took more than 1 hour 
>with SQlite. Obviously there is room for improvement. If I manage to 
>find out what makes the difference I will post it here.

Did you already try to run ANALYZE; on the fully populated
database? It gathers statistics about indexes and those are
used by the optimizer to choose a query plan.
It might not help in your case, but it doesn't hurt to try.

>Thanks again and best regards,
>Hilmar
-- 
  (  Kees Nuyt
  )
c[_]
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Re: [sqlite] How to optimize a multi-condition query

[Hilmar Berger]

  Hi,

thanks to everybody that answered. I tried your suggestions but there 
was no measurable improvement. Possibly this is the best what I can get 
out of Sqlite.
However, I tried a similar query on a larger table using both SQlite and 
Postgresql (same machine, same table structure + indices, same data).
Postrgresql took 25secs for this query while it took more than 1 hour 
with SQlite. Obviously there is room for improvement. If I manage to 
find out what makes the difference I will post it here.

Thanks again and best regards,
Hilmar


El 10/15/2010 4:44 PM, Igor Tandetnik escribió:
> Hilmar Berger  wrote:
>> Indexes has been created for all fields in A and B (e.g. create index
>> name on A(chr, start, stop, strand));
>>
>> The query is as follows:
>>
>> select * from
>>  a, b
>>  where a.chr = b.chr and a.strand = b.strand and a.start<= b.start
>> and  a.stop>= b.stop  and b.start<= a.stop and a.start<= b.stop ;
> Drop those indexes you created, change the query to
>
> select * from a, b
>   where a.chr = b.chr and a.strand = b.strand
>   and b.start between a.start and a.stop
>   and b.stop<= a.stop;
>
> and create a single index on b(chr, strand, start) or b(chr, strand, start, 
> stop), listing fields in this exact order  (adding stop to the index may or 
> may not result in marginal performance improvement - experiment).
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Re: [sqlite] How to optimize a multi-condition query

[Igor Tandetnik]

Hilmar Berger  wrote:
> I used EXPLAIN QUERY PLAN on the query and it looks like it does not use
> any index on b at all, only if I use hardcoded conditions like b > 0.
> 
> It appears that the real problem is that SQlite does not use indices for
> both tables

For your problem, there's no way to use indices on both tables. An index is 
only helpful if it allows one to look at only some, but not all, rows in the 
table. In your query, one has to look at all records in A and find suitable 
matching records in B, or else look at all records in B and find matching 
records in A. You have to look at all records in at least one table, there's no 
way around that.
-- 
Igor Tandetnik

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Re: [sqlite] How to optimize a multi-condition query

[Igor Tandetnik]

Hilmar Berger  wrote:
> Indexes has been created for all fields in A and B (e.g. create index
> name on A(chr, start, stop, strand));
> 
> The query is as follows:
> 
> select * from
> a, b
> where a.chr = b.chr and a.strand = b.strand and a.start <= b.start
> and  a.stop >= b.stop  and b.start <= a.stop and a.start <= b.stop ;

Drop those indexes you created, change the query to

select * from a, b
 where a.chr = b.chr and a.strand = b.strand
 and b.start between a.start and a.stop
 and b.stop <= a.stop;

and create a single index on b(chr, strand, start) or b(chr, strand, start, 
stop), listing fields in this exact order  (adding stop to the index may or may 
not result in marginal performance improvement - experiment).
-- 
Igor Tandetnik

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Re: [sqlite] How to optimize a multi-condition query

[Igor Tandetnik]

Black, Michael (IS)  wrote:
> I love simple examples like this can help people with understanding 
> things...so I tried this which I thought would do what Hilmar
> wants...but alaswhat concept am I missing? 
> 
> SQLite version 3.7.2
> sqlite> create table c(achr char,bchr char);
> sqlite> create index c_chr on c(achr,bchr);
> sqlite> explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
> 
> Why no use of the index in this case?

Try this:

select t.achr, t.bchr
from (select distinct achr from c) as alphabet
join c as t on (t.achr=alphabet.achr and t.bchr=alphabet.achr);

Under some circumstances - achr only has a small number of distinct values, the 
number of rows where achr=bchr is a small percentage of all rows in the table - 
this may be significantly faster than full table scan.
-- 
Igor Tandetnik

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Re: [sqlite] How to optimize a multi-condition query

[Pavel Ivanov]

> sqlite> create table c(achr char,bchr char);
> sqlite> create index c_chr on c(achr,bchr);
> sqlite> explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
>
> Why no use of the index in this case?

How do you think it should be used here? It's not that rows with the
same values of achr and bchr stored together in the index - they are
spread all over the place. And thus using index it will have to make
full scan of it which is less efficient than full scan of the table.
Or should I say it's more efficient than full scan of the table in
very rare situations, so that I'm not sure if SQLite implements it at
all.


Pavel

On Fri, Oct 15, 2010 at 8:34 AM, Black, Michael (IS)
<michael.bla...@ngc.com> wrote:
> I love simple examples like this can help people with understanding 
> things...so I tried this which I thought would do what Hilmar wants...but 
> alaswhat concept am I missing?
>
> SQLite version 3.7.2
> sqlite> create table c(achr char,bchr char);
> sqlite> create index c_chr on c(achr,bchr);
> sqlite> explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
>
> Why no use of the index in this case?
>
> Michael D. Black
> Senior Scientist
> Advanced Analytics Directorate
> Northrop Grumman Information Systems
>
>
> 
>
> From: sqlite-users-boun...@sqlite.org on behalf of Simon Davies
> Sent: Fri 10/15/2010 5:16 AM
> To: General Discussion of SQLite Database
> Subject: EXTERNAL:Re: [sqlite] How to optimize a multi-condition query
>
>
>
> On 15 October 2010 10:43, Hilmar Berger <hilmar.ber...@integromics.com> wrote:
>>  Thanks !
>>
>> However, I tried what you suggested and there was no change.
>>
>> I used EXPLAIN QUERY PLAN on the query and it looks like it does not use
>> any index on b at all, only if I use hardcoded conditions like b > 0.
>>
>> It appears that the real problem is that SQlite does not use indices for
>> both tables, e.g.:
>>
>> CREATE INDEX a_chr on a(chr)
>> CREATE INDEX b_chr on b(chr)
>>
>> explain query plan
>>   select a.chr, b.chr
>>     from b, a
>>     where b.chr = a.chr;
>>
>> Output:
>> 0    0    TABLE b
>> 1    1    TABLE a WITH INDEX a_chr
>
> There is no benefit in using an index on b for this query.
>
> Change the query to:
>  select a.chr, b.chr
>    from b, a
>    where b.chr = a.chr and b.chr>0;
>
> and the query plan becomes:
> 0|0|TABLE b WITH INDEX b_chr
> 1|1|TABLE a WITH INDEX a_chr
>
>>
>>
>> There is an example on how to use multiple indices on the same table
>> here: http://www.sqlite.org/cvstrac/wiki?p=PerformanceTuning
>> However, I'm not sure how to extend this to joined tables.
>>
>> Thanks !
>>
>> Best regards,
>> Hilmar
>>
>
> Regarding
>
> "select * from
>    a, b
>    where a.chr = b.chr and a.strand = b.strand and
> a.start <= b.start and  a.stop >= b.stop  and
> b.start <= a.stop and a.start <= b.stop ;"
>
> surely the last 2 conditions are redundant assuming a.start<a.stop,
> and b.start
>
> Regards,
> Simon
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>
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Re: [sqlite] How to optimize a multi-condition query

[Martin.Engelschalk]

  Hi,

the condition in your query

select achr,bchr from c where achr=bchr

involves 2 columns of the table. In this case, an index is useless.
If you do

select achr,bchr from c where achr='foo'

then the index will be used.

Martin



Am 15.10.2010 15:09, schrieb Black, Michael (IS):
> Ok then... I added 67,600 records like this and still no index use.
>
> SQLite version 3.7.2
> sqlite>  select count(*) from c;
> 67600
> sqlite>  explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
> sqlite>  create index c_chr on c(achr,bchr);
> sqlite>  explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
>
> Here's my record add:
> #include
> #include
> #include "sqlite3.h"
> int main()
> {
>   sqlite3 *db;
>   char *errmsg=NULL;
>   int rc;
>   int i,j,k;
>   sqlite3_open("test.db",);
>   rc=sqlite3_exec(db, "CREATE TABLE c (achr char, bchr 
> char)",NULL,NULL,);
>   if (rc != SQLITE_OK) {
>puts(errmsg);
>sqlite3_free(errmsg);
>   }
>   sqlite3_exec(db,"BEGIN",NULL,NULL,);
>   for(k=0;k<100;k++) {
>for(i=0;i<26;i++) {
> char sql[4096];
> for(j=0;j<26;j++) {
>  sprintf(sql,"INSERT INTO c VALUES ('%c','%c')",'a'+i,'a'+j);
>  rc=sqlite3_exec(db, sql,NULL,NULL,);
>  if (rc != SQLITE_OK) {
>   puts(sql);
>   puts(errmsg);
>   sqlite3_free(errmsg);
>   exit(-1);
>  }
> }
>}
>   }
>   sqlite3_exec(db,"COMMIT",NULL,NULL,);
>   sqlite3_close(db);
>   return 0;
> }
>
> Michael D. Black
> Senior Scientist
> Advanced Analytics Directorate
> Northrop Grumman Information Systems
>
>
> 
>
> From: sqlite-users-boun...@sqlite.org on behalf of luuk34
> Sent: Fri 10/15/2010 7:40 AM
> To: General Discussion of SQLite Database
> Subject: EXTERNAL:Re: [sqlite] How to optimize a multi-condition query
>
>
>
>
>On 15-10-10 14:34, Black, Michael (IS) wrote:
>> I love simple examples like this can help people with understanding 
>> things...so I tried this which I thought would do what Hilmar wants...but 
>> alaswhat concept am I missing?
>>
>> SQLite version 3.7.2
>> sqlite>   create table c(achr char,bchr char);
>> sqlite>   create index c_chr on c(achr,bchr);
>> sqlite>   explain query plan select achr,bchr from c where achr=bchr;
>> 0|0|TABLE c
>>
>> Why no use of the index in this case?
>>
> because there are no records in the database,
> so its quicker to read just all records,
> than to read all record in the order of the index...
>
> --
> Luuk
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>
>
>
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Re: [sqlite] How to optimize a multi-condition query

[Black, Michael (IS)]

Ok then... I added 67,600 records like this and still no index use.  
 
SQLite version 3.7.2
sqlite> select count(*) from c;
67600
sqlite> explain query plan select achr,bchr from c where achr=bchr;
0|0|TABLE c
sqlite> create index c_chr on c(achr,bchr);
sqlite> explain query plan select achr,bchr from c where achr=bchr;
0|0|TABLE c
 
Here's my record add:
#include 
#include 
#include "sqlite3.h"
int main()
{
 sqlite3 *db;
 char *errmsg=NULL;
 int rc;
 int i,j,k;
 sqlite3_open("test.db",);
 rc=sqlite3_exec(db, "CREATE TABLE c (achr char, bchr char)",NULL,NULL,);
 if (rc != SQLITE_OK) {
  puts(errmsg);
  sqlite3_free(errmsg);
 }
 sqlite3_exec(db,"BEGIN",NULL,NULL,);
 for(k=0;k<100;k++) {
  for(i=0;i<26;i++) {
   char sql[4096];
   for(j=0;j<26;j++) {
sprintf(sql,"INSERT INTO c VALUES ('%c','%c')",'a'+i,'a'+j);
rc=sqlite3_exec(db, sql,NULL,NULL,);
if (rc != SQLITE_OK) {
 puts(sql);
 puts(errmsg);
 sqlite3_free(errmsg);
 exit(-1);
}
   }
  }
 }
 sqlite3_exec(db,"COMMIT",NULL,NULL,);
 sqlite3_close(db);
 return 0;
}

Michael D. Black
Senior Scientist
Advanced Analytics Directorate
Northrop Grumman Information Systems
 



From: sqlite-users-boun...@sqlite.org on behalf of luuk34
Sent: Fri 10/15/2010 7:40 AM
To: General Discussion of SQLite Database
Subject: EXTERNAL:Re: [sqlite] How to optimize a multi-condition query




  On 15-10-10 14:34, Black, Michael (IS) wrote:
> I love simple examples like this can help people with understanding 
> things...so I tried this which I thought would do what Hilmar wants...but 
> alaswhat concept am I missing?
>
> SQLite version 3.7.2
> sqlite>  create table c(achr char,bchr char);
> sqlite>  create index c_chr on c(achr,bchr);
> sqlite>  explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
>
> Why no use of the index in this case?
>

because there are no records in the database,
so its quicker to read just all records,
than to read all record in the order of the index...

--
Luuk
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Re: [sqlite] How to optimize a multi-condition query

[luuk34]

  On 15-10-10 14:34, Black, Michael (IS) wrote:
> I love simple examples like this can help people with understanding 
> things...so I tried this which I thought would do what Hilmar wants...but 
> alaswhat concept am I missing?
>
> SQLite version 3.7.2
> sqlite>  create table c(achr char,bchr char);
> sqlite>  create index c_chr on c(achr,bchr);
> sqlite>  explain query plan select achr,bchr from c where achr=bchr;
> 0|0|TABLE c
>
> Why no use of the index in this case?
>

because there are no records in the database,
so its quicker to read just all records,
than to read all record in the order of the index...

-- 
Luuk
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Re: [sqlite] How to optimize a multi-condition query

[Black, Michael (IS)]

I love simple examples like this can help people with understanding things...so 
I tried this which I thought would do what Hilmar wants...but alaswhat 
concept am I missing?  
 
SQLite version 3.7.2
sqlite> create table c(achr char,bchr char);
sqlite> create index c_chr on c(achr,bchr);
sqlite> explain query plan select achr,bchr from c where achr=bchr;
0|0|TABLE c
 
Why no use of the index in this case?  
 
Michael D. Black
Senior Scientist
Advanced Analytics Directorate
Northrop Grumman Information Systems
 



From: sqlite-users-boun...@sqlite.org on behalf of Simon Davies
Sent: Fri 10/15/2010 5:16 AM
To: General Discussion of SQLite Database
Subject: EXTERNAL:Re: [sqlite] How to optimize a multi-condition query



On 15 October 2010 10:43, Hilmar Berger <hilmar.ber...@integromics.com> wrote:
>  Thanks !
>
> However, I tried what you suggested and there was no change.
>
> I used EXPLAIN QUERY PLAN on the query and it looks like it does not use
> any index on b at all, only if I use hardcoded conditions like b > 0.
>
> It appears that the real problem is that SQlite does not use indices for
> both tables, e.g.:
>
> CREATE INDEX a_chr on a(chr)
> CREATE INDEX b_chr on b(chr)
>
> explain query plan
>   select a.chr, b.chr
> from b, a
> where b.chr = a.chr;
>
> Output:
> 00TABLE b
> 11TABLE a WITH INDEX a_chr

There is no benefit in using an index on b for this query.

Change the query to:
  select a.chr, b.chr
from b, a
where b.chr = a.chr and b.chr>0;

and the query plan becomes:
0|0|TABLE b WITH INDEX b_chr
1|1|TABLE a WITH INDEX a_chr

>
>
> There is an example on how to use multiple indices on the same table
> here: http://www.sqlite.org/cvstrac/wiki?p=PerformanceTuning
> However, I'm not sure how to extend this to joined tables.
>
> Thanks !
>
> Best regards,
> Hilmar
>

Regarding

"select * from
a, b
where a.chr = b.chr and a.strand = b.strand and
a.start <= b.start and  a.stop >= b.stop  and
b.start <= a.stop and a.start <= b.stop ;"

surely the last 2 conditions are redundant assuming a.start<a.stop,
and b.starthttp://sqlite.org:8080/cgi-bin/mailman/listinfo/sqlite-users


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Re: [sqlite] How to optimize a multi-condition query

[Simon Davies]

On 15 October 2010 10:43, Hilmar Berger  wrote:
>  Thanks !
>
> However, I tried what you suggested and there was no change.
>
> I used EXPLAIN QUERY PLAN on the query and it looks like it does not use
> any index on b at all, only if I use hardcoded conditions like b > 0.
>
> It appears that the real problem is that SQlite does not use indices for
> both tables, e.g.:
>
> CREATE INDEX a_chr on a(chr)
> CREATE INDEX b_chr on b(chr)
>
> explain query plan
>   select a.chr, b.chr
>     from b, a
>     where b.chr = a.chr;
>
> Output:
> 0    0    TABLE b
> 1    1    TABLE a WITH INDEX a_chr

There is no benefit in using an index on b for this query.

Change the query to:
  select a.chr, b.chr
from b, a
where b.chr = a.chr and b.chr>0;

and the query plan becomes:
0|0|TABLE b WITH INDEX b_chr
1|1|TABLE a WITH INDEX a_chr

>
>
> There is an example on how to use multiple indices on the same table
> here: http://www.sqlite.org/cvstrac/wiki?p=PerformanceTuning
> However, I'm not sure how to extend this to joined tables.
>
> Thanks !
>
> Best regards,
> Hilmar
>

Regarding

"select * from
a, b
where a.chr = b.chr and a.strand = b.strand and
a.start <= b.start and  a.stop >= b.stop  and
b.start <= a.stop and a.start <= b.stop ;"

surely the last 2 conditions are redundant assuming a.start

Re: [sqlite] How to optimize a multi-condition query

[Hilmar Berger]

  Thanks !

However, I tried what you suggested and there was no change.

I used EXPLAIN QUERY PLAN on the query and it looks like it does not use 
any index on b at all, only if I use hardcoded conditions like b > 0.

It appears that the real problem is that SQlite does not use indices for 
both tables, e.g.:

CREATE INDEX a_chr on a(chr)
CREATE INDEX b_chr on b(chr)

explain query plan
   select a.chr, b.chr
 from b, a
 where b.chr = a.chr;

Output:
00TABLE b
11TABLE a WITH INDEX a_chr


There is an example on how to use multiple indices on the same table 
here: http://www.sqlite.org/cvstrac/wiki?p=PerformanceTuning
However, I'm not sure how to extend this to joined tables.

Thanks !

Best regards,
Hilmar

El 10/14/2010 7:12 PM, Simon Slavin escribió:
> On 14 Oct 2010, at 5:46pm, Hilmar Berger wrote:
>
>> The query is as follows:
>>
>> select * from
>>  a, b
>>  where a.chr = b.chr and a.strand = b.strand and a.start<= b.start
>> and  a.stop>= b.stop  and b.start<= a.stop and a.start<= b.stop ;
>> Indexes has been created for all fields in A and B (e.g.
>> create index name on A(chr, start, stop, strand));
> I not certain from your phrasing, but this may not do what you think.  It is 
> different matter to do
>
> create index Achr on A (chr)
> create index Astart on A (start)
> create index Astop on A (stop)
> ...
>
> to what you did above.  One creates one index on the sequence of four 
> variables, the other creates four indexes each on one variable.
>
> However, to make this SELECT go fast,
> CREAT INDEX Bkey ON B (chr,strand)
> CREAT INDEX Bstart ON B (start)
> CREAT INDEX Bstop ON B (stop)
>
> May help.
>
> Also I recommend doing this:
>
> http://www.sqlite.org/lang_analyze.html
>
> Simon.
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Re: [sqlite] How to optimize a multi-condition query

[Simon Slavin]

On 14 Oct 2010, at 5:46pm, Hilmar Berger wrote:

> The query is as follows:
> 
> select * from
> a, b
> where a.chr = b.chr and a.strand = b.strand and a.start <= b.start 
> and  a.stop >= b.stop  and b.start <= a.stop and a.start <= b.stop ;

> Indexes has been created for all fields in A and B (e.g.
> create index name on A(chr, start, stop, strand));

I not certain from your phrasing, but this may not do what you think.  It is 
different matter to do

create index Achr on A (chr)
create index Astart on A (start)
create index Astop on A (stop)
...

to what you did above.  One creates one index on the sequence of four 
variables, the other creates four indexes each on one variable.

However, to make this SELECT go fast,
CREAT INDEX Bkey ON B (chr,strand)
CREAT INDEX Bstart ON B (start)
CREAT INDEX Bstop ON B (stop)

May help.

Also I recommend doing this:

http://www.sqlite.org/lang_analyze.html

Simon.
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[sqlite] How to optimize a multi-condition query

[Hilmar Berger]

  Hi all,

I have a query that does not perform as fast as expected and would like 
to know if anyone here has an idea on how to optimize it.

There are two tables, A and B. Both have fields chr, start, stop and 
strand. A has about 50k entries, B about 12k.
Both contain intervals defined by start...stop. The intervals in B have 
length 1, those in A any possible length.
I want to identify all intervals in B that fall into one of those in A 
and get the corresponding interval data from A for each match of B.
Indexes has been created for all fields in A and B (e.g. create index 
name on A(chr, start, stop, strand));

The query is as follows:

select * from
 a, b
 where a.chr = b.chr and a.strand = b.strand and a.start <= b.start 
and  a.stop >= b.stop  and b.start <= a.stop and a.start <= b.stop ;

This query takes about 130 seconds, but if when I remove the two last 
conditions it drops to 0.5 seconds. Replacing both last conditions with 
conditions like b.start > 1000 or b.start <> 0 the execution time 
will stay at 0.5 seconds.

Any help appreciated.

Thanks !

Hilmar

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