I've made a bit of progress, I think:

Adding this composite index to smw_rels2 appears to decrease the
time of the 'SELECT DISTINCT...' query to about 10% of original,
and decreases the time of the 'runJobs' jobs to about 20-25%.

ALTER TABLE smw_rels2 ADD INDEX idx_o_id_p_id USING BTREE (o_id, p_id);

I assume this could replace the existing index on o_id, but I have
not actually tried it.  I also don't know what compatibility issues
arise with composite indexes.

Excerpts from Daniel Ring's message of Tue Sep 21 13:38:59 -0400 2010:
> I'm having an issue with seemingly slow and redundant queries during
> runJobs.  I'm using MW 1.15.5 and SMW 1.5.2, upgraded from 1.15.1 and
> 1.5.1 respectively.  (The upgrade didn't noticably change the speed 
> or redundancy).
> 
> There are a few templates which are used by many pages, the worst
> case so far being ~120k uses of a single template which turns the
> ~15 template parameters into ~10 properties, a category, and a page.
> It uses #if and uses other templates, (wrapping the other template
> calls in 'noinclude' doesn't appear to affect the runtime) and is
> basically unremarkable.
> 
> So, running 'runJobs' gives output like the following:
> 
> With --procs=1
> 
> 
>   2010-09-21 16:14:17 refreshLinks2 Template:TX_Facility start=361172 
> end=362192 t=2407915 good
>   2010-09-21 16:53:19 refreshLinks2 Template:TX_Facility start=362193 
> end=363233 t=2341932 good
> 
> (E.g. ~40min per refreshLinks2 with start-end range ~1000)
> 
> With --procs=? (I don't remember, but with --procs=1, these were
> t=~3500 and increase proportionally with procs, so I think the DB
> is the bottleneck.)
> 
> 
>   2010-09-18 14:00:07 refreshLinks 42-009-34059_(TX_Facility) t=22856 good
>   2010-09-18 14:00:35 refreshLinks 42-001-31705_(TX_Facility) t=28058 good
>   2010-09-18 14:01:04 refreshLinks 42-003-01936_(TX_Facility) t=28900 good
> 
> 
> Watching the SQL log, I see it pause at this query:
>   SELECT /* SMW::getInProperties 127.0.0.1 */  DISTINCT smw_title,smw_sortkey
>     FROM `smw_ids` INNER JOIN `smw_rels2` AS t1 ON t1.p_id=smw_id  WHERE 
> t1.o_id='42720'
> 
> 
> And in the MySQL shell I get:
> 
> 
> mysql> SELECT    DISTINCT smw_title,smw_sortkey   FROM `smw_ids` INNER JOIN 
> `smw_rels2` AS t1 ON t1.p_id=smw_id  WHERE t1.o_id='42720';
> +--------------+--------------+
> | smw_title    | smw_sortkey  |
> +--------------+--------------+
> | Well_number  | Well number  | 
> | State_number | State number | 
> +--------------+--------------+
> 2 rows in set (5.98 sec)
> 
> mysql> SELECT    COUNT(*)   FROM `smw_ids` INNER JOIN `smw_rels2` AS t1 ON 
> t1.p_id=smw_id  WHERE t1.o_id='42720';
> +----------+
> | COUNT(*) |
> +----------+
> |   123037 | 
> +----------+
> 1 row in set (5.56 sec)
> 
> 
> The redundancy is that the SELECT DISTINCT output is the same
> every time.  MySQL query cache is on, and Memcached is used, but
> neither made a noticable difference.  (I assume some other query
> during runJobs invalidates it...)
> 
> So, is this a bug or am I doing something totally wrong?
> 
> Thanks,
> Dan

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