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Best way to alter primary key on large innodb tables?

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  • Best way to alter primary key on large innodb tables?

    Hi,

    We're trying to alter the primary key on a large table to be more efficient with Innodb (we've noticed a significant drop in performance on the table since migrating from myisam and we're hypothesizing that the pk is a large factor).

    The current primary key is a 2-column pair - a randomly generated varhchar(16) "id" and an integer "version". We'd like to replace this with an auto-increment integer and make (id,version)a unique index instead.

    The other columns of the table are all longtext or longblob (full schema below). There are ~300k records, totaling ~20GB.

    We've been experimenting with different approaches on our test environment to try and find the fastest way to make the change, but it's going a lot slower than we'd like (ideally we'd like to make the change on our production db with max 2 hours downtime).

    So far we've tried two approaches:
    1. Change existing table
    - drop pk,
    - alter table add new auto_inc pk
    - add unique index

    2. create new table and copy records
    - create new table with auto_inc pk, no indexes
    - INSERT (...) INTO newTable SELECT (...) from oldTable
    - add unique index
    - rename tables

    The first approach took 5 hours, 3 of which just to drop the primary key. We're running the second test now, but it's already taken over 1.5 hours and hasn't finished copying the rows over.

    Can anyone suggest any other ways which might be faster? Is 2 hours just completely unrealistic?

    Server details:
    mysql-5.0.72-enterprise-gpl-log
    8GB ram
    quad core


    Thanks,
    Stephen


    schema (columns renamed):

    CREATE TABLE `largeTable` ( `id` varchar(16) collate utf8_unicode_ci NOT NULL, `version` int(11) NOT NULL, `col_1` longblob NOT NULL, `col_2` longblob NOT NULL, `col_3` longblob NOT NULL, `col_4` longblob NOT NULL, `col_5` longblob NOT NULL, `col_6` longblob NOT NULL, `col_7` longblob NOT NULL, `col_8` longblob NOT NULL, `col_9` longblob NOT NULL, `col_10` longtext collate utf8_unicode_ci NOT NULL, `col_11` longtext collate utf8_unicode_ci NOT NULL, `col_12` longtext collate utf8_unicode_ci NOT NULL, `col_13` longblob NOT NULL, `col_14` longblob NOT NULL, `col_15` longblob NOT NULL, `col_16` longblob NOT NULL, `col_17` text collate utf8_unicode_ci NOT NULL, `col_18` longblob NOT NULL, PRIMARY KEY (`id`,`version`))

  • #2
    3.
    a.create new table with pk and index
    b.fetch 100(0/00) rows from old table
    c.no rows? exit
    d.insert them into new table
    e.jump to b

    b-d could be in script executed by cron

    Comment


    • #3
      Thanks! Copying rows in batches sped it up a bit, but unfortunately it still took 3.5 hours in total (

      It looks like the bottleneck is reading the rows from disk. It takes 40 seconds on average to copy a batch of 1000 rows (we tried different batch sizes from 10-10,000 but it didn't make much difference).

      Our best guess is that the table has become badly fragmented due to the poor primary key which means table scans involve a lot of jumping around on disc.

      Looks like we'll have to resort to something more fiddly while the service is running

      current plan:
      - get ids of all records at time X (there's a small secondary table with a a 1-to-1 relationship we can use to do this quickly)
      - in the background copy records with these ids to a new table with the new pk and index. Probably in small batches with sleep time inbetween to limit service impact.
      - once finished, lock the table and copy over any new/updated records which have come in since time X (the fiddly bit).

      Comment


      • #4
        What was the query that fetched x rows ?
        Could You post it + explain result ?

        Comment


        • #5
          Hi,

          Thanks for your help with this.

          I tried two ways:
          a) Select as part of insert: "INSERT INTO ... (SELECT ... LIMIT offset, X);"
          b) Separate select and insert queries:
          "SELECT ... LIMIT offset,X"
          <process result set>
          "INSERT ..."

          With b) the select was taking 99% of the total time per batch. Here's the per-batch select with explain output:


          EXPLAIN SELECT `id`, `version`, `col_1`, `col_2`, `col_3`, `col_4`, `col_5`,`col_6`, `col_7`, `col_8`, `col_9`,`col_10`, `col_11`, `col_12`, `col_13`, `col_14`,`col_15`,`col_16`, `col_17`,`col_18` FROM largeTableLIMIT 1000, 3000+----+-------------+------------+------+---------------+------+---------+------+--------+-------+| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |+----+-------------+------------+------+---------------+------+---------+------+--------+-------+| 1 | SIMPLE | largeTable | ALL | NULL | NULL | NULL | NULL | 288412 | |+----+-------------+------------+------+---------------+------+---------+------+--------+-------+


          I tried adding an explicit "ORDER BY id, version" clause to the query, but it didn't give any improvement in query time. Here's the explain:


          +----+-------------+------------+-------+---------------+---------+---------+------+--------+-------+| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |+----+-------------+------------+-------+---------------+---------+---------+------+--------+-------+| 1 | SIMPLE | largeTable | index | NULL | PRIMARY | 56 | NULL | 288412 | |+----+-------------+------------+-------+---------------+---------+---------+------+--------+-------+



          NB. the size of the records doesn't seem to be a major factor, if the records are in the query cache the time drops from 40 seconds to 0.4 seconds per batch (we can see this when we forget to reset the cache inbetween test runs).

          Comment


          • #6
            Innodb has got inner primary key (as I remember), maybe You could use it ?

            Or You could order by WITH where. First run should be very slow, but second, third etc. should fetch less rows than in previous runs.

            Comment


            • #7
              stephenhenderson wrote on Mon, 20 July 2009 19:56


              I tried adding an explicit "ORDER BY id, version" clause to the query, but it didn't give any improvement in query time.

              You should still add it, because else I am not so sure that rows will be in the same order every time you retrieve them with LIMIT.

              Quote:



              SELECT `id`, `version`, `col_1`, `col_2`, `col_3`, `col_4`, `col_5`,`col_6`, `col_7`, `col_8`, `col_9`,`col_10`, `col_11`, `col_12`, `col_13`, `col_14`,`col_15`,`col_16`, `col_17`,`col_18` FROM largeTableLIMIT 1000, 3000


              The LIMIT will be a PITA for the last set of rows (for which almost all rows have to be retrieved but discarded). Januzi is correct: you should use WHERE instead.


              januzi wrote on Mon, 20 July 2009 20:54

              Innodb has got inner primary key (as I remember), maybe You could use it ?

              Or You could order by WITH where. First run should be very slow, but second, third etc. should fetch less rows than in previous runs.

              The only primary key is also the clustered key and it is (id,version).

              Comment

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