MariaDB – How to Avoid Slow Query Writing to Temporary Disk Table

mariadbperformancequery-performance

I have this query which is flagged as a "slow query" by MariaDB and also causes Created_tmp_disk_tables to increase each time it is run:

SELECT `articles`.`id`, `articles`.`title_id`, `articles`.`title`, 
`articles`.`created_on`, `articles`.`abstract`, 'article' AS 'doctype' 
FROM `articles` WHERE (published = 1) AND (highlight = 1)  
UNION  
SELECT `guides`.`id`, `guides`.`title_id`, `guides`.`title`, 
`guides`.`created_on`, `guides`.`abstract`, 'guide' AS 'doctype' 
FROM `guides` WHERE (published = 1) AND (highlight = 1)  
ORDER BY `created_on` DESC LIMIT 2;

At first, I thought the root cause to be the abstract field, since it was a TEXT. Then I changed it to VARCHAR(1024) but it didn't solve the issue (it-s still flagged as slow and still causes the tmp disk table).

Please note that if I remove the abstract columns from the select-ed columns, the query is still flagged as slow, but it does not cause the tmp disk table.

Please could you help me understand what needs to be done to avoid temporary disk tables in this case?

The tables are as such:

Create table articles (
id Char(32) NOT NULL,
id_category Tinyint UNSIGNED NOT NULL,
title_id Varchar(255) NOT NULL,
title Varchar(255) NOT NULL,
author Varchar(100),
created_on Datetime NOT NULL,
modified_on Datetime,
published Bool NOT NULL DEFAULT true,
highlight Bool NOT NULL DEFAULT false,
abstract Varchar(1024),
content Mediumtext,
UNIQUE (title_id),
Primary Key (id)) ENGINE = InnoDB
DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci;

Create table guides (
id Char(32) NOT NULL,
id_category Tinyint UNSIGNED NOT NULL,
title_id Varchar(255) NOT NULL,
title Varchar(255) NOT NULL,
author Varchar(100),
created_on Datetime NOT NULL,
modified_on Datetime,
published Bool NOT NULL DEFAULT true,
highlight Bool NOT NULL DEFAULT false,
abstract Varchar(1024),
content Mediumtext,
UNIQUE (title_id),
Primary Key (id)) ENGINE = InnoDB
DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci;

Create Index visibility ON articles (published,highlight);

Create Index visibility ON guides (published,highlight);

This is the EXPLAIN:

| id   | select_type  | table      | type | possible_keys | key        | key_len | ref         | rows | Extra          |
+------+--------------+------------+------+---------------+------------+---------+-------------+------+----------------+
|    1 | PRIMARY      | articles   | ref  | visibility    | visibility | 2       | const,const |    2 |                |
|    2 | UNION        | guides     | ref  | visibility    | visibility | 2       | const,const |    4 |                |
| NULL | UNION RESULT | <union1,2> | ALL  | NULL          | NULL       | NULL    | NULL        | NULL | Using filesort |

And here is my MariaDB 10.1.26 configuration (I truncated entries supposed to be non-relevant):

innodb                                                     ON
innodb-adaptive-flushing                                   TRUE
innodb-adaptive-flushing-lwm                               10
innodb-adaptive-hash-index                                 TRUE
innodb-adaptive-hash-index-partitions                      1
innodb-adaptive-max-sleep-delay                            150000
innodb-additional-mem-pool-size                            8388608
innodb-api-bk-commit-interval                              5
innodb-api-disable-rowlock                                 FALSE
innodb-api-enable-binlog                                   FALSE
innodb-api-enable-mdl                                      FALSE
innodb-api-trx-level                                       0
innodb-autoextend-increment                                64
innodb-autoinc-lock-mode                                   1
innodb-background-scrub-data-check-interval                3600
innodb-background-scrub-data-compressed                    FALSE
innodb-background-scrub-data-interval                      604800
innodb-background-scrub-data-uncompressed                  FALSE
innodb-buf-dump-status-frequency                           0
innodb-buffer-page                                         ON
innodb-buffer-page-lru                                     ON
innodb-buffer-pool-dump-at-shutdown                        FALSE
innodb-buffer-pool-dump-now                                FALSE
innodb-buffer-pool-dump-pct                                100
innodb-buffer-pool-filename                                ib_buffer_pool
innodb-buffer-pool-instances                               1
innodb-buffer-pool-load-abort                              FALSE
innodb-buffer-pool-load-at-startup                         FALSE
innodb-buffer-pool-load-now                                FALSE
innodb-buffer-pool-populate                                FALSE
innodb-buffer-pool-size                                    67108864
innodb-buffer-pool-stats                                   ON
innodb-change-buffer-max-size                              25
innodb-change-buffering                                    all
innodb-changed-pages                                       ON
innodb-checksum-algorithm                                  INNODB
innodb-checksums                                           TRUE
innodb-cleaner-lsn-age-factor                              HIGH_CHECKPOINT
innodb-cmp                                                 ON
innodb-cmp-per-index                                       ON
innodb-cmp-per-index-enabled                               FALSE
innodb-cmp-per-index-reset                                 ON
innodb-cmp-reset                                           ON
innodb-cmpmem                                              ON
innodb-cmpmem-reset                                        ON
innodb-commit-concurrency                                  0
innodb-compression-algorithm                               zlib
innodb-compression-failure-threshold-pct                   5
innodb-compression-level                                   6
innodb-compression-pad-pct-max                             50
innodb-concurrency-tickets                                 5000
innodb-corrupt-table-action                                assert
innodb-data-file-path                                      (No default value)
innodb-data-home-dir                                       (No default value)
innodb-default-encryption-key-id                           1
innodb-defragment                                          FALSE
innodb-defragment-fill-factor                              0.9
innodb-defragment-fill-factor-n-recs                       20
innodb-defragment-frequency                                40
innodb-defragment-n-pages                                  7
innodb-defragment-stats-accuracy                           0
innodb-disable-sort-file-cache                             FALSE
innodb-doublewrite                                         TRUE
innodb-empty-free-list-algorithm                           BACKOFF
innodb-encrypt-log                                         FALSE
innodb-encrypt-tables                                      OFF
innodb-encryption-rotate-key-age                           1
innodb-encryption-rotation-iops                            100
innodb-encryption-threads                                  0
innodb-fake-changes                                        FALSE
innodb-fast-shutdown                                       1
innodb-fatal-semaphore-wait-threshold                      600
innodb-file-format                                         Antelope
innodb-file-format-check                                   TRUE
innodb-file-format-max                                     Antelope
innodb-file-io-threads                                     4
innodb-file-per-table                                      TRUE
innodb-flush-log-at-timeout                                1
innodb-flush-log-at-trx-commit                             1
innodb-flush-method                                        (No default value)
innodb-flush-neighbors                                     1
innodb-flushing-avg-loops                                  30
innodb-force-load-corrupted                                FALSE
innodb-force-primary-key                                   FALSE
innodb-force-recovery                                      0
innodb-foreground-preflush                                 EXPONENTIAL_BACKOFF
innodb-ft-aux-table                                        (No default value)
innodb-ft-being-deleted                                    ON
innodb-ft-cache-size                                       8000000
innodb-ft-config                                           ON
innodb-ft-default-stopword                                 ON
innodb-ft-deleted                                          ON
innodb-ft-enable-diag-print                                FALSE
innodb-ft-enable-stopword                                  TRUE
innodb-ft-index-cache                                      ON
innodb-ft-index-table                                      ON
innodb-ft-max-token-size                                   84
innodb-ft-min-token-size                                   3
innodb-ft-num-word-optimize                                2000
innodb-ft-result-cache-limit                               2000000000
innodb-ft-server-stopword-table                            (No default value)
innodb-ft-sort-pll-degree                                  2
innodb-ft-total-cache-size                                 640000000
innodb-ft-user-stopword-table                              (No default value)
innodb-idle-flush-pct                                      100
innodb-immediate-scrub-data-uncompressed                   FALSE
innodb-instrument-semaphores                               FALSE
innodb-io-capacity                                         200
innodb-io-capacity-max                                     18446744073709551615
innodb-kill-idle-transaction                               0
innodb-large-prefix                                        FALSE
innodb-lock-schedule-algorithm                             fcfs
innodb-lock-wait-timeout                                   50
innodb-lock-waits                                          ON
innodb-locking-fake-changes                                TRUE
innodb-locks                                               ON
innodb-locks-unsafe-for-binlog                             FALSE
innodb-log-arch-dir                                        (No default value)
innodb-log-arch-expire-sec                                 0
innodb-log-archive                                         FALSE
innodb-log-block-size                                      512
innodb-log-buffer-size                                     16777216
innodb-log-checksum-algorithm                              INNODB
innodb-log-compressed-pages                                TRUE
innodb-log-file-size                                       8388608
innodb-log-files-in-group                                  2
innodb-log-group-home-dir                                  (No default value)
innodb-lru-scan-depth                                      1024
innodb-max-bitmap-file-size                                104857600
innodb-max-changed-pages                                   1000000
innodb-max-dirty-pages-pct                                 75
innodb-max-dirty-pages-pct-lwm                             0.001
innodb-max-purge-lag                                       0
innodb-max-purge-lag-delay                                 0
innodb-metrics                                             ON
innodb-mirrored-log-groups                                 0
innodb-monitor-disable                                     (No default value)
innodb-monitor-enable                                      all
innodb-monitor-reset                                       (No default value)
innodb-monitor-reset-all                                   (No default value)
innodb-mtflush-threads                                     8
innodb-mutexes                                             ON
innodb-old-blocks-pct                                      37
innodb-old-blocks-time                                     1000
innodb-online-alter-log-max-size                           134217728
innodb-open-files                                          0
innodb-optimize-fulltext-only                              FALSE
innodb-page-size                                           16384
innodb-prefix-index-cluster-optimization                   FALSE
innodb-print-all-deadlocks                                 FALSE
innodb-purge-batch-size                                    300
innodb-purge-threads                                       1
innodb-random-read-ahead                                   FALSE
innodb-read-ahead-threshold                                56
innodb-read-io-threads                                     4
innodb-read-only                                           FALSE
innodb-replication-delay                                   0
innodb-rollback-on-timeout                                 FALSE
innodb-rollback-segments                                   128
innodb-sched-priority-cleaner                              19
innodb-scrub-log                                           FALSE
innodb-scrub-log-speed                                     256
innodb-show-locks-held                                     10
innodb-show-verbose-locks                                  0
innodb-simulate-comp-failures                              0
innodb-sort-buffer-size                                    1048576
innodb-spin-wait-delay                                     6
innodb-stats-auto-recalc                                   TRUE
innodb-stats-include-delete-marked                         FALSE
innodb-stats-method                                        nulls_equal
innodb-stats-modified-counter                              0
innodb-stats-on-metadata                                   FALSE
innodb-stats-persistent                                    TRUE
innodb-stats-persistent-sample-pages                       20
innodb-stats-sample-pages                                  8
innodb-stats-traditional                                   TRUE
innodb-stats-transient-sample-pages                        8
innodb-status-file                                         FALSE
innodb-status-output                                       FALSE
innodb-status-output-locks                                 FALSE
innodb-strict-mode                                         TRUE
innodb-support-xa                                          TRUE
innodb-sync-array-size                                     1
innodb-sync-spin-loops                                     30
innodb-sys-columns                                         ON
innodb-sys-datafiles                                       ON
innodb-sys-fields                                          ON
innodb-sys-foreign                                         ON
innodb-sys-foreign-cols                                    ON
innodb-sys-indexes                                         ON
innodb-sys-semaphore-waits                                 ON
innodb-sys-tables                                          ON
innodb-sys-tablespaces                                     ON
innodb-sys-tablestats                                      ON
innodb-table-locks                                         TRUE
innodb-tablespaces-encryption                              ON
innodb-tablespaces-scrubbing                               ON
innodb-thread-concurrency                                  0
innodb-thread-sleep-delay                                  10000
innodb-tmpdir                                              (No default value)
innodb-track-changed-pages                                 FALSE
innodb-trx                                                 ON
innodb-undo-directory                                      .
innodb-undo-logs                                           128
innodb-undo-tablespaces                                    0
innodb-use-atomic-writes                                   FALSE
innodb-use-fallocate                                       FALSE
innodb-use-global-flush-log-at-trx-commit                  TRUE
innodb-use-mtflush                                         FALSE
innodb-use-native-aio                                      TRUE
innodb-use-stacktrace                                      FALSE
innodb-use-sys-malloc                                      TRUE
innodb-use-trim                                            FALSE
innodb-write-io-threads                                    4
interactive-timeout                                        28800
join-buffer-size                                           262144
join-buffer-space-limit                                    2097152
join-cache-level                                           2
keep-files-on-create                                       FALSE
key-buffer-size                                            131072
key-cache-age-threshold                                    300
key-cache-block-size                                       1024
key-cache-division-limit                                   100
key-cache-file-hash-size                                   512
key-cache-segments                                         0
large-files-support                                        TRUE
large-pages                                                FALSE
lc-messages                                                en_US
lc-messages-dir                                            /usr/share/mysql
lc-time-names                                              en_US
local-infile                                               TRUE
lock-wait-timeout                                          31536000
max-allowed-packet                                         16777216
max-binlog-cache-size                                      18446744073709547520
max-binlog-size                                            104857600
max-binlog-stmt-cache-size                                 18446744073709547520
max-connect-errors                                         100
max-connections                                            51
max-delayed-threads                                        20
max-digest-length                                          1024
max-error-count                                            64
max-heap-table-size                                        16777216
max-join-size                                              18446744073709551615
max-length-for-sort-data                                   1024
max-long-data-size                                         16777216
max-prepared-stmt-count                                    16382
max-relay-log-size                                         104857600
max-seeks-for-key                                          4294967295
max-session-mem-used                                       9223372036854775807
max-sort-length                                            1024
max-sp-recursion-depth                                     0
max-statement-time                                         0
max-tmp-tables                                             32
max-user-connections                                       0
max-write-lock-count                                       4294967295
memlock                                                    FALSE
metadata-locks-cache-size                                  1024
metadata-locks-hash-instances                              8
min-examined-row-limit                                     0
mrr-buffer-size                                            262144
multi-range-count                                          256
open-files-limit                                           1024
optimizer-prune-level                                      1
optimizer-search-depth                                     62
optimizer-selectivity-sampling-limit                       100
optimizer-switch                                           index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,index_merge_sort_intersection=off,engine_condition_pushdown=off,index_condition_pushdown=on,derived_merge=on,derived_with_keys=on,firstmatch=on,loosescan=on,materialization=on,in_to_exists=on,semijoin=on,partial_match_rowid_merge=on,partial_match_table_scan=on,subquery_cache=on,mrr=off,mrr_cost_based=off,mrr_sort_keys=off,outer_join_with_cache=on,semijoin_with_cache=on,join_cache_incremental=on,join_cache_hashed=on,join_cache_bka=on,optimize_join_buffer_size=off,table_elimination=on,extended_keys=on,exists_to_in=on
optimizer-use-condition-selectivity                        1
partition                                                  ON
performance-schema                                         TRUE
pid-file                                                   /var/run/mysqld/mysqld.pid
plugin-dir                                                 /usr/lib/x86_64-linux-gnu/mariadb18/plugin/
plugin-maturity                                            unknown
port                                                       0
port-open-timeout                                          0
preload-buffer-size                                        32768
profiling-history-size                                     15
progress-report-time                                       5
protocol-version                                           10
query-alloc-block-size                                     16384
query-cache-limit                                          1048576
query-cache-min-res-unit                                   4096
query-cache-size                                           0
query-cache-strip-comments                                 FALSE
query-cache-type                                           OFF
query-cache-wlock-invalidate                               FALSE
query-prealloc-size                                        24576
range-alloc-block-size                                     4096
read-buffer-size                                           131072
read-only                                                  FALSE
read-rnd-buffer-size                                       262144
sort-buffer-size                                           2097152
sql-mode                                                   STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION
stack-trace                                                TRUE
stored-program-cache                                       256
strict-password-validation                                 TRUE
super-large-pages                                          FALSE
symbolic-links                                             TRUE
sync-binlog                                                0
sync-frm                                                   TRUE
sync-master-info                                           10000
sync-relay-log                                             10000
sync-relay-log-info                                        10000
sysdate-is-now                                             FALSE
system-time-zone                                           CET
table-cache                                                400
table-definition-cache                                     400
table-open-cache                                           400
tc-heuristic-recover                                       OFF
temp-pool                                                  TRUE
thread-cache-size                                          8
thread-concurrency                                         10
thread-handling                                            one-thread-per-connection
thread-pool-idle-timeout                                   60
thread-pool-max-threads                                    1000
thread-pool-oversubscribe                                  3
thread-pool-size                                           4
thread-pool-stall-limit                                    500
thread-stack                                               196608
time-format                                                %H:%i:%s
timed-mutexes                                              FALSE
tmp-table-size                                             16777216
tmpdir                                                     /tmp

Best Answer

One factor that can cause the creation of temp disk tables is the inclusion of TEXT or BLOB columns in the SELECTs. To avoid this you can use the SUBSTR function in the SELECT to shorten the data as you may not need the full contents of that column in the result set. However, it seems a BLOB/TEXT query will only create a temporary disk table if other factors in the query cause the creation of temporary (non-disk) tables.

Also, UNION is really shorthand for UNION DISTINCT which means the database needs to eliminate duplicates to produce the result set. Use UNION ALL instead of just UNION to avoid what in this case looks like wasted effort. In many cases you will see that the UNION RESULT line disappears from the EXPLAIN because the database no longer needs to create a temporary table. According to the MariaDB Knowledge Base on UNION/UNION ALL:

Until MariaDB 10.1.1, all UNION ALL statements required the server to create a temporary table. Since MariaDB 10.1.1, the server can in most cases execute UNION ALL without creating a temporary table, improving performance (see MDEV-334).

However, in your case, because of the ORDER BY at the end it will still create a temporary table, though it might not necessarily be a disk table. If you really want to avoid the temporary table, then you'll have to decide if you really need this ordering in the query. You will avoid the temporary table if you instead ORDER BY on each SELECT. (Note that you then need to wrap each SELECT in parenthesis.)

And just a thought, given that these two tables are identical except for their names, why not just merge them into one table and avoid the UNION ... ORDER BY -> temporary table problem?

YOUR QUERY

SELECT post.postid, post.attach FROM newbb_innopost AS post WHERE post.threadid = 51506;

At first glance, that query should only touches 1.1597% (62510 out of 5390146) of the table. It should be fast given the key distribution of threadid 51506.

REALITY CHECK

No matter which version of MySQL (Oracle, Percona, MariaDB) you use, none of them can fight to one enemy they all have in common : The InnoDB Architecture.

InnoDB Architecture

CLUSTERED INDEX

Please keep in mind that the each threadid entry has a primary key attached. This means that when you read from the index, it must do a primary key lookup within the ClusteredIndex (internally named gen_clust_index). In the ClusteredIndex, each InnoDB page contains both data and PRIMARY KEY index info. See my post Best of MyISAM and InnoDB for more info.

REDUNDANT INDEXES

You have a lot of clutter in the table because some indexes have the same leading columns. MySQL and InnoDB has to navigate through the index clutter to get to needed BTREE nodes. You should reduced that clutter by running the following:

ALTER TABLE newbb_innopost
    DROP INDEX threadid,
    DROP INDEX threadid_2,
    DROP INDEX threadid_visible_dateline,
    ADD INDEX threadid_visible_dateline_index (`threadid`,`visible`,`dateline`,`userid`)
;

Why strip down these indexes ?

The first three indexes start with threadid
threadid_2 and threadid_visible_dateline start with the same three columns
threadid_visible_dateline does not need postid since it's the PRIMARY KEY and it's embedded

BUFFER CACHING

The InnoDB Buffer Pool caches data and index pages. MyISAM only caches index pages.

Just in this area alone, MyISAM does not waste time caching data. That's because it's not designed to cache data. InnoDB caches every data page and index page (and its grandmother) it touches. If your InnoDB Buffer Pool is too small, you could be caching pages, invalidating pages, and removing pages all in one query.

TABLE LAYOUT

You could shave of some space from the row by considering importthreadid and importpostid. You have them as BIGINTs. They take up 16 bytes in the ClusteredIndex per row.

You should run this

SELECT importthreadid,importpostid FROM newbb_innopost PROCEDURE ANALYSE();

This will recommend what data types these columns should be for the given dataset.

CONCLUSION

MyISAM has a lot less to contend with than InnoDB, especially in the area of caching.

While you revealed the amount of RAM (32GB) and the version of MySQL (Server version: 10.0.12-MariaDB-1~trusty-wsrep-log mariadb.org binary distribution, wsrep_25.10.r4002), there are still other pieces to this puzzle you have not revealed

The InnoDB settings
The Number of Cores
Other settings from my.cnf

If you can add these things to the question, I can further elaborate.

UPDATE 2014-08-28 11:27 EDT

You should increase threading

innodb_read_io_threads = 64
innodb_write_io_threads = 16
innodb_log_buffer_size = 256M

I would consider disabling the query cache (See my recent post Why query_cache_type is disabled by default start from MySQL 5.6?)

query_cache_size = 0

I would preserve the Buffer Pool

innodb_buffer_pool_dump_at_shutdown=1
innodb_buffer_pool_load_at_startup=1

Increase purge threads (if you do DML on multiple tables)

innodb_purge_threads = 4

Best Answer

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