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.

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

GIVE IT A TRY !!!

Observations:

Version: 5.5.41-0ubuntu0.14.04.1
64 GB of RAM
Uptime = 3d 03:40:44
You are not running on Windows.
Running 64-bit version
You appear to be running entirely (or mostly) InnoDB.

The More Important Issues

Increase innodb_buffer_pool_size to at least 1G (not more than 45G). Sounds like most of your 64GB is unused? Or do you expect a huge growth in data?

Turn off the Query Cache; it does not seem to be useful:

query_cache_size = 0
query_cache_type = OFF

Set long_query_time = 2 and turn on the slowlog. After a day, run pt-query-digest to find the worst queries. Then work on optimizing them. (Composite indexes, reformulating queries, etc. Ask for help if needed.)

Supporting details and other suggestions

( innodb_buffer_pool_size / _ram ) = 128M / 65536M = 0.20% -- % of RAM used for InnoDB buffer_pool ( (key_buffer_size / 0.20 + innodb_buffer_pool_size / 0.70) / _ram ) = (16M / 0.20 + 128M / 0.70) / 65536M = 0.40% -- Most of available ram should be made available for caching. -- http://mysql.rjweb.org/doc.php/memory

[!!] InnoDB buffer pool / data size: 128.0M/873.0M
So innodb_buffer_pool_size should be at least 1G.

[!!] InnoDB Write buffer efficiency: 0.00% (0 hits/ 1 total)
0 out of 1 -- bogus to mark it "!!"

( Innodb_pages_written / Innodb_buffer_pool_write_requests ) = 2,068,247 / 5340758 = 38.7% -- Write requests that had to hit disk -- Check innodb_buffer_pool_size

( innodb_file_per_table ) = OFF -- Put each file in its own tablespace -- (Mildly recommended, especially for large tables)

( Qcache_hits / Qcache_inserts ) = 1,765,289 / 2,509,742 = 0.703 -- Hit to insert ratio -- high is good -- Consider turning off the query cache.

( (query_cache_size - Qcache_free_memory) / Qcache_queries_in_cache / query_alloc_block_size ) = (16M - 14960424) / 1477 / 8192 = 0.15 -- query_alloc_block_size vs formula -- Adjust query_alloc_block_size

[!!] Query cache prunes per day: 15154

( Created_tmp_disk_tables / (Created_tmp_disk_tables + Created_tmp_tables) ) = 3,090 / (3090 + 4930) = 38.5% -- Percent of temp tables that spilled to disk -- maybe increase tmp_table_size and max_heap_table_size; avoid blobs, etc.

( Select_scan ) = 459,980 / 272444 = 1.7 /sec -- full table scans -- Add indexes / optimize queries (unless they are tiny tables)

( Select_scan / Com_select ) = 459,980 / 2518409 = 18.3% -- % of selects doing full table scan. (May be fooled by Stored Routines.) -- Add indexes / optimize queries

( binlog_format ) = STATEMENT -- STATEMENT/ROW/MIXED. ROW is preferred; it may become the default.

( log_slow_queries ) = OFF -- Whether to log slow queries. (Before 5.1.29, 5.6.1)

( slow_query_log ) = OFF -- Whether to log slow queries. (5.1.12)

( long_query_time ) = 10.000000 = 10 -- Cutoff (Seconds) for defining a "slow" query. -- Suggest 2

( Connections ) = 2,305,560 / 272,444 = 8.5 /sec -- Connections -- Increase wait_timeout; use pooling?

( Max_used_connections ) = 66 -- How many simultaneous connections you had (highwater mark).
[!!] Highest connection usage: 100% (152/151)
Those disagree; perhaps you restarted?

( open_files_limit ) = 1,024 -- ulimit -n -- To allow more files, change ulimit or /etc/security/limits.conf or in sysctl.conf (kern.maxfiles & kern.maxfilesperproc) or something else (OS dependent) -- If you get more tables, raising this will be important.

( Opened_tables ) = 43/hour
[!!] Table cache hit rate: 6% (400 open / 5K opened)
These disagree; perhaps there is no problem here.

[!!] Key buffer used: 18.3% (3M used / 16M cache)
[!!] Read Key buffer hit rate: 91.7% (743 cached / 62 reads)
Not a problem since there is virtually no MyISAM usage and key_buffer_size is only a tiny percentage of RAM.

19 issues flagged, out of 133 computed Variables/Status/Expressions

My take on Tuner's recommendations:

Run OPTIMIZE TABLE to defragment tables for better performance -- waste of time!
Enable the slow query log to troubleshoot bad queries -- yes
Reduce or eliminate persistent connections to reduce connection usage -- ok
Adjust your join queries to always utilize indexes -- yes (use slowlog to find them)
When making adjustments, make tmp_table_size/max_heap_table_size equal -- ok
Reduce your SELECT DISTINCT queries which have no LIMIT clause -- yawn
Increase table_open_cache gradually to avoid file descriptor limits --
    ok, but may not be critical
Read this before increasing table_open_cache over 64: http://bit.ly/1mi7c4C
Beware that open_files_limit (1024) variable -- noted
should be greater than table_open_cache ( 400) -- it is

max_connections (> 151) -- No; figure out why there are so many connections
wait_timeout ( 16M) -- probably not important
join_buffer_size (> 128.0K, or always use indexes with joins) -- might help, might not
tmp_table_size (> 16M) -- first look for other ways to improve queries
max_heap_table_size (> 16M)
table_open_cache (> 400)
innodb_buffer_pool_size (>= 872M) if possible. -- yes