path: root/docs/performance/slow-probesetdata-sql.org

* Slow ProbeSetData SQL query

** The case

We were looking to optimize a query for correlations. On Penguin2 (standard
drives, RAID5) the query took 1 hour. On Tux01 (solid state NVME) it took 6
minutes. Adding an index for StrainId (see explorations below) reduced that
query to 3 minutes - which is kinda acceptable. The real problem, however is
that this is a quadratic search - so it will get worse quickly - and we need
to solve it.

So what does ProbeSetData contain?

#+BEGIN_SRC SQL
select * from ProbeSetData limit 5;
+----+----------+-------+
| Id | StrainId | value |
+----+----------+-------+
|  1 |        1 | 5.742 |
|  1 |        2 | 5.006 |
|  1 |        3 | 6.079 |
|  1 |        4 | 6.414 |
|  1 |        5 | 4.885 |
+----+----------+-------+
#+END_SRC

You can see Id is sectioned in the file (and there are not that many Ids) but
StrainId is *distributed* through the database file and some 'StrainIds' match
many data points. Id stands for Dataset and StrainId really means Measurement(!)

Our query looked for 1,236,088 measurement distributed over a 53Gb file (and
an even larger index file). Turns out the full table is read many many times
over for one particular query pivoting on strainid...

We have the following options:

1. Reorder the table
2. Use column based storage
3. Use compression
4. Use a different storage layout

*** Reorder the table

We could reorder the table on StrainID which would make this search much
faster but it would many common (dataset) queries slower. So, that is not a
great idea. One thing we could try is create a copy of the first table.

*** Use column based storage

Column-based storage works when you need a subset of the data in the table. In
this case it won't help much because, even though the pivot itself would be
faster, we still traverse all data to get IDs and values.

*** Use compression

Compression reduces the size on disk and may be beneficial. Real life metrics
on the internet don't show that much improvement, but we could try native
compression and/or ZFS.

*** Use a different storage layout

My prediction is that we can not get around this.


** Exploration

In the following steps I reduce the complex case to a simple case explaining
the performance bottleneck we are seeing today. I did not add comments, but
you can see what I did.

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select * from ProbeSetXRef limit 2;
+------------------+------------+--------+------------+--------------------+------------+------------------+---------------------+------------+------------------+--------+--------------------+------+
| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old  | LRS_old            | pValue_old | mean             | se                  | Locus      | LRS              | pValue | additive           | h2   |
+------------------+------------+--------+------------+--------------------+------------+------------------+---------------------+------------+------------------+--------+--------------------+------+
|                1 |          1 |      1 | 10.095.400 |   13.3971627898894 |      0.163 | 5.48794285714286 | 0.08525787814808819 | rs13480619 |  12.590069931048 |  0.269 |        -0.28515625 | NULL |
|                1 |          2 |      2 | D15Mit189  | 10.042057464356201 |      0.431 | 9.90165714285714 |  0.0374686634976217 | rs29535974 | 10.5970737900941 |  0.304 | -0.116783333333333 | NULL |
+------------------+------------+--------+------------+--------------------+------------+------------------+---------------------+------------+------------------+--------+--------------------+------+
2 rows in set (0.001 sec)
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> SELECT ProbeSet.Name,T4.value FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)  left join ProbeSetData as T4 on T4.Id = ProbeSetXRef.DataId
    ->                         and T4.StrainId=4
    -> limit 5;
+------+-------+
| Name | value |
+------+-------+
| NULL | 6.414 |
| NULL | 6.414 |
| NULL | 6.414 |
| NULL | 6.414 |
| NULL | 6.414 |
+------+-------+
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> SELECT ProbeSet.Name,T4.value,T5.value FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
left join ProbeSetData as T4 on T4.Id = ProbeSetXRef.DataId and T4.StrainId=4
left join ProbeSetData as T5 on T5.Id = ProbeSetXRef.DataId and T5.StrainId=5
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id  limit 5;

+---------+---------+
| Name    | value   |
+---------+---------+
| 4331726 | 5.52895 |
| 5054239 | 6.29465 |
| 4642578 | 9.13706 |
| 4398221 | 6.77672 |
| 5543360 | 4.30016 |
+---------+---------+
#+END_SRC

#+BEGIN_SRC SQL
SELECT ProbeSet.Name,T4.value FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
left join ProbeSetData as T4 on T4.Id = ProbeSetXRef.DataId and T4.StrainId=4
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id ;

1236087 rows in set (19.173 sec)
#+END_SRC

#+BEGIN_SRC SQL
SELECT ProbeSet.Name,T4.value FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
left join ProbeSetData as T4 on T4.StrainId=4 and T4.Id = ProbeSetXRef.DataId
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id ;

1236087 rows in set (19.173 sec)
#+END_SRC

#+BEGIN_SRC SQL
SELECT ProbeSet.Name FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id ;
#+END_SRC

Find all the probeset 'names' (probe sequence included) for one dataset:

#+BEGIN_SRC SQL
SELECT count(DISTINCT ProbeSet.Name) FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)          WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id                       and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'            and ProbeSet.Id = ProbeSetXRef.ProbeSetId                                   order by ProbeSet.Id;
+-------------------------------+
| count(DISTINCT ProbeSet.Name) |
+-------------------------------+
|                       1236087 |
+-------------------------------+
#+END_SRC

Now for each of those probesets:

#+BEGIN_SRC SQL
SELECT ProbeSet.Name,T4.value FROM (ProbeSet, ProbeSetXRef)
left join ProbeSetData as T4 on T4.StrainId=4 and T4.Id = ProbeSetXRef.DataId
WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id limit 5;
#+END_SRC

ProbeSetXRef contains the p-values:

#+BEGIN_SRC SQL
select * from ProbeSetXRef limit 5;
+------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+------------+------------------+--------+--------------------+------+
| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old  | LRS_old            | pValue_old | mean              | se                  | Locus      | LRS              | pValue | additive           | h2   |
+------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+------------+------------------+--------+--------------------+------+
|                1 |          1 |      1 | 10.095.400 |   13.3971627898894 |      0.163 |  5.48794285714286 | 0.08525787814808819 | rs13480619 |  12.590069931048 |  0.269 |        -0.28515625 | NULL |
|                1 |          2 |      2 | D15Mit189  | 10.042057464356201 |      0.431 |  9.90165714285714 |  0.0374686634976217 | rs29535974 | 10.5970737900941 |  0.304 | -0.116783333333333 | NULL |
#+END_SRC


#+BEGIN_SRC SQL
SELECT count(T4.value) FROM (ProbeSet, ProbeSetXRef)
left join ProbeSetData as T4 on T4.StrainId=4 and T4.Id = ProbeSetXRef.DataId
WHERE ProbeSet.Id = ProbeSetXRef.ProbeSetId ;
#+END_SRC


#+BEGIN_SRC SQL
SELECT count(T4.value) FROM (ProbeSet, ProbeSetXRef) left join ProbeSetData as T4 on T4.StrainId=4 limit 5;
#+END_SRC

#+BEGIN_SRC SQL
select value from (ProbeSetData) where StrainId=4 limit 5;
#+END_SRC

So, this is the sloooow baby:

#+BEGIN_SRC SQL
select count(id) from (ProbeSetData) where StrainId=4;

| ProbeSetData |          0 | DataId   |            2 | StrainId    | A         |  4852908856 |     NULL | NULL   |      | BTREE      |         |               |

-rw-rw---- 1 mysql mysql  53G Mar  3 23:49 ProbeSetData.MYD
-rw-rw---- 1 mysql mysql  66G Mar  4 03:00 ProbeSetData.MYI
#+END_SRC

#+BEGIN_SRC SQL
create index strainid on ProbeSetData(StrainId);
Stage: 1 of 2 'Copy to tmp table'   8.77% of stage done
Stage: 2 of 2 'Enabling keys'      0% of stage done
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> create index strainid on ProbeSetData(StrainId);
Query OK, 5111384047 rows affected (2 hours 56 min 25.807 sec)
Records: 5111384047  Duplicates: 0  Warnings: 0
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(id) from (ProbeSetData) where StrainId=4;

+-----------+
| count(id) |
+-----------+
|  14267545 |
+-----------+
1 row in set (19.707 sec)
#+END_SRC


#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(*) from ProbeSetData where strainid = 140;
+----------+
| count(*) |
+----------+
| 10717771 |
+----------+
1 row in set (10.161 sec)
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(*) from ProbeSetData where strainid = 140 and id=4;
+----------+
| count(*) |
+----------+
|        0 |
+----------+
1 row in set (0.000 sec)
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(*) from ProbeSetData where strainid = 4 and id=4;
+----------+
| count(*) |
+----------+
|        1 |
+----------+
1 row in set (0.000 sec)
#+END_SRC


#+BEGIN_SRC SQL
select id from ProbeSetFreeze where id=1;

WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
order by ProbeSet.Id  limit 5;
#+END_SRC

#+BEGIN_SRC SQL
select count(ProbeSetId) from ProbeSetXRef where ProbeSetFreezeId=1;
+-------------------+
| count(ProbeSetId) |
+-------------------+
|             12422 |
+-------------------+
1 row in set (0.006 sec)
#+END_SRC


#+BEGIN_SRC SQL
select count(ProbeSetId) from (ProbeSetXRef,ProbeSetFreeze) where
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA';
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(ProbeSetId) from (ProbeSetXRef,ProbeSetFreeze) where
    -> ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
    -> and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA';
+-------------------+
| count(ProbeSetId) |
+-------------------+
|           1236087 |
+-------------------+
1 row in set (0.594 sec)
#+END_SRC

ProbeSetXRef.ProbeSetFreezeId is 206, so

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(ProbeSetId) from (ProbeSetXRef) where ProbeSetXRef.ProbeSetFreezeId = 206;
+-------------------+
| count(ProbeSetId) |
+-------------------+
|           1236087 |
+-------------------+
1 row in set (0.224 sec)
#+END_SRC

#+BEGIN_SRC SQL
MariaDB [db_webqtl]> select count(*) from ProbeSetData where strainid = 1 and id=4;
+----------+
| count(*) |
+----------+
|        1 |
+----------+
1 row in set (0.000 sec)
#+END_SRC