aboutsummaryrefslogtreecommitdiff
path: root/docs/performance/slow-probesetdata-sql.org
diff options
context:
space:
mode:
Diffstat (limited to 'docs/performance/slow-probesetdata-sql.org')
-rw-r--r--docs/performance/slow-probesetdata-sql.org703
1 files changed, 703 insertions, 0 deletions
diff --git a/docs/performance/slow-probesetdata-sql.org b/docs/performance/slow-probesetdata-sql.org
new file mode 100644
index 0000000..919eb37
--- /dev/null
+++ b/docs/performance/slow-probesetdata-sql.org
@@ -0,0 +1,703 @@
+* 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. This table has doubled in size in the last 5 years.
+
+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 (item) and StrainId really means
+measurement type or trait measured(!)
+
+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 add a copy of the first table. Not exactly
+elegant but a quick fix for sure. We'll need an embedded procedure to keep it
+up-to-data.
+
+*** 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.
+
+** Result
+
+The final query is shown at the bottom of 'Exploration'. It takes 2 minutes
+on Penguin2 and Tux01. Essentially I took out the joins (which parsed the same
+table repeatedly) and added an index. The trick is to keep minimizing the query.
+
+The 2 minute query will do for now and it probably is no longer quadratic.
+
+We can probably improve things in the future by changing the way ProbeSetData
+is stored.
+
+
+** 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 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;
++-----------+-------+
+| Name | value |
++-----------+-------+
+| 100001_at | 6.414 |
+| 100001_at | 6.414 |
+| 100001_at | 6.414 |
+| 100001_at | 8.414 |
+| 100001_at | 8.414 |
++-----------+-------+
+5 rows in set (20.064 sec)
+#+END_SRC SQL
+
+#+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
+
+Now this query is fast because it traverses the ProbeSetData table only once and uses id as a starting point:
+
+#+BEGIN_SRC SQL
+MariaDB [db_webqtl]> select count(*) from (ProbeSetData,ProbeSetXRef) where ProbeSetXRef.ProbeSetFreezeId = 206 and id=ProbeSetId;
++----------+
+| count(*) |
++----------+
+| 10699448 |
++----------+
+1 row in set (4.429 sec)
+#+END_SRC
+
+#+BEGIN_SRC SQL
+select id,strainid,value from (ProbeSetData,ProbeSetXRef) where
+ ProbeSetXRef.ProbeSetFreezeId = 206 and id=ProbeSetId
+limit 5;
++--------+----------+-------+
+| id | strainid | value |
++--------+----------+-------+
+| 225088 | 1 | 7.33 |
+| 225088 | 2 | 7.559 |
+| 225088 | 3 | 7.84 |
+| 225088 | 4 | 7.835 |
+| 225088 | 5 | 7.652 |
++--------+----------+-------+
+5 rows in set (0.001 sec)
+#+END_SRC
+
+
+#+BEGIN_SRC SQL
+select id,strainid,value from (ProbeSetData,ProbeSetXRef) where ProbeSetXRef.ProbeSetFreezeId = 206 and id=ProbeSetId and strainid=4 limit 5;
++--------+----------+-------+
+| id | strainid | value |
++--------+----------+-------+
+| 225088 | 4 | 7.835 |
+| 225089 | 4 | 9.595 |
+| 225090 | 4 | 8.982 |
+| 225091 | 4 | 8.153 |
+| 225092 | 4 | 7.111 |
++--------+----------+-------+
+5 rows in set (0.000 sec)
+#+END_SRC
+
+#+BEGIN_SRC SQL
+select ProbeSet.name,strainid,probesetfreezeid,value from (ProbeSet,ProbeSetData,ProbeSetFreeze,ProbeSetXRef)
+where ProbeSetData.id=ProbeSetId
+ and (strainid=4 or strainid=5)
+ and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
+limit 5;
++---------+----------+------------------+-------+
+| name | strainid | probesetfreezeid | value |
++---------+----------+------------------+-------+
+| 4331726 | 4 | 206 | 7.835 |
+| 5054239 | 4 | 206 | 9.595 |
+| 4642578 | 4 | 206 | 8.982 |
+| 4398221 | 4 | 206 | 8.153 |
+| 5543360 | 4 | 206 | 7.111 |
++---------+----------+------------------+-------+
+5 rows in set (2.174 sec)
+#+END_SRC
+
+No more joins and super fast!!
+
+#+BEGIN_SRC SQL
+SELECT ProbeSet.Name,T4.StrainID,Probesetfreezeid,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 limit 5;
++---------+----------+------------------+---------+
+| Name | StrainID | Probesetfreezeid | value |
++---------+----------+------------------+---------+
+| 4331726 | 4 | 206 | 5.52895 |
+| 5054239 | 4 | 206 | 6.29465 |
+| 4642578 | 4 | 206 | 9.13706 |
+| 4398221 | 4 | 206 | 6.77672 |
+| 5543360 | 4 | 206 | 4.30016 |
++---------+----------+------------------+---------+
+5 rows in set (0.000 sec)
+#+END_SRC
+
+The difference is the use of ProbeSetId and DataId in ProbeSetFreeze
+
+: left join ProbeSetData as T4 on T4.StrainId=4 and T4.Id = ProbeSetXRef.DataId
+
+#+BEGIN_SRC SQL
+select ProbeSetData.id,ProbeSet.name,strainid,probesetfreezeid,value from (ProbeSet,ProbeSetData,ProbeSetFreeze,ProbeSetXRef)
+where ProbeSetData.id=ProbeSetId
+ and (strainid=4 or strainid=5)
+ and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
+limit 5;
++---------+----------+------------------+-------+
+| name | strainid | probesetfreezeid | value |
++---------+----------+------------------+-------+
+| 4331726 | 4 | 206 | 7.835 |
+| 5054239 | 4 | 206 | 9.595 |
+| 4642578 | 4 | 206 | 8.982 |
+| 4398221 | 4 | 206 | 8.153 |
+| 5543360 | 4 | 206 | 7.111 |
++---------+----------+------------------+-------+
+5 rows in set (2.174 sec)
+#+END_SRC
+
+
+#+BEGIN_SRC SQL
+MariaDB [db_webqtl]> select ProbeSetData.id,ProbeSet.name,strainid,probesetfreezeid,value from (ProbeSet,ProbeSetData,ProbeSetFreeze,ProbeSetXRef)
+ where ProbeSetData.id=ProbeSetId
+ and (strainid=4 or strainid=5)
+ and ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
+ limit 5;
++--------+---------+----------+------------------+-------+
+| id | name | strainid | probesetfreezeid | value |
++--------+---------+----------+------------------+-------+
+| 225088 | 4331726 | 4 | 206 | 7.835 |
+| 225089 | 5054239 | 4 | 206 | 9.595 |
+| 225090 | 4642578 | 4 | 206 | 8.982 |
+| 225091 | 4398221 | 4 | 206 | 8.153 |
+| 225092 | 5543360 | 4 | 206 | 7.111 |
++--------+---------+----------+------------------+-------+
+5 rows in set (2.085 sec)
+#+END_SRC
+
+
+#+BEGIN_SRC SQL
+MariaDB [db_webqtl]> SELECT T4.id,ProbeSet.Name,T4.StrainID,Probesetfreezeid,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 limit 5;
++----------+---------+----------+------------------+---------+
+| id | Name | StrainID | Probesetfreezeid | value |
++----------+---------+----------+------------------+---------+
+| 38574432 | 4331726 | 4 | 206 | 5.52895 |
+| 39254882 | 5054239 | 4 | 206 | 6.29465 |
+| 38867352 | 4642578 | 4 | 206 | 9.13706 |
+| 38637053 | 4398221 | 4 | 206 | 6.77672 |
+| 39715382 | 5543360 | 4 | 206 | 4.30016 |
++----------+---------+----------+------------------+---------+
+5 rows in set (0.001 sec)
+#+END_SRC
+
+Now you can see the difference.
+
+#+BEGIN_SRC SQL
+select ProbeSetData.id,ProbeSet.name,strainid,probesetfreezeid,value from (ProbeSet,ProbeSetData,ProbeSetFreeze,ProbeSetXRef)
+ where ProbeSetData.id=ProbeSetXRef.DataId
+ and (strainid=4 or strainid=5)
+ and ProbeSetXRef.ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSet.name = '4331726'
+ limit 5;
+
++----------+---------+----------+------------------+---------+
+| id | name | strainid | probesetfreezeid | value |
++----------+---------+----------+------------------+---------+
+| 38574432 | 4331726 | 4 | 206 | 5.52895 |
++----------+---------+----------+------------------+---------+
+#+END_SRC
+
+It worked!
+
+BUT IT IS SLOW for the full query. This is now due to this table being huge
+and DataID distributed through the table (sigh!).
+
+#+BEGIN_SRC SQL
+MariaDB [db_webqtl]> select count(*) from ProbeSetXRef;
++----------+
+| count(*) |
++----------+
+| 47713039 |
++----------+
+1 row in set (0.000 sec)
+#+END_SRC
+
+
+#+BEGIN_SRC SQL
+select ProbeSetData.id,ProbeSet.name,strainid,probesetfreezeid,value from (ProbeSet,ProbeSetData,ProbeSetFreeze,ProbeSetXRef)
+ where
+ ProbeSetXRef.ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetFreeze.Id = 206
+ and ProbeSetData.id=ProbeSetXRef.DataId
+ and (strainid=4 or strainid=5)
+ limit 5;
+
++----------+---------+----------+------------------+---------+
+| id | name | strainid | probesetfreezeid | value |
++----------+---------+----------+------------------+---------+
+| 38549183 | 4304920 | 4 | 206 | 4.97269 |
+| 38549184 | 4304921 | 4 | 206 | 6.25133 |
+| 38549185 | 4304922 | 4 | 206 | 6.03701 |
+| 38549186 | 4304923 | 4 | 206 | 9.10316 |
+| 38549187 | 4304925 | 4 | 206 | 8.90826 |
++----------+---------+----------+------------------+---------+
+5 rows in set (23.995 sec)
+
+select count(ProbeSetId) from ProbeSetXRef where ProbeSetFreezeId = 206;
++-------------------+
+| count(ProbeSetId) |
++-------------------+
+| 1236087 |
++-------------------+
+
+select count(ProbeSet.name) from (ProbeSet,ProbeSetXRef)
+ where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId;
++----------------------+
+| count(ProbeSet.name) |
++----------------------+
+| 1236087 |
++----------------------+
+1 row in set (7.126 sec)
+
+select ProbeSet.name,ProbeSetData.id from (ProbeSet,ProbeSetXRef,ProbeSetData)
+ where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetData.id = ProbeSetXRef.DataId
+;
+
+MariaDB [db_webqtl]> select count(ProbeSetData.id) from (ProbeSet,ProbeSetXRef,ProbeSetData) where ProbeSetFreezeId = 206 and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetData.id = ProbeSetXRef.DataId;
++------------------------+
+| count(ProbeSetData.id) |
++------------------------+
+| 114956091 |
++------------------------+
+1 row in set (35.836 sec)
+
+select count(*) from (ProbeSet,ProbeSetXRef,ProbeSetData) where ProbeSetFreezeId = 206 and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetData.id = ProbeSetXRef.DataId ;
++-----------+
+| count(*) |
++-----------+
+| 114956091 |
++-----------+
+1 row in set (35.392 sec)
+
+
+select ProbeSet.name,ProbeSetData.value from (ProbeSet,ProbeSetXRef,ProbeSetData)
+ where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetData.id = ProbeSetXRef.DataId
+;
+
+select count(value) from (ProbeSet,ProbeSetXRef,ProbeSetData) where ProbeSetFreezeId = 206 and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetData.id = ProbeSetXRef.DataId and strainid=5 ;
++--------------+
+| count(value) |
++--------------+
+| 1236087 |
++--------------+
+1 row in set (14.819 sec)
+
+
+select count(value) from (ProbeSet,ProbeSetXRef,ProbeSetData)
+where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetData.id = ProbeSetXRef.DataId
+ and ((strainid>=4 and strainid<=31) or strainid in (33,35,36,37,39,98,100,103))
+;
+
++--------------+
+| count(value) |
++--------------+
+| 43263045 |
++--------------+
+1 row in set (1 min 40.498 sec)
+
+select name,strainid,value from (ProbeSet,ProbeSetXRef,ProbeSetData)
+where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetData.id = ProbeSetXRef.DataId
+ and ((strainid>=4 and strainid<=31) or strainid in (33,35,36,37,39,98,100,103))
+limit 5;
++---------+----------+---------+
+| name | strainid | value |
++---------+----------+---------+
+| 4331726 | 4 | 5.52895 |
+| 4331726 | 5 | 6.76158 |
+| 4331726 | 6 | 6.06911 |
+| 4331726 | 7 | 6.24858 |
+| 4331726 | 8 | 6.36076 |
++---------+----------+---------+
+
+select name,strainid,value from (ProbeSet,ProbeSetXRef,ProbeSetData)
+where ProbeSetFreezeId = 206
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetData.id = ProbeSetXRef.DataId
+ and ((strainid>=4 and strainid<=31) or strainid in (33,35,36,37,39,98,100,103))
+;
+
+#+END_SRC
+
+The final query works in 2.2 minutes on both Penguin2 and Tux01.
+
+** Original query
+
+This is the original query generated by GN2 that takes 1 hour on
+Penguin2 and 3 minutes on Tux01. Note it fetches all values for these 'traits' so essentially
+traverses the full 53GB database table (and even larger index) for each of
+them.
+
+#+BEGIN_SRC SQL
+SELECT ProbeSet.Name,T4.value, T5.value, T6.value, T7.value, T8.value, T9.value, T10.value, T11.value, T12.value, T13.value, T14.value, T15.value, T16.value, T17.value, T18.value, T19.value, T20.value, T21.value, T22.value, T23.value, T24.value, T25.value, T26.value, T28.value,
+ T29.value, T30.value, T31.value, T33.value, T35.value, T36.value, T37.value, T39.value,
+ T98.value, T100.value, T103.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
+ left join ProbeSetData as T6 on T6.Id = ProbeSetXRef.DataId and T6.StrainId=6
+ left join ProbeSetData as T7 on T7.Id = ProbeSetXRef.DataId and T7.StrainId=7
+ left join ProbeSetData as T8 on T8.Id = ProbeSetXRef.DataId and T8.StrainId=8
+ left join ProbeSetData as T9 on T9.Id = ProbeSetXRef.DataId and T9.StrainId=9
+ left join ProbeSetData as T10 on T10.Id = ProbeSetXRef.DataId and T10.StrainId=10
+ left join ProbeSetData as T11 on T11.Id = ProbeSetXRef.DataId and T11.StrainId=11
+ left join ProbeSetData as T12 on T12.Id = ProbeSetXRef.DataId and T12.StrainId=12
+ left join ProbeSetData as T13 on T13.Id = ProbeSetXRef.DataId and T13.StrainId=13
+ left join ProbeSetData as T14 on T14.Id = ProbeSetXRef.DataId and T14.StrainId=14
+ left join ProbeSetData as T15 on T15.Id = ProbeSetXRef.DataId and T15.StrainId=15
+ left join ProbeSetData as T16 on T16.Id = ProbeSetXRef.DataId and T16.StrainId=16
+ left join ProbeSetData as T17 on T17.Id = ProbeSetXRef.DataId and T17.StrainId=17
+ left join ProbeSetData as T18 on T18.Id = ProbeSetXRef.DataId and T18.StrainId=18
+ left join ProbeSetData as T19 on T19.Id = ProbeSetXRef.DataId and T19.StrainId=19
+ left join ProbeSetData as T20 on T20.Id = ProbeSetXRef.DataId and T20.StrainId=20
+ left join ProbeSetData as T21 on T21.Id = ProbeSetXRef.DataId and T21.StrainId=21
+ left join ProbeSetData as T22 on T22.Id = ProbeSetXRef.DataId and T22.StrainId=22
+ left join ProbeSetData as T23 on T23.Id = ProbeSetXRef.DataId and T23.StrainId=23
+ left join ProbeSetData as T24 on T24.Id = ProbeSetXRef.DataId and T24.StrainId=24
+ left join ProbeSetData as T25 on T25.Id = ProbeSetXRef.DataId and T25.StrainId=25
+ left join ProbeSetData as T26 on T26.Id = ProbeSetXRef.DataId and T26.StrainId=26
+ left join ProbeSetData as T28 on T28.Id = ProbeSetXRef.DataId and T28.StrainId=28
+ left join ProbeSetData as T29 on T29.Id = ProbeSetXRef.DataId and T29.StrainId=29
+ left join ProbeSetData as T30 on T30.Id = ProbeSetXRef.DataId and T30.StrainId=30
+ left join ProbeSetData as T31 on T31.Id = ProbeSetXRef.DataId and T31.StrainId=31
+ left join ProbeSetData as T33 on T33.Id = ProbeSetXRef.DataId and T33.StrainId=33
+ left join ProbeSetData as T35 on T35.Id = ProbeSetXRef.DataId and T35.StrainId=35
+ left join ProbeSetData as T36 on T36.Id = ProbeSetXRef.DataId and T36.StrainId=36
+ left join ProbeSetData as T37 on T37.Id = ProbeSetXRef.DataId and T37.StrainId=37
+ left join ProbeSetData as T39 on T39.Id = ProbeSetXRef.DataId and T39.StrainId=39
+ left join ProbeSetData as T98 on T98.Id = ProbeSetXRef.DataId and T98.StrainId=98
+ left join ProbeSetData as T100 on T100.Id = ProbeSetXRef.DataId and T100.StrainId=100
+ left join ProbeSetData as T103 on T103.Id = ProbeSetXRef.DataId and T103.StrainId=103
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSetFreeze.Name = 'UMUTAffyExon_0209_RMA'
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ order by ProbeSet.Id
+#+END_SRC
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-27 08:03:50 +0000