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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 |