Improving performance for simple left join in postgreSQL - sql

I am trying to do a left join between two tables in a postgreSQL database and finding it takes about 14 minutes to run. From existing SO posts, it seems like this type of join should be on the order of seconds, so I'd like to know how to improve the performance of this join. I'm running 64-bit postgreSQL version 9.4.4 on a Windows 8 machine w/ 8 GB RAM, using pgAdmin III. The table structures are as follows:
Table A: "parcels_qtr":
parcel (text) | yr (int) | qtr (text) | lpid (pk, text) |
Has 15.5 million rows, each column is indexed, and "lpid" is the primary key. I also ran this table through a standard vacuum process.
Table B: "postalvac_qtr":
parcel (text) | yr (int) | qtr (text) | lpid (pk, text) | vacCountY (int) |
Has 618,000 records, all fields except "vacCountY" are indexed and "lpid" is the primary key. This also has gone through a standard vacuum process.
When running with data output, it takes about 14 min. When running with explain (analyze, buffers) it takes a little over a minute. First question - is this difference in performance wholly attributable to printing the data or is something else going on here?
And second question, can I get this run time down to a few seconds?
Here is my SQL code:
EXPLAIN (ANALYZE, BUFFERS)
select a.parcel,
a.lpid,
a.yr,
a.qtr,
b."vacCountY"
from parcels_qtr as a
left join postalvac_qtr as b
on a.lpid = b.lpid;
And here are the results of my explain statement: https://explain.depesz.com/s/uKkK
I'm pretty new to postgreSQL so patience and explanations would be greatly appreciated!

You're asking the DB to do quite a bit of work. Just looking at the explain plan, it's:
Read in an entire table (postalvac_qtr)
Build a hash based on lpid
Read in an entire other, much larger, table (parcels_qtr)
Hash each of the 15MM lpids, and match them to the existing hash table
How large are these tables? You can check this by issuing:
SELECT pg_size_pretty(pg_relation_size('parcels_qtr'));
I'm almost certain that this hash join is spilling out to disk, and the way it's structured ("give me all of the data from both of these tables"), there's no way it won't.
The indices don't help, and can't. As long as you're asking for the entirety of a table, using an index would only make things slower -- postgres has to traverse the entire table anyway, so it might as well issue a sequential scan.
As for why the query has different performance than the explain analyze, I suspect you're correct. A combination of 1- sending 15M rows to your client, and 2- trying to display it, is going to cause a significant slowdown above and beyond the actual query.
So, what can you do about it?
First, what is this query trying to do? How often do you want to grab all of the data in those two tables, completely unfiltered? If it's very common, you may want to consider going back to the requirements stage and figuring out another way to address that need (e.g. would it be reasonable to grab all the data for a given year and quarter instead?). If it's uncommon (say, a daily export), then 1-14min might be fine.
Second, you should make sure that your tables aren't bloated. If you experience significant update or delete traffic on your tables, that can grow them over time. The autovacuum daemon is there to help deal with this, but occasionally issuing a vacuum full will also help.
Third, you can try tuning your DB config. In postgresql.conf, there are parameters for things like the expected amount of RAM that your server can use for disk cache, and the amount of RAM the server can use for sorting or joining (before it spills out to disk). By tinkering with these sorts of parameters, you might be able to improve the speed.
Fourth, you might want to revisit your schema. Do you want year and quarter as two separate columns, or would you be better off with a single column of the date type? Do you want a text key, or would you be better off with a bigint (either serial or derived from the text column), which will likely join more quickly? Are the parcel, yr, and qtr fields actually needed in both tables, or are they duplicate data in one table?
Anyway, I hope this helps.

Related

SQL Table causes slow running Queries

I have a sql table that has approximately 6,000 records with 17 columns each. If I do a basic search on the table (i.e. Select * from table_Orders)... it takes 1.5 minutes to return all the records! Any query that I run using this table is also very slow. I have reindexed the table so fragmentation is not an issue. This table has 2 nvarchar(max) columns in it that is storing xml data. Returning the table without these columns is extremely fast (less than 1 second). So, i'm guessing it's the xml data that is bogging down the queries. Is there anything I can do to speed up performance of queries that utilize columns with xml in them? Any insight will be greatly appreciated. I don't typically work with xml within sql, so I don't even know where to start.
This sounds like network speed and NOT search times. Even a table scan of 6000 rows only takes a fraction of a second - to search all the rows. Returning those rows to a client though... you're downloading all that data, so you're going to see a difference when you retrieve a lot of it. This has nothing to do with "query performance" and there isn't anything you can do about it unless you can make the network faster or deliver less data.
You can test this by issuing queries searching for a key in your clustered index. Assuming you have a clustered index on RowID...
select RowId, NonXmlColumn where RowId = 3 -- or some other reasonable key
select RowId, XmlColumn where RowId = 3
The search time for those queries will be the same. So, any difference in speed can be attributed to the network.
I would not store that data in a table. I would not store in VARCHAR if I did. Not to sound like a jerk.
SQL Server has a xml datatype: http://msdn.microsoft.com/en-us/library/hh403385.aspx
It says there is limitations. You should see what applies to your scenario.
If you need to preserve the XML - stick it somewhere else and pull from it what ever fields you'll need to search on.

Simple Select, returns 1400 rows, takes 360ms?

I have a query that returns me 1400 rows.
It's basic.
SELECT * FROM dbo.entity_event ee
That is taking between 250 and 380ms, averaging though, on the 360ms. I'd expect this to be much quicker. I am running it on a laptop though, but an i7, 8gb, SSD. Does that seem normal, or should it be quicker? The table only has the total result set. No Where clause.
Running:
SELECT * FROM dbo.entity_event ee WHERE entity_event_type_id = 1
Takes the same time.
There is a clustered index on the primary key (id) in the table.
The table has around 15 columns. Mainly dates, ints and decimal(16,2).
If it seems slow, what can I look at to improve this? I do expect the table to become rather large as the system gets used.
I'm unable to track this on my live site, as the host doesn't allow SQL Profile to connect (Permissions). I can only check on my dev machine. It doesn't seem quick when live though.
The issue originates from a VIEW that I have, which is taking 643ms average. It has 8 joined tables, 4 of which are OUTER joins, ruling out the option of an indexed view.
The view, however, does use the column names, including other logic (CASE... ISNULL etc).
EDIT: I notice that SELECT TOP 10 ... Takes 1ms. SELECT TOP 500 .. Takes 161ms... So, it does seem liniar, and related to the volume of data. I'm wondering if this can be improved?
Execution plan:
This looks normal to me as it appears it's doing a full scan regardless of the WHERE clause--because the entity_event_type_id is not your PK nor indexed. So putting that WHERE clause will not help since it's not indexed.
Doing the Top N will help because it knows it doesn't need to scan the whole clustered pk index.
So...Yes it can be improved--if you index entity_event_type_id you would expect a faster time with that WHERE clause. But as always...index it only if you really will be using that field in WHERE clauses often.
--Jim

Will one query run faster than multiple queries, if they are deleting the same amount of records

I have a table like this:
Table company
companyid | companyname | owner |
5 |coffecompany |Mike |
6 |juicecompany |Mike |
For some reason, I need to use this:
DELETE FROM company WHERE companyid='5';
DELETE FROM company WHERE companyid='6';
instead of
DELETE FROM company WHERE owner='Mike';
But I wonder if the second choice run faster, if it does, will it run much faster? In the future, I may have to use it to delete a large amount of records, so I really need to know.
delete from company where companyId in (5, 6); should always be faster, even though the difference might be negligible if eg. you've got proper indexes, no concurrent queries, no issues with locking etc.
Note that my query is for MS SQL, if your database server allows using the same construct (ie. specifying all the values in such concise way), you should probably use it, if not, go with something like delete from company where companyId = 5 or companyId = 6; Also, don't use string literals if companyid is a number (is the table column actually a number, or a text?).
In any case, it gives the server more lee-way in implementing the actual operation, and DB servers tend to be very good at query optimization.
One possible bottle-neck for deletion could be in the transaction logs, however. It might very well be that if you're deleting a huge amount of rows at once, it would be better to do a few separate deletes in separate transactions to fit within transaction size limits.
Generally, SQL is language operating on sets of data so second query will be much faster for huge amount of rows.
First choice might be slower as you'll have to send query text as many times as you have rows to delete. Imagine network traffic if you want to delete 1 000 000 rows.
On small amounts of rows probably you won't be able to see any difference.
If you are using Oracle, think of using bind variable :
execute immediate 'DELETE FROM company WHERE companyid=:ID' USING 6;
But other than that, there is no specific answer to your question, you need to benchmark yourself, it depends on the amount of data, your indexes etc...
When using Where clause in a query, RDBMS will go to find the result set applying the condition.
Normally RDBMS will do a full-table-scan to find the result set, it means that any records will be investigated to see if the condition is matched. Based on the table size that will be time consuming.
Above approach will differed when when the column(s) listed in the where condition are indexed.
Indexing is a way of sorting a number of records on multiple fields. Creating an index on a field in a table creates another data structure which holds the field value, and pointer to the record it relates to. This index structure is then sorted, allowing Binary Searches to be performed on it.
As a simplified sample:
A linear search (full-table-scan) on the field A of table T containing N records would require an average of N/2 accesses to find a value.
If 'A' field is indexed then a sorted binary search will requiring an average of log2 N block accesses. Asuming that N=1,000,000 then we will have
N/2 = 500,000
log2 1000000 = 19.93 = 20
Instantly we can see this is a drastic improvement.
It looks like the companyid is the primary key of company table, if so any primary key column will be indexed automatically by RDMS and the search will be more effective than searching by owner.

SQL Query Slow? Should it be?

Using SQLite, Got a table with ~10 columns. Theres ~25million rows.
That table has an INDEX on 'sid, uid, area, type'.
I run a select like so:
SELECT sid from actions where uid=1234 and area=1 and type=2
That returns me 1571 results, and takes 4 minutes to complete.
Is that sane?
I'm far from an SQL expert, so hopefully someone can fill me in on what I'm missing. Why could this possibly take 4+ minutes with everything indexed?
Any recommended resources to learn about achieving high SQL performance? I feel like a lot of the Google results just give me opinions or anecdotes, I wouldn't mind a solid book.
Create uid+area+type index instead, or uid+area+type+sid
Since the index starts with the sid column, it must do a scan (start at the beginning, read to the end) of either the index or the table to find your data matching the other 3 columns. This means it has to read all 25 million rows to find the answer. Even if it's reading just the rows of the index rather than the table, that's a lot of work.
Imagine a phone book of the greater New York metropolitan area, organized by (with an 'index' on) Last Name, First Name.
You submit SELECT [Last Name] FROM NewYorkPhoneBook WHERE [First Name] = 'Thelma'
It has to read all 25 million entries to find all those Thelmas. Unless you either specify the last name and can then turn directly to the page where that last name first appers (a seek), or have an index organized by First Name (a seek on the index followed by a seek on the table, aka a "bookmark lookup"), there's no way around it.
The index you would create to make your query faster is on uid, area, type. You could include sid, though leave it out if sid is part of the primary key.
Note: Tables often do have multiple indexes. Just note that the more indexes, the slower the write performance. Unnecessary indexes can slow overall performance, sometimes radically so. Testing and eventually experience will help guide you in this. Also, reasoning it out as a real-world problem (like my phone book examples) can really help. If it wouldn't make sense with phone books (and separate phone book indexes) then it probably won't make sense in the database.
One more thing: even if you put an index on those columns, if your query is going to end up pulling a great percentage of the rows in the main table, it will still be cheaper to scan the table rather than do the bookmark lookup (seek the index then seek the table for each row found). The exact "tipping point" of whether to do a bookmark lookup with a seek, or to do a table scan isn't something I can tell you off the top of my head, but it is based on solid math.
The index is not really usefull as it does start with the wrong field... which means a table scan.
Looks like you have a normal computer there, not something made for databases. I run table scans over 650 million rows in about a minute on my lower end db server, but that means reading about a gigabyte per second from the discs, which are a RAID of 10k RM discs - RAID 10. Just to say that basically... that databases love IO, and that in a degree that you have never seen before. Basically larger db servers have many discs to satisfy the IOPS (IO per second) requirement. I have seen a server with 190 discs.
So, you ahve two choices: beed up your IOPS capability (means spending money), or set up indices that get used because they are "proper".
Proper means: an index only is usefull if the fields it contains are used from left to right. Not necessarily in the same order... but if a field is missed there is a chance the SQL System decides it is not worth pursuing the index and instead goes table scan (as in your case).
When you create your new index on uid, area and type, you should also do a select distinct on each one to determine which has the fewest distinct entries, then create your index such that the fewer the differences the earlier they show up in the index definition.

SQL: Inner joining two massive tables

I have two massive tables with about 100 million records each and I'm afraid I needed to perform an Inner Join between the two. Now, both tables are very simple; here's the description:
BioEntity table:
BioEntityId (int)
Name (nvarchar 4000, although this is an overkill)
TypeId (int)
EGM table (an auxiliar table, in fact, resulting of bulk import operations):
EMGId (int)
PId (int)
Name (nvarchar 4000, although this is an overkill)
TypeId (int)
LastModified (date)
I need to get a matching Name in order to associate BioEntityId with the PId residing in the EGM table. Originally, I tried to do everything with a single inner join but the query appeared to be taking way too long and the logfile of the database (in simple recovery mode) managed to chew up all the available disk space (that's just over 200 GB, when the database occupies 18GB) and the query would fail after waiting for two days, If I'm not mistaken. I managed to keep the log from growing (only 33 MB now) but the query has been running non-stop for 6 days now and it doesn't look like it's gonna stop anytime soon.
I'm running it on a fairly decent computer (4GB RAM, Core 2 Duo (E8400) 3GHz, Windows Server 2008, SQL Server 2008) and I've noticed that the computer jams occasionally every 30 seconds (give or take) for a couple of seconds. This makes it quite hard to use it for anything else, which is really getting on my nerves.
Now, here's the query:
SELECT EGM.Name, BioEntity.BioEntityId INTO AUX
FROM EGM INNER JOIN BioEntity
ON EGM.name LIKE BioEntity.Name AND EGM.TypeId = BioEntity.TypeId
I had manually setup some indexes; both EGM and BioEntity had a non-clustered covering index containing TypeId and Name. However, the query ran for five days and it did not end either, so I tried running Database Tuning Advisor to get the thing to work. It suggested deleting my older indexes and creating statistics and two clustered indexes instead (one on each table, just containing the TypeId which I find rather odd - or just plain dumb - but I gave it a go anyway).
It has been running for 6 days now and I'm still not sure what to do...
Any ideas guys? How can I make this faster (or, at least, finite)?
Update:
- Ok, I've canceled the query and rebooted the server to get the OS up and running again
- I'm rerunning the workflow with your proposed changes, specifically cropping the nvarchar field to a much smaller size and swapping "like" for "=". This is gonna take at least two hours, so I'll be posting further updates later on
Update 2 (1PM GMT time, 18/11/09):
- The estimated execution plan reveals a 67% cost regarding table scans followed by a 33% hash match. Next comes 0% parallelism (isn't this strange? This is the first time I'm using the estimated execution plan but this particular fact just lifted my eyebrow), 0% hash match, more 0% parallelism, 0% top, 0% table insert and finally another 0% select into. Seems the indexes are crap, as expected, so I'll be making manual indexes and discard the crappy suggested ones.
I'm not an SQL tuning expert, but joining hundreds of millions of rows on a VARCHAR field doesn't sound like a good idea in any database system I know.
You could try adding an integer column to each table and computing a hash on the NAME field that should get the possible matches to a reasonable number before the engine has to look at the actual VARCHAR data.
For huge joins, sometimes explicitly choosing a loop join speeds things up:
SELECT EGM.Name, BioEntity.BioEntityId INTO AUX
FROM EGM
INNER LOOP JOIN BioEntity
ON EGM.name LIKE BioEntity.Name AND EGM.TypeId = BioEntity.TypeId
As always, posting your estimated execution plan could help us provide better answers.
EDIT: If both inputs are sorted (they should be, with the covering index), you can try a MERGE JOIN:
SELECT EGM.Name, BioEntity.BioEntityId INTO AUX
FROM EGM
INNER JOIN BioEntity
ON EGM.name LIKE BioEntity.Name AND EGM.TypeId = BioEntity.TypeId
OPTION (MERGE JOIN)
First, 100M-row joins are not at all unreasonable or uncommon.
However, I suspect the cause of the poor performance you're seeing may be related to the INTO clause. With that, you are not only doing a join, you are also writing the results to a new table. Your observation about the log file growing so huge is basically confirmation of this.
One thing to try: remove the INTO and see how it performs. If the performance is reasonable, then to address the slow write you should make sure that your DB log file is on a separate physical volume from the data. If it isn't, the disk heads will thrash (lots of seeks) as they read the data and write the log, and your perf will collapse (possibly to as little as 1/40th to 1/60th of what it could be otherwise).
Maybe a bit offtopic, but:
" I've noticed that the computer jams occasionally every 30 seconds (give or take) for a couple of seconds."
This behavior is characteristic for cheap RAID5 array (or maybe for single disk) while copying (and your query mostly copies data) gigabytes of information.
More about problem - can't you partition your query into smaller blocks? Like names starting with A, B etc or IDs in specific ranges? This could substantially decrease transactional/locking overhead.
I'd try maybe removing the 'LIKE' operator; as you don't seem to be doing any wildcard matching.
As recommended, I would hash the name to make the join more reasonable. I would strongly consider investigating assigning the id during the import of batches through a lookup if it is possible, since this would eliminate the need to do the join later (and potentially repeatedly having to perform such an inefficient join).
I see you have this index on the TypeID - this would help immensely if this is at all selective. In addition, add the column with the hash of the name to the same index:
SELECT EGM.Name
,BioEntity.BioEntityId
INTO AUX
FROM EGM
INNER JOIN BioEntity
ON EGM.TypeId = BioEntity.TypeId -- Hopefully a good index
AND EGM.NameHash = BioEntity.NameHash -- Should be a very selective index now
AND EGM.name LIKE BioEntity.Name
Another suggestion I might offer is try to get a subset of the data instead of processing all 100 M rows at once to tune your query. This way you don't have to spend so much time waiting to see when your query is going to finish. Then you could consider inspecting the query execution plan which may also provide some insight to the problem at hand.
100 million records is HUGE. I'd say to work with a database that large you'd require a dedicated test server. Using the same machine to do other work while performing queries like that is not practical.
Your hardware is fairly capable, but for joins that big to perform decently you'd need even more power. A quad-core system with 8GB would be a good start. Beyond that you have to make sure your indexes are setup just right.
do you have any primary keys or indexes? can you select it in stages? i.e. where name like 'A%', where name like 'B%', etc.
I had manually setup some indexes; both EGM and BioEntity had a non-clustered covering index containing TypeId and Name. However, the query ran for five days and it did not end either, so I tried running Database Tuning Advisor to get the thing to work. It suggested deleting my older indexes and creating statistics and two clustered indexes instead (one on each table, just containing the TypeId which I find rather odd - or just plain dumb - but I gave it a go anyway).
You said you made a clustered index on TypeId in both tables, although it appears you have a primary key on each table already (BioEntityId & EGMId, respectively). You do not want your TypeId to be the clustered index on those tables. You want the BioEntityId & EGMId to be clustered (that will physically sort your data in order of the clustered index on disk. You want non-clustered indexes on foreign keys you will be using for lookups. I.e. TypeId. Try making the primary keys clustered, and adding a non-clustered index on both tables that ONLY CONTAINS TypeId.
In our environment we have a tables that are roughly 10-20 million records apiece. We do a lot of queries similar to yours, where we are combining two datasets on one or two columns. Adding an index for each foreign key should help out a lot with your performance.
Please keep in mind that with 100 million records, those indexes are going to require a lot of disk space. However, it seems like performance is key here, so it should be worth it.
K. Scott has a pretty good article here which explains some issues more in depth.
Reiterating a few prior posts here (which I'll vote up)...
How selective is TypeId? If you only have 5, 10, or even 100 distinct values across your 100M+ rows, the index does nothing for you -- particularly since you're selecting all the rows anyway.
I'd suggest creating a column on CHECKSUM(Name) in both tables seems good. Perhaps make this a persisted computed column:
CREATE TABLE BioEntity
(
BioEntityId int
,Name nvarchar(4000)
,TypeId int
,NameLookup AS checksum(Name) persisted
)
and then create an index like so (I'd use clustered, but even nonclustered would help):
CREATE clustered INDEX IX_BioEntity__Lookup on BioEntity (NameLookup, TypeId)
(Check BOL, there are rules and limitations on building indexes on computed columns that may apply to your environment.)
Done on both tables, this should provide a very selective index to support your query if it's revised like this:
SELECT EGM.Name, BioEntity.BioEntityId INTO AUX
FROM EGM INNER JOIN BioEntity
ON EGM.NameLookup = BioEntity.NameLookup
and EGM.name = BioEntity.Name
and EGM.TypeId = BioEntity.TypeId
Depending on many factors it will still run long (not least because you're copying how much data into a new table?) but this should take less than days.
Why an nvarchar? Best practice is, if you don't NEED (or expect to need) the unicode support, just use varchar. If you think the longest name is under 200 characters, I'd make that column a varchar(255). I can see scenarios where the hashing that has been recommended to you would be costly (it seems like this database is insert intensive). With that much size, however, and the frequency and random nature of the names, your indexes will become fragmented quickly in most scenarios where you index on a hash (dependent on the hash) or the name.
I would alter the name column as described above and make the clustered index TypeId, EGMId/BioentityId (the surrogate key for either table). Then you can join nicely on TypeId, and the "rough" join on Name will have less to loop through. To see how long this query might run, try it for a very small subset of your TypeIds, and that should give you an estimate of the run time (although it might ignore factors like cache size, memory size, hard disk transfer rates).
Edit: if this is an ongoing process, you should enforce the foreign key constraint between your two tables for future imports/dumps. If it's not ongoing, the hashing is probably your best best.
I would try to solve the issue outside the box, maybe there is some other algorithm that could do the job much better and faster than the database. Of course it all depends on the nature of the data but there are some string search algorithm that are pretty fast (Boyer-Moore, ZBox etc), or other datamining algorithm (MapReduce ?) By carefully crafting the data export it could be possible to bend the problem to fit a more elegant and faster solution. Also, it could be possible to better parallelize the problem and with a simple client make use of the idle cycles of the systems around you, there are framework that can help with this.
the output of this could be a list of refid tuples that you could use to fetch the complete data from the database much faster.
This does not prevent you from experimenting with index, but if you have to wait 6 days for the results I think that justifies resources spent exploring other possible options.
my 2 cent
Since you're not asking the DB to do any fancy relational operations, you could easily script this. Instead of killing the DB with a massive yet simple query, try exporting the two tables (can you get offline copies from the backups?).
Once you have the tables exported, write a script to perform this simple join for you. It'll take about the same amount of time to execute, but won't kill the DB.
Due to the size of the data and length of time the query takes to run, you won't be doing this very often, so an offline batch process makes sense.
For the script, you'll want to index the larger dataset, then iterate through the smaller dataset and do lookups into the large dataset index. It'll be O(n*m) to run.
If the hash match consumes too many resources, then do your query in batches of, say, 10000 rows at a time, "walking" the TypeID column. You didn't say the selectivity of TypeID, but presumably it is selective enough to be able to do batches this small and completely cover one or more TypeIDs at a time. You're also looking for loop joins in your batches, so if you still get hash joins then either force loop joins or reduce the batch size.
Using batches will also, in simple recovery mode, keep your tran log from growing very large. Even in simple recovery mode, a huge join like you are doing will consume loads of space because it has to keep the entire transaction open, whereas when doing batches it can reuse the log file for each batch, limiting its size to the largest needed for one batch operation.
If you truly need to join on Name, then you might consider some helper tables that convert names into IDs, basically repairing the denormalized design temporarily (if you can't repair it permanently).
The idea about checksum can be good, too, but I haven't played with that very much, myself.
In any case, such a huge hash match is not going to perform as well as batched loop joins. If you could get a merge join it would be awesome...
I wonder, whether the execution time is taken by the join or by the data transfer.
Assumed, the average data size in your Name column is 150 chars, you will actually have 300 bytes plus the other columns per record. Multiply this by 100 million records and you get about 30GB of data to transfer to your client. Do you run the client remote or on the server itself ?
Maybe you wait for 30GB of data being transferred to your client...
EDIT: Ok, i see you are inserting into Aux table. What is the setting of the recovery model of the database?
To investigate the bottleneck on the hardware side, it might be interesting whether the limiting resource is reading data or writing data. You can start a run of the windows performance monitor and capture the length of the queues for reading and writing of your disks for example.
Ideal, you should place the db log file, the input tables and the output table on separate physical volumes to increase speed.