The performance of this Spark SQL query is bad due to skew data distribution:
select c.*, coalesce(
sum(revenue)
OVER (PARTITION BY cid, pid, code
ORDER BY (cTime div (1000*3600))
RANGE BETWEEN 336 PRECEDING and 1 PRECEDING), 0L) as totalRevenue
from records c
I see in SparkUI that single task stack and the cluster fail if I increase the scanned range.
I am using Yarn at AWS EMR, with Spark 2.2.0
How can I overcome this issue?
Thanks
I can only recommend several approaches to alleviate your condition for investigation. I would actually try two approaches that don’t treat the skew first:
Try increasing the executor memory per the message. On YARN you may additionally need to increase the maximum container memory as well. The default on Spark IIRC is 2gb and its not uncommon to need to increase it.
Try switching to memory_and_disk or disk_only persistence levels. I believe this should work for your query although it can be hard to eyeball the full query plan
The reason for this is that at least to my eye your data is fundamentally skewed. You’re setting yourself up for maintenance difficulties if you start reshaping the data to address the skew in specific ways to the current shape of the data because the shape of the data may change over time. In my opinion at least you want to preserve the most straightforward implementation of your query for as long as you can, and only optimize skew issues programmatically if you hit problems with SLA violations, etc.
If those don’t work then you can try to address the skew directly. A simple approach for this is to create a third column that is populated by a random number for the column values that are known to be problematic. Do one pass of your summing operation with this in place, using it as a key, then a second pass with the extra random column removed. Alternatively you can do two queries and concatenate them: one with the random number for skewed data (which must still be handled in two passes) and another unaltered query for the non problematic data.
Edit - compute partial sums through two frames
The fundamentally useful observation here is that addition is commutative and associative. My original proposal based on random numbers won't work but this will. Basically, you want to compute the partial sum of the frame you want in several parts. The easiest way to do this is probably as a set of ranges (two used here for simplicity):
create temporary table partial_revenue_1 as select c.*, coalesce(
sum(revenue)
OVER (PARTITION BY cid, pid, code
ORDER BY (cTime div (1000*3600))
RANGE BETWEEN 336 PRECEDING and 118 PRECEDING), 0L) as partialTotalRevenue
from records c
create temporary table partial_revenue_2 as select c.*, coalesce(
sum(revenue)
OVER (PARTITION BY cid, pid, code
ORDER BY (cTime div (1000*3600))
RANGE BETWEEN 117 PRECEDING and 1 PRECEDING), 0L) as partialTotalRevenue
from records c
create temporary table combined_partials as select * from
partial_reveneue_1 union all select * from partial_revenue_2
select sum(partialTotalRevenue), first(c.some_col) ... from
combined_partials c group by cid, pid, code
Notice you need to use the first aggregate function to cull the duplicate fields that you will have from the earlier select * operations on the records table. Don't worry, this will be fine since both values came from the same table.
Related
I need to check my solution for idempotency and check how much it's different with past solution.
I tried next:
spark.sql('''
select * from t1
except
select * from t2
''').count()
It's gives me information how much this tables different (t1 - my solution, t2 - primal data). If here is many different data, I want to check, where it different.
So, I tried that:
diff = {}
columns = t1.columns
for col in columns:
cntr = spark.sql('''
select {col} from t1
except
select {col} from t2
''').count()
diff[col] = cntr
print(diff)
It's not good for me, because it's works about 1-2 hours (both tables have 30 columns and 30 million lines of data).
Do you guys have an idea how to calculate this quickly?
Except is a kind of a join on all columns at the same time. Does your data have a primary key? It could even be complex, comprising of multiple columns, but it's still much better then taking all 30 columns into account.
Once you figure out the primary key you can do the FULL OUTER JOIN and:
check NULLs on the left
check NULLs on the right
check other columns of matching rows (it's much cheaper to compare the values after the join)
Given that your resource remains unchanged, I think there are three ways that you can optimize:
Join two dataframe once but not looping the except: I assume your dataset should have a key / index, otherwise there is no ordering in your both dataframe and you can't perform except to check the difference. Unless you have limited resource, just do join once to concat two dataframe first instead of multiple except.
Check your data partitioning: Even you use point 1 / the method that you're using, make sure that data partition is in even distribution with optimal number of partition. Most of the time, data skew is one of the critical parts to lower your performance. If your key is a string, use repartition. If you're using a sequence number, use repartitionByRange.
Use the when-otherwise pair to check the difference: once you join two dataframe, you can use a when-otherwise condition to compare the difference, for example: df.select(func.sum(func.when(func.col('df1.col_a')!=func.col('df2.col_a'), func.lit(1))).otherwise(func.lit(0)).alias('diff_in_col_a_count')). Therefore, you can calculate all the difference within one action but not multiple action.
Why does the order of rows displayed differ, when I take a subset of the dataframe columns to display, via show?
Here is the original dataframe:
Here dates are in the given order, as you can see, via show.
Now the order of rows displayed via show changes when I select a subset of predict_df by method of column selection for a new dataframe.
Because of Spark dataframe itself is unordered. It's due to parallel processing principles wich Spark uses. Different records may be located in different files (and on different nodes) and different executors may read the data in different time and in different sequence.
So You have to excplicitly specify order in Spark action using orderBy (or sort) method. E.g.:
df.orderBy('date').show()
In this case result will be ordered by date column and would be more predictible. But, if many records have equal date value then within those date subset records also would be unordered. So in this case, in order to obtain strongly ordered data, we have to perform orderBy on set of columns. And values in all rows of those set of columns must be unique. E.g.:
df.orderBy(col("date").asc, col("other_column").desc)
In general unordered datasets is a normal case for data processing systems. Even "traditional" DBMS like PostgeSQL or MS SQL Server in general return unordered records and we have to explicitly use ORDER BY clause in SELECT statement. And even if sometime we may see the same results of one query it isn't guarenteed by DBMS that by another execution result will be the same also. Especially if data reading is performed on a large amout of data.
The situation occurs because the show is an action that is called twice.
As no .cache is applied the whole cycle starts again from the start. Moreover, I tried this a few times and got the same order and not the same order as the questioner observed. Processing is non-deterministic.
As soon as I used .cache, the same result was always gotten.
This means that there is ordering preserved over a narrow transformation on a dataframe, if caching has been applied, otherwise the 2nd action will invoke processing from the start again - the basics are evident here as well. And may be the bottom line is always do ordering explicitly - if it matters.
Like #Ihor Konovalenko and #mck mentioned, Sprk dataframe is unordered by its nature. Also, looks like your dataframe doesn’t have a reliable key to order, so one solution is using monotonically_increasing_id https://spark.apache.org/docs/latest/api/python/reference/api/pyspark.sql.functions.monotonically_increasing_id.html to create id and that will keep your dataframe always ordered. However if your dataframe is big, be aware this function might take some time to generate id for each row.
I want to return the first N rows from a Cassandra database filtering on some criterion, where the filtering is done on ordinary (not clustering) columns.
Let's assume a simple table like this:
CREATE TABLE test(
id UUID,
timestamp TIMESTAMP,
value DOUBLE,
PRIMARY KEY ((id), timestamp)
) WITH CLUSTERING ORDER BY (timestamp ASC)
Option 1
SELECT timestamp, value FROM test WHERE id=? AND value<? LIMIT ? ALLOW FILTERING
This is allowed, but ALLOW FILTERING is generally to be avoided. Having said that, is it really that bad if the query touches only the one partition?
Option 2
Set a very small paging size, e.g. N*10 (say) and then:
SELECT timestamp, value FROM test WHERE id=?
Read the results a page at a time, and stop reading as soon as sufficient suitable rows have been read. Is there any cost associated with the pages that have not yet been fetched? If not I'd guess this is the clear winner.
Option 3
Default paging, LIMIT the number of results to N*10, issue a new query if insufficient suitable rows returned:
SELECT timestamp, value FROM test WHERE id=? AND timestamp>? LIMIT ?
If there are insufficient suitable rows in the results, issue a new query starting just after the previous query result's last timestamp.
I'd like to know what is likely to be the best option.
I did some rough-and-ready benchmarking. To my surprise, I found that the ALLOW FILTERING option was orders of magnitude faster, at least in my test scenario. The other two options were heavily dependent on the LIMIT or page size, with smaller a LIMIT/page performing very much worse.
If the first suitable row is found in the first page/first query result then the three options are not far off comparable, but ALLOW FILTERING is still fastest.
The biggest surprise to me was that paging through results of a single large query performs little better than serial execution (i.e. non-concurrent) of multiple small queries. Could it be that each time the driver requests the next page of results, Cassandra in effect executes a new query for that page?
Clearly, these conclusions are heavily biased by the dataset being queried. However, the superiority of ALLOW FILTERING was so stark that I'd make the working assumption that this will be applicable in almost all cases.
I am new to column store db family and some of the concepts are not yet completely clear to me. I want to use MemSQL to store sparse matrix.
The table would look something like this:
CREATE TABLE matrix (
r_id INT,
c_id INT,
cell_data VARCHAR(10),
KEY (`r_id`, `c_id`) USING CLUSTERED COLUMNSTORE,
);
The Queries:
SELECT c_id, cell_data FROM matrix WHERE r_id=<val>; i.e. whole row
SELECT r_id, cell_data FROM matrix WHERE c_id=<val>; i.e. whole column
SELECT cell_data FROM matrix WHERE r_id=<val1> AND c_id=<val2>; i.e. one cell
UPDATE matrix SET cell_data=<val> WHERE r_id=<val1> AND c_id=<val2>;
INSERT INTO matrix VALUES (<v1>, <v2>, <v3>);
The queries 1 and 2 are about equally frequent and 3, 4 and 5 are also equally frequent. One of Q1,2 are equally frequent as one of Q3,4,5 (i.e. Q1,2:Q3,4,5 ~= 1:1).
I do realize that inserting into column store one row at a time creates Row segment group for each insert and thus degrading performance. I cannot batch the inserts. Also I cannot use in-memory row store (the matrix is too big).
I have three questions:
Does the issue with single row inserts concern updates too if only cell_data is changed (i.e. Q4)?
Would it be possible to have in-memory row table in which I would do INSERT (?and UPDATE?) operations and periodically batch the contents to column table?
How would I perform Q1,2 if I need most recent data (?UNION ALL?)?
Is it possible avoid executing Q3 for both tables (?which would mean two round trips?)?
I am concerned by execution speed of Q1 and Q2. Is the Clustered key optimal for those. I am not sure how the records would be stored with table above.
1.
Yes, single-row updates also perform poorly - they are essentially a delete and an insert.
2.
Yes, and in fact we automatically do this behind the scenes - the most recently inserted data (if it is too small a number of rows to be a good columnar segment) is kept in an in-memory rowstore form, and read queries are essentially looking at a UNION ALL of that data and the column-oriented data. We then batch up this data to write into column-oriented form.
If that doesn't work well enough, depending on your workload, you may benefit from explicitly keeping some of your data in a rowstore table instead of relying on the above behavior, in which case:
2a. yes, to see the most recent data you would use UNION ALL
2b. the data could be in either table, so you would have to query both (like for Q1,2, using UNION ALL works). This does not do two round trips, just one.
3.
You can either order by r or c first in the columnstore key - r in your current schema. This makes queries for a row efficient, but queries for a column are going to be very inefficient, they may have to scan basically the full table (depending on the patterns in your data). Unfortunately columnstore tables do not support using multiple keys, so there is no good way to solve this. One potential hacky solution is to maintain two copies of your table, one with key (r, c) and one with key (c, r) - this is essentially manually maintaining two indexes.
Based on the workload you're describing, it sounds like you are doing many single-row queries (Q3,4,5, which is 50% of the workload), which rowstore is much better suited for than columnstore (see http://docs.memsql.com/latest/concepts/columnstore/). Unfortunately, if it doesn't fit in memory, there isn't really a good way around this other than perhaps to add more memory.
I have a following CQL table (a bit simplified for clarity):
CREATE TABLE test_table (
user uuid,
app_id ascii,
domain_id ascii,
props map<ascii,blob>,
PRIMARY KEY ((user), app_id, domain_id)
)
The idea is that this table would contain many users (i.e. rows, say, dozens of millions). For each user there would be a few domains of interest and there would be a few apps per domain. And for each user/domain/app there would be a small set of properties.
I need to scan this entire table and load its contents in chunks for given app_id and domain_id. My idea was to use the TOKEN function to be able to read the whole data set in several iterations. So, something like this:
SELECT props FROM test_table WHERE app_id='myapp1'
AND domain_id='mydomain1'
AND TOKEN(user) > -9223372036854775808
AND TOKEN(user) < 9223372036854775807;
I was assuming that this query would be efficient because I specify the range of the row keys and by specifying the values of the clustering keys I effectively specify the column range. But when I try to run this query I get the error message "Bad Request: Cannot execute this query as it might involve data filtering and thus may have unpredictable performance. If you want to execute this query despite the performance unpredictability, use ALLOW FILTERING".
I have limited experience with Cassandra and I assumed that this sort of query would map into get_range_slices() call, which accepts the slice predicate (i.e. the range of columns defined by my app_id/domain_id values) and the key range defined by my token range. It seems either I misunderstand how this sort of query is handled or maybe I misunderstand about the efficiency of get_range_slices() call.
To be more specific, my questions are:
- if this data model does make sense for the kind of query I have in mind
- if this query is expected to be efficient
- if it is efficient, then why am I getting this error message asking me to ALLOW FILTERING
My only guess about the last one was that the rows that do not have the given combination of app_id/domain_id would need to be skipped from the result.
--- update ----
Thank for all the comments. I have been doing more research on this and there is still something that I do not fully understand.
In the given structure what I am trying to get is like a rectangular area from my data set (assuming that all rows have the same columns). Where top and the bottom of the rectangle is determined by the token range (range) and the left/right sides are defined as column range (slice). So, this should naturally transform into get_range_slices request. My understanding (correct me if I am wrong) that the reason why CQL requires me to put ALLOW FILTERING clause is because there will be rows that do not contain the columns I am looking for, so they will have to be skipped. And since nobody knows if it will have to skip every second row or first million rows before finding one that fits my criteria (in the given range) - this is what causes the unpredictable latency and possibly even timeout. Am I right? I have tried to write a test that does the same kind of query but using low-level Astyanax API (over the same table, I had to read the data generated with CQL, it turned out to be quite simple) and this test does work - except that it returns keys with no columns where the row does not contain the slice of columns I am asking for. Of course I had to implement some kind of simple paging based on the starting token and limit to fetch the data in small chunks.
Now I am wondering - again, considering that I would need to deal with dozens of millions of users: would it be better to partially "rotate" this table and organize it in something like this:
Row key: domain_id + app_id + partition no (something like hash(user) mod X)
Clustering key: column partition no (something like hash(user) >> 16 mod Y) + user
For the "column partition no"...I am not sure if it is really needed. I assume that if I go with this model I will have relatively small number of rows (X=1000..10000) for each domain + app combination. This will allow me to query the individual partitions, even in parallel if I want to. But (assuming the user is random UUID) for 100M users it will result in dozens or hundreds of thousands of columns per row. Is it a good idea to read one such a row in one request? It should created some memory pressure for Cassandra, I am sure. So maybe reading them in groups (say, Y=10..100) would be better?
I realize that what I am trying to do is not what Cassandra does well - reading "all" or large subset of CF data in chunks that can be pre-calculated (like token range or partition keys) for parallel fetching from different hosts. But I am trying to find a pattern that is the most efficient for such a use case.
By the way, the query like "select * from ... where TOKEN(user)>X and TOKEN(user)
Short answer
This warning means that Cassandra would have to read non-indexed data and filter out the rows that don't satisfy the criteria. If you add ALLOW FILTERING to the end of query, it will work, however it will scan a lot of data:
SELECT props FROM test_table
WHERE app_id='myapp1'
AND domain_id='mydomain1'
AND TOKEN(user) > -9223372036854775808
AND TOKEN(user) < 9223372036854775807
ALLOW FILTERING;
Longer explanation
In your example primary key consists of two parts: user is used as partition key, and <app_id, domain_id> form remaining part. Rows for different users are distributed across the cluster, each node responsible for specific range of token ring.
Rows on a single node are sorted by the hash of partition key (token(user) in your example). Different rows for single user are stored on a single node, sorted by <app_id, domain_id> tuple.
So, the primary key forms a tree-like structure. Partition key adds one level of hierarchy, and each remaining field of a primary key adds another one. By default, Cassandra processes only the queries that return all rows from the continuos range of the tree (or several ranges if you use key in (...) construct). If Cassandra should filter out some rows, ALLOW FILTERING must be specified.
Example queries that don't require ALLOW FILTERING:
SELECT * FROM test_table
WHERE user = 'user1';
//OK, returns all rows for a single partition key
SELECT * FROM test_table
WHERE TOKEN(user) > -9223372036854775808
AND TOKEN(user) < 9223372036854775807;
//OK, returns all rows for a continuos range of the token ring
SELECT * FROM test_table
WHERE user = 'user1'
AND app_id='myapp1';
//OK, the rows for specific user/app combination
//are stored together, sorted by domain_id field
SELECT * FROM test_table
WHERE user = 'user1'
AND app_id > 'abc' AND app_id < 'xyz';
//OK, since rows for a single user are sorted by app
Example queries that do require ALLOW FILTERING:
SELECT props FROM test_table
WHERE app_id='myapp1';
//Must scan all the cluster for rows,
//but return only those with specific app_id
SELECT props FROM test_table
WHERE user='user1'
AND domain_id='mydomain1';
//Must scan all rows having user='user1' (all app_ids),
//but return only those having specific domain
SELECT props FROM test_table
WHERE user='user1'
AND app_id > 'abc' AND app_id < 'xyz'
AND domain_id='mydomain1';
//Must scan the range of rows satisfying <user, app_id> condition,
//but return only those having specific domain
What to do?
In Cassandra it's not possible to create a secondary index on the part of the primary key. There are few options, each having its pros and cons:
Add a separate table that has primary key ((app_id), domain_id, user) and duplicate the necessary data in two tables. It will allow you to query necessary data for a specific app_id or <app_id, domain_id> combination. If you need to query specific domain and all apps - third table is necessary. This approach is called materialized views
Use some sort of parallel processing (hadoop, spark, etc) to perform necessary calculations for all app/domain combinations. Since Cassandra needs to read all the data anyway, there probably won't be much difference from a single pair. If the result for other pairs might be cached for later use, it will probably save some time.
Just use ALLOW FILTERING if query performance is acceptable for your needs. Dozens of millions partition keys is probably not too much for Cassandra.
Presuming you are using the Murmur3Partitioner (which is the right choice), you do not want to run range queries on the row key. This key is hashed to determine which node holds the row, and is therefore not stored in sorted order. Doing this kind of range query would therefore require a full scan.
If you want to do this query, you should store some known value as a sentinel for your row key, such that you can query for equality rather than range. From your data it appears that either app_id or domain_id would be a good choice, since it sounds like you always know these values when performing your query.