I have a large partitioned Iceberg table ordered by some columns. Now I want to scan through some filtered parts of that table using Spark and toLocalIterator(), preserving the order.
When my filter condition outputs the data from single partition everything is OK - the rows are ordered as expected.
The problem happens when there are multiple partitions in result - they come to me in random order. Of course I can add ORDER BY to my select statement, but that triggers expensive sorting, which is totally unnecessary if I only could explicitly specify the order for partitions.
The question is: how to tell Spark to use that order (or some other order)? Or broader: how to leverage from ordering columns in Iceberg schema?
Related
I have a case where i am trying to write some results using dataframe write into S3 using the below query with input_table_1 size is 13 Gb and input_table_2 as 1 Mb
input_table_1 has columns account, membership and
input_table_2 has columns role, id , membership_id, quantity, start_date
SELECT
/*+ BROADCASTJOIN(input_table_2) */
account,
role,
id,
quantity,
cast(start_date AS string) AS start_date
FROM
input_table_1
INNER JOIN
input_table_2
ON array_contains(input_table_1.membership, input_table_2.membership_id)
where membership array contains list of member_ids
This dataset write using Spark dataframe is generating around 1.1TiB of data in S3 with around 700 billion records.
We identified that there are duplicates and used dataframe.distinct.write.parquet("s3path") to remove the duplicates . The record count is reduced to almost 1/3rd of the previous total count with around 200 billion rows but we observed that the output size in S3 is now 17.2 TiB .
I am very confused how this can happen.
I have used the following spark conf settings
spark.sql.shuffle.partitions=20000
I have tried to do a coalesce and write to s3 but it did not work.
Please suggest if this is expected and when can be done ?
There's two sides to this:
1) Physical translation of distinct in Spark
The Spark catalyst optimiser turns a distinct operation into an aggregation by means of the ReplaceDeduplicateWithAggregate rule (Note: in the execution plan distinct is named Deduplicate).
This basically means df.distinct() on all columns is translated into a groupBy on all columns with an empty aggregation:
df.groupBy(df.columns:_*).agg(Map.empty).
Spark uses a HashPartitioner when shuffling data for a groupBy on respective columns. Since the groupBy clause in your case contains all columns (well, implicitly, but it does), you're more or less randomly shuffling data to different nodes in the cluster.
Increasing spark.sql.shuffle.partitions in this case is not going to help.
Now on to the 2nd side, why does this affect the size of your parquet files so much?
2) Compression in parquet files
Parquet is a columnar format, will say your data is organised in columns rather than row by row. This allows for powerful compression if data is adequately laid-out & ordered. E.g. if a column contains the same value for a number of consecutive rows, it is enough to write that value just once and make a note of the number of repetitions (a strategy called run length encoding). But Parquet also uses various other compression strategies.
Unfortunately, data ends up pretty randomly in your case after shuffling to remove duplicates. The original partitioning of input_table_1 was much better fitted.
Solutions
There's no single answer how to solve this, but here's a few pointers I'd suggest doing next:
What's causing the duplicates? Could these be removed upstream? Or is there a problem with the join condition causing duplicates?
A simple solution is to just repartition the dataset after distinct to match the partitioning of your input data. Adding a secondary sorting (sortWithinPartition) is likely going to give you even better compression. However, this comes at the cost of an additional shuffle!
As #matt-andruff pointed out below, you can also achieve this in SQL using cluster by. Obviously, that also requires you to move the distinct keyword into your SQL statement.
Write your own deduplication algorithm as Spark Aggregator and group / shuffle the data just once in a meaningful way.
We know in SQL, an index can be created on a column if it is frequently used for filtering. Is there anything similar I can do in spark? Let's say I have a big table T containing a column C I want to filter on. I want to filter 10s of thousands of id sets on the column C. Can I sort/orderBy column C, cache the result, and then filter all the id sets with the sorted table? Will it help like indexing in SQL?
You should absolutely build the table/dataset/dataframe with a sorted id if you will query on it often. It will help predicate pushdown. and in general give a boost in performance.
When executing queries in the most generic and basic manner, filtering
happens very late in the process. Moving filtering to an earlier phase
of query execution provides significant performance gains by
eliminating non-matches earlier, and therefore saving the cost of
processing them at a later stage. This group of optimizations is
collectively known as predicate pushdown.
Even if you aren't sorting data you may want to look at storing the data in file with 'distribute by' or 'cluster by'. It is very similar to repartitionBy. And again only boosts performance if you intend to query the data as you have distributed the data.
If you intend to requery often yes, you should cache data, but in general there aren't indexes. (There are file types that help boost performance if you have specific query type needs. (Row based/columnar based))
You should look at the Spark Specific Performance tuning options. Adaptive query is a next generation that helps boost performance, (without indexes)
If you are working with Hive: (Note they have their own version of partitions)
Depending on how you will query the data you may also want to look at partitioning or :
[hive] Partitioning is mainly helpful when we need to filter our data based
on specific column values. When we partition tables, subdirectories
are created under the table’s data directory for each unique value of
a partition column. Therefore, when we filter the data based on a
specific column, Hive does not need to scan the whole table; it rather
goes to the appropriate partition which improves the performance of
the query. Similarly, if the table is partitioned on multiple columns,
nested subdirectories are created based on the order of partition
columns provided in our table definition.
Hive Partitioning is not a magic bullet and will slow down querying if the pattern of accessing data is different than the partitioning. It make a lot of sense to partition by month if you write a lot of queries looking at monthly totals. If on the other hand the same table was used to look at sales of product 'x' from the beginning of time, it would actually run slower than if the table wasn't partitioned. (It's a tool in your tool shed.)
Another hive specific tip:
The other thing you want to think about, and is keeping your table stats. The Cost Based Optimizer uses those statistics to query your data. You should make sure to keep them up to date. (Re-run after ~30% of your data has changed.)
ANALYZE TABLE [db_name.]tablename [PARTITION(partcol1[=val1], partcol2[=val2], ...)] -- (Note: Fully support qualified table name
since Hive 1.2.0, see HIVE-10007.)
COMPUTE STATISTICS
[FOR COLUMNS] -- (Note: Hive 0.10.0 and later.)
[CACHE METADATA] -- (Note: Hive 2.1.0 and later.)
[NOSCAN];
With Apache Spark we can partition a dataframe into separate files when saving into Parquet format.
In the way Parquet files are written, each partition contains multiple row groups each of include column statistics pertaining to each group (e.g., min/max values, as well as number of NULL values).
Now, it would seem ideal in some situations to organize the Parquet file such that related data appears together in one or more row groups. This would be a secondary level of partitioning within each partition file (which constitutes the first level).
This is possible using for example pyarrow, but how can we do this with a distributed SQL engine such as Spark?
Besides partitioning you can order your data to group related data together in a limited set of partitions. Statement from Databricks:
Z-Ordering is a technique to colocate related information in the same
set of files
(
df
.write.option("header", True)
.orderBy(df.col_1.desc())
.partitionBy("col_2")
)
I am trying to understand the performance impact on the partitioning scheme when Spark is used to query a hive table. As an example:
Table 1 has 3 partition columns, and data is stored in paths like
year=2021/month=01/day=01/...data...
Table 2 has 1 partition column
date=20210101/...data...
Anecdotally I have found that queries on the second type of table are faster, but I don't know why, and I don't why. I'd like to understand this so I know how to design the partitioning of larger tables that could have more partitions.
Queries being tested:
select * from table limit 1
I realize this won't benefit from any kind of query pruning.
The above is meant as an example query to demonstrate what I am trying to understand. But in case details are important
This is using s3 not HDFS
The data in the table is very small, and there are not a large number of partitons
The time for running the query on the first table is ~2 minutes, and ~10 seconds on the second
Data is stored as parquet
Except all other factors which you did not mention: storage type, configuration, cluster capacity, the number of files in each case, your partitioning schema does not correspond to the use-case.
Partitioning schema should be chosen based on how the data will be selected or how the data will be written or both. In your case partitioning by year, month, day separately is over-partitioning. Partitions in Hive are hierarchical folders and all of them should be traversed (even if using metadata only) to determine the data path, in case of single date partition, only one directory level is being read. Two additional folders: year+month+day instead of date do not help with partition pruning because all columns are related and used together always in the where.
Also, partition pruning probably does not work at all with 3 partition columns and predicate like this: where date = concat(year, month, day)
Use EXPLAIN and check it and compare with predicate like this where year='some year' and month='some month' and day='some day'
If you have one more column in the WHERE clause in the most of your queries, say category, which does not correlate with date and the data is big, then additional partition by it makes sense, you will benefit from partition pruning then.
I am using Spark 2.2. I have a join query on a partitioning column and also have some filter conditions on other columns. So, when I checked the execution plan, it looks like below.
It checks for non-null partition columns.
It applies predicates on entire table even before joining with second table. This is causing Spark to read/apply filters on all partitions, then join to get data. My join clause actually hits only one partition.
Why does my query need to scan all partitions? Is there any way to control predicates push down in Spark when doing joins?