A spark inner SortMerge Join on using a column containing a ml Vector appears to give non-deterministic and inaccurate result on larger datasets.
I was using the approxNearestNeighbors method of BucketRandomLSH projection of Spark v2.4.3, and discovered it gives different numbers of results for large data sets.
This problem only appears when executing a SortMerge join; a broadcast join gives the same result every time.
I tracked the problem down to the join on the LSH hash keys. A reproducible example is below...
import org.apache.spark.sql.functions._
import org.apache.spark.ml.linalg.Vectors
import scala.util.Random
spark.conf.set("spark.sql.autoBroadcastJoinThreshold", -1)
//create a large dataframe containing an Array (length two) of ml Vectors of length one.
val df = Seq.fill(30000)(
(java.util.UUID.randomUUID.toString,
Seq(
Vectors.dense(Random.nextInt(10).toDouble),
Vectors.dense(Random.nextInt(10).toDouble))
)
).toDF
//ensure it's caches
df.cache.count()
//positional explode the vector column
val dfExploded = df.select(col("*"), posexplode(col("_2")))
// now self join on the exploded 'col' and 'pos' fields
dfExploded.join(dfExploded, Seq("pos","col")).drop("pos","col").distinct.count
Different result each time...
scala>dfExploded.join(dfExploded,Seq("pos","col")).drop("pos","col").distinct.count
res139: Long = 139663581
scala>dfExploded.join(dfExploded,Seq("pos","col")).drop("pos","col").distinct.count
res140: Long = 156349630
Related
I'm creating an index using the monotonically_increasing_id() function in Pyspark 3.1.1.
I'm aware of the specific characteristics of that function, but they don't explain my issue.
After creating the index I do a simple aggregation applying the collect_list() function on the created index.
If I compare the results the index changes in certain cases, that is specifically on the upper end of the long-range when the input data is not too small.
Full example code:
import random
import string
from pyspark.sql import SparkSession
from pyspark.sql import functions as f
from pyspark.sql.types import StructType, StructField, StringType
spark = SparkSession.builder\
.appName("test")\
.master("local")\
.config('spark.sql.shuffle.partitions', '8')\
.getOrCreate()
# Create random input data of around length 100000:
input_data = []
ii = 0
while ii <= 100000:
L = random.randint(1, 3)
B = ''.join(random.choices(string.ascii_uppercase, k=5))
for i in range(L):
C = random.randint(1,100)
input_data.append((B,))
ii += 1
# Create Spark DataFrame:
input_rdd = sc.parallelize(tuple(input_data))
schema = StructType([StructField("B", StringType())])
dg = spark.createDataFrame(input_rdd, schema=schema)
# Create id and aggregate:
dg = dg.sort("B").withColumn("ID0", f.monotonically_increasing_id())
dg2 = dg.groupBy("B").agg(f.collect_list("ID0"))
Output:
dg.sort('B', ascending=False).show(10, truncate=False)
dg2.sort('B', ascending=False).show(5, truncate=False)
This of course creates different data with every run, but if the length is large enough (problem appears slightly at 10000, but not at 1000), it should appear everytime. Here's an example result:
+-----+-----------+
|B |ID0 |
+-----+-----------+
|ZZZVB|60129554616|
|ZZZVB|60129554617|
|ZZZVB|60129554615|
|ZZZUH|60129554614|
|ZZZRW|60129554612|
|ZZZRW|60129554613|
|ZZZNH|60129554611|
|ZZZNH|60129554609|
|ZZZNH|60129554610|
|ZZZJH|60129554606|
+-----+-----------+
only showing top 10 rows
+-----+---------------------------------------+
|B |collect_list(ID0) |
+-----+---------------------------------------+
|ZZZVB|[60129554742, 60129554743, 60129554744]|
|ZZZUH|[60129554741] |
|ZZZRW|[60129554739, 60129554740] |
|ZZZNH|[60129554736, 60129554737, 60129554738]|
|ZZZJH|[60129554733, 60129554734, 60129554735]|
+-----+---------------------------------------+
only showing top 5 rows
The entry ZZZVB has the three IDs 60129554615, 60129554616, and 60129554617 before aggregation, but after aggregation the numbers have changed to 60129554742, 60129554743, 60129554744.
Why? I can't imagine this is supposed to happen. Isn't the result of monotonically_increasing_id() a simple long that keeps its value after having been created?
EDIT: As expected a workaround is to coalesce(1) the DataFrame before creating the id.
dg and df2 are two different dataframes, each with their own DAG. These DAGs are executed independently from each other when an action on one of the dataframes is called. So each time show() is called, the DAG of the respective dataframe is evaluated and during that evaluation, f.monotonically_increasing_id() is called.
To prevent f.monotonically_increasing_id() being called twice, you could add a cache after the withColumn transformation:
dg = dg.sort("B").withColumn("ID0", f.monotonically_increasing_id()).cache()
With the cache, the result of the first evaluation of f.monotonically_increasing_id() is cached and reused when evaluating the second dataframe.
I have a large RDD (more than 1,000,000 lines), while each line has four elements A,B,C,D in a tuple. A head scan of the RDD looks like
[(492,3440,4215,794),
(6507,6163,2196,1332),
(7561,124,8558,3975),
(423,1190,2619,9823)]
Now I want to find the mean of each position in this RDD. For example for the data above I need an output list has values:
(492+6507+7561+423)/4
(3440+6163+124+1190)/4
(4215+2196+8558+2619)/4
(794+1332+3975+9823)/4
which is:
[(3745.75,2729.25,4397.0,3981.0)]
Since the RDD is very large, it is not convenient to calculate the sum of each position and then divide by the length of RDD. Are there any quick way for me to get the output? Thank you very much.
I don't think there is anything faster than calculating the mean (or sum) for each column
If you are using the DataFrame API you can simply aggregate multiple columns:
import os
import time
from pyspark.sql import functions as f
from pyspark.sql import SparkSession
# start local spark session
spark = SparkSession.builder.getOrCreate()
# load as rdd
def localpath(path):
return 'file://' + os.path.join(os.path.abspath(os.path.curdir), path)
rdd = spark._sc.textFile(localpath('myPosts/'))
# create data frame from rdd
df = spark.createDataFrame(rdd)
means_df = df.agg(*[f.avg(c) for c in df.columns])
means_dict = means_df.first().asDict()
print(means_dict)
Note that the dictionary keys will be the default spark column names ('0', '1', ...). If you want more speaking column names you can give them as an argument to the createDataFrame command
I'm struggling to understand how the conversion among RDDs, DataSets and DataFrames works.
I'm pretty new to Spark, and I get stuck every time I need to pass from a data model to another (especially from RDDs to Datasets and Dataframes).
Could anyone explain me the right way to do it?
As an example, now I have a RDD[org.apache.spark.ml.linalg.Vector] and I need to pass it to my machine learning algorithm, for example a KMeans (Spark DataSet MLlib). So, I need to convert it to Dataset with a single column named "features" which should contain Vector typed rows. How should I do this?
All you need is an Encoder. Imports
import org.apache.spark.sql.Encoder
import org.apache.spark.sql.catalyst.encoders.ExpressionEncoder
import org.apache.spark.ml.linalg
RDD:
val rdd = sc.parallelize(Seq(
linalg.Vectors.dense(1.0, 2.0), linalg.Vectors.sparse(2, Array(), Array())
))
Conversion:
val ds = spark.createDataset(rdd)(ExpressionEncoder(): Encoder[linalg.Vector])
.toDF("features")
ds.show
// +---------+
// | features|
// +---------+
// |[1.0,2.0]|
// |(2,[],[])|
// +---------+
ds.printSchema
// root
// |-- features: vector (nullable = true)
To convert a RDD to a dataframe, the easiest way is to use toDF() in Scala. To use this function, it is necessary to import implicits which is done using the SparkSession object. It can be done as follows:
val spark = SparkSession.builder().getOrCreate()
import spark.implicits._
val df = rdd.toDF("features")
toDF() takes an RDD of tuples. When the RDD is built up of common Scala objects they will be implicitly converted, i.e. there is no need to do anything, and when the RDD has multiple columns there is no need to do anything either, the RDD already contains a tuple. However, in this special case you need to first convert RDD[org.apache.spark.ml.linalg.Vector] to RDD[(org.apache.spark.ml.linalg.Vector)]. Therefore, it is necessary to do a convertion to tuple as follows:
val df = rdd.map(Tuple1(_)).toDF("features")
The above will convert the RDD to a dataframe with a single column called features.
To convert to a dataset the easiest way is to use a case class. Make sure the case class is defined outside the Main object. First convert the RDD to a dataframe, then do the following:
case class A(features: org.apache.spark.ml.linalg.Vector)
val ds = df.as[A]
To show all possible convertions, to access the underlying RDD from a dataframe or dataset can be done using .rdd:
val rdd = df.rdd
Instead of converting back and forth between RDDs and dataframes/datasets it's usually easier to do all the computations using the dataframe API. If there is no suitable function to do what you want, usually it's possible to define an UDF, user defined function. See for example here: https://jaceklaskowski.gitbooks.io/mastering-spark-sql/spark-sql-udfs.html
I am using Spark 2.0.0 with DataFrames API (DataSet[Row]) to join some dataframes as follows. I want to get all the rows from both usages and activations (hence the full outer join) and then do an inner join on the resulting dataset so that I consider only the rows that are also having a corresponding row in appDetails dataset (hence the inner join).
val result = usages
.join(activations, Seq("DATE", "APP_ID"), "outer")
.join(appDetails, Seq("APP_ID"), "inner")
This query does not return any results. However, if I change the full outer join to a left outer join, like this, it returns results.
val result = usages
.join(activations, Seq("DATE", "APP_ID"), "left")
.join(appDetails, Seq("APP_ID"), "inner")
However this doesn't work for me because I want all the rows from activations table as well. What's happening here? Why doesn't the full outer join work as expected in this case?
This question explains how Spark's random split works, How does Sparks RDD.randomSplit actually split the RDD, but I don't understand how spark keeps track of what values went to one split so that those same values don't go to the second split.
If we look at the implementation of randomSplit:
def randomSplit(weights: Array[Double], seed: Long): Array[DataFrame] = {
// It is possible that the underlying dataframe doesn't guarantee the ordering of rows in its
// constituent partitions each time a split is materialized which could result in
// overlapping splits. To prevent this, we explicitly sort each input partition to make the
// ordering deterministic.
val sorted = Sort(logicalPlan.output.map(SortOrder(_, Ascending)), global = false, logicalPlan)
val sum = weights.sum
val normalizedCumWeights = weights.map(_ / sum).scanLeft(0.0d)(_ + _)
normalizedCumWeights.sliding(2).map { x =>
new DataFrame(sqlContext, Sample(x(0), x(1), withReplacement = false, seed, sorted))
}.toArray
}
we can see that it creates two DataFrames that share the same sqlContext and with two different Sample(rs).
How are these two DataFrame(s) communicating with each other so that a value that fell in the first one is not included in the second one?
And is the data being fetched twice? (Assume the sqlContext is selecting from a DB, is the select being executed twice?).
It's exactly the same as sampling an RDD.
Assuming you have the weight array (0.6, 0.2, 0.2), Spark will generate one DataFrame for each range (0.0, 0.6), (0.6, 0.8), (0.8, 1.0).
When it's time to read the result DataFrame, Spark will just go over the parent DataFrame. For each item, generate a random number, if that number fall in the the specified range, then emit the item. All child DataFrame share the same random number generator (technically, different generators with the same seed), so the sequence of random number is deterministic.
For your last question, if you did not cache the parent DataFrame, then the data for the input DataFrame will be re-fetch each time an output DataFrame is computed.