Make Python dictionary available to all spark partitions - apache-spark

I am trying to develop an algorithm in pyspark for which I am working with linalg.SparseVector class. I need to create a dictionary of key value pairs as input to each SparseVector object. Here the keys have to be integers as they represent integers (in my case representing user ids). I have a separate method that reads the input file and returns a dictionary where each user ID ( string) is mapped to an integer index. When I go through the file again and do a
FileRdd.map( lambda x: userid_idx[ x[0] ] ) . I receive a KeyError. I'm thinking this is because my dict is unavailable to all partitions. Is there a way to make userid_idx dict available to all partitions similar to a distributed map in MapReduce? Also I apologize for the mess. I am posting this using my phone. Will update in a while from my laptop.
The code as promised:
from pyspark.mllib.linalg import SparseVector
from pyspark import SparkContext
import glob
import sys
import time
"""We create user and item indices starting from 0 to #users and 0 to #items respectively. This is done to store them in sparseVectors as dicts."""
def create_indices(inputdir):
items=dict()
user_id_to_idx=dict()
user_idx_to_id=dict()
item_idx_to_id=dict()
item_id_to_idx=dict()
item_idx=0
user_idx=0
for inputfile in glob.glob(inputdir+"/*.txt"):
print inputfile
with open(inputfile) as f:
for line in f:
toks=line.strip().split("\t")
try:
user_id_to_idx[toks[1].strip()]
except KeyError:
user_id_to_idx[toks[1].strip()]=user_idx
user_idx_to_id[user_idx]=toks[1].strip()
user_idx+=1
try:
item_id_to_idx[toks[0].strip()]
except KeyError:
item_id_to_idx[toks[0].strip()]=item_idx
item_idx_to_id[item_idx]=toks[0].strip()
item_idx+=1
return user_idx_to_id,user_id_to_idx,item_idx_to_id,item_id_to_idx,user_idx,item_idx
# pass in the hdfs path to the input files and the spark context.
def runKNN(inputdir,sc,user_id_to_idx,item_id_to_idx):
rdd_text=sc.textFile(inputdir)
try:
new_rdd = rdd_text.map(lambda x: (item_id_to_idx[str(x.strip().split("\t")[0])],{user_id_to_idx[str(x.strip().split("\t")[1])]:1})).reduceByKey(lambda x,y: x.update(y))
except KeyError:
sys.exit(1)
new_rdd.saveAsTextFile("hdfs:path_to_output/user/hadoop/knn/output")
if __name__=="__main__":
sc = SparkContext()
u_idx_to_id,u_id_to_idx,i_idx_to_id,i_id_to_idx,u_idx,i_idx=create_indices(sys.argv[1])
u_idx_to_id_b=sc.broadcast(u_idx_to_id)
u_id_to_idx_b=sc.broadcast(u_id_to_idx)
i_idx_to_idx_b=sc.broadcast(i_idx_to_id)
i_id_to_idx_b=sc.broadcast(i_id_to_idx)
num_users=sc.broadcast(u_idx)
num_items=sc.broadcast(i_idx)
runKNN(sys.argv[1],sc,u_id_to_idx_b.value,i_id_to_idx_b.value)

In Spark, that dictionary will already be available to you as it is in all tasks. For example:
dictionary = {1:"red", 2:"blue"}
rdd = sc.parallelize([1,2])
rdd.map(lambda x: dictionary[x]).collect()
# Prints ['red', 'blue']
You will probably find that your issue is actually that your dictionary does not contain the key you are looking up!
From the Spark documentation:
Normally, when a function passed to a Spark operation (such as map or reduce) is executed on a remote cluster node, it works on separate copies of all the variables used in the function. These variables are copied to each machine, and no updates to the variables on the remote machine are propagated back to the driver program.
A copy of local variables referenced will be sent to the node along with the task.
Broadcast variables will not help you here, they are simply a tool to improve performance by sending once per node rather than a once per task.

Related

Network bound transformation and threading

I am trying to use a REST API to enrich data I have in a spark dataframe. The REST API isn't built by me and requires a single input at a time (no batch option). Unfortunately the REST API latency is slower than I would like so my spark applications seem to spend a lot of time waiting for the API to iterate over each row. Although my REST API has higher latency, it does have very high throughput/capacity which does not seem to get fully used by my spark application.
Since my application appears to be network bound, I was wondering if it would make sense to use threading to help improve the speed of my application. Does spark already capable of doing this internally? If using threads does make sense, is there an easy way to accomplish this? Has anybody successfully done this?
I’ve encountered the same problem when fetching data from a blob storage.
Below is a small self-contained dummy example that I think you can easily modify for your needs.
In the example you should be able to register that it takes a lot longer to construct df_slow vs constructing df_fast.
It works by making each worker process a list of rows in parallel, instead of processing one row at a time sequentially.
You might be able to just swap the slowAdd function with your own Row transforming function. The slowAdd function simulates network latency by sleeping 0.1 seconds.
import pyspark.sql.functions as F
import pyspark.sql.types as T
from pyspark.sql import Row
# Just some dataframe with numbers
data = [(i,) for i in range(0, 1000)]
df = spark.createDataFrame(data, ["Data"], T.IntegerType())
# Get an rdd that contains 'list of Rows' instead of 'Row'
standardRdd = df.rdd # contains [row1, row3, row3,...]
number_of_partitions = 10
repartionedRdd = standardRdd.repartition(number_of_partitions) # contains [row1, row2, row3,...] but repartioned to increase parallelism
glomRdd = repartionedRdd.glom() # contains roughly [[row1, row2, row3,..., row100], [row101, row102, row103, ...], ...]
# where the number of sublists corresponds to the number of partitions
# Define a transformation function with an artificial delay.
# Substitute this with your own transformation function.
import time
def slowAdd(r):
d = r.asDict()
d["Data"] = d["Data"] + 100
time.sleep(0.1)
return Row(**d)
# Define a function that maps the slowAdd function from 'list of Rows' to 'list of Rows' in parallel
import concurrent.futures
def slowAdd_with_thread_pool(list_of_rows):
thread_pool = concurrent.futures.ThreadPoolExecutor(max_workers=100)
return [result for result in thread_pool.map(slowAdd, list_of_rows)]
# Perform a fast mapping from 'list of Rows' to 'Rows'.
transformed_fast_rdd = glomRdd.flatMap(slowAdd_with_thread_pool)
# For reference, perform a slow mapping from 'Rows' to 'Rows'
transformed_slow_rdd = repartionedRdd.map(slowAdd)
# Convert the rdds back to dataframes from the rdd's
df_fast = spark.createDataFrame(transformed_fast_rdd)
#This sum operation will be fast (~100 threads sleeping in parallel on each worker)
df_fast.agg(F.sum(F.col("Data"))).show()
df_slow = spark.createDataFrame(transformed_slow_rdd)
#This sum operation will be slow (1 thread sleeping in parallel on each worker)
df_slow.agg(F.sum(F.col("Data"))).show()

How to convert specific rows in a column into a separate column using pyspark and enumerate each row with an increasing numerical index? [duplicate]

I'm trying to read in retrosheet event file into spark. The event file is structured as such.
id,TEX201403310
version,2
info,visteam,PHI
info,hometeam,TEX
info,site,ARL02
info,date,2014/03/31
info,number,0
info,starttime,1:07PM
info,daynight,day
info,usedh,true
info,umphome,joycj901
info,attendance,49031
start,reveb001,"Ben Revere",0,1,8
start,rollj001,"Jimmy Rollins",0,2,6
start,utlec001,"Chase Utley",0,3,4
start,howar001,"Ryan Howard",0,4,3
start,byrdm001,"Marlon Byrd",0,5,9
id,TEX201404010
version,2
info,visteam,PHI
info,hometeam,TEX
As you can see for each game the events loops back.
I've read the file into a RDD, and then via a second for loop added a key for each iteration, which appears to work. But I was hoping to get some feedback on if there was a cleaning way to do this using spark methods.
logFile = '2014TEX.EVA'
event_data = (sc
.textFile(logfile)
.collect())
idKey = 0
newevent_list = []
for line in event_dataFile:
if line.startswith('id'):
idKey += 1
newevent_list.append((idKey,line))
else:
newevent_list.append((idKey,line))
event_data = sc.parallelize(newevent_list)
PySpark since version 1.1 supports Hadoop Input Formats.You can use textinputformat.record.delimiter option to use a custom format delimiter as below
from operator import itemgetter
retrosheet = sc.newAPIHadoopFile(
'/path/to/retrosheet/file',
'org.apache.hadoop.mapreduce.lib.input.TextInputFormat',
'org.apache.hadoop.io.LongWritable',
'org.apache.hadoop.io.Text',
conf={'textinputformat.record.delimiter': '\nid,'}
)
(retrosheet
.filter(itemgetter(1))
.values()
.filter(lambda x: x)
.map(lambda v: (
v if v.startswith('id') else 'id,{0}'.format(v)).splitlines()))
Since Spark 2.4 you can also read data into DataFrame using text reader
spark.read.option("lineSep", '\nid,').text('/path/to/retrosheet/file')

Pyspark applying foreach

I'm nooby in Pyspark and I pretend to play a bit with a couple of functions to understand better how could I use them in more realistic scenarios. for a while, I trying to apply a specific function to each number coming in a RDD. My problem is basically that, when I try to print what I grabbed from my RDD the result is None
My code:
from pyspark import SparkConf , SparkContext
conf = SparkConf().setAppName('test')
sc = SparkContext(conf=conf)
sc.setLogLevel("WARN")
changed = []
def div_two (n):
opera = n / 2
return opera
numbers = [8,40,20,30,60,90]
numbersRDD = sc.parallelize(numbers)
changed.append(numbersRDD.foreach(lambda x: div_two(x)))
#result = numbersRDD.map(lambda x: div_two(x))
for i in changed:
print(i)
I appreciate a clear explanation about why this is coming Null in the list and what should be the right approach to achieve that using foreach whether it's possible.
thanks
Your function definition of div_two seems fine which can yet be reduced to
def div_two (n):
return n/2
And you have converted the arrays of integers to rdd which is good too.
The main issue is that you are trying to add rdds to an array changed by using foreach function. But if you look at the definition of foreach
def foreach(self, f) Inferred type: (self: RDD, f: Any) -> None
which says that the return type is None. And thats what is getting printed.
You don't need an array variable for printing the changed elements of an RDD. You can simply write a function for printing and call that function in foreach function
def printing(x):
print x
numbersRDD.map(div_two).foreach(printing)
You should get the results printed.
You can still add the rdd to an array variable but rdds are distributed collection in itself and Array is a collection too. So if you add rdd to an array you will have collection of collection which means you should write two loops
changed.append(numbersRDD.map(div_two))
def printing(x):
print x
for i in changed:
i.foreach(printing)
The main difference between your code and mine is that I have used map (which is a transformation) instead of foreach ( which is an action) while adding rdd to changed variable. And I have use two loops for printing the elements of rdd

pandas group by in parallel

I'm having some trouble splitting the aggregation step of a group-by operation across multiple cores. I have the following working code, and would like to apply it over several processors:
import pandas as pd
import numpy as np
from multiprocessing import Pool, cpu_count
mydf = pd.DataFrame({'v1':[1,2,3,4]*6,'v2':['a','b','c']*8,'v3':np.arange(20,44)})
Which I can then apply the following GroupBy operation:
(the step I wish to do in parallel)
pd.groupby(mydf,by=['v1','v2']).apply(lambda x: np.percentile(x['v3'],[20,30]))
yielding the series:
1 a [22.4, 23.6]
b [26.4, 27.6]
c [30.4, 31.6]
2 a [31.4, 32.6]
b [23.4, 24.6]
c [27.4, 28.6]
I Tried the following, with reference to:parallel groupby
def applyParallel(dfGrouped, func):
with Pool(1) as p:
ret_list = p.map(func, [group for name, group in dfGrouped])
return pd.concat(ret_list)
def myfunc(df):
df['pct1'] = df.loc[:,['v3']].apply(np.percentile,args=([20],))
df['pct2'] = df.loc[:,['v3']].apply(np.percentile,args=([80],))
return(df)
grouped = pd.groupby(mydf,by=['v1','v2'])
applyParallel(grouped,myfunc)
But I'm losing the index structure and getting duplicates. I could probably solve this step with a further group by operation, but I think it shouldn't be too difficult to avoid it entirely. Any suggestions?
Not that I'm still looking for an answer, but It'd probably be better to use a library that handles parallel manipulations of pandas DataFrames, rather than trying to do so manually.
Dask is one option which is intended to scale Pandas operations with little code modification.
Another option (but is maybe a little more difficult to set up) is PySpark

PySpark isin function

I am converting my legacy Python code to Spark using PySpark.
I would like to get a PySpark equivalent of:
usersofinterest = actdataall[actdataall['ORDValue'].isin(orddata['ORDER_ID'].unique())]['User ID']
Both, actdataall and orddata are Spark dataframes.
I don't want to use toPandas() function given the drawback associated with it.
If both dataframes are big, you should consider using an inner join which will work as a filter:
First let's create a dataframe containing the order IDs we want to keep:
orderid_df = orddata.select(orddata.ORDER_ID.alias("ORDValue")).distinct()
Now let's join it with our actdataall dataframe:
usersofinterest = actdataall.join(orderid_df, "ORDValue", "inner").select('User ID').distinct()
If your target list of order IDs is small then you can use the pyspark.sql isin function as mentioned in furianpandit's post, don't forget to broadcast your variable before using it (spark will copy the object to every node making their tasks a lot faster):
orderid_list = orddata.select('ORDER_ID').distinct().rdd.flatMap(lambda x:x).collect()[0]
sc.broadcast(orderid_list)
The most direct translation of your code would be:
from pyspark.sql import functions as F
# collect all the unique ORDER_IDs to the driver
order_ids = [x.ORDER_ID for x in orddata.select('ORDER_ID').distinct().collect()]
# filter ORDValue column by list of order_ids, then select only User ID column
usersofinterest = actdataall.filter(F.col('ORDValue').isin(order_ids)).select('User ID')
However, you should only filter like this only if number of 'ORDER_ID' is definitely small (perhaps <100,000 or so).
If the number of 'ORDER_ID's is large, you should use a broadcast variable which sends the list of order_ids to each executor so it can compare against the order_ids locally for faster processing. Note, this will work even if 'ORDER_ID' is small.
order_ids = [x.ORDER_ID for x in orddata.select('ORDER_ID').distinct().collect()]
order_ids_broadcast = sc.broadcast(order_ids) # send to broadcast variable
usersofinterest = actdataall.filter(F.col('ORDValue').isin(order_ids_broadcast.value)).select('User ID')
For more information on broadcast variables, check out: https://jaceklaskowski.gitbooks.io/mastering-apache-spark/spark-broadcast.html
So, you have two spark dataframe. One is actdataall and other is orddata, then use following command to get your desire result.
usersofinterest = actdataall.where(actdataall['ORDValue'].isin(orddata.select('ORDER_ID').distinct().rdd.flatMap(lambda x:x).collect()[0])).select('User ID')

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