How to measure the execution time of a query on Spark - sql

I need to measure the execution time of query on Apache spark (Bluemix).
What I tried:
import time
startTimeQuery = time.clock()
df = sqlContext.sql(query)
df.show()
endTimeQuery = time.clock()
runTimeQuery = endTimeQuery - startTimeQuery
Is it a good way? The time that I get looks too small relative to when I see the table.

To do it in a spark-shell (Scala), you can use spark.time().
See another response by me: https://stackoverflow.com/a/50289329/3397114
df = sqlContext.sql(query)
spark.time(df.show())
The output would be:
+----+----+
|col1|col2|
+----+----+
|val1|val2|
+----+----+
Time taken: xxx ms
Related: On Measuring Apache Spark Workload Metrics for Performance Troubleshooting.

I use System.nanoTime wrapped around a helper function, like this -
def time[A](f: => A) = {
val s = System.nanoTime
val ret = f
println("time: "+(System.nanoTime-s)/1e6+"ms")
ret
}
time {
df = sqlContext.sql(query)
df.show()
}

Update:
No, using time package is not the best way to measure execution time of Spark jobs. The most convenient and exact way I know of is to use the Spark History Server.
On Bluemix, in your notebooks go to the "Paelette" on the right side. Choose the "Evironment" Panel and you will see a link to the Spark History Server, where you can investigate the performed Spark jobs including computation times.

SPARK itself provides much granular information about each stage of your Spark Job.
You can view your running job on http://IP-MasterNode:4040 or You can enable History server for analyzing the jobs at a later time.
Refer here for more info on History server.

If you are using spark-shell (scala) you can use the time module:
import time
df = sqlContext.sql(query)
spark.time(df.show())
However, SparkSession.time() is not available in pyspark. For python, a simple solution would be to use time:
import time
start_time = time.time()
df.show()
print(f"Execution time: {time.time() - start_time}")

You can also try using sparkMeasure which simplify the collection of performance metrics

For those looking for / needing a python version
(as pyspark google search leads to this post) :
from time import time
from datetime import timedelta
class T():
def __enter__(self):
self.start = time()
def __exit__(self, type, value, traceback):
self.end = time()
elapsed = self.end - self.start
print(str(timedelta(seconds=elapsed)))
Usage :
with T():
//spark code goes here
As inspired by :
https://blog.usejournal.com/how-to-create-your-own-timing-context-manager-in-python-a0e944b48cf8
Proved useful when using console or whith notebooks
(jupyter magic %%time an %timeit are limited to cell scope, which is inconvenient when you have shared objects across notebook context)

Related

AWS lambda 10x slower running pandas preprocessing compared to endpoint

I have been experimenting with reducing prediction request latency. On the one hand I have a sagemaker inference pipeline, which has a single endpoint with a preprocessing container and a model container. The preprocessing container runs a script extracting some date features and numerical features using pandas.
I've also tested creating a a lambda deployment package with pandas following this post. So here I would do the feature extraction inside the lambda, and then call the model endpoint using the response from the lambda.
I noticed a big difference in response time, and when I looked closer I noticed the pandas operations take 10x longer in the lambda?
Here's an example of a feature extraction function that takes 5x longer, but some are over 10x longer (one function goes from 30 ms to 380).
def extract_date_features(df):
print('Getting date features.')
df['date'] = pd.to_datetime(df.date)
df['weekday'] = df.date.dt.weekday
df['year'] = df.date.dt.year
df['month'] = df.date.dt.month
df['day'] = df.date.dt.day
df['weekday'] = df.date.dt.weekday
df['dayofyear'] = df.date.dt.dayofyear
#df['week'] = df.date.dt.isocalendar().week.apply(int)
df['dayofweek'] = df.date.dt.dayofweek
df['is_weekend'] = np.where(df.date.dt.dayofweek.isin([5,6]), 1,0)
df['quarter'] = df.date.dt.quarter
What would be the reason for this? And it is my understanding that the compute provided for a lambda is all handled by aws, so there's no way to select a "faster" lambda, and I'm stuck with this speed if I'm using pandas in lambda.

Can I apply a function to a pandas dataframe asyncronously?

In my use case I need to fetch data from remote server. The code is roughly equivalent to:
def get_user_data(user_id):
time.sleep(5)
...
return data
df = pd.DataFrame({'user_id': ['uid1', 'uid2', 'uid3', ..., 'uid9999']})
answer = df['user_id'].apply(get_user_data)
It seems to me pandas could be running the get_user_data function asynchronously.
Note:
I've tried df['user_id'].swifter.apply(get_user_data) and using dask. They both give me an good speedup by running multiple functions in parallel, but my CPU, network, and remote server utilization remain very low.
Is there a way to do an asynchronous .apply() ?

How to parallelize groupby() in dask?

I tried:
df.groupby('name').agg('count').compute(num_workers=1)
df.groupby('name').agg('count').compute(num_workers=4)
They take the same time, why num_workers does not work?
Thanks
By default, Dask will work with multi-threaded tasks which means it uses a single processor on your computer. (Note that using dask is nevertheless interesting if you have data that can't fit in memory)
If you want to use several processors to compute your operation, you have to use a different scheduler:
from dask import dataframe as dd
from dask.distributed import LocalCluster, Client
df = dd.read_csv("data.csv")
def group(num_workers):
start = time.time()
res = df.groupby("name").agg("count").compute(num_workers=num_workers)
end = time.time()
return res, end-start
print(group(4))
clust = LocalCluster()
clt = Client(clust, set_as_default=True)
print(group(4))
Here, I create a local cluster using 4 parallel processes (because I have a quadcore) and then set a default scheduling client that will use this local cluster to perform the Dask operations. With a CSV two columns file of 1.5 Gb, the standard groupby takes around 35 seconds on my laptop whereas the multiprocess one only takes around 22 seconds.

Pyspark: Serialized task exceeds max allowed. Consider increasing spark.rpc.message.maxSize or using broadcast variables for large values

I'm doing calculations on a cluster and at the end when I ask summary statistics on my Spark dataframe with df.describe().show() I get an error:
Serialized task 15:0 was 137500581 bytes, which exceeds max allowed: spark.rpc.message.maxSize (134217728 bytes). Consider increasing spark.rpc.message.maxSize or using broadcast variables for large values
In my Spark configuration I already tried to increase the aforementioned parameter:
spark = (SparkSession
.builder
.appName("TV segmentation - dataprep for scoring")
.config("spark.executor.memory", "25G")
.config("spark.driver.memory", "40G")
.config("spark.dynamicAllocation.enabled", "true")
.config("spark.dynamicAllocation.maxExecutors", "12")
.config("spark.driver.maxResultSize", "3g")
.config("spark.kryoserializer.buffer.max.mb", "2047mb")
.config("spark.rpc.message.maxSize", "1000mb")
.getOrCreate())
I also tried to repartition my dataframe using:
dfscoring=dfscoring.repartition(100)
but still I keep on getting the same error.
My environment: Python 3.5, Anaconda 5.0, Spark 2
How can I avoid this error ?
i'm in same trouble, then i solve it.
the cause is spark.rpc.message.maxSize if default set 128M, you can change it when launch a spark client, i'm work in pyspark and set the value to 1024, so i write like this:
pyspark --master yarn --conf spark.rpc.message.maxSize=1024
solve it.
I had the same issue and it wasted a day of my life that I am never getting back. I am not sure why this is happening, but here is how I made it work for me.
Step 1: Make sure that PYSPARK_PYTHON and PYSPARK_DRIVER_PYTHON are correctly set.
Turned out that python in worker(2.6) had a different version than in driver(3.6). You should check if environment variables PYSPARK_PYTHON and PYSPARK_DRIVER_PYTHON are correctly set.
I fixed it by simply switching my kernel from Python 3 Spark 2.2.0 to Python Spark 2.3.1 in Jupyter. You may have to set it up manually. Here is how to make sure your PySpark is set up correctly https://mortada.net/3-easy-steps-to-set-up-pyspark.html
STEP 2: If that doesn't work, try working around it:
This kernel switch worked for DFs that I haven't added any columns to:
spark_df -> panda_df -> back_to_spark_df .... but it didn't work on the DFs where I had added 5 extra columns. So what I tried and it worked was the following:
# 1. Select only the new columns:
df_write = df[['hotel_id','neg_prob','prob','ipw','auc','brier_score']]
# 2. Convert this DF into Spark DF:
df_to_spark = spark.createDataFrame(df_write)
df_to_spark = df_to_spark.repartition(100)
df_to_spark.registerTempTable('df_to_spark')
# 3. Join it to the rest of your data:
final = df_to_spark.join(data,'hotel_id')
# 4. Then write the final DF.
final.write.saveAsTable('schema_name.table_name',mode='overwrite')
Hope that helps!
I had the same problem but using Watson studio. My solution was:
sc.stop()
configura=SparkConf().set('spark.rpc.message.maxSize','256')
sc=SparkContext.getOrCreate(conf=configura)
spark = SparkSession.builder.getOrCreate()
I hope it help someone...
I had faced the same issue while converting the sparkDF to pandasDF.
I am working on Azure-Databricks , first you need to check the memory set in the spark config using below -
spark.conf.get("spark.rpc.message.maxSize")
Then we can increase the memory-
spark.conf.set("spark.rpc.message.maxSize", "500")
For those folks, who are looking for AWS Glue script pyspark based way of doing this. The below code snippet might be useful
from awsglue.context import GlueContext
from pyspark.context import SparkContext
from pyspark import SparkConf
myconfig=SparkConf().set('spark.rpc.message.maxSize','256')
#SparkConf can be directly used with its .set property
sc = SparkContext(conf=myconfig)
glueContext = GlueContext(sc)
..
..

Make Pandas DataFrame apply() use all cores?

As of August 2017, Pandas DataFame.apply() is unfortunately still limited to working with a single core, meaning that a multi-core machine will waste the majority of its compute-time when you run df.apply(myfunc, axis=1).
How can you use all your cores to run apply on a dataframe in parallel?
You may use the swifter package:
pip install swifter
(Note that you may want to use this in a virtualenv to avoid version conflicts with installed dependencies.)
Swifter works as a plugin for pandas, allowing you to reuse the apply function:
import swifter
def some_function(data):
return data * 10
data['out'] = data['in'].swifter.apply(some_function)
It will automatically figure out the most efficient way to parallelize the function, no matter if it's vectorized (as in the above example) or not.
More examples and a performance comparison are available on GitHub. Note that the package is under active development, so the API may change.
Also note that this will not work automatically for string columns. When using strings, Swifter will fallback to a “simple” Pandas apply, which will not be parallel. In this case, even forcing it to use dask will not create performance improvements, and you would be better off just splitting your dataset manually and parallelizing using multiprocessing.
The simplest way is to use Dask's map_partitions. You need these imports (you will need to pip install dask):
import pandas as pd
import dask.dataframe as dd
from dask.multiprocessing import get
and the syntax is
data = <your_pandas_dataframe>
ddata = dd.from_pandas(data, npartitions=30)
def myfunc(x,y,z, ...): return <whatever>
res = ddata.map_partitions(lambda df: df.apply((lambda row: myfunc(*row)), axis=1)).compute(get=get)
(I believe that 30 is a suitable number of partitions if you have 16 cores). Just for completeness, I timed the difference on my machine (16 cores):
data = pd.DataFrame()
data['col1'] = np.random.normal(size = 1500000)
data['col2'] = np.random.normal(size = 1500000)
ddata = dd.from_pandas(data, npartitions=30)
def myfunc(x,y): return y*(x**2+1)
def apply_myfunc_to_DF(df): return df.apply((lambda row: myfunc(*row)), axis=1)
def pandas_apply(): return apply_myfunc_to_DF(data)
def dask_apply(): return ddata.map_partitions(apply_myfunc_to_DF).compute(get=get)
def vectorized(): return myfunc(data['col1'], data['col2'] )
t_pds = timeit.Timer(lambda: pandas_apply())
print(t_pds.timeit(number=1))
28.16970546543598
t_dsk = timeit.Timer(lambda: dask_apply())
print(t_dsk.timeit(number=1))
2.708152851089835
t_vec = timeit.Timer(lambda: vectorized())
print(t_vec.timeit(number=1))
0.010668013244867325
Giving a factor of 10 speedup going from pandas apply to dask apply on partitions. Of course, if you have a function you can vectorize, you should - in this case the function (y*(x**2+1)) is trivially vectorized, but there are plenty of things that are impossible to vectorize.
you can try pandarallel instead: A simple and efficient tool to parallelize your pandas operations on all your CPUs (On Linux & macOS)
Parallelization has a cost (instanciating new processes, sending data via shared memory, etc ...), so parallelization is efficiant only if the amount of calculation to parallelize is high enough. For very little amount of data, using parallezation not always worth it.
Functions applied should NOT be lambda functions.
from pandarallel import pandarallel
from math import sin
pandarallel.initialize()
# FORBIDDEN
df.parallel_apply(lambda x: sin(x**2), axis=1)
# ALLOWED
def func(x):
return sin(x**2)
df.parallel_apply(func, axis=1)
see https://github.com/nalepae/pandarallel
If you want to stay in native python:
import multiprocessing as mp
with mp.Pool(mp.cpu_count()) as pool:
df['newcol'] = pool.map(f, df['col'])
will apply function f in a parallel fashion to column col of dataframe df
Just want to give an update answer for Dask
import dask.dataframe as dd
def your_func(row):
#do something
return row
ddf = dd.from_pandas(df, npartitions=30) # find your own number of partitions
ddf_update = ddf.apply(your_func, axis=1).compute()
On my 100,000 records, without Dask:
CPU times: user 6min 32s, sys: 100 ms, total: 6min 32s
Wall time: 6min 32s
With Dask:
CPU times: user 5.19 s, sys: 784 ms, total: 5.98 s
Wall time: 1min 3s
To use all (physical or logical) cores, you could try mapply as an alternative to swifter and pandarallel.
You can set the amount of cores (and the chunking behaviour) upon init:
import pandas as pd
import mapply
mapply.init(n_workers=-1)
...
df.mapply(myfunc, axis=1)
By default (n_workers=-1), the package uses all physical CPUs available on the system. If your system uses hyper-threading (usually twice the amount of physical CPUs would show up as logical cores), mapply will spawn one extra worker to prioritise the multiprocessing pool over other processes on the system.
Depending on your definition of all your cores, you could also use all logical cores instead (beware that like this the CPU-bound processes will be fighting for physical CPUs, which might slow down your operation):
import multiprocessing
n_workers = multiprocessing.cpu_count()
# or more explicit
import psutil
n_workers = psutil.cpu_count(logical=True)
Here is an example of sklearn base transformer, in which pandas apply is parallelized
import multiprocessing as mp
from sklearn.base import TransformerMixin, BaseEstimator
class ParllelTransformer(BaseEstimator, TransformerMixin):
def __init__(self,
n_jobs=1):
"""
n_jobs - parallel jobs to run
"""
self.variety = variety
self.user_abbrevs = user_abbrevs
self.n_jobs = n_jobs
def fit(self, X, y=None):
return self
def transform(self, X, *_):
X_copy = X.copy()
cores = mp.cpu_count()
partitions = 1
if self.n_jobs <= -1:
partitions = cores
elif self.n_jobs <= 0:
partitions = 1
else:
partitions = min(self.n_jobs, cores)
if partitions == 1:
# transform sequentially
return X_copy.apply(self._transform_one)
# splitting data into batches
data_split = np.array_split(X_copy, partitions)
pool = mp.Pool(cores)
# Here reduce function - concationation of transformed batches
data = pd.concat(
pool.map(self._preprocess_part, data_split)
)
pool.close()
pool.join()
return data
def _transform_part(self, df_part):
return df_part.apply(self._transform_one)
def _transform_one(self, line):
# some kind of transformations here
return line
for more info see https://towardsdatascience.com/4-easy-steps-to-improve-your-machine-learning-code-performance-88a0b0eeffa8
The native Python solution (with numpy) that can be applied on the whole DataFrame as the original question asks (not only on a single column)
import numpy as np
import multiprocessing as mp
dfs = np.array_split(df, 8000) # divide the dataframe as desired
def f_app(df):
return df.apply(myfunc, axis=1)
with mp.Pool(mp.cpu_count()) as pool:
res = pd.concat(pool.map(f_app, dfs))
Here another one using Joblib and some helper code from scikit-learn. Lightweight (if you already have scikit-learn), good if you prefer more control over what it is doing since joblib is easily hackable.
from joblib import parallel_backend, Parallel, delayed, effective_n_jobs
from sklearn.utils import gen_even_slices
from sklearn.utils.validation import _num_samples
def parallel_apply(df, func, n_jobs= -1, **kwargs):
""" Pandas apply in parallel using joblib.
Uses sklearn.utils to partition input evenly.
Args:
df: Pandas DataFrame, Series, or any other object that supports slicing and apply.
func: Callable to apply
n_jobs: Desired number of workers. Default value -1 means use all available cores.
**kwargs: Any additional parameters will be supplied to the apply function
Returns:
Same as for normal Pandas DataFrame.apply()
"""
if effective_n_jobs(n_jobs) == 1:
return df.apply(func, **kwargs)
else:
ret = Parallel(n_jobs=n_jobs)(
delayed(type(df).apply)(df[s], func, **kwargs)
for s in gen_even_slices(_num_samples(df), effective_n_jobs(n_jobs)))
return pd.concat(ret)
Usage: result = parallel_apply(my_dataframe, my_func)
Instead of
df["new"] = df["old"].map(fun)
do
from joblib import Parallel, delayed
df["new"] = Parallel(n_jobs=-1, verbose=10)(delayed(fun)(i) for i in df["old"])
To me this is a slight improvement over
import multiprocessing as mp
with mp.Pool(mp.cpu_count()) as pool:
df["new"] = pool.map(fun, df["old"])
as you get a progress indication and automatic batching if the jobs are very small.
Since the question was "How can you use all your cores to run apply on a dataframe in parallel?", the answer can also be with modin. You can run all cores in parallel, though the real time is worse.
See https://github.com/modin-project/modin . It runs of top of dask or ray. They say "Modin is a DataFrame designed for datasets from 1MB to 1TB+." I tried: pip3 install "modin"[ray]". Modin vs pandas was - 12 sec on six cores vs. 6 sec.
In case you need to do something based on the column name inside the function beware that .apply function may give you some trouble. In my case I needed to change the column type using astype() function based on the column name. This is probably not the most efficient way of doing it but suffices the purpose and keeps the column names as the original one.
import multiprocessing as mp
def f(df):
""" the function that you want to apply to each column """
column_name = df.columns[0] # this is the same as the original column name
# do something what you need to do to that column
return df
# Here I just make a list of all the columns. If you don't use .to_frame()
# it will pass series type instead of a dataframe
dfs = [df[column].to_frame() for column in df.columns]
with mp.Pool(mp.cpu_num) as pool:
processed_df = pd.concat(pool.map(f, dfs), axis=1)