I have a Process pool in python that is starting processes as normal, however, I have just realized that these processes are not closed after the completion (I know that they completed as the last statement is a file write).
Below the code, with an example function ppp:
from multiprocessing import Pool
import itertools
def ppp(element):
window,day = element
print(window,day)
time.sleep(10)
if __name__ == '__main__': ##The line marked
print('START')
start_time = current_milli_time()
days = ['0808', '0810', '0812', '0813', '0814', '0817', '0818', '0827']
windows = [1000,2000,3000,4000,5000,10000,15000, 20000,30000,60000,120000,180000]
processes_args = list(itertools.product(windows, days))
pool = Pool(8)
results = pool.map(ppp, processes_args)
pool.close()
pool.join()
print('END', current_milli_time()-start_time)
I am working on Linux, Ubuntu 16.04. Everything was working fine before I added the line marked in the example. I am wondering if that behavior can be related to the missing of a return statement. Anyway, that is what looks like my 'htop':
As you can see, no process is closed, but all have completed their work.
I found that related question: Python Multiprocessing pool.close() and join() does not close processes, however, I have not understood if the solution to this problem is to use map_async instead of map.
EDIT: real function code:
def process_day(element):
window,day = element
noise = 0.2
print('Processing day:', day,', window:', window)
individual_files = glob.glob('datan/'+day+'/*[0-9].csv')
individual = readDataset(individual_files)
label_time = individual.loc[(individual['LABEL_O'] != -2) | (individual['LABEL_F'] != -2), 'TIME']
label_time = list(np.unique(list(label_time)))
individual = individual[individual['TIME'].isin(label_time)]
#Saving IDs for further processing
individual['ID'] = individual['COLLAR']
#Time variable in seconds for aggregation and merging
individual['TIME_S'] = individual['TIME'].copy()
noise_x = np.random.normal(0,noise,len(individual))
noise_y = np.random.normal(0,noise,len(individual))
noise_z = np.random.normal(0,noise,len(individual))
individual['X_AXIS'] = individual['X_AXIS'] + noise_x
individual['Y_AXIS'] = individual['Y_AXIS'] + noise_y
individual['Z_AXIS'] = individual['Z_AXIS'] + noise_z
#Time syncronization (applying milliseconds for time series processing)
print('Time syncronization:')
with progressbar.ProgressBar(max_value=len(individual.groupby('ID'))) as bar:
for baboon,df_baboon in individual.groupby('ID'):
times = list(df_baboon['TIME'].values)
d = Counter(times)
result = []
for timestamp in np.unique(times):
for i in range(0,d[timestamp]):
result.append(str(timestamp+i*1000/d[timestamp]))
individual.loc[individual['ID'] == baboon,'TIME'] = result
bar.update(1)
#Time series process
ts_process = time_series_processing(window, 'TIME_S', individual, 'COLLAR', ['COLLAR', 'TIME', 'X_AXIS','Y_AXIS','Z_AXIS'])
#Aggregation and tsfresh
ts_process.do_process()
individual = ts_process.get_processed_dataframe()
individual.to_csv('noise2/processed_data/'+str(window)+'/agg/'+str(day)+'.csv', index = False)
#NEtwork inference process
ni = network_inference_process(individual, 'TIME_S_mean')
#Inference
ni.do_process()
final = ni.get_processed_dataframe()
final.to_csv('noise2/processed_data/'+str(window)+'/net/'+str(day)+'.csv', index = False)
#Saving not aggregated ground truth
ground_truth = final[['ID_mean', 'TIME_S_mean', 'LABEL_O_values', 'LABEL_F_values']].copy()
#Neighbor features process
neighbors_features_f = ni.get_neighbor_features(final, 'TIME_S_mean', 'ID_mean')
neighbors_features_f = neighbors_features_f.drop(['LABEL_O_values_n', 'LABEL_F_values_n'], axis=1)
neighbors_features_f.to_csv('noise2/processed_data/'+str(window)+'/net/'+str(day)+'_neigh.csv', index = False)
# Final features dataframe
final_neigh = pd.merge(final, neighbors_features_f, how='left', left_on=['TIME_S_mean','ID_mean'], right_on = ['TIME_S_mean_n','BABOON_NODE_n'])
final_neigh.to_csv('noise2/processed_data/'+str(window)+'/complete/'+str(day)+'.csv', index = False)
return
So as you can see, the last statement is a write to file, and it is executed by all the processes, I do not actually think that the problem is inside this function.
Related
downloadStart = datetime.now()
while (True):
requestURL = transactionAPI.format(page = tempPage,limit = 5000)
response = requests.get(requestURL,headers=headers)
json_data = json.loads(response.content)
tempMomosTransactionHistory.extend(json_data["list"])
if(datetime.fromtimestamp(json_data["list"][-1]["crtime"]) < datetime(datetime.today().year,datetime.today().month,datetime.today().day - dateRange)):
break
tempPage += 1
downloadEnd = datetime.now()
Any suggestions please threading or something like that ?
Outputs here
downloadtime 0:00:02.056010
downloadtime 0:00:05.680806
downloadtime 0:00:05.447945
You need to improve it in two ways.
Optimise code within loop
Parallelize code execution
#1
By looking at your code I can see one improvement ie. create datetime.today object instead of doing 3 times. Check other methods like transactionAPI optimise further.
#2:
If you multi core CPU machine then you take advantage of machine by spanning thread per page. Refer to modified code of above.
import threading
def processRequest(tempPage):
requestURL = transactionAPI.format(page = tempPage,limit = 5000)
response = requests.get(requestURL,headers=headers)
json_data = json.loads(response.content)
tempMomosTransactionHistory.extend(json_data["list"])
downloadStart = datetime.now()
while (True):
#create thread per page
t1 = threading.Thread(target=processRequest, args=(tempPage, ))
t1.start()
#Fetch datetime today object once instaed 3 times
datetimetoday = datetime()
if(datetime.fromtimestamp(json_data["list"][-1]["crtime"]) < datetime(datetimetoday.year,datetimetoday.month,datetimetoday.day - dateRange)):
break
tempPage += 1
downloadEnd = datetime.now()
I have a list containing ID Number's, I want to implement every unique ID Number in an API call for each Multiprocessor whilst running the same corresponding functions, implementing the same conditional statements to each processor etc. I have tried to make sense of it but there is not a lot online about this procedure.
I thought to use a for loop but I don't want every processor running this for loop picking up every item in a list. I just need each item to be associated to each processor.
I was thinking something like this:
from multiprocessing import process
import requests, json
ID_NUMBERS = ["ID 1", "ID 2", "ID 3".... ETC]
BASE_URL = "www.api.com"
KEY = {"KEY": "12345"}
a = 0
for x in ID_NUMBERS:
def[a]():
while Active_live_data == True:
# continuously loops over, requesting data from the website
unique_api_call = "{}/livedata[{}]".format(BASE_URL, x)
request_it = requests.get(unique_api_call, headers=KEY)
show_it = (json.loads(request_it.content))
#some extra conditional code...
a += 1
processes = []
b = 0
for _ in range(len(ID_NUMBERS))
p = multiprocessing.Process(target = b)
p.start()
processes.append(p)
b += 1
Any help would be greatly appreciated!
Kindest regards,
Andrew
You can use the map function:
import multiprocessing as mp
num_cores = mp.cpu_count()
pool = mp.Pool(processes=num_cores)
results = pool.map(your_function, list_of_IDs)
This will execute the function your_function, each time with a different item from the list list_of_IDs, and the values returned by your_function will be stored in a list of values (results).
Same approach as #AlessiaM but uses the high-level api in the concurrent.futures module.
import concurrent.futures as mp
import requests, json
BASE_URL = ''
KEY = {"KEY": "12345"}
ID_NUMBERS = ["ID 1", "ID 2", "ID 3"]
def job(id):
unique_api_call = "{}/livedata[{}]".format(BASE_URL, id)
request_it = requests.get(unique_api_call, headers=KEY)
show_it = (json.loads(request_it.content))
return show_it
# Default to as many workers as there are processors,
# But since your job is IO bound (vs CPU bound),
# you could increase this to an even bigger figure by giving the `max_workers` parameter
with mp.ProcessPoolExecutor() as pool:
results = pool.map(job,ID_NUMBERS)
# Process results here
I store QuertyText within a pandas dataframe. Once I've loaded all the queries into I want to conduct an analysis again each query. Currently, I have ~50k to evaluate. So, doing it one by one, will take a long time.
So, I wanted to implement concurrent.futures. How do I take the individual QueryText stored within fullAnalysis as pass it to concurrent.futures and return the output as a variable?
Here is my entire code:
import pandas as pd
import time
import gensim
import sys
import warnings
from concurrent.futures import ThreadPoolExecutor
from concurrent.futures import as_completed
fullAnalysis = pd.DataFrame()
def fetch_data(jFile = 'ProcessingDetails.json'):
print("Fetching data...please wait")
#read JSON file for latest dictionary file name
baselineDictionaryFileName = 'Dictionary/Dictionary_05-03-2020.json'
#copy data to pandas dataframe
labelled_data = pd.read_json(baselineDictionaryFileName)
#Add two more columns to get the most similar text and score
labelled_data['SimilarText'] = ''
labelled_data['SimilarityScore'] = float()
print("Data fetched from " + baselineDictionaryFileName + " and there are " + str(labelled_data.shape[0]) + " rows to be evalauted")
return labelled_data
def calculateScore(inputFunc):
warnings.filterwarnings("ignore", category=DeprecationWarning)
model = gensim.models.Word2Vec.load('w2v_model_bigdata')
inp = inputFunc
print(inp)
out = dict()
strEvaluation = inp.split("most_similar ",1)[1]
#while inp != 'quit':
split_inp = inp.split()
try:
if split_inp[0] == 'help':
pass
elif split_inp[0] == 'similarity' and len(split_inp) >= 3:
pass
elif split_inp[0] == 'most_similar' and len(split_inp) >= 2:
for pair in model.most_similar(positive=[split_inp[1]]):
out.update({pair[0]: pair[1]})
except KeyError as ke:
#print(str(ke) + "\n")
inp = input()
return out
def main():
with ThreadPoolExecutor(max_workers=5) as executor:
for i in range(len(fullAnalysis)):
text = fullAnalysis['QueryText'][i]
arg = 'most_similar'+ ' ' + text
#for item in executor.map(calculateScore, arg):
output = executor.map(calculateScore, arg)
return output
if __name__ == "__main__":
fullAnalysis = fetch_data()
results = main()
print(f'results: {results}')
The Python Global Interpreter Lock or GIL allows only one thread to hold control of the Python interpreter. Since your function calculateScore might be cpu-bound and requires the interpreter to execute its byte code, you may be gaining little by using threading. If, on the other hand, it were doing mostly I/O operations, it would be giving up the GIL for most of its running time allowing other threads to run. But that does not seem to be the case here. You probably should be using the ProcessPoolExecutor from concurrent.futures (try it both ways and see):
def main():
with ProcessPoolExecutor(max_workers=None) as executor:
the_futures = {}
for i in range(len(fullAnalysis)):
text = fullAnalysis['QueryText'][i]
arg = 'most_similar'+ ' ' + text
future = executor.submit(calculateScore, arg)
the_futures[future] = i # map future to request
for future in as_completed(the_futures): # results as they become available not necessarily the order of submission
i = the_futures[future] # the original index
result = future.result() # the result
If you omit the max_workers parameter (or specify a value of None) from the ProcessPoolExecutor constructor, the default will be the number of processors you have on your machine (not a bad default). There is no point in specifying a value larger than the number of processors you have.
If you do not need to tie the future back to the original request, then the_futures can just be a list to which But simplest yest in not even to bother to use the as_completed method:
def main():
with ProcessPoolExecutor(max_workers=5) as executor:
the_futures = []
for i in range(len(fullAnalysis)):
text = fullAnalysis['QueryText'][i]
arg = 'most_similar'+ ' ' + text
future = executor.submit(calculateScore, arg)
the_futures.append(future)
# wait for the completion of all the results and return them all:
results = [f.result() for f in the_futures()] # results in creation order
return results
It should be mentioned that code that launches the ProcessPoolExecutor functions should be in a block governed by a if __name__ = '__main__':. If it isn't you will get into a recursive loop with each subprocess launching the ProcessPoolExecutor. But that seems to be the case here. Perhaps you meant to use the ProcessPoolExecutor all along?
Also:
I don't know what the line ...
model = gensim.models.Word2Vec.load('w2v_model_bigdata')
... in function calculateStore does. It may be the one i/o-bound statement. But this appears to be something that does not vary from call to call. If that is the case and model is not being modified in the function, shouldn't this statement be moved out of the function and computed just once? Then this function would clearly run faster (and be clearly cpu-bound).
Also:
The exception block ...
except KeyError as ke:
#print(str(ke) + "\n")
inp = input()
... is puzzling. You are inputting a value that will never be used right before returning. If this is to pause execution, there is no error message being output.
With Booboo assistance, I was able to update code to include ProcessPoolExecutor. Here is my updated code. Overall, processing has been speed up by more than 60%.
I did run into a processing issue and found this topic BrokenPoolProcess that addresses the issue.
output = {}
thePool = {}
def main(labelled_data, dictionaryRevised):
args = sys.argv[1:]
with ProcessPoolExecutor(max_workers=None) as executor:
for i in range(len(labelled_data)):
text = labelled_data['QueryText'][i]
arg = 'most_similar'+ ' '+ text
output = winprocess.submit(
executor, calculateScore, arg
)
thePool[output] = i #original index for future to request
for output in as_completed(thePool): # results as they become available not necessarily the order of submission
i = thePool[output] # the original index
text = labelled_data['QueryText'][i]
result = output.result() # the result
maximumKey = max(result.items(), key=operator.itemgetter(1))[0]
maximumValue = result.get(maximumKey)
labelled_data['SimilarText'][i] = maximumKey
labelled_data['SimilarityScore'][i] = maximumValue
return labelled_data, dictionaryRevised
if __name__ == "__main__":
start = time.perf_counter()
print("Starting to evaluate Query Text for labelling...")
output_Labelled_Data, output_dictionary_revised = preProcessor()
output,dictionary = main(output_Labelled_Data, output_dictionary_revised)
finish = time.perf_counter()
print(f'Finished in {round(finish-start, 2)} second(s)')
I'm working on a Raspberry Pi (3 B+) making a data collection device and I'm
trying to spawn a process to record the data coming in and write it to a file. I have a function for the writing that works fine when I call it directly.
When I call it using the multiprocess approach however, nothing seems to happen. I can see in task monitors in Linux that the process does in fact get spawned but no file gets written, and when I try to pass a flag to it to shut down it doesn't work, meaning I end up terminating the process and nothing seems to have happened.
I've been over this every which way and can't see what I'm doing wrong; does anyone else? In case it's relevant, these are functions inside a parent class, and one of the functions is meant to spawn another as a thread.
Code I'm using:
from datetime import datetime, timedelta
import csv
from drivers.IMU_SEN0 import IMU_SEN0
import multiprocessing, os
class IMU_data_logger:
_output_filename = ''
_csv_headers = []
_accelerometer_headers = ['Accelerometer X','Accelerometer Y','Accelerometer Z']
_gyroscope_headers = ['Gyroscope X','Gyroscope Y','Gyroscope Z']
_magnetometer_headers = ['Bearing']
_log_accelerometer = False
_log_gyroscope= False
_log_magnetometer = False
IMU = None
_writer=[]
_run_underway = False
_process=[]
_stop_value = 0
def __init__(self,output_filename='/home/pi/blah.csv',log_accelerometer = True,log_gyroscope= True,log_magnetometer = True):
"""data logging device
NOTE! Multiple instances of this class should not use the same IMU devices simultaneously!"""
self._output_filename = output_filename
self._log_accelerometer = log_accelerometer
self._log_gyroscope = log_gyroscope
self._log_magnetometer = log_magnetometer
def __del__(self):
# TODO Update this
if self._run_underway: # If there's still a run underway, end it first
self.end_recording()
def _set_up(self):
self.IMU = IMU_SEN0(self._log_accelerometer,self._log_gyroscope,self._log_magnetometer)
self._set_up_headers()
def _set_up_headers(self):
"""Set up the headers of the CSV file based on the header substrings at top and the input flags on what will be measured"""
self._csv_headers = []
if self._log_accelerometer is not None:
self._csv_headers+= self._accelerometer_headers
if self._log_gyroscope is not None:
self._csv_headers+= self._gyroscope_headers
if self._log_magnetometer is not None:
self._csv_headers+= self._magnetometer_headers
def _record_data(self,frequency,stop_value):
self._set_up() #Run setup in thread
"""Record data function, which takes a recording frequency, in herz, as an input"""
previous_read_time=datetime.now()-timedelta(1,0,0)
self._run_underway = True # Note that a run is now going
Period = 1/frequency # Period, in seconds, of a recording based on the input frequency
print("Writing output data to",self._output_filename)
with open(self._output_filename,'w',newline='') as outcsv:
self._writer = csv.writer(outcsv)
self._writer.writerow(self._csv_headers) # Write headers to file
while stop_value.value==0: # While a run continues
if datetime.now()-previous_read_time>=timedelta(0,1,0): # If we've waited a period, collect the data; otherwise keep looping
print("run underway value",self._run_underway)
if datetime.now()-previous_read_time>=timedelta(0,Period,0): # If we've waited a period, collect the data; otherwise keep looping
previous_read_time = datetime.now() # Update previous readtime
next_row = []
if self._log_accelerometer:
# Get values in m/s^2
axes = self.IMU.read_accelerometer_values()
next_row += [axes['x'],axes['y'],axes['z']]
if self._log_gyroscope:
# Read gyro values
gyro = self.IMU.read_gyroscope_values()
next_row += [gyro['x'],gyro['y'],gyro['z']]
if self._log_magnetometer:
# Read magnetometer value
b= self.IMU.read_magnetometer_bearing()
next_row += b
self._writer.writerow(next_row)
# Close the csv when done
outcsv.close()
def start_recording(self,frequency_in_hz):
# Create recording process
self._stop_value = multiprocessing.Value('i',0)
self._process = multiprocessing.Process(target=self._record_data,args=(frequency_in_hz,self._stop_value))
# Start recording process
self._process.start()
print(datetime.now().strftime("%H:%M:%S.%f"),"Data logging process spawned")
print("Logging Accelerometer:",self._log_accelerometer)
print("Logging Gyroscope:",self._log_gyroscope)
print("Logging Magnetometer:",self._log_magnetometer)
print("ID of data logging process: {}".format(self._process.pid))
def end_recording(self,terminate_wait = 2):
"""Function to end the recording multithread that's been spawned.
Args: terminate_wait: This is the time, in seconds, to wait after attempting to shut down the process before terminating it."""
# Get process id
id = self._process.pid
# Set stop event for process
self._stop_value.value = 1
self._process.join(terminate_wait) # Wait two seconds for the process to terminate
if self._process.is_alive(): # If it's still alive after waiting
self._process.terminate()
print(datetime.now().strftime("%H:%M:%S.%f"),"Process",id,"needed to be terminated.")
else:
print(datetime.now().strftime("%H:%M:%S.%f"),"Process",id,"successfully ended itself.")
====================================================================
ANSWER: For anyone following up here, it turns out the problem was my use of the VS Code debugger which apparently doesn't work with multiprocessing and was somehow preventing the success of the spawned process. Many thanks to Tomasz Swider below for helping me work through issues and, eventually, find my idiocy. The help was very deeply appreciated!!
I can see few thing wrong in your code:
First thing
stop_value == 0 will not work as the multiprocess.Value('i', 0) != 0, change that line to
while stop_value.value == 0
Second, you never update previous_read_time so it will write the readings as fast as it can, you will run out of disk quick
Third, try use time.sleep() the thing you are doing is called busy looping and it is bad, it is wasting CPU cycles needlessly.
Four, terminating with self._stop_value = 1 probably will not work there must be other way to set that value maybe self._stop_value.value = 1.
Well here is a pice of example code based on the code that you have provided that is working just fine:
import csv
import multiprocessing
import time
from datetime import datetime, timedelta
from random import randint
class IMU(object):
#staticmethod
def read_accelerometer_values():
return dict(x=randint(0, 100), y=randint(0, 100), z=randint(0, 10))
class Foo(object):
def __init__(self, output_filename):
self._output_filename = output_filename
self._csv_headers = ['xxxx','y','z']
self._log_accelerometer = True
self.IMU = IMU()
def _record_data(self, frequency, stop_value):
#self._set_up() # Run setup functions for the data collection device and store it in the self.IMU variable
"""Record data function, which takes a recording frequency, in herz, as an input"""
previous_read_time = datetime.now() - timedelta(1, 0, 0)
self._run_underway = True # Note that a run is now going
Period = 1 / frequency # Period, in seconds, of a recording based on the input frequency
print("Writing output data to", self._output_filename)
with open(self._output_filename, 'w', newline='') as outcsv:
self._writer = csv.writer(outcsv)
self._writer.writerow(self._csv_headers) # Write headers to file
while stop_value.value == 0: # While a run continues
if datetime.now() - previous_read_time >= timedelta(0, 1,
0): # If we've waited a period, collect the data; otherwise keep looping
print("run underway value", self._run_underway)
if datetime.now() - previous_read_time >= timedelta(0, Period,
0): # If we've waited a period, collect the data; otherwise keep looping
next_row = []
if self._log_accelerometer:
# Get values in m/s^2
axes = self.IMU.read_accelerometer_values()
next_row += [axes['x'], axes['y'], axes['z']]
previous_read_time = datetime.now()
self._writer.writerow(next_row)
# Close the csv when done
outcsv.close()
def start_recording(self, frequency_in_hz):
# Create recording process
self._stop_value = multiprocessing.Value('i', 0)
self._process = multiprocessing.Process(target=self._record_data, args=(frequency_in_hz, self._stop_value))
# Start recording process
self._process.start()
print(datetime.now().strftime("%H:%M:%S.%f"), "Data logging process spawned")
print("ID of data logging process: {}".format(self._process.pid))
def end_recording(self, terminate_wait=2):
"""Function to end the recording multithread that's been spawned.
Args: terminate_wait: This is the time, in seconds, to wait after attempting to shut down the process before terminating it."""
# Get process id
id = self._process.pid
# Set stop event for process
self._stop_value.value = 1
self._process.join(terminate_wait) # Wait two seconds for the process to terminate
if self._process.is_alive(): # If it's still alive after waiting
self._process.terminate()
print(datetime.now().strftime("%H:%M:%S.%f"), "Process", id, "needed to be terminated.")
else:
print(datetime.now().strftime("%H:%M:%S.%f"), "Process", id, "successfully ended itself.")
if __name__ == '__main__':
foo = Foo('/tmp/foometer.csv')
foo.start_recording(20)
time.sleep(5)
print('Ending recording')
foo.end_recording()
I have a piece of code that queries a DB and returns a set of IDs. For each ID, I need to run a related query to get a dataset. I would like to run the queries in parallel to speed up the processing. Once all the processes are run, then I build a block of text and write that to a file, then move to the next id.
How do I ensure that all the processes start at the same time, then wait for all of them to complete before moving to the page =... and writefile operations?
If run as it, I get the following error: Process object is not iterable (on line 9).
Here is what I have so far:
from helpers import *
import multiprocessing
idSet = getIDset(10)
for id in idSet:
ds1 = multiprocessing.Process(target = getDS1(id))
ds1list1, ds1Item1, ds1Item2 = (ds1)
ds2 = multiprocessing.Process(target = getDS2(id))
ds3 = multiprocessing.Process(target = getDS3(id))
ds4 = multiprocessing.Process(target = getDS4(id))
ds5 = multiprocessing.Process(target = getDS5(id))
movefiles = multiprocessing.Process(moveFiles(srcPath = r'Z://', src = ds1Item2 , dstPath=r'E:/new_data_dump//'))
## is there a better way to get them to start in unison than this?
ds1.start()
ds2.start()
ds3.start()
ds4.start()
ds5.start()
## how do I know all processes are finished before moving on?
page = +ds1+'\n' \
+ds2+'\n' \
+ds3+'\n' \
+ds4+'\n' \
+ds5+'\n'
writeFile(r'E:/new_data_dump/',filename+'.txt',page)
I usually keep my "processes" in a list.
plist = []
for i in range(0, 5) :
p = multiprocessing.Process(target = getDS2(id))
plist.append(p)
for p in plist :
p.start()
... do stuff ...
for p in plist :
p.join() # <---- this will wait for each process to finish before continuing
Also I think you have an issue with creating your Process. "target" is supposed to be a function. Not the result of a function as it seems you have it (unless your function returns functions).
It should look like this:
p = Process(target=f, args=('bob',))
Where target is the function, and args is a tuple of arguemnts passed like so:
def f(name) :
print name