Question :
I am running several cat | zgrep commands on a remote server and gathering their output individually for further processing:
class MainProcessor(mp.Process):
def __init__(self, peaks_array):
super(MainProcessor, self).__init__()
self.peaks_array = peaks_array
def run(self):
for peak_arr in self.peaks_array:
peak_processor = PeakProcessor(peak_arr)
peak_processor.start()
class PeakProcessor(mp.Process):
def __init__(self, peak_arr):
super(PeakProcessor, self).__init__()
self.peak_arr = peak_arr
def run(self):
command = 'ssh remote_host cat files_to_process | zgrep --mmap "regex" '
log_lines = (subprocess.check_output(command, shell=True)).split('n')
process_data(log_lines)
This, however, results in sequential execution of the subprocess(‘ssh … cat …’) commands. Second peak waits for first to finish and so on.
How can I modify this code so that the subprocess calls run in parallel, while still being able to collect the output for each individually?
Answer #1:
Another approach (rather than the other suggestion of putting shell processes in the background) is to use multithreading.
The run method that you have would then do something like this:
thread.start_new_thread ( myFuncThatDoesZGrep)
To collect results, you can do something like this:
class MyThread(threading.Thread):
def run(self):
self.finished = False
# Your code to run the command here.
blahBlah()
# When finished....
self.finished = True
self.results = []
Run the thread as stated above in the link on multithreading. When your thread object has myThread.finished == True, then you can collect the results via myThread.results.
Answer #2:
You don’t need neither multiprocessing nor threading to run subprocesses in parallel e.g.:
#!/usr/bin/env python
from subprocess import Popen
# run commands in parallel
processes = [Popen("echo {i:d}; sleep 2; echo {i:d}".format(i=i), shell=True)
for i in range(5)]
# collect statuses
exitcodes = [p.wait() for p in processes]
it runs 5 shell commands simultaneously. Note: neither threads nor multiprocessing module are used here. There is no point to add ampersand & to the shell commands: Popen doesn’t wait for the command to complete. You need to call .wait() explicitly.
It is convenient but it is not necessary to use threads to collect output from subprocesses:
#!/usr/bin/env python
from multiprocessing.dummy import Pool # thread pool
from subprocess import Popen, PIPE, STDOUT
# run commands in parallel
processes = [Popen("echo {i:d}; sleep 2; echo {i:d}".format(i=i), shell=True,
stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
for i in range(5)]
# collect output in parallel
def get_lines(process):
return process.communicate()[0].splitlines()
outputs = Pool(len(processes)).map(get_lines, processes)
Related: Python threading multiple bash subprocesses?.
Here’s code example that gets output from several subprocesses concurrently in the same thread:
#!/usr/bin/env python3
import asyncio
import sys
from asyncio.subprocess import PIPE, STDOUT
@asyncio.coroutine
def get_lines(shell_command):
p = yield from asyncio.create_subprocess_shell(shell_command,
stdin=PIPE, stdout=PIPE, stderr=STDOUT)
return (yield from p.communicate())[0].splitlines()
if sys.platform.startswith('win'):
loop = asyncio.ProactorEventLoop() # for subprocess' pipes on Windows
asyncio.set_event_loop(loop)
else:
loop = asyncio.get_event_loop()
# get commands output in parallel
coros = [get_lines('"{e}" -c "print({i:d}); import time; time.sleep({i:d})"'
.format(i=i, e=sys.executable)) for i in range(5)]
print(loop.run_until_complete(asyncio.gather(*coros)))
loop.close()
