Python 3 subprocesses slower than equivalent bash - python

I'm using a python3 script to automatize some jobs.
I need to measure the time of such external jobs. So I decided to use python 3 built-in time() combined with the subprocess module:
with open(in_files[i],'r') as f, open(sol_files[i],'w') as f_sol:
start = time.time()
process = subprocess.run(['./'+src_files[i]], stdin = f, stdout=f_sol)
end = time.time()
The calculated elapsed time by this python snippet is 0.73 seconds
However, the equivalent bash command:
time ./file < input_file > output_file
Is significantly faster: 0.5 seconds
Which could be causing this huge discrepancy? Maybe the context switching with the python interpreter due the redirection usage? Maybe something related to buffering?
A similar code without the redirection usage does not show this behavior:
start = time.time()
process = subprocess.run(['sleep','1'])
end = time.time()
The above code time is elapsed in 1s + negligible time.
Best regards

It was a stupid mistake.
time.time() does not have a good precision in most systems.
Note that even though the time is always returned as a floating point number, not all systems provide time with a better precision than 1 second. While this function normally returns non-decreasing values, it can return a lower value than a previous call if the system clock has been set back between the two calls.
Python 3 Time Module Documentation
perf_counter() or process_time() works just fine. Nothing wrong with subprocesses.

Related

How to measure the time of a subprocess containing a delay in Python?

I have a process which contains a delay of 2 seconds and I'm trying to measure the time that the delayed process takes to run in a different program. I've tried a lot of different time tools, including time.time(), time.clock(), timeit, resource, os.wait4(), etc. Any way I do it, none of the measurements are accounting for the 2 second delay in the child process (they all return some very small number like 0.00113...). In contrast, when I run the same code around a time delay in the current program (rather than measuring the subprocess), it outputs the correct elapsed time (something like 2.002...). I know for sure that the delay is working correctly in the child process, it's just not being measured correctly. My code looks like the following (this is just one implementation I've tried, using time.time()):
import subprocess
now = time.clock()
response = subprocess.Popen(['python3', 'oracle.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
response.wait()
then = time.clock()
time_elapsed = then - now
print("time elapsed: ", str(time_elapsed))```
The problem is not that time.clock() doesn't work, the problem is that your subprocess is either not actually taking 2 seconds to run, or is failing to run at all.
Try using subprocess.check_output() instead of subprocess.Popen() and let us know what that shows. That way you won't need response.wait(), because the waiting and error checking is all handled inside check_output().

My python code occasionally takes 15 milliseconds to execute an empty method

I created a simple application, and I realised that my code is running extremely slow. This application included calling the same method over and over again. I tried investigating the problem, and it turned out that calling the same function / method several times resulted in Python sometimes taking 15 milliseconds to execute an empty function (pass).
I'm running windows 10 Home 64 bit on a Lenovo ThinkPad, i7 CPU
The less code the function / method has, the smaller the chance of having a 15ms runtime, however, it never goes away.
Here's the code:
import time
class Clock:
def __init__(self):
self.t = time.time()
def restart(self):
dt = time.time() - self.t
t = time.time()
return dt * 1000
def method():
pass
for i in range(100000):
c = Clock()
dt = c.restart()
if dt > 1.:
print(str(i) + ' ' + str(dt))
I'd expect that I never get anything printed out, however an average result looks like this:
6497 15.619516372680664
44412 15.622615814208984
63348 15.621185302734375
On average 1-4 out of 100000 times the time elapsed between starting the clock and getting the result (which is an empty function call and a simple subtraction and variable assignment) the elapsed time is 15.62.. milliseconds, which makes the run time really slow.
Occasionally the elapsed time is 1 millisecond.
Thank you for your help!
In your code you are making the call to time.time() twice which would require the system to retrieve the time from the OS. You can read here
How does python's time.time() method work?
As you mentioned you used Windows, it is probably better for you to use time.clock() instead and will defer you to read this link instead since they do a much better job explaining. https://www.pythoncentral.io/measure-time-in-python-time-time-vs-time-clock/
Also the link takes garbage collection into account of performance and gives the ability to remove it during testing.
Hope it answers your questions!

Benchmark Python programs

I'm new to Python. It is my first interpreted language. I used to study Java so far.
So, when Java program runs for the first time, it is execueted slower than for the next times.
The reasi is caching.
import time
def procedure():
time.sleep(2.5)
# measure process time
t0 = time.clock()
procedure()
print (time.clock() - t0), "seconds process time"
I tried this for several times. The result is always equal. So, am I right that no cashe interferes and that the benchmark is pretty reliable?
it's OK to do benchmarks like this, the accuracy is good enough for functions which run "long" and pretty constant, like in your example.
But there are some pitfalls: for "quick" functions (like the empty one), you run into precision limits. And for functions which vary in execution time (like net i/o, for example), you have to measure multiple times to find min/max/avg runtime.
And in addition to that, the clock best used differs on platforms: on windows, time.clock() is preferred, on *nix, time.time().
luckily, there is a module which takes care of all that: timeit:
>>> import time
>>> def procedure():
pass
>>> def time_this(f):
t0=time.clock()
f()
print((time.clock() - t0), "seconds process time")
>>> time_this(procedure)
1.9555558310457855e-06 seconds process time
>>> time_this(procedure)
1.9555557742023666e-06 seconds process time
>>> time_this(procedure)
1.9555557742023666e-06 seconds process time
>>> import timeit
>>> timeit.Timer(procedure).timeit()
0.09460783423588737
>>> timeit.Timer(procedure).repeat()
[0.09791419021132697, 0.09721947901198291, 0.09598943441130814]
you might want to look at it's source. Or just use it ;)
As for caching: python code compiles to bytecode when first used. This bytecode is cached by default - but this won't affect your benchmark as long as you don't do imports in your function.

Sleep for exact time in python

I need to wait for about 25ms in one of my functions. Sometimes this function is called when the processor is occupied with other things and other times it has the processor all to itself.
I've tried time.sleep(.25) but sometimes its actually 25ms and other times it takes much longer. Is there a way to sleep for an exact amount of time regardless of processor availability?
Because you're working with a preemptive operating system, there's no way you can guarantee that your process will be able to have control of the CPU in 25ms.
If you'd still like to try, it would be better to have a busy loop that polls until 25ms has passed. Something like this might work:
import time
target_time = time.clock() + 0.025
while time.clock() < target_time:
pass
0.25 seconds are 250 ms, not 25. Apart from this, there is no way to wait for exactly 25 ms on common operating systems – you would need some real-time operating system.
What system are you on? If you're on Windows you may want to do something like this for exact timing:
import ctypes
kernel32 = ctypes.windll.kernel32
# This sets the priority of the process to realtime--the same priority as the mouse pointer.
kernel32.SetThreadPriority(kernel32.GetCurrentThread(), 31)
# This creates a timer. This only needs to be done once.
timer = kernel32.CreateWaitableTimerA(ctypes.c_void_p(), True, ctypes.c_void_p())
# The kernel measures in 100 nanosecond intervals, so we must multiply .25 by 10000
delay = ctypes.c_longlong(.25 * 10000)
kernel32.SetWaitableTimer(timer, ctypes.byref(delay), 0, ctypes.c_void_p(), ctypes.c_void_p(), False)
kernel32.WaitForSingleObject(timer, 0xffffffff)
This code will pretty much guarentee your process will sleep .25 seconds. Watch out though- you may want to lower the priority to 2 or 3 unless it's absolutely critical that this sleeps for .25 seconds. Certainly don't change the priority too high for a user-end product.
Edit: in Windows 10 this nonsense seems unnecessary. Try it like so:
>>> from time import sleep
>>> import timeit
>>> '%.2f%% overhead' % (timeit.timeit('sleep(0.025)', number=100, globals=globals()) / 0.025 - 100)
'0.29% overhead'
.29%, or thereabout, is fairly low overhead, and usually more than accurate enough.
Previous Windows versions will by default have a sleep resolution of 55 msecs, which means your sleep call will take somewhere between 25 and 55 msecs. To get the sleep resolution down to 1 millisecond you need to set the resolution used by Windows by calling timeBeginPeriod:
import ctypes
winmm = ctypes.WinDLL('winmm')
winmm.timeBeginPeriod(1)
Another solution for accurate timings and delay is to use the perf_counter() function from module time. Especially useful in windows as time.sleep is not accurate in milliseconds. See below example where function accurate_delay creates a delay in millisecond.
import time
def accurate_delay(delay):
''' Function to provide accurate time delay in millisecond
'''
_ = time.perf_counter() + delay/1000
while time.perf_counter() < _:
pass
delay = 10
t_start = time.perf_counter()
print('Wait for {:.0f} ms. Start: {:.5f}'.format(delay, t_start))
accurate_delay(delay)
t_end = time.perf_counter()
print('End time: {:.5f}. Delay is {:.5f} ms'.
format(t_end, 1000*(t_end - t_start)))
sum = 0
ntests = 1000
for _ in range(ntests):
t_start = time.perf_counter()
accurate_delay(delay)
t_end = time.perf_counter()
print('Test completed: {:.2f}%'.format(_/ntests * 100), end='\r', flush=True)
sum = sum + 1000*(t_end - t_start) - delay
print('Average difference in time delay is {:.5f} ms.'.format(sum/ntests))
What you intend to do is a real time application. Python (and probably the OS you are using) is not intended to program this kind of applications, where time restriction is so strict.
In order for you to achieve what you are looking for you need a RTOS (Real Time Operating System) and develop your application using a suitable programming language (usually C) following RT best practises.
From the docs of the sleep method:
Suspend execution for the given number of seconds. The argument may be
a floating point number to indicate a more precise sleep time. The
actual suspension time may be less than that requested because any
caught signal will terminate the sleep() following execution of that
signal’s catching routine. Also, the suspension time may be longer
than requested by an arbitrary amount because of the scheduling of
other activity in the system.
The fact is that it depends on your underlying OS.

Python's time.clock() vs. time.time() accuracy?

Which is better to use for timing in Python? time.clock() or time.time()? Which one provides more accuracy?
for example:
start = time.clock()
... do something
elapsed = (time.clock() - start)
vs.
start = time.time()
... do something
elapsed = (time.time() - start)
As of 3.3, time.clock() is deprecated, and it's suggested to use time.process_time() or time.perf_counter() instead.
Previously in 2.7, according to the time module docs:
time.clock()
On Unix, return the current processor time as a floating point number
expressed in seconds. The precision, and in fact the very definition
of the meaning of “processor time”, depends on that of the C function
of the same name, but in any case, this is the function to use for
benchmarking Python or timing algorithms.
On Windows, this function returns wall-clock seconds elapsed since the
first call to this function, as a floating point number, based on the
Win32 function QueryPerformanceCounter(). The resolution is typically
better than one microsecond.
Additionally, there is the timeit module for benchmarking code snippets.
The short answer is: most of the time time.clock() will be better.
However, if you're timing some hardware (for example some algorithm you put in the GPU), then time.clock() will get rid of this time and time.time() is the only solution left.
Note: whatever the method used, the timing will depend on factors you cannot control (when will the process switch, how often, ...), this is worse with time.time() but exists also with time.clock(), so you should never run one timing test only, but always run a series of test and look at mean/variance of the times.
Others have answered re: time.time() vs. time.clock().
However, if you're timing the execution of a block of code for benchmarking/profiling purposes, you should take a look at the timeit module.
One thing to keep in mind:
Changing the system time affects time.time() but not time.clock().
I needed to control some automatic tests executions. If one step of the test case took more than a given amount of time, that TC was aborted to go on with the next one.
But sometimes a step needed to change the system time (to check the scheduler module of the application under test), so after setting the system time a few hours in the future, the TC timeout expired and the test case was aborted. I had to switch from time.time() to time.clock() to handle this properly.
clock() -> floating point number
Return the CPU time or real time since the start of the process or since
the first call to clock(). This has as much precision as the system
records.
time() -> floating point number
Return the current time in seconds since the Epoch.
Fractions of a second may be present if the system clock provides them.
Usually time() is more precise, because operating systems do not store the process running time with the precision they store the system time (ie, actual time)
Depends on what you care about. If you mean WALL TIME (as in, the time on the clock on your wall), time.clock() provides NO accuracy because it may manage CPU time.
time() has better precision than clock() on Linux. clock() only has precision less than 10 ms. While time() gives prefect precision.
My test is on CentOS 6.4, python 2.6
using time():
1 requests, response time: 14.1749382019 ms
2 requests, response time: 8.01301002502 ms
3 requests, response time: 8.01491737366 ms
4 requests, response time: 8.41021537781 ms
5 requests, response time: 8.38804244995 ms
using clock():
1 requests, response time: 10.0 ms
2 requests, response time: 0.0 ms
3 requests, response time: 0.0 ms
4 requests, response time: 10.0 ms
5 requests, response time: 0.0 ms
6 requests, response time: 0.0 ms
7 requests, response time: 0.0 ms
8 requests, response time: 0.0 ms
As others have noted time.clock() is deprecated in favour of time.perf_counter() or time.process_time(), but Python 3.7 introduces nanosecond resolution timing with time.perf_counter_ns(), time.process_time_ns(), and time.time_ns(), along with 3 other functions.
These 6 new nansecond resolution functions are detailed in PEP 564:
time.clock_gettime_ns(clock_id)
time.clock_settime_ns(clock_id, time:int)
time.monotonic_ns()
time.perf_counter_ns()
time.process_time_ns()
time.time_ns()
These functions are similar to the version without the _ns suffix, but
return a number of nanoseconds as a Python int.
As others have also noted, use the timeit module to time functions and small code snippets.
The difference is very platform-specific.
clock() is very different on Windows than on Linux, for example.
For the sort of examples you describe, you probably want the "timeit" module instead.
I use this code to compare 2 methods .My OS is windows 8 , processor core i5 , RAM 4GB
import time
def t_time():
start=time.time()
time.sleep(0.1)
return (time.time()-start)
def t_clock():
start=time.clock()
time.sleep(0.1)
return (time.clock()-start)
counter_time=0
counter_clock=0
for i in range(1,100):
counter_time += t_time()
for i in range(1,100):
counter_clock += t_clock()
print "time() =",counter_time/100
print "clock() =",counter_clock/100
output:
time() = 0.0993799996376
clock() = 0.0993572257367
time.clock() was removed in Python 3.8 because it had platform-dependent behavior:
On Unix, return the current processor time as a floating point number expressed in seconds.
On Windows, this function returns wall-clock seconds elapsed since the first call to this function, as a floating point number
print(time.clock()); time.sleep(10); print(time.clock())
# Linux : 0.0382 0.0384 # see Processor Time
# Windows: 26.1224 36.1566 # see Wall-Clock Time
So which function to pick instead?
Processor Time: This is how long this specific process spends actively being executed on the CPU. Sleep, waiting for a web request, or time when only other processes are executed will not contribute to this.
Use time.process_time()
Wall-Clock Time: This refers to how much time has passed "on a clock hanging on the wall", i.e. outside real time.
Use time.perf_counter()
time.time() also measures wall-clock time but can be reset, so you could go back in time
time.monotonic() cannot be reset (monotonic = only goes forward) but has lower precision than time.perf_counter()
On Unix time.clock() measures the amount of CPU time that has been used by the current process, so it's no good for measuring elapsed time from some point in the past. On Windows it will measure wall-clock seconds elapsed since the first call to the function. On either system time.time() will return seconds passed since the epoch.
If you're writing code that's meant only for Windows, either will work (though you'll use the two differently - no subtraction is necessary for time.clock()). If this is going to run on a Unix system or you want code that is guaranteed to be portable, you will want to use time.time().
Short answer: use time.clock() for timing in Python.
On *nix systems, clock() returns the processor time as a floating point number, expressed in seconds. On Windows, it returns the seconds elapsed since the first call to this function, as a floating point number.
time() returns the the seconds since the epoch, in UTC, as a floating point number. There is no guarantee that you will get a better precision that 1 second (even though time() returns a floating point number). Also note that if the system clock has been set back between two calls to this function, the second function call will return a lower value.
To the best of my understanding, time.clock() has as much precision as your system will allow it.
Right answer : They're both the same length of a fraction.
But which faster if subject is time ?
A little test case :
import timeit
import time
clock_list = []
time_list = []
test1 = """
def test(v=time.clock()):
s = time.clock() - v
"""
test2 = """
def test(v=time.time()):
s = time.time() - v
"""
def test_it(Range) :
for i in range(Range) :
clk = timeit.timeit(test1, number=10000)
clock_list.append(clk)
tml = timeit.timeit(test2, number=10000)
time_list.append(tml)
test_it(100)
print "Clock Min: %f Max: %f Average: %f" %(min(clock_list), max(clock_list), sum(clock_list)/float(len(clock_list)))
print "Time Min: %f Max: %f Average: %f" %(min(time_list), max(time_list), sum(time_list)/float(len(time_list)))
I am not work an Swiss labs but I've tested..
Based of this question : time.clock() is better than time.time()
Edit : time.clock() is internal counter so can't use outside, got limitations max 32BIT FLOAT, can't continued counting if not store first/last values. Can't merge another one counter...
Comparing test result between Ubuntu Linux and Windows 7.
On Ubuntu
>>> start = time.time(); time.sleep(0.5); (time.time() - start)
0.5005500316619873
On Windows 7
>>> start = time.time(); time.sleep(0.5); (time.time() - start)
0.5

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