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Python script execution time increases when executed multiple time parallely

I have a python script whose execution time is 1.2 second while it is being executed standalone.
But when I execute it 5-6 time parallely ( Am using postman to ping the url multiple times) the execution time shoots up.
Adding the breakdown of the time taken.
1 run -> ~1.2seconds
2 run -> ~1.8seconds
3 run -> ~2.3seconds
4 run -> ~2.9seconds
5 run -> ~4.0seconds
6 run -> ~4.5seconds
7 run -> ~5.2seconds
8 run -> ~5.2seconds
9 run -> ~6.4seconds
10 run -> ~7.1seconds
Screenshot of top command(Asked in the comment):
This is a sample code:
import psutil
import os
import time
start_time = time.time()
import cgitb
cgitb.enable()
import numpy as np
import MySQLdb as mysql
import cv2
import sys
import rpy2.robjects as robj
import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri.activate()
from rpy2.robjects.packages import importr
R = robj.r
DTW = importr('dtw')
process= psutil.Process(os.getpid())
print " Memory Consumed after libraries load: "
print process.memory_info()[0]/float(2**20)
st_pt=4
# Generate our data (numpy arrays)
template = np.array([range(84),range(84),range(84)]).transpose()
query = np.array([range(2500000),range(2500000),range(2500000)]).transpose()
#time taken
print(" --- %s seconds ---" % (time.time() - start_time))
I also checked my memory consumption using watch -n 1 free -m and memory consumption also increases noticeably.
1) How do I make sure that the execution time of script remain constant everytime.
2) Can I load the libraries permanently so that the time taken by the script to load the libraries and the memory consumed can be minimized?
I made an enviroment and tried using
#!/home/ec2-user/anaconda/envs/test_python/
but it doesn't make any difference whatsoever.
EDIT:
I have AMAZON's EC2 server with 7.5GB RAM.
My php file with which am calling the python script.
<?php
$response = array("error" => FALSE);
if($_SERVER['REQUEST_METHOD']=='GET'){
$response["error"] = FALSE;
$command =escapeshellcmd(shell_exec("sudo /home/ec2-user/anaconda/envs/anubhaw_python/bin/python2.7 /var/www/cgi-bin/dtw_test_code.py"));
session_write_close();
$order=array("\n","\\");
$cleanData=str_replace($order,'',$command);
$response["message"]=$cleanData;
} else
{
header('HTTP/1.0 400 Bad Request');
$response["message"] = "Bad Request.";
}
echo json_encode($response);
?>
Thanks

1) You really can't ensure the execution will take always the same time, but at least you can avoid performance degradation by using a "locking" strategy like the ones described in this answer.
Basically you can test if the lockfile exists, and if so, put your program to sleep a certain amount of time, then try again.
If the program does not find the lockfile, it creates it, and delete the lockfile at the end of its execution.
Please note: in the below code, when the script fails to get the lock for a certain number of retries, it will exit (but this choice is really up to you).
The following code exemplifies the use of a file as a "lock" against parallel executions of the same script.
import time
import os
import sys
lockfilename = '.lock'
retries = 10
fail = True
for i in range(retries):
try:
lock = open(lockfilename, 'r')
lock.close()
time.sleep(1)
except Exception:
print('Got after {} retries'.format(i))
fail = False
lock = open(lockfilename, 'w')
lock.write('Locked!')
lock.close()
break
if fail:
print("Cannot get the lock, exiting.")
sys.exit(2)
# program execution...
time.sleep(5)
# end of program execution
os.remove(lockfilename)
2) This would mean that different python instances share the same memory pool and I think it's not feasible.

1)
More servers equals more availability
Hearsay tells me that one effective way to ensure consistent request times is to use multiple requests to a cluster. As I heard it the idea goes something like this.
The chance of a slow request
(Disclaimer I'm not much of a mathematician or statistician.)
If there is a 1% chance a request is going to take an abnormal amount of time to finish then one-in-a-hundred requests can be expected to be slow. If you as a client/consumer make two requests to a cluster instead of just one, the chance that both of them turn out to be slow would be more like 1/10000, and with three 1/1000000, et cetera. The downside is doubling your incoming requests means needing to provide (and pay for) as much as twice the server power to fulfill your requests with a consistent time, this additional cost scales with how much chance is acceptable for a slow request.
To my knowledge this concept is optimized for consistent fulfillment times.
The client
A client interfacing with a service like this has to be able to spawn multiple requests and handle them gracefully, probably including closing the unfulfilled connections as soon as it can.
The servers
On the backed there should be a load balancer that can associate multiple incoming client requests to multiple unique cluster workers. If a single client makes multiple requests to an overburdened node, its just going to compound its own request time like you see in your simple example.
In addition to having the client opportunistically close connections it would be best to have a system of sharing job fulfilled status/information so that backlogged request on other other slower-to-process nodes have a chance of aborting an already-fulfilled request.
This this a rather informal answer, I do not have direct experience with optimizing a service application in this manner. If someone does I encourage and welcome more detailed edits and expert implementation opinions.
2)
Caching imports
yes that is a thing, and its awesome!
I would personally recommend setting up django+gunicorn+nginx. Nginx can cache static content and keep a request backlog, gunicorn provides application caching and multiple threads&worker management (not to mention awesome administration and statistic tools), django embeds best practices for database migrations, auth, request routing, as well as off-the-shelf plugins for providing semantic rest endpoints and documentation, all sorts of goodness.
If you really insist on building it from scratch yourself you should study uWsgi, a great Wsgi implementation that can be interfaced with gunicorn to provide application caching. Gunicorn isn't the only option either, Nicholas Piël has a Great write up comparing performance of various python web serving apps.

Here's what we have:
EC2 instance type is m3.large box which has only 2 vCPUs https://aws.amazon.com/ec2/instance-types/?nc1=h_ls
We need to run a CPU- and memory-hungry script which takes over a second to execute when CPU is not busy
You're building an API than needs to handle concurrent requests and running apache
From the screenshot I can conclude that:
your CPUs are 100% utilized when 5 processes are run. Most likely they would be 100% utilized even when fewer processes are run. So this is the bottleneck and no surprise that the more processes are run the more time is required — you CPU resources just get shared among concurrently running scripts.
each script copy eats about ~300MB of RAM so you have lots of spare RAM and it's not a bottleneck. The amount of free + buffers memory on your screenshot confirms that.
The missing part is:
are requests directly sent to your apache server or there's a balancer/proxy in front of it?
why do you need PHP in your example? There are plently of solutions available using python ecosystem only without a php wrapper ahead of it
Answers to your questions:
That's infeasible in general case
The most you can do is to track your CPU usage and make sure its idle time doesn't drop below some empirical threshold — in this case your scripts would be run in more or less fixed amount of time.
To guarantee that you need to limit the number of requests being processed concurrently.
But if 100 requests are sent to your API concurrently you won't be able to handle them all in parallel! Only some of them will be handled in parallel while others waiting for their turn. But your server won't be knocked down trying to serve them all.
Yes and no
No because unlikely can you do something in your present architecture when a new script is launched on every request through a php wrapper. BTW it's a very expensive operation to run a new script from scratch each time.
Yes if a different solution is used. Here are the options:
use a python-aware pre-forking webserver which will handle your requests directly. You'll spare CPU resources on python startup + you might utilize some preloading technics to share RAM among workers, i.e http://docs.gunicorn.org/en/stable/settings.html#preload-app. You'd also need to limit the number of parallel workers to be run http://docs.gunicorn.org/en/stable/settings.html#workers to adress your first requirement.
if you need PHP for some reason you might setup some intermediary between PHP script and python workers — i.e. a queue-like server.
Than simply run several instances of your python scripts which would wait for some request to be availble in the queue. Once it's available it would handle it and put the response back to the queue and php script would slurp it and return back to the client. But it's a more complex to build this that the first solution (if you can eliminate your PHP script of course) and more components would be involved.
reject the idea to handle such heavy requests concurrently, and instead assign each request a unique id, put the request into a queue and return this id to the client immediately. The request will be picked up by an offline handler and put back into the queue once it's finished. It will be client's responsibility to poll your API for readiness of this particular request
1st and 2nd combined — handle requests in PHP and request another HTTP server (or any other TCP server) handling your preloaded .py-scripts

The ec2 cloud does not guarantee 7.5gb of free memory on the server. This would mean that the VM performance is severely impacted like you are seeing where the server has less than 7.5gb of physical free ram. Try reducing the amount of memory the server thinks it has.
This form of parallel performance is very expensive. Typically with 300mb requirement, the ideal would be a script which is long running, and re-uses the memory for multiple requests. The Unix fork function allows a shared state to be re-used. The os.fork gives this in python, but may not be compatible with your libraries.

It might be because of the way computers are run.
Each program gets a slice of time on a computer (quote Help Your Kids With Computer Programming, say maybe 1/1000 of a second)
Answer 1: Try using multiple threads instead of parallel processes.
It'll be less time-consuming, but the program's time to execute still won't be completely constant.
Note: Each program has it's own slot of memory, so that is why memory consumption is shooting up.

How to show a 'processing' or 'in progress' view while pyramid is running a process?

I've got a simple pyramid app up and running, most of the views are a fairly thin wrapper around an sqlite database, with forms thrown in to edit/add some information.
A couple of times a month a new chunk of data will need to be added to this system (by csv import). The data is saved in an SQL table (the whole process right till commit takes about 4 seconds).
Every time a new chunk of data is uploaded, this triggers a recalculation of other tables in the database. The recalculation process takes a fairly long time (about 21-50 seconds for a month's worth of data).
Currently I just let the browser/client sit there waiting for the process to finish, but I do foresee the calculation process taking more and more time as the system gets more usage. From a UI perspective, this obviously looks like a hung process.
What can I do to indicate to the user that:-
That the long wait is normal/expected?
How MUCH longer they should have to wait (progress bar etc.)?
Note: I'm not asking about long-polling or websockets here, as this isn't really an interactive application and based on my basic knowledge websockets/async are overkill for my purposes.
I guess a follow-on question at this point, am I doing the wrong thing running processes in my view functions? Hardly seem to see that being done in examples/tutorials around the web. Am I supposed to be using celery or similar in this situation?

You're right, doing long calculations in a view function is generally frowned upon - I mean, if it's a typical website with random visitors who are able to hung a webserver thread for a minute then it's a recipe for a DoS vulnerability. But in some situations (internal website, few users, only admin has access to the "upload csv" form) you may get away with it. In fact, I used to have maintenance scripts which ran for hours :)
The trick here is to avoid browser timeouts - at the moment your client sends the data to the server and just sits there waiting for any reply, without any idea whether their request is being processed or not. Generally, at about 60 seconds the browser (or proxy, or frontend webserver) may become impatient and close the connection. Your server process will then get an error trying writing anything to the already closed connection and crash/raise an error.
To prevent this from happening the server needs to write something to the connection periodically, so the client sees that the server is alive and won't close the connection.
"Normal" Pyramid templates are buffered - i.e. the output is not sent to the client until the whole template to generated. Because of that you need to directly use response.app_iter / response.body_file and output some data there periodically.
As an example, you can duplicate the Todo List Application in One File example from Pyramid Cookbook and replace the new_view function with the following code (which itself has been borrowed from this question):
#view_config(route_name='new', request_method='GET', renderer='new.mako')
def new_view(request):
return {}
#view_config(route_name='new', request_method='POST')
def iter_test(request):
import time
if request.POST.get('name'):
request.db.execute(
'insert into tasks (name, closed) values (?, ?)',
[request.POST['name'], 0])
request.db.commit()
def test_iter():
i = 0
while True:
i += 1
if i == 5:
yield str('<p>Done! Click here to see the results</p>')
raise StopIteration
yield str('<p>working %s...</p>' % i)
print time.time()
time.sleep(1)
return Response(app_iter=test_iter())
(of cource, this solution is not too fancy UI-wise, but you said you didn't want to mess with websockets and celery)

So is the long running process triggered by browser action? I.e., the user is uploading the CSV that gets processed and then the view is doing the processing right there? For short-ish running browser processes I've used a loading indicator via jQuery or javascript, basically popping a modal animated spinner or something while a process runs, then when it completes hiding the spinner.
But if you're getting into longer and longer processes I think you should really look at some sort of background processing that will offload it from the UI. It doesn't have to be a message based worker, but even something like the end user uploads the file and a "to be processed" entry gets set in a database. Then you could have a pyramid script scheduled periodically in the background polling the status table and running anything it finds. You can move your file processing that is in the view to a separate method, and that can be called from the command line script. Then when the processing is finished it can update the status table indicating it is finished and that feedback could be presented back to the user somewhere, and not blocking their UI the whole time.

Console output consuming much CPU? (about 140 lines per second)

I am doing my bachelor's thesis where I wrote a program that is distributed over many servers and exchaning messages via IPv6 multicast and unicast. The network usage is relatively high but I think it is not too high when I have 15 servers in my test where there are 2 requests every second that are going like that:
Server 1 requests information from server 3-15 via multicast. every of 3-15 must respond. if one response is missing after 0.5 sec, the multicast is resent, but only the missing servers must respond (so in most cases this is only one server)
Server 2 does exactly the same. If there are missing results after 5 retries the missing servers are marked as dead and the change is synced with the other server (1/2)
So there are 2 multicasts every second and 26 unicasts every second. I think this should not be too much?
Server 1 and 2 are running python web servers which I use to do the request every second on each server (via a web client)
The whole szenario is running in a mininet environment which is running in a virtual box ubuntu that has 2 cores (max 2.8ghz) and 1GB RAM. While running the test, i see via htop that the CPUs are at 100% while the RAM is at 50%. So the CPU is the bottleneck here.
I noticed that after 2-5 minutes (1 minute = 60 * (2+26) messages = 1680 messages) there are too many missing results causing too many sending repetitions while new requests are already coming in, so that the "management server" thinks the client servers (3-15) are down and deregisters them. After syncing this with the other management server, all client servers are marked as dead on both management servers which is not true...
I am wondering if the problem could be my debug outputs? I am printing 3-5 messages for every message that is sent and received. So that are about (let's guess it are 5 messages per sent/recvd msg) (26 + 2)*5 = 140 lines that are printed on the console.
I use python 2.6 for the servers.
So the question here is: Can the console output slow down the whole system that simple requests take more than 0.5 seconds to complete 5 times in a row? The request processing is simple in my test. No complex calculations or something like that. basically it is something like "return request_param in ["bla", "blaaaa", ...] (small list of 5 items)"
If yes, how can I disable the output completely without having to comment out every print statement? Or is there even the possibility to output only lines that contain "Error" or "Warning"? (not via grep, because when grep becomes active all the prints already have finished... I mean directly in python)
What else could cause my application to be that slow? I know this is a very generic question, but maybe someone already has some experience with mininet and network applications...

I finally found the real problem. It was not because of the prints (removing them improved performance a bit, but not significantly) but because of a thread that was using a shared lock. This lock was shared over multiple CPU cores causing the whole thing being very slow.
It even got slower the more cores I added to the executing VM which was very strange...
Now the new bottleneck seems to be the APScheduler... I always get messages like "event missed" because there is too much load on the scheduler. So that's the next thing to speed up... :)

Django, sleep() pauses all processes, but only if no GET parameter?

Using Django (hosted by Webfaction), I have the following code
import time
def my_function(request):
time.sleep(10)
return HttpResponse("Done")
This is executed via Django when I go to my url, www.mysite.com
I enter the url twice, immediately after each other. The way I see it, both of these should finish after 10 seconds. However, the second call waits for the first one and finishes after 20 seconds.
If, however, I enter some dummy GET parameter, www.mysite.com?dummy=1 and www.mysite.com?dummy=2 then they both finish after 10 seconds. So it is possible for both of them to run simultaneously.
It's as though the scope of sleep() is somehow global?? Maybe entering a parameter makes them run as different processes instead of the same???
It is hosted by Webfaction. httpd.conf has:
KeepAlive Off
Listen 30961
MaxSpareThreads 3
MinSpareThreads 1
ServerLimit 1
SetEnvIf X-Forwarded-SSL on HTTPS=1
ThreadsPerChild 5
I do need to be able to use sleep() and trust that it isn't stopping everything. So, what's up and how to fix it?
Edit: Webfaction runs this using Apache.

As Gjordis pointed out, sleep will pause the current thread. I have looked at Webfaction and it looks like their are using WSGI for running the serving instance of Django. This means, every time a request comes in, Apache will look at how many worker processes (that are processes that each run a instance of Django) are currently running. If there are none/to view it will spawn additonally workers and hand the requests to them.
Here is what I think is happening in you situation:
first GET request for resource A comes in. Apache uses a running worker (or starts a new one)
the worker sleeps 10 seconds
during this, a new request for resource A comes in. Apache sees it is requesting the same resource and sends it to the same worker as for request A. I guess the assumption here is that a worker that recently processes a request for a specific resource it is more likely that the worker has some information cached/preprocessed/whatever so it can handle this request faster
this results in a 20 second block since there is only one worker that waits 2 times 10 seconds
This behavior makes complete sense 99% of the time so it's logical to do this by default.
However, if you change the requested resource for the second request (by adding GET parameter) Apache will assume that this is a different resource and will start another worker (since the first one is already "busy" (Apache can not know that you are not doing any hard work). Since there are now two worker, both waiting 10 seconds the total time goes down to 10 seconds.
Additionally I assume that something is **wrong** with your design. There are almost no cases which I can think of where it would be sensible to not respond to a HTTP request as fast as you can. After all, you want to serve as many requests as possible in the shortest amount of time, so sleeping 10 seconds is the most counterproductive thing you can do. I would recommend the you create a new question and state what you actual goal is that you are trying to achieve. I'm pretty sure there is a more sensible solution to this!

Assuming you run your Django-server just with run() , by default this makes a single threaded server. If you use sleep on a single threaded process, the whole application freezes for that sleep time.

It may simply be that your browser is queuing the second request to be performed only after the first one completes. If you are opening your URLs in the same browser, try using the two different ones (e.g. Firefox and Chrome), or try performing requests from the command line using wget or curl instead.

Google AppEngine startup times

I've already read how to avoid slow ("cold") startup times on AppEngine, and implemented the solution from the cookbook using 10 second polls, but it doesn't seem to help a lot.
I use the Python runtime, and have installed several handlers to handle my requests, none of them doing something particularly time consuming (mostly just a DB fetch).
Although the Hot Handler is active, I experience slow load times (up to 15 seconds or more per handler) and the log shows frequently the This request caused a new process to be started for your application, and thus caused your application code to be loaded for the first time ... message after the app was IDLE for a while.
This is very odd. Do I have to fetch each URL separately in the Hot Handler?

The "appropriate" way of avoiding slow too many slow startup times is to use the "always on" option. Of course, this is not a free option ($0.30 per day).