Im currently writing a python3 script that checks out a C source file by running the C code with various of input files. the compilation is done by GCC if it matters.
in some case, the C code enters into an infinite loop (I figured it out because I ran out of memory).
is there a way that I can "protect" my code like a watchdog or something that
tells me a after X minutes that I ran into an infinite loop?
I cant assume anything about the input so i cant have answers like change it or something...
#runfile is an exe file, code file is .c file, inputlist/outputlist are directories
import subprocess as sbp
import os
sbp.call('gcc -o {0} {1}'.format(runfile,codefile), shell = True)
for i in range(numoFiles):
#run the file with input i and save it to output i in outdir
os.system("./{0} <{1} >{2}".format(ID,inputList[i],outputList[i]))
Look up the "Halting Problem". It is not possible to determine whether an arbitrary program will eventually finish or if it will be stuck in a loop forever.
I figured out a way to avoid enter infinite loop by this method:
import subprocess
for i in range(numofiles):
cmd="gcc -o {0} {1}".format(runfile,codefile)
subprocess.call(cmd, shell = True)
try:
cmd="./{0} <{1} >'/dev/null'".format(Cfile,inputfile) #check if runtime>100 sec
subprocess.run(cmd,shell=True,timeout=100)
except subprocess.TimeoutExpired:
print("infinite loop")
continue
cmd="./{0} <{1} >{2}".format(Cfile,inputfile,outputfile)
subprocess.run(cmd,shell=True) #print output to txt file
Related
I am using a third-party C++ program to generate intermediate results for the python program that I am working on. The terminal command that I use looks like follows, and it works fine.
./ukb/src/ukb_wsd --ppr_w2w -K ukb/scripts/wn30g.bin -D ukb/scripts/wn30_dict.txt ../data/glass_ukb_input2.txt > ../data/glass_ukb_output2w2.txt
If I break it down into smaller pieces:
./ukb/src/ukb_wsd - executable program
--ppr_w2w - one of the options/switches
-K ukb/scripts/wn30g.bin - parameter K indicates that the next item is a file (network file)
-D ukb/scripts/wn30_dict.txt - parameter D indicate that the next item is a file (dictionary file)
../data/glass_ukb_input2.txt - input file
> - shell command to write the output to a file
../data/glass_ukb_output2w2.txt - output file
The above works fine for one instance. I am trying to do this for around 70000 items (input files). So found a way by using the subprocess module in Python. The body of the python function that I created looks like this.
with open('../data/glass_ukb_input2.txt', 'r') as input, open('../data/glass_ukb_output2w2w_subproc.txt', 'w') as output:
subprocess.run(['./ukb/src/ukb_wsd', '--ppr_w2w', '-K', 'ukb/scripts/wn30g.bin', '-D', 'ukb/scripts/wn30_dict.txt'],
stdin=input,
stdout=output)
This error is no longer there
When I execute the function, it gives an error as follows:
...
STDOUT = subprocess.STDOUT
AttributeError: module 'subprocess' has no attribute 'STDOUT'
Can anyone shed some light about solving this problem.
EDIT
The error was due to a file named subprocess.py in the source dir which masked Python's subprocess file. Once it was removed no error.
But the program could not identify the input file given in stdin. I am thinking it has to do with having 3 input files. Is there a way to provide more than one input file?
EDIT 2
This problem is now solved with the current approach:
subprocess.run('./ukb/src/ukb_wsd --ppr_w2w -K ukb/scripts/wn30g.bin -D ukb/scripts/wn30_dict.txt ../data/glass_ukb_input2.txt > ../data/glass_ukb_output2w2w_subproc.txt',shell=True)
I have a very simple (test) code which I'm running either from a Linux shell, or in interactive mode, and I have two different behaviours I cannot figure out the reason of.
I have a file generated by a Popen call, previously, where each line is a file path. This is the code used to generate the file:
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
(Incidentally, I was trying to build a PIPE originally, namely inputting the output of this command to a grep command, and since I wasn't successful in any way, I decided to break the problem down and just read the file paths from a file, and process them one by one. So maybe there is a common issue that is blocking me somewhere in this procedure).
Since in this second step I wasn't even able to open and process the files by opening the addresses contained in each line of the find.txt file, I just tried to print the file lines out, because for sure they're available in there:
with open('find.txt','r') as g:
for l in g.readlines():
print(l)
Now, the interesting part:
if I paste the lines above into a python shell, everything works fine and I get my outputs as expected
if, on the other hand, I try to run python test.py, where test.py is the name of the file containing the lines above, no output appears in the shell's stdout.
I've tried sys.stdout.flush() to no avail. I've also inserted some dummy print() statements along the way: everything gets printed but what's after the g.readlines() statement.
Here's the full script I'm trying to make work (a pre-precursor of what I'm actually after, tbh).
#!/usr/bin/env python3
import subprocess
import sys
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
print('hello')
with open('find.txt','r') as g:
print('hello?')
for l in g.readlines():
print('help me!')
print(l)
sys.stdout.flush()
output being:
{ancis:>106> python test.py
hello
hello?
{ancis:>106>
EDIT
I've quickly tried the very same lines (but without the call to find, which isn't available) on my python installation in Windows: it works as expected)
Based on that, I've tried to run the simpler code below:
print('hello')
with open('find.txt','r') as g:
print('hello?')
for l in g.readlines():
print('help me!')
print(l)
sys.stdout.flush()
as a script, in Linux - This also works w/o problems.
This should mean that somehow I'm messing things up with the call to Popen... But what?
This is a race condition.
Your call to
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
is opening another process and running your find command which takes a bit of time to fully execute.
Python then continues on and reaches the reading of the file portion before the command is fully executed and the file is generated.
Want to test it out?
Add a time.sleep(1) just before the opening of the file.
Full test script:
#!/usr/bin/env python3
import subprocess
import time
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
time.sleep(1)
with open('find.txt','r') as g:
for l in g:
print(l)
To block until the process is complete you can use find.communicate().
With this you can also optionally set a timeout if that's something that you want.
#!/usr/bin/env python3
import subprocess
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
find.communicate()
with open('find.txt','r') as g:
for l in g:
print(l)
Source:
https://docs.python.org/3/library/subprocess.html#subprocess.Popen.communicate
Up front confession... I'm a python neophyte. Please forgive any ignorance on my part.
As just a way to learn more, I'm trying to write a script that will take my latest Quicken backup and with 7-Zip, create a compressed and encrypted file with a timestamp in the name. I then want to copy it two two locations.
I have succeeded up the the name part. I've created a variable for the time the script starts and I want to append this to a base file name, but I don't seem to be able to do it. When I've tried, the script runs, but nothing is ever created, no compressed file that is. If I remove what I have with regard to the variable for the filename, I do get a compressed and encrypted file as expected.
Here is what I have so far. The print commands are just there for me making sure I've done the 'today' and 'newfile' variables correctly. Also, I'm doing the testing with just an empty .docx file so that it processes quicker.
Thanks in advance for any/all help or suggestions. I really appreciate it.
from datetime import datetime
from pathlib import Path
today = datetime.now()
print(today.strftime('%Y-%m-%d %H:%M:%S'))
newfile = 'Q2020_' + (today.strftime('%m-%d-%Y_%H%M%S'))
print(newfile)
os.chdir('D:/Quicken Backups')
print(os.getcwd())
import subprocess
cmd= ['C:\\Program Files\\7-Zip\\7z.exe', 'a', '-t7z', '-mx9', '"D:\\Quicken Backups\\Quicken2020\\" + newfile ".7z"', '-ppassword', '-mhe', 'D:\\Quicken Backups\\test.docx']
subprocess.Popen(cmd, stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
Have you thought about using a python package made for zipping, like zipfile?
This way you dont need to deal with opening a subprocess
import zipfile
dest_zip_folder = '2020_backup.zip' # new file name
file_to_zip = 'D:\\Quicken Backups\\test.docx'
zipfile.ZipFile(dest_zip_folder, mode='w').write(file_to_zip)
If you dont want to use that way, I see an error in your code.
You are missing a + after newfile
cmd = [ ...., .... + newfile + '.7zip', ... ]
Also give subprocess.call() a try
import subproccess
cmd = [. . . . . .]
subprocess.call(cmd)
It took a LOT of mucking around with Windows variables syntax and running the subprocess a little differently, but I finally got the thing working, outputting an encrypted file with a date/time stamp in the file name.
For troubleshooting I added the /K to the cmd command so that the window would not close upon completion. This was a HUGE help in trouble shooting this.
Thanks to everyone who even looked at my posted. I hope someday this thread will help someone else!
import os
from pathlib import Path
os.chdir('D:/Quicken Backups')
print(os.getcwd())
import subprocess
cmd = subprocess.Popen('cmd.exe /K ""C:\\Program Files\\7-Zip\\7z.exe" a -t7z -mx9 "D:\\Quicken Backups\\Quicken2020\\Q2020_%DATE:~4,2%-%DATE:~7,2%-%DATE:~-4%_%TIME:~0,2%%TIME:~3,2%%TIME:~8%.7z" -ppassword -mhe "D:\\Quicken Backups\\test.docx"')
I'm new to Linux, and have been trying to solve an assignment but to no avail.
I have a shell script which prints out lines of a text file in a certain manner (a line within every few seconds):
python << END
import time,random
a= open ('/home/ch/pshety/course/fielding_history.txt','r')
flag =False
for i in range(1000):
b=a.readline()
if i==402 or flag:
print(a.readline())
flag=True
time.sleep(2)
END
sh th.sh
If I run it without trying to redirect it anywhere, I get the output on the terminal. However, when I tried to redirect it into a new text file, it doesn't do anything - the text remains empty:
sh th.sh > debug.txt
I've tried looking for answers, I've stumbled upon a lot of suggestions including tee but nothing helps - the file remains empty.
What am I doing wrong?
Try this:
import time,random
a = open('/home/ch/pshety/course/fielding_history.txt', 'r')
for i in range(1000):
b = a.readline()
if i >= 402:
print(b, flush=True)
time.sleep(2)
Your Python script likely needs to flush the contents of the output buffer before you can see it.
Note: aside from the sleep() call, Unix provides other ways of accomplishing this. I would take a look at man tail and read about the -f and -n switches.
Edit: didn't realize that tail has a switch (-s) to sleep as well!
I would like to easily test my python programs without constantly using the python shell since each time the program is modified you have to quit, re-enter the python shell and import the program again. I am using a 2012 Macbook pro with OSX. I have the following code:
import sys
def read_strings(filename):
with open(filename) as file:
return file.read().split('>')[1:0]
file1 = sys.argv[1]
filename = read_strings(file1)
Essentially I would like to read into and split a txt file containing:
id1>id2>id3>id4
I am entering this into my command line:
pal-nat184-102-127:python_stuff ceb$ python3 program.py string.txt
However when I try the sys.argv approach on the command line my program returns nothing. Is this a good approach to testing code, could anyone point me in the correct direction?
This is what I would like to happen:
pal-nat184-102-127:python_stuff ceb$ python3 program.py string.txt
['id1', 'id2', 'id3', 'id4']
Let's take this a piece at a time:
However when I try the sys.argv approach on the command line my
program returns nothing
The final result of your program is that it writes a string into the variable filename. It's a little strange to have a program "return" a value. Generally, you want a program to print it's something out or save something to a file. I'm guessing it would ease your debugging if you modified your program by adding,
print (filename)
at the end: you'd be able to see the result of your program.
could anyone point me in the correct direction?
One other debugging note: It can be useful to write your .py files so that they can be run both independently at the command line or in a python shell. How you've currently structured your code, this will work semi-poorly. (Starting a shell and then importing your file will cause an error because sys.argv[1] isn't defined.)
A solution to this is to change your the bottom section of your code as follows:
if __name__ == '__main__':
file1 = sys.argv[1]
filename = read_strings(file1)
The if guard at the top says, "If running as a standalone script, then run what's below me. If you imported me from some place else, then do not execute what's below me."
Feel free to follow up below if I misinterpreted your question.
You never do anything with the result of read_strings. Try:
print(read_strings(file1))