I have a problem that I seriously spent months on now!
Essentially I am running code that requires to read from and save to HD5 files. I am using h5py for this.
It's very hard to debug because the problem (whatever it is) only occurs in like 5% of the cases (each run takes several hours) and when it gets there it crashes python completely so debugging with python itself is impossible. Using simple logs it's also impossible to pinpoint to the exact crashing situation - it appears to be very random, crashing at different points within the code, or with a lag.
I tried using OllyDbg to figure out whats happening and can safely conclude that it consistently crashes at the following location: http://i.imgur.com/c4X5W.png
It seems to be shortly after calling the python native PyObject_ClearWeakRefs, with an access violation error message. The weird thing is that the file is successfully written to. What would cause the access violation error? Or is that python internal (e.g. the stack?) and not file (i.e. my code) related?
Has anyone an idea whats happening here? If not, is there a smarter way of finding out what exactly is happening? maybe some hidden python logs or something I don't know about?
Thank you
PyObject_ClearWeakRefs is in the python interpreter itself. But if it only happens in a small number of runs, it could be hardware related. Things you could try:
Run your program on a different machine. if it doesn't crash there, it is probably a hardware issue.
Reinstall python, in case the installed version has somehow become corrupted.
Run a memory test program.
Thanks for all the answers. I ran two versions this time, one with a new python install and my same program, another one on my original computer/install, but replacing all HDF5 read/write procedures with numpy read/write procedures.
The program continued to crash on my second computer at odd times, but on my primary computer I had zero crashes with the changed code. I think it is thus safe to conclude that the problems were HDF5 or more specifically h5py related. It appears that more people encountered issues with h5py in that respect. Given that any error in my application translates to potentially large financial losses I decided to dump HDF5 completely in favor of other stable solutions.
Use a try catch statement. This can be put into the program in order to stop the program from crashing when erroneous data is entered
Related
I am having a Bus error in a Python script.
I could believe there is some issue with the memory there, but I don't know exactly what the source is.
I would expect it to be possible somehow to trace the line of Python code where this happens (even without a full stack).
It does say "core dumped", but no core is dumped, and I am not sure if Python core dumps can easily be used with gdb or the like to trace the line of code where the error happened.
What are my options? The error at the moment is cryptic in the sense that I don't know where the faulty memory access happens or why.
(I should mention that I did try to investigate for answers online before asking this, but didn't find anything useful. Just small pieces of "I am stuck" kind of things. I am guessing this error is very rare.)
EDIT:
$ python3 --version
Python 3.9.12
Yes, I am using C/C++ libraries, I believe, like numpy, copy (not sure if it is C/C++), torch.
I am not sure it is a good idea to post the code here, as it is quite a long .py file, and I am not sure exactly where the code gives that error, especially without a core dump actually being written to the disk.
I will mention that there are several parts where I am slightly concerned about unnecessary memory use that accumulates (this part is called a lot):
This loop:
for key in self.parameters.keys():
new = self.parameters[key]['x'].parameter
self.parser.parameters[key]['x'].parameter = new.detach().clone()
I am facing a problem with a python script getting killed. I had always used this script with no problem at all until two days ago, then it started to print, without any change in the code, the string 'killed' before aborting the execution.
Other people have tried to run the same code on their system and it works fine, as it used to do with me until two days ago.
I have read some old similar question, and I have got the problem could be an out-of-memory issue due to a bad memory management in my code. It sounds a little strange to me, since it used to work perfectly until some days ago and the problem appears on my system only.
Do you have any idea on how to inspect the problem and find a possible solution, please?
Python version: Python 2.7.14+
System: Scientific Linux CERN 7
In your case, it's highly probale that the script you're processing reached some given limit of the amount of resources it's able to use and that depends on your OS and other parameters, are you running something else with the script ? or are there many open files etc ?
The most likely reason for such an error is exceeding memory use, whiwh forces the system to not take risks and break when allocating more starts failing. Maybe you can print in parallel the total memory you're using to have a glimpse of what's happening since the information you've given are not enough to help you :
import os, psutil
process = psutil.Process(os.getpid())
then: (for python 3)
print(process.memory_info().rss)
or: (for python 2.7) (tested)
print(process.memory_info()[0])
begin TLDR;
I want to write a python3 script to scan through the memory of a running windows process and find strings.
end TLDR;
This is for a CTF binary. It's a typical Windows x86 PE file. The goal is simply to get a flag from the processes memory as it runs. This is easy with ProcessHacker you can search through the strings in the memory of the running application and find the flag with a regex. Now because I'm a masochistic geek I strive to script out solutions for CTFs (for everything really). Specifically I want to use python3, C# is also an option but would really like to keep all of the solution scripts in python.
Thought this would be a very simple task. You know... pip install some library written by someone that's already solved the problem and use it. Couldn't find anything that would let me do what I need for this task. Here are the libraries I tried out already.
ctypes - This was the first one I used, specifically ReadProcessMemory. Kept getting 299 errors which was because the buffer I was passing in was larger than that section of memory so I made a recursive function that would catch that exception, divide the buffer length by 2 until it got something THEN would read one byte at a time until it hit a 299 error. May have been on the right track there but I wasn't able to get the flag. I WAS able to find the flag only if I knew the exact address of the flag (which I'd get from process hacker). I may make a separate question on SO to address that, this one is really just me asking the community if something already exists before diving into this.
pymem - A nice wrapper for ctypes but had the same issues as above.
winappdbg - python2.x only. I don't want to use python 2.x.
haystack - Looks like this depends on winappdbg which depends on python 2.x.
angr - This is a possibility, Only scratched the surface with it so far. Looks complicated and it's on the to learn list but don't want to dive into something right now that's not going to solve the issue.
volatility - Looks like this is meant for working with full RAM dumps not for hooking into currently running processes and reading the memory.
My plan at the moment is to dive a bit more into angr to see if that will work, go back to pymem/ctypes and try more things. If all else fails ProcessHacker IS opensource. I'm not fluent in C so it'll take time to figure out how they're doing it. Really hoping there's some python3 library I'm missing or maybe I'm going about this the wrong way.
Ended up writing the script using the frida library. Also have to give soutz to rootbsd because his or her code in the fridump3 project helped greatly.
I have a python script, which is used to perform a lab measurement using several devices. The whole setup is rather involved, including communication over serial devices, API calls as well as the use of self-written and commercial drivers. In the end, however, everything boils down to two nested loops, which vary some parameters, collect data and write it to a file.
My problem is that I observe random occurences of a MemoryError, typically after 10 hours, equivalent to ~15k runs of the loops. At the moment, I don't have an idea, where it comes from or how I can trace it further. So I would be happy for suggestions, how to work on my problem. My observations up to this moment are as follows.
The error occurs at random states of the program. Different runs will throw the MemoryError at different lines of my script.
There is never any helpful error message. Python only says MemoryError without any error string. The traceback leads me to some point in the script, where memory is needed (e.g. when building a list), but it appears to be no specific instruction, which is the problem.
My RAM is far from full. The python process in question typically consumes some ten MB of RAM when viewed in the task manager. In addition, the RAM usage appears to be stable for hours. Usually, it increases slowly for some time, just to drop to down to the previous level quickly, which I interpret as the garbage collector kicking in periodically.
So far I did not find any indications for a memory leak. I used memory_profiler to trace the memory usage of my functions and found it to be stable. In addition, I followed this blog entry to observe what the garbage collector does in detail. Again, I could not find any hints for undeleted objects.
I am stuck to Win7 x86 due to a driver, which will only work on a 32bit system. So I cannot follow suggestions like this to go to a 64 bit version of Windows. Anyway, I do not see, how this would help in my situation.
The iPython console, from which the script is being launched, often behaves strange after the error occurred. Sometimes, a new MemoryError is thrown even for very simple operations. Often, the console is marked by Windows as "not responding" after some time. A menu pops up, where besides the usual options to wait for the process or to terminate it, there is a third option to "restore" the program (whatever that means). Doing so usually causes the console to work normal again.
At this point, I am somewhat out of ideas on how to proceed. The general receipe to comment out parts of the script until it works is highly undesirable in my case. As stated above, each test run will take several hours, meaning a potential downtime of weeks for my lab equipment. Going that direction, appears unfeasable to me. Is there any more direct approach to learn, what is crashing behind the scenes? How can I understand that python apparently fails to malloc?
In the PyCharm debugger we can pause a process. I have a program to debug that takes a lot of time before we arrive to the part I'm debugging.
The program can be modeled like that: GOOD_CODE -> CODE_TO_DEBUG.
I'm wondering if there is a way to..
run GOOD_CODE
save the process
edit the code in CODE_TO_DEBUG
restore the process and with the edited CODE_TO_DEBUG
Is serialization the good way to do it or is there some tool to do that?
I'm working on OSX with PyCharm.
Thank you for your kind answers.
The classic method is to write a program that reproduces the conditions that lead into the buggy code, without taking a bunch of time -- say, read in the data from a file instead of generating it -- and then paste in the code you're trying to fix. If you get it fixed in the test wrapper, and it still doesn't work in the original program, you then "only" have to find the interaction with the rest of the program that's faulty (global variables, bad parameters passes, etc.)