How to destroy Python objects and free up memory

Question

I am trying to iterate over 100,000 images and capture some image features and store the resulting dataFrame on disk as a pickle file.

Unfortunately due to RAM constraints, i am forced to split the images into chunks of 20,000 and perform operations on them before saving the results onto disk.

The code written below is supposed to save the dataframe of results for 20,000 images before starting the loop to process the next 20,000 images.

However - This does not seem to be solving my problem as the memory is not getting released from RAM at the end of the first for loop

So somewhere while processing the 50,000th record, the program crashes due to Out of Memory Error.

I tried deleting the objects after saving them to disk and invoking the garbage collector, however the RAM usage does not seem to be going down.

What am i missing?

#file_list_1 contains 100,000 images
file_list_chunks = list(divide_chunks(file_list_1,20000))
for count,f in enumerate(file_list_chunks):
    # make the Pool of workers
    pool = ThreadPool(64) 
    results = pool.map(get_image_features,f)
    # close the pool and wait for the work to finish 
    list_a, list_b = zip(*results)
    df = pd.DataFrame({'filename':list_a,'image_features':list_b})
    df.to_pickle("PATH_TO_FILE"+str(count)+".pickle")
    del list_a
    del list_b
    del df
    gc.collect()
    pool.close() 
    pool.join()
    print("pool closed")

Answer 1

Now, it could be that something in the 50,000th is very large, and that's causing the OOM, so to test this I'd first try:

file_list_chunks = list(divide_chunks(file_list_1,20000))[30000:]

If it fails at 10,000 this will confirm whether 20k is too big a chunksize, or if it fails at 50,000 again, there is an issue with the code...

---

Okay, onto the code...

Firstly, you don't need the explicit list constructor, it's much better in python to iterate rather than generate the entire the list into memory.

file_list_chunks = list(divide_chunks(file_list_1,20000))
# becomes
file_list_chunks = divide_chunks(file_list_1,20000)

I think you might be misusing ThreadPool here:

Prevents any more tasks from being submitted to the pool. Once all the tasks have been completed the worker processes will exit.

This reads like close might have some thinks still running, although I guess this is safe it feels a little un-pythonic, it's better to use the context manager for ThreadPool:

with ThreadPool(64) as pool: 
    results = pool.map(get_image_features,f)
    # etc.

The explicit dels in python aren't actually guaranteed to free memory.

You should collect after the join/after the with:

with ThreadPool(..):
    ...
    pool.join()
gc.collect()

You could also try chunk this into smaller pieces e.g. 10,000 or even smaller!

---

Hammer 1

One thing, I would consider doing here, instead of using pandas DataFrames and large lists is to use a SQL database, you can do this locally with sqlite3:

import sqlite3
conn = sqlite3.connect(':memory:', check_same_thread=False)  # or, use a file e.g. 'image-features.db'

and use context manager:

with conn:
    conn.execute('''CREATE TABLE images
                    (filename text, features text)''')

with conn:
    # Insert a row of data
    conn.execute("INSERT INTO images VALUES ('my-image.png','feature1,feature2')")

That way, we won't have to handle the large list objects or DataFrame.

You can pass the connection to each of the threads... you might have to something a little weird like:

results = pool.map(get_image_features, zip(itertools.repeat(conn), f))

Then, after the calculation is complete you can select all from the database, into which ever format you like. E.g. using read_sql.

---

Hammer 2

Use a subprocess here, rather than running this in the same instance of python "shell out" to another.

Since you can pass start and end to python as sys.args, you can slice these:

# main.py
# a for loop to iterate over this
subprocess.check_call(["python", "chunk.py", "0", "20000"])

# chunk.py a b
for count,f in enumerate(file_list_chunks):
    if count < int(sys.argv[1]) or count > int(sys.argv[2]):
         pass
    # do stuff

That way, the subprocess will properly clean up python (there's no way there'll be memory leaks, since the process will be terminated).

---

My bet is that Hammer 1 is the way to go, it feels like you're gluing up a lot of data, and reading it into python lists unnecessarily, and using sqlite3 (or some other database) completely avoids that.