Question

I need to run a function for the each of the elements of my database.

When I try the following:

from multiprocessing import Pool
from pymongo import Connection

def foo():
...


connection1 = Connection('127.0.0.1', 27017)
db1 = connection1.data

my_pool = Pool(6)
my_pool.map(foo, db1.index.find())

I’m getting the following error:

Job 1, ‘python myscript.py ‘ terminated by signal SIGKILL (Forced quit)

Which is, I think, caused by db1.index.find() eating all the available ram while trying to return millions of database elements…

How should I modify my code for it to work?

Some logs are here:

dmesg | tail -500 | grep memory
[177886.768927] Out of memory: Kill process 3063 (python) score 683 or sacrifice child
[177891.001379]  [<ffffffff8110e51a>] out_of_memory+0xfa/0x250
[177891.021362] Out of memory: Kill process 3063 (python) score 684 or sacrifice child
[177891.025399]  [<ffffffff8110e51a>] out_of_memory+0xfa/0x250

The actual function below:

def create_barrel(item):
    connection = Connection('127.0.0.1', 27017)
    db = connection.data
    print db.index.count()
    barrel = []
    fls = []
    if 'name' in item.keys():
        barrel.append(WhitespaceTokenizer().tokenize(item['name']))
        name = item['name']
    elif 'name.utf-8' in item.keys():
        barrel.append(WhitespaceTokenizer().tokenize(item['name.utf-8']))
        name = item['name.utf-8']
    else:
        print item.keys()
    if 'files' in item.keys():
        for file in item['files']:
            if 'path' in file.keys():
                barrel.append(WhitespaceTokenizer().tokenize(" ".join(file['path'])))
                fls.append(("\\".join(file['path']),file['length']))
            elif 'path.utf-8'  in file.keys():
                barrel.append(WhitespaceTokenizer().tokenize(" ".join(file['path.utf-8'])))
                fls.append(("\\".join(file['path.utf-8']),file['length']))
            else:
                print file
                barrel.append(WhitespaceTokenizer().tokenize(file))
    if len(fls) < 1:
        fls.append((name,item['length']))
    barrel = sum(barrel,[])
    for s in barrel:
        vs = re.findall("\d[\d|\.]*\d", s) #versions i.e. numbes such as 4.2.7500 
    b0 = []
    for s in barrel:
        b0.append(re.split("[" + string.punctuation + "]", s))
    b1 = filter(lambda x: x not in string.punctuation, sum(b0,[]))
    flag = True
    while flag:
        bb = []
        flag = False
        for bt in b1:
            if bt[0] in string.punctuation:
                bb.append(bt[1:])
                flag = True
            elif bt[-1] in string.punctuation:
                bb.append(bt[:-1])
                flag = True
            else:
                bb.append(bt)
        b1 = bb
    b2 = b1 + barrel + vs
    b3 = list(set(b2))
    b4 = map(lambda x: x.lower(), b3)
    b_final = {}
    b_final['_id'] = item['_id']
    b_final['tags'] = b4
    b_final['name'] = name
    b_final['files'] = fls
    print db.barrels.insert(b_final)

I’ve noticed interesting thing. Then I press ctrl+c to stop process I’m getting the following:

python index2barrel.py 
Traceback (most recent call last):
  File "index2barrel.py", line 83, in <module>
    my_pool.map(create_barrel, db1.index.find, 6)
  File "/usr/lib/python2.7/multiprocessing/pool.py", line 227, in map
    return self.map_async(func, iterable, chunksize).get()
  File "/usr/lib/python2.7/multiprocessing/pool.py", line 280, in map_async
    iterable = list(iterable)
TypeError: 'instancemethod' object is not iterable

I mean, why multiprocessing is trying to convert somethin to the list? Isn’t it the source of the problem?

from the stack trace:

brk(0x231ccf000)                        = 0x231ccf000
futex(0x1abb150, FUTEX_WAKE_PRIVATE, 1) = 1
sendto(3, "+\0\0\0\260\263\355\356\0\0\0\0\325\7\0\0\0\0\0\0data.index\0\0"..., 43, 0, NULL, 0) = 43
recvfrom(3, "Some text from my database."..., 491663, 0, NULL, NULL) = 491663
... [manymany times]
brk(0x2320d5000)                        = 0x2320d5000
.... manymany times

The above sample goes and goes in strace output and for some reason strace -o logfile python myscript.py
does not halt. It just eats all the available ram and writes in log file.

UPDATE. Using imap instead of map solved my problem.

Answer 1

Since the find() operation is returning the cursor the the map function and since you say that this runs without a problem when you do
for item in db1.index.find(): create_barrel(item)
it looks like the create_barrel function is OK.

Can you try to limit the number of results returned in the cursor and see if this helps? I think the syntax would be:

db1.index.find().limit(100)

If you could try this and see if it helps it might help to get the cause of the problem.

EDIT1: I think you are going about this the wrong way by using the map function – I think you should be using map_reduce in the mongo python driver – that way the map function will be executed by the mongod process.