What is a python "cksum" equivalent for very large files and how does it work?

2

I have a problem that i need to validate huge compressed files after download (usually more than 10-20gb per file) against reference checksums that have apparently been generated using cksum

(To be more precise: My python script needs to download large compressed files from the ncbi ftp-server that was supposed to provide md5 checksums for validating the downloads, but instead only provided some different unspecified filehash/checksum values. After some trial and error I found that these checksums were identical to the output of the unix tool cksum, which apparently genereates CRC-checksums. So to compare/validate these i need to generate cksum-equivalent checksums for the downloaded files.)

It appears that the unix tool cksum yields totally different checksum values than the supposed equivalent unix tool crc32 (or the python zlib.crc32() function, for that matter). When googling the problem I could not understand the explanations for why this occurs, especially since they appear to be identical on some systems? So maybe this is because I work on a 64 bit system (but then: who doesn't nowadays)?

using built-in python modules I can easily generate md5- and CRC32 checksums, but none of these are equivalent to the cksum output, neither in decimal nor in hexadecimal representation.

I did find a previous post here on stackoverflow pointing to a snippet that seems to solve this. But while it works for small files, A.) I do not understand a word of it, so I have a hard time adapting it and B.) it does not seem to work well with large files.

for completeness sake: here is the snippet (python3 version):

#!/usr/bin/env python
import sys

crctab = [ 0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9, 0x130476dc,
        0x17c56b6b, 0x1a864db2, 0x1e475005, 0x2608edb8, 0x22c9f00f,
        0x2f8ad6d6, 0x2b4bcb61, 0x350c9b64, 0x31cd86d3, 0x3c8ea00a,
        0x384fbdbd, 0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9,
        0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75, 0x6a1936c8,
        0x6ed82b7f, 0x639b0da6, 0x675a1011, 0x791d4014, 0x7ddc5da3,
        0x709f7b7a, 0x745e66cd, 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e,
        0x95609039, 0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5,
        0xbe2b5b58, 0xbaea46ef, 0xb7a96036, 0xb3687d81, 0xad2f2d84,
        0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d, 0xd4326d90, 0xd0f37027,
        0xddb056fe, 0xd9714b49, 0xc7361b4c, 0xc3f706fb, 0xceb42022,
        0xca753d95, 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
        0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d, 0x34867077,
        0x30476dc0, 0x3d044b19, 0x39c556ae, 0x278206ab, 0x23431b1c,
        0x2e003dc5, 0x2ac12072, 0x128e9dcf, 0x164f8078, 0x1b0ca6a1,
        0x1fcdbb16, 0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca,
        0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde, 0x6b93dddb,
        0x6f52c06c, 0x6211e6b5, 0x66d0fb02, 0x5e9f46bf, 0x5a5e5b08,
        0x571d7dd1, 0x53dc6066, 0x4d9b3063, 0x495a2dd4, 0x44190b0d,
        0x40d816ba, 0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e,
        0xbfa1b04b, 0xbb60adfc, 0xb6238b25, 0xb2e29692, 0x8aad2b2f,
        0x8e6c3698, 0x832f1041, 0x87ee0df6, 0x99a95df3, 0x9d684044,
        0x902b669d, 0x94ea7b2a, 0xe0b41de7, 0xe4750050, 0xe9362689,
        0xedf73b3e, 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
        0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686, 0xd5b88683,
        0xd1799b34, 0xdc3abded, 0xd8fba05a, 0x690ce0ee, 0x6dcdfd59,
        0x608edb80, 0x644fc637, 0x7a089632, 0x7ec98b85, 0x738aad5c,
        0x774bb0eb, 0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f,
        0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53, 0x251d3b9e,
        0x21dc2629, 0x2c9f00f0, 0x285e1d47, 0x36194d42, 0x32d850f5,
        0x3f9b762c, 0x3b5a6b9b, 0x0315d626, 0x07d4cb91, 0x0a97ed48,
        0x0e56f0ff, 0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623,
        0xf12f560e, 0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7, 0xe22b20d2,
        0xe6ea3d65, 0xeba91bbc, 0xef68060b, 0xd727bbb6, 0xd3e6a601,
        0xdea580d8, 0xda649d6f, 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604,
        0xc960ebb3, 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
        0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b, 0x9b3660c6,
        0x9ff77d71, 0x92b45ba8, 0x9675461f, 0x8832161a, 0x8cf30bad,
        0x81b02d74, 0x857130c3, 0x5d8a9099, 0x594b8d2e, 0x5408abf7,
        0x50c9b640, 0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c,
        0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8, 0x68860bfd,
        0x6c47164a, 0x61043093, 0x65c52d24, 0x119b4be9, 0x155a565e,
        0x18197087, 0x1cd86d30, 0x029f3d35, 0x065e2082, 0x0b1d065b,
        0x0fdc1bec, 0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088,
        0x2497d08d, 0x2056cd3a, 0x2d15ebe3, 0x29d4f654, 0xc5a92679,
        0xc1683bce, 0xcc2b1d17, 0xc8ea00a0, 0xd6ad50a5, 0xd26c4d12,
        0xdf2f6bcb, 0xdbee767c, 0xe3a1cbc1, 0xe760d676, 0xea23f0af,
        0xeee2ed18, 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
        0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0, 0x9abc8bd5,
        0x9e7d9662, 0x933eb0bb, 0x97ffad0c, 0xafb010b1, 0xab710d06,
        0xa6322bdf, 0xa2f33668, 0xbcb4666d, 0xb8757bda, 0xb5365d03,
        0xb1f740b4 ]

UNSIGNED = lambda n: n & 0xffffffff

def memcrc(b):
    n = len(b)
    i = c = s = 0
    for c in b:
        tabidx = (s>>24)^c
        s = UNSIGNED((s << 8)) ^ crctab[tabidx]
    while n:
        c = n & 0o0377
        n = n >> 8
        s = UNSIGNED(s << 8) ^ crctab[(s >> 24) ^ c]
    return UNSIGNED(~s)

if __name__ == '__main__':
    fname = sys.argv[-1]
    buffer = open(fname, 'rb').read()
    print("%d\t%d\t%s" %  (memcrc(buffer), len(buffer), fname))

Could someone please help me understand this?

  • what exactly is the problem with the difference between cksum and crc32?
  • is it simply the fact that the one is 32bit based and the other 64 bit?
  • Can i simply convert between the values produced by both, and if yes how?
  • what is the purpose of the crctab in the above snippet and how does the conversion work there?
python
python-3.x
checksum
crc
filehash
asked on Stack Overflow Dec 3, 2020 by jov14 • edited Dec 3, 2020 by jov14

2 Answers

1

I've tried refactoring your code into a class following a similar api to the standard Python hashlib:

class crc32:
    def __init__(self):
        self.nchars = 0
        self.crc = 0
    
    def update(self, buf):
        crc = self.crc
        for c in buf:
            crc = crctab[(crc >> 24) ^ c] ^ ((crc << 8) & 0xffffffff)
        self.crc = crc
        self.nchars += len(buf)

    def digest(self):
        crc = self.crc
        n = self.nchars
        while n:
            c = n & 0xff
            crc = crctab[(crc >> 24) ^ c] ^ ((crc << 8) & 0xffffffff)
            n >>= 8
        return UNSIGNED(~crc)

I've expanded out UNSIGNED to try and make it faster and reordered some of the statements to be more similar to the standard zlib library (as used by Python) while I was trying to understand the differences. It seems they use a different polynomial to generate the table, but otherwise it's the same.

The above code can be used as:

with open('largefile', 'rb') as fd:
  digest = crc32()
  while buf := fd.read(4096):
    digest.update(buf)
  print(digest.digest())

which prints out the expected 1135714720 for a file created by:

echo -n hello world > test.txt

The above code should work for large files, but given the performance of Python this would take far too long to be useful. A 75MB file I have takes ~11 seconds, while cksum takes just ~0.2 seconds. You should be able to get somewhere with using Cython to speed it up, but that's a bit more fiddly and if your're struggling with the existing code it's going to be quite a learning curve!

I've had another play and got performance similar to cksum with Cython, the code looks like:

cdef unsigned int *crctab_c = [
  // copy/paste crctab from above
]

cdef class crc32_c:
    cdef unsigned int crc, nchars

    def __init__(self):
        self.nchars = 0
        self.crc = 0
    
    cdef _update(self, bytes buf):
        cdef unsigned int crc, i, j
        cdef unsigned char c
        crc = self.crc
        for c in buf:
            i = (crc >> 24) ^ c
            j = crc << 8
            crc = crctab_c[i] ^ j
        self.crc = crc
        self.nchars += len(buf)

    def update(self, buf):
        return self._update(buf)

    def digest(self):
        crc = self.crc
        n = self.nchars
        while n:
            c = n & 0xff
            crc = crctab_c[(crc >> 24) ^ c] ^ ((crc << 8) & 0xffffffff)
            n >>= 8
        return (~crc) & 0xffffffff

after compiling this code with Cython, it can be used in a similar manner to the previous class. Performance is pretty good: Python now takes ~200ms for a 75MiB file and is basically the same as cksum, but much slower than zlib which only takes ~80ms.

answered on Stack Overflow Dec 3, 2020 by Sam Mason • edited Dec 4, 2020 by Sam Mason
1

I don't know the why part of your question. All I can say is that the great thing about standards is that you have so many to choose from.

cksum is specified by POSIX to use a different CRC than the more common CRC-32 you find in zlib, Python, used in zip and gzip files, etc. The CRC-32/CKSUM has this specification (from Greg Cook's CRC catalog):

width=32 poly=0x04c11db7 init=0x00000000 refin=false refout=false xorout=0xffffffff check=0x765e7680 residue=0xc704dd7b name="CRC-32/CKSUM"

The more common CRC-32 has this specification:

width=32 poly=0x04c11db7 init=0xffffffff refin=true refout=true xorout=0xffffffff check=0xcbf43926 residue=0xdebb20e3 name="CRC-32/ISO-HDLC"

The cksum utility on my system (macOS) computes the CRC-32/CKSUM, but it also has options to compute the CRC-32/ISO_HDLC, as well as two other actual checksums, the first from the BSD Unix sum command, and the second from the AT&T System V Unix sum command.

There is apparently no shortage of results that cksum might produce.

No, it has nothing to do with 32 vs. 64 bit systems.

No, you cannot convert between the values.

The purpose of the table is to speed up the CRC calculation by precomputing the CRC of every byte value.

answered on Stack Overflow Dec 4, 2020 by Mark Adler • edited Dec 4, 2020 by Mark Adler

User contributions licensed under CC BY-SA 3.0