I was recently presented with a repository with a corrupted packfile, and was asked if the data was recoverable. This post-mortem describes the steps I took to investigate and fix the problem. I thought others might find the process interesting, and it might help somebody in the same situation.

Note: In this case, no good copy of the repository was available. For the much easier case where you can get the corrupted object from elsewhere, see this howto.

I started with an fsck, which found a problem with exactly one object (I’ve used $pack and $obj below to keep the output readable, and also because I’ll refer to them later):

    $ git fsck
    error: $pack SHA1 checksum mismatch
    error: index CRC mismatch for object $obj from $pack at offset 51653873
    error: inflate: data stream error (incorrect data check)
    error: cannot unpack $obj from $pack at offset 51653873

The pack checksum failing means a byte is munged somewhere, and it is presumably in the object mentioned (since both the index checksum and zlib were failing).

Reading the zlib source code, I found that "incorrect data check" means that the adler-32 checksum at the end of the zlib data did not match the inflated data. So stepping the data through zlib would not help, as it did not fail until the very end, when we realize the CRC does not match. The problematic bytes could be anywhere in the object data.

The first thing I did was pull the broken data out of the packfile. I needed to know how big the object was, which I found out with:

    $ git show-index <$idx | cut -d' ' -f1 | sort -n | grep -A1 51653873
    51653873
    51664736

Show-index gives us the list of objects and their offsets. We throw away everything but the offsets, and then sort them so that our interesting offset (which we got from the fsck output above) is followed immediately by the offset of the next object. Now we know that the object data is 10863 bytes long, and we can grab it with:

  dd if=$pack of=object bs=1 skip=51653873 count=10863

I inspected a hexdump of the data, looking for any obvious bogosity (e.g., a 4K run of zeroes would be a good sign of filesystem corruption). But everything looked pretty reasonable.

Note that the "object" file isn’t fit for feeding straight to zlib; it has the git packed object header, which is variable-length. We want to strip that off so we can start playing with the zlib data directly. You can either work your way through it manually (the format is described in Documentation/technical/pack-format.txt), or you can walk through it in a debugger. I did the latter, creating a valid pack like:

    # pack magic and version
    printf 'PACK\0\0\0\2' >tmp.pack
    # pack has one object
    printf '\0\0\0\1' >>tmp.pack
    # now add our object data
    cat object >>tmp.pack
    # and then append the pack trailer
    /path/to/git.git/test-sha1 -b <tmp.pack >trailer
    cat trailer >>tmp.pack

and then running "git index-pack tmp.pack" in the debugger (stop at unpack_raw_entry). Doing this, I found that there were 3 bytes of header (and the header itself had a sane type and size). So I stripped those off with:

    dd if=object of=zlib bs=1 skip=3

I ran the result through zlib’s inflate using a custom C program. And while it did report the error, I did get the right number of output bytes (i.e., it matched git’s size header that we decoded above). But feeding the result back to "git hash-object" didn’t produce the same sha1. So there were some wrong bytes, but I didn’t know which. The file happened to be C source code, so I hoped I could notice something obviously wrong with it, but I didn’t. I even got it to compile!

I also tried comparing it to other versions of the same path in the repository, hoping that there would be some part of the diff that didn’t make sense. Unfortunately, this happened to be the only revision of this particular file in the repository, so I had nothing to compare against.

So I took a different approach. Working under the guess that the corruption was limited to a single byte, I wrote a program to munge each byte individually, and try inflating the result. Since the object was only 10K compressed, that worked out to about 2.5M attempts, which took a few minutes.

The program I used is here:

#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <signal.h>
#include <zlib.h>

static int try_zlib(unsigned char *buf, int len)
{
        /* make this absurdly large so we don't have to loop */
        static unsigned char out[1024*1024];
        z_stream z;
        int ret;

        memset(&z, 0, sizeof(z));
        inflateInit(&z);

        z.next_in = buf;
        z.avail_in = len;
        z.next_out = out;
        z.avail_out = sizeof(out);

        ret = inflate(&z, 0);
        inflateEnd(&z);
        return ret >= 0;
}

/* eye candy */
static int counter = 0;
static void progress(int sig)
{
        fprintf(stderr, "\r%d", counter);
        alarm(1);
}

int main(void)
{
        /* oversized so we can read the whole buffer in */
        unsigned char buf[1024*1024];
        int len;
        unsigned i, j;

        signal(SIGALRM, progress);
        alarm(1);

        len = read(0, buf, sizeof(buf));
        for (i = 0; i < len; i++) {
                unsigned char c = buf[i];
                for (j = 0; j <= 0xff; j++) {
                        buf[i] = j;

                        counter++;
                        if (try_zlib(buf, len))
                                printf("i=%d, j=%x\n", i, j);
                }
                buf[i] = c;
        }

        alarm(0);
        fprintf(stderr, "\n");
        return 0;
}

I compiled and ran with:

  gcc -Wall -Werror -O3 munge.c -o munge -lz
  ./munge <zlib

There were a few false positives early on (if you write "no data" in the zlib header, zlib thinks it’s just fine :) ). But I got a hit about halfway through:

  i=5642, j=c7

I let it run to completion, and got a few more hits at the end (where it was munging the CRC to match our broken data). So there was a good chance this middle hit was the source of the problem.

I confirmed by tweaking the byte in a hex editor, zlib inflating the result (no errors!), and then piping the output into "git hash-object", which reported the sha1 of the broken object. Success!

I fixed the packfile itself with:

  chmod +w $pack
  printf '\xc7' | dd of=$pack bs=1 seek=51659518 conv=notrunc
  chmod -w $pack

The \xc7 comes from the replacement byte our "munge" program found. The offset 51659518 is derived by taking the original object offset (51653873), adding the replacement offset found by "munge" (5642), and then adding back in the 3 bytes of git header we stripped.

After that, "git fsck" ran clean.

As for the corruption itself, I was lucky that it was indeed a single byte. In fact, it turned out to be a single bit. The byte 0xc7 was corrupted to 0xc5. So presumably it was caused by faulty hardware, or a cosmic ray.

And the aborted attempt to look at the inflated output to see what was wrong? I could have looked forever and never found it. Here’s the diff between what the corrupted data inflates to, versus the real data:

  -       cp = strtok (arg, "+");
  +       cp = strtok (arg, ".");

It tweaked one byte and still ended up as valid, readable C that just happened to do something totally different! One takeaway is that on a less unlucky day, looking at the zlib output might have actually been helpful, as most random changes would actually break the C code.

But more importantly, git’s hashing and checksumming noticed a problem that easily could have gone undetected in another system. The result still compiled, but would have caused an interesting bug (that would have been blamed on some random commit).

The adventure continues…

I ended up doing this again! Same entity, new hardware. The assumption at this point is that the old disk corrupted the packfile, and then the corruption was migrated to the new hardware (because it was done by rsync or similar, and no fsck was done at the time of migration).

This time, the affected blob was over 20 megabytes, which was far too large to do a brute-force on. I followed the instructions above to create the zlib file. I then used the inflate program below to pull the corrupted data from that. Examining that output gave me a hint about where in the file the corruption was. But now I was working with the file itself, not the zlib contents. So knowing the sha1 of the object and the approximate area of the corruption, I used the sha1-munge program below to brute-force the correct byte.

Here’s the inflate program (it’s essentially gunzip but without the .gz header processing):

#include <stdio.h>
#include <string.h>
#include <zlib.h>
#include <stdlib.h>

int main(int argc, char **argv)
{
        /*
         * oversized so we can read the whole buffer in;
         * this could actually be switched to streaming
         * to avoid any memory limitations
         */
        static unsigned char buf[25 * 1024 * 1024];
        static unsigned char out[25 * 1024 * 1024];
        int len;
        z_stream z;
        int ret;

        len = read(0, buf, sizeof(buf));
        memset(&z, 0, sizeof(z));
        inflateInit(&z);

        z.next_in = buf;
        z.avail_in = len;
        z.next_out = out;
        z.avail_out = sizeof(out);

        ret = inflate(&z, 0);
        if (ret != Z_OK && ret != Z_STREAM_END)
                fprintf(stderr, "initial inflate failed (%d)\n", ret);

        fprintf(stderr, "outputting %lu bytes", z.total_out);
        fwrite(out, 1, z.total_out, stdout);
        return 0;
}

And here is the sha1-munge program:

#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <signal.h>
#include <openssl/sha.h>
#include <stdlib.h>

/* eye candy */
static int counter = 0;
static void progress(int sig)
{
        fprintf(stderr, "\r%d", counter);
        alarm(1);
}

static const signed char hexval_table[256] = {
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 00-07 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 08-0f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 10-17 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 18-1f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 20-27 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 28-2f */
          0,  1,  2,  3,  4,  5,  6,  7,                /* 30-37 */
          8,  9, -1, -1, -1, -1, -1, -1,                /* 38-3f */
         -1, 10, 11, 12, 13, 14, 15, -1,                /* 40-47 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 48-4f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 50-57 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 58-5f */
         -1, 10, 11, 12, 13, 14, 15, -1,                /* 60-67 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 68-67 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 70-77 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 78-7f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 80-87 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 88-8f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 90-97 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* 98-9f */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* a0-a7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* a8-af */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* b0-b7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* b8-bf */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* c0-c7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* c8-cf */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* d0-d7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* d8-df */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* e0-e7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* e8-ef */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* f0-f7 */
         -1, -1, -1, -1, -1, -1, -1, -1,                /* f8-ff */
};

static inline unsigned int hexval(unsigned char c)
{
return hexval_table[c];
}

static int get_sha1_hex(const char *hex, unsigned char *sha1)
{
        int i;
        for (i = 0; i < 20; i++) {
                unsigned int val;
                /*
                 * hex[1]=='\0' is caught when val is checked below,
                 * but if hex[0] is NUL we have to avoid reading
                 * past the end of the string:
                 */
                if (!hex[0])
                        return -1;
                val = (hexval(hex[0]) << 4) | hexval(hex[1]);
                if (val & ~0xff)
                        return -1;
                *sha1++ = val;
                hex += 2;
        }
        return 0;
}

int main(int argc, char **argv)
{
        /* oversized so we can read the whole buffer in */
        static unsigned char buf[25 * 1024 * 1024];
        char header[32];
        int header_len;
        unsigned char have[20], want[20];
        int start, len;
        SHA_CTX orig;
        unsigned i, j;

        if (!argv[1] || get_sha1_hex(argv[1], want)) {
                fprintf(stderr, "usage: sha1-munge <sha1> [start] <file.in\n");
                return 1;
        }

        if (argv[2])
                start = atoi(argv[2]);
        else
                start = 0;

        len = read(0, buf, sizeof(buf));
        header_len = sprintf(header, "blob %d", len) + 1;
        fprintf(stderr, "using header: %s\n", header);

        /*
         * We keep a running sha1 so that if you are munging
         * near the end of the file, we do not have to re-sha1
         * the unchanged earlier bytes
         */
        SHA1_Init(&orig);
        SHA1_Update(&orig, header, header_len);
        if (start)
                SHA1_Update(&orig, buf, start);

        signal(SIGALRM, progress);
        alarm(1);

        for (i = start; i < len; i++) {
                unsigned char c;
                SHA_CTX x;

#if 0
                /*
                 * deletion -- this would not actually work in practice,
                 * I think, because we've already committed to a
                 * particular size in the header. Ditto for addition
                 * below. In those cases, you'd have to do the whole
                 * sha1 from scratch, or possibly keep three running
                 * "orig" sha1 computations going.
                 */
                memcpy(&x, &orig, sizeof(x));
                SHA1_Update(&x, buf + i + 1, len - i - 1);
                SHA1_Final(have, &x);
                if (!memcmp(have, want, 20))
                        printf("i=%d, deletion\n", i);
#endif

                /*
                 * replacement -- note that this tries each of the 256
                 * possible bytes. If you suspect a single-bit flip,
                 * it would be much shorter to just try the 8
                 * bit-flipped variants.
                 */
                c = buf[i];
                for (j = 0; j <= 0xff; j++) {
                        buf[i] = j;

                        memcpy(&x, &orig, sizeof(x));
                        SHA1_Update(&x, buf + i, len - i);
                        SHA1_Final(have, &x);
                        if (!memcmp(have, want, 20))
                                printf("i=%d, j=%02x\n", i, j);
                }
                buf[i] = c;

#if 0
                /* addition */
                for (j = 0; j <= 0xff; j++) {
                        unsigned char extra = j;
                        memcpy(&x, &orig, sizeof(x));
                        SHA1_Update(&x, &extra, 1);
                        SHA1_Update(&x, buf + i, len - i);
                        SHA1_Final(have, &x);
                        if (!memcmp(have, want, 20))
                                printf("i=%d, addition=%02x", i, j);
                }
#endif

                SHA1_Update(&orig, buf + i, 1);
                counter++;
        }

        alarm(0);
        fprintf(stderr, "\r%d\n", counter);
        return 0;
}