Re: Help with "fatal: unable to read ...." error during GC?

From: Paul Smith <paul@mad-scientist.net>
Date: Aug 11, 2018, 12:13 UTC
Message-ID: <be46349efde84f158b80e96f2fbbcf4304a71208.camel@mad-scientist.net>
In-Reply-To: <20180808182436.GA19096@sigill.intra.peff.net>

On Wed, 2018-08-08 at 14:24 -0400, Jeff King wrote:

Show 12 quoted lines

> If so, can you try running it under gdb and getting a stack trace?
> Something like:
> 
>   gdb git
>   [and then inside gdb...]
>   set args pack-objects --all --reflog --indexed-objects foo </dev/null
>   break die
>   run
>   bt
> 
> That might give us a clue where the broken object reference is coming
> from.

Oh no.  I messed up :(.

I rebuilt Git 2.18.0 without optimization to try to get more debug information. Unfortunately I didn't think to create a backup of my problematic .git directory.

When I ran the above command under the debugger using the non-optimized version of Git... it worked! That fixed the problem so that now when I run "git gc" using the original optimized version I no longer see the issue there either.

So... clearly something is wrong but because I was dumb and didn't make a backup I can no longer reproduce the problem :(. On the other hand, my repository is no longer throwing errors so that's good.

I do still have these warnings and no amount of git gc/git fsck/etc. has reduced them in any way:

$ git gc warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits Enumerating objects: 506556, done. Counting objects: 100% (506556/506556), done. Delta compression using up to 8 threads. Compressing objects: 100% (101199/101199), done. Writing objects: 100% (506556/506556), done. Total 506556 (delta 358957), reused 506556 (delta 358957) warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits warning: reflog of 'HEAD' references pruned commits Checking connectivity: 506556, done.

I've run git gc --prune=all then git fsck reports only these dangling commits:

dangling commit cef0678a5e0765506e3fac41286696fd37a9b1e9 dangling commit 1729195f021a1b95ea8ca10b9c32e76bf2257e67 dangling commit 08385b9731291607a8c6d4bf10272002d8f31e1f dangling commit c4ddfb2139eeb5a3c132dbfc84cc6e27fdeb46d1 dangling commit 1df8ebcc1cd5f59dd224ce1f3ba39f24370cf4e7

(this is down from probably 50 or so "dangling ..." commits, blobs, and trees before).