GNU bug report logs - #34006
Guix gc killed live roots - broke git

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: swedebugia <at> riseup.net
To: bug-guix <at> gnu.org
Subject: Guix gc killed live roots - broke git
Date: Mon, 07 Jan 2019 02:07:42 -0800

[Message part 1 (text/plain, inline)]

Hi

Yesterday I hacked on guix. Everything was fine. Store was 43G.
I ran guix gc to clean up.

Afterwards git broke:

$ git pull swedebugia 
fatal: unable to fork

Stracing it reveals that it is missing something (see full attached):
execve("/home/sdb/.guix-profile/bin/git", ["git", "pull", "swedebugia"],
0x7ffe05bad790 /* 66 vars */) = 0
brk(NULL)                               = 0xbfe000
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0)
= 0x7f61627a1000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or
directory)
...

$ which git
/home/sdb/.guix-profile/bin/git
$ guix --version
guix (GNU Guix) 0.16.0 <- vanilla 0.16 initted from the installer

$ guix package -l|grep -5 git
Generation 1	Dec 24 2018 07:36:14
 
emacs-paredit	24	out	/gnu/store/1zha5anxg029qfl7r569aap5lfyrb66a-emacs-paredit-24
 
emacs-no-x	26.1	out	/gnu/store/9v7m3c83rm1rgi99ph5xdkpnnd0c62x4-emacs-no-x-26.1
 
setxkbmap	1.3.1	out	/gnu/store/3px1119mhx9q7xzmi5jlg5wylhkx84cr-setxkbmap-1.3.1
  git	2.19.2	out	/gnu/store/iffgahfxnk13narndlaqf9xm0yhyhyyv-git-2.19.2

Is this a bug?

If yes I think it is serious.

-- 
Cheers 
Swedebugia

[strace-git.txt (text/plain, attachment)]

Message #8 received at 34006 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: swedebugia <at> riseup.net
Cc: 34006 <at> debbugs.gnu.org
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Mon, 07 Jan 2019 12:31:48 +0100

Hi swedebugia,

> $ git pull swedebugia 
> fatal: unable to fork
>
> Stracing it reveals that it is missing something (see full attached):

Where do you see that?

-- 
Ricardo

Message #11 received at 34006 <at> debbugs.gnu.org (full text, mbox):

From: swedebugia <swedebugia <at> riseup.net>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 34006 <at> debbugs.gnu.org
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Mon, 7 Jan 2019 17:58:21 +0100

On 2019-01-07 12:31, Ricardo Wurmus wrote:
> 
> Hi swedebugia,
> 
>> $ git pull swedebugia
>> fatal: unable to fork
>>
>> Stracing it reveals that it is missing something (see full attached):
> 
> Where do you see that?

Ah, sorry the full command was:
strace git pull swedebugia

I tried installing git again with guix package -i git, but it seems no 
substitutes are available anymore to my surprise (0.16 is not even 2 
months old).

-- 
Cheers Swedebugia

Message #14 received at 34006 <at> debbugs.gnu.org (full text, mbox):

From: Mark H Weaver <mhw <at> netris.org>
To: swedebugia <swedebugia <at> riseup.net>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 34006 <at> debbugs.gnu.org
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Tue, 08 Jan 2019 02:50:53 -0500

Hi,

swedebugia <swedebugia <at> riseup.net> writes:

> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>
>>> $ git pull swedebugia
>>> fatal: unable to fork
>>>
>>> Stracing it reveals that it is missing something (see full attached):
>>
>> Where do you see that?
>
> Ah, sorry the full command was:
> strace git pull swedebugia

I looked at the strace output you provided, and didn't find any evidence
of a missing file, which I doubt would lead to the error message "unable
to fork" anyway.  The short excerpt that you quoted in your earlier mail
showed the failure to find "/etc/ld.so.preload", but that's expected,
and does not indicate a problem.  The problem might be happening in the
child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
the -f option to strace, i.e. "strace -f git pull swedebugia", might
yield more useful information.

If I'm not mistaken, "unable to fork" more likely indicates a lack of
available resources, possibly due to configured resource limits (see
ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
Otherwise, I guess it could be due to restrictions imposed by the use of
a security framework.

       Mark

Message #17 received at 34006 <at> debbugs.gnu.org (full text, mbox):

From: swedebugia <swedebugia <at> riseup.net>
To: Mark H Weaver <mhw <at> netris.org>
Cc: Ricardo Wurmus <rekado <at> elephly.net>,
 "34006 <at> debbugs.gnu.org" <34006 <at> debbugs.gnu.org>
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Tue, 08 Jan 2019 09:50:19 +0100

[Message part 1 (text/html, inline)]

[Message part 2 (text/plain, inline)]

Mark H Weaver <mhw <at> netris.org> skrev: (8 januari 2019 08:50:53 CET)
>Hi,
>
>swedebugia <swedebugia <at> riseup.net> writes:
>
>> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>>
>>>> $ git pull swedebugia
>>>> fatal: unable to fork
>>>>
>>>> Stracing it reveals that it is missing something (see full
>attached):
>>>
>>> Where do you see that?
>>
>> Ah, sorry the full command was:
>> strace git pull swedebugia
>
>I looked at the strace output you provided, and didn't find any
>evidence
>of a missing file, which I doubt would lead to the error message
>"unable
>to fork" anyway.  The short excerpt that you quoted in your earlier
>mail
>showed the failure to find "/etc/ld.so.preload", but that's expected,
>and does not indicate a problem.  The problem might be happening in the
>child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
>the -f option to strace, i.e. "strace -f git pull swedebugia", might
>yield more useful information.
>
>If I'm not mistaken, "unable to fork" more likely indicates a lack of
>available resources, possibly due to configured resource limits (see
>ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
>Otherwise, I guess it could be due to restrictions imposed by the use
>of
>a security framework.
>
>       Mark

Thanks for the -f tip. I thought the errors were significant, but now I understood they are not.
I will reply to the thread with more information if upgrading does not solve it. 
It is a vanilla 0.16 with a few packages installed, no security framework. 
I will share the whole environment also.
Git has been upgraded so I will try installing the newer version next.
-- 
Sent from my p≡p for Android.

[pEpkey.asc (application/pgp-keys, attachment)]

Message #20 received at 34006 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: swedebugia <swedebugia <at> riseup.net>
Cc: 34006 <at> debbugs.gnu.org
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Mon, 07 Jan 2019 18:52:32 +0100

swedebugia <swedebugia <at> riseup.net> writes:

> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>
>> Hi swedebugia,
>>
>>> $ git pull swedebugia
>>> fatal: unable to fork
>>>
>>> Stracing it reveals that it is missing something (see full attached):
>>
>> Where do you see that?
>
> Ah, sorry the full command was:
> strace git pull swedebugia

What I meant is that the excerpt you showed does not reveal that
“missing something” is the cause of the error.  Having a bunch of things
not found is pretty normal given that search paths are used.

> I tried installing git again with guix package -i git, but it seems no
> substitutes are available anymore to my surprise (0.16 is not even 2
> months old).

Substitutes from berlin / ci.guix.info?

-- 
Ricardo

Message #25 received at 34006-done <at> debbugs.gnu.org (full text, mbox):

From: swedebugia <at> riseup.net
To: Mark H Weaver <mhw <at> netris.org>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 34006-done <at> debbugs.gnu.org
Subject: Re: bug#34006: Guix gc killed live roots - broke git
Date: Sat, 12 Jan 2019 11:02:16 -0800

On 2019-01-08 07:50, Mark H Weaver wrote:
> Hi,
> 
> swedebugia <swedebugia <at> riseup.net> writes:
> 
>> On 2019-01-07 12:31, Ricardo Wurmus wrote:
>>>
>>>> $ git pull swedebugia
>>>> fatal: unable to fork
>>>>
>>>> Stracing it reveals that it is missing something (see full attached):
>>>
>>> Where do you see that?
>>
>> Ah, sorry the full command was:
>> strace git pull swedebugia
> 
> I looked at the strace output you provided, and didn't find any evidence
> of a missing file, which I doubt would lead to the error message "unable
> to fork" anyway.  The short excerpt that you quoted in your earlier mail
> showed the failure to find "/etc/ld.so.preload", but that's expected,
> and does not indicate a problem.  The problem might be happening in the
> child process (/home/sdb/.guix-profile/libexec/git-core/git), so adding
> the -f option to strace, i.e. "strace -f git pull swedebugia", might
> yield more useful information.
> 
> If I'm not mistaken, "unable to fork" more likely indicates a lack of
> available resources, possibly due to configured resource limits (see
> ulimit(3) and the 'ulimit' bash builtin, e.g. try "ulimit -a").
> Otherwise, I guess it could be due to restrictions imposed by the use of
> a security framework.

Tried again with "strace -f" and got this:

stat("/home/sdb/.guix-profile/libexec/git-core/ssh", 0x7ffe26617620) =
-1 ENOENT (No such file or directory)
stat("/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/bin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/gnu/store/6ff29rxibnfzabp17qj3mzpc8jggrmsn-profile/sbin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/home/sdb/.local/bin;/home/sdb/.guix-profile/bin/ssh",
0x7ffe26617620) = -1 ENOENT (No such file or directory)
stat("/home/sdb/.guix-profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/run/setuid-programs/ssh", 0x7ffe26617620) = -1 ENOENT (No such
file or directory)
stat("/home/sdb/.config/guix/current/bin/ssh", 0x7ffe26617620) = -1
ENOENT (No such file or directory)
stat("/home/sdb/.guix-profile/bin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/home/sdb/.guix-profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT (No
such file or directory)
stat("/run/current-system/profile/bin/ssh", 0x7ffe26617620) = -1 ENOENT
(No such file or directory)
stat("/run/current-system/profile/sbin/ssh", 0x7ffe26617620) = -1 ENOENT
(No such file or directory)
close(14)                               = 0

So installing ssh might be a good idea >D

Solved! :D

-- 
Cheers 
Swedebugia

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