fix-attrs broken in v2.2.0.1 #329

b-m-f · 2021-02-14T19:00:28Z

I am using the fix-attrs.d directory to change permissions on a file that is mounted into the container at launch.

This worked fine in 2.1.0.2 but breaks in 2.2.0.1.

Working in 2.1.0.2
https://github.com/b-m-f/WirtBot/runs/1894909984#step:3:1813

Breaking with 2.2.0.1
https://github.com/b-m-f/WirtBot/runs/1898569667?check_suite_focus=true#step:3:2244

The text was updated successfully, but these errors were encountered:

b-m-f · 2021-02-14T19:39:04Z

Let me know if there is any more info I can provide to help :)

The only suspect I could make out is this change: 3e7bc9f

jprjr · 2021-02-15T21:42:56Z

Can you come up with a small example? I can't seem to get it to fail

b-m-f · 2021-02-16T18:34:32Z

Hi @jprjr ,

I have created a reproduction at https://github.com/b-m-f/s6-overlay-bug-reproduction . It is based on the nginx example from the README.

Simply clone and run docker-compose up. It should fail with:

s6-bug-test    | [fix-attrs.d] 01-fix-mounted: applying...
s6-bug-test    | [fix-attrs.d] 01-fix-mounted: exited 1.

Versions:
Docker version 20.10.3
docker-compose version 1.28.2

rakheshster · 2021-02-21T18:10:40Z

FWIW I too encountered this issue with my containers today. Upgraded to the latest 2.2.0.3 and that didn't help either.

Docker version 20.10.2, build 2291f61
docker-compose version 1.27.4, build 40524192

andrewzah · 2021-03-11T21:35:33Z

fix-attrs.d just hangs for me. on 2.2.0.1 and 2.2.0.3

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...

timothydlister · 2021-03-12T18:02:42Z

Not sure if this will help anyone but I had this problem when using the s6-overlay package in the Alpine repository. When I installed using a release from this repo, the problem went away.

dermotbradley · 2021-03-12T18:42:34Z

On Friday, March 12, 2021, 6:03:03 PM GMT, Timothy Lister ***@***.***> wrote: Not sure if this will help anyone but I had this problem when using the package in the Alpine repository. When I installed using a release from this repo, the problem went away.

Hi there, Alpine maintainer for s6-overlay here. Which Alpine release was this with? Edge? v3.13.0/v3.13.1/v3.13.2? Which version of the s6-overlay package? Which version of s6-overlay? Alpine Edge has the current release of s6-overlay packaged whereas v3.13.x has an older version, likewise the version of the other s6 packages differ between Edge and v3.13.x. Dermot

timothydlister · 2021-03-12T18:56:47Z

On Friday, March 12, 2021, 6:03:03 PM GMT, Timothy Lister @.***> wrote: Not sure if this will help anyone but I had this problem when using the package in the Alpine repository. When I installed using a release from this repo, the problem went away.
Hi there, Alpine maintainer for s6-overlay here. Which Alpine release was this with? Edge? v3.13.0/v3.13.1/v3.13.2? Which version of the s6-overlay package? Which version of s6-overlay? Alpine Edge has the current release of s6-overlay packaged whereas v3.13.x has an older version, likewise the version of the other s6 packages differ between Edge and v3.13.x. Dermot

Hi there,

I just reran my test to make sure, from my dockerfile:

FROM alpine:3.13
RUN apk add --no-cache s6-overlay
...
ENTRYPOINT ["/init"]

Shows when run:

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...

From inside 3.13:

/ # apk info s6-overlay
WARNING: Ignoring https://dl-cdn.alpinelinux.org/alpine/v3.13/main: No such file or directory
WARNING: Ignoring https://dl-cdn.alpinelinux.org/alpine/v3.13/community: No such file or directory
s6-overlay-2.1.0.0-r1 description:
s6 overlay for containers

s6-overlay-2.1.0.0-r1 webpage:
https://github.com/just-containers/s6-overlay/

Trying with alpine:edge gives:

export: fatal: unable to exec /etc/s6/init/init-stage1: Permission denied

dermotbradley · 2021-03-12T19:21:26Z

On Friday, March 12, 2021, 6:57:04 PM GMT, Timothy Lister ***@***.***> wrote: Trying with alpine:edge gives: export: fatal: unable to exec /etc/s6/init/init-stage1: Permission denied

Ah, I see the problem with that, several files that should be marked executable are not: /etc/s6/init-no-catchall/init-stage1 /etc/s6/init-no-catchall/init-stage2 /etc/s6/init/init-stage1 /etc/s6/init/init-stage3 and possibly some other files. When I create the Alpine package I unpack the upstream tarfile and any file permissions come from this tarfile. I'll raise an Issue in Github s6-overlay to log this. Separately I'll fix this in the Alpine package and push out a new minor release for Edge - hopefully tonight, if not then tomorrow. Looks like this has been an issue for the last few s6-overlay versions - unfortunately I've been busy with some other stuff and haven't been actively using s6-overlay for the past couple of months and so didn't spot this earlier. Dermot

dermotbradley · 2021-03-13T03:06:31Z

@timothydlister

I've figured out the problem with the Alpine Edge package for s6-overlay and raised a MR for a new package release to resolve it in Edge, https://gitlab.alpinelinux.org/alpine/aports/-/merge_requests/19251. I'm not part of the core Alpine and so can't do the merge myself - hopefully it will be merged in the next few hours and then the revised package will be rolled out to the repository mirrors, however it might take a day or two with it being the weekend.

In the meantime you could modify your Dockerfile for Alpine Edge to do the chmod and mkdir commands after the "apk add" for s6-overlay as a workaround.

I haven't looked at the older package for Alpine 3.13 yet but its probably the same issue.

I've raised #334 regarding the s6-overlay Source Code tarfile i'm using for the packaging.

cnt0 · 2021-03-18T10:13:44Z

looks like I can reproduce this issue with s6-overlay package from alpine:3.13.

FROM alpine:3.13
RUN apk add --no-cache s6-overlay
ENTRYPOINT ["/init"]

just hangs. @dermotbradley can you please fix this as well?

dermotbradley · 2021-03-19T01:17:22Z

looks like I can reproduce this issue with s6-overlay package from alpine:3.13.
FROM alpine:3.13
RUN apk add --no-cache s6-overlay
ENTRYPOINT ["/init"]
just hangs. @dermotbradley can you please fix this as well?

Hi. The issue I fixed in Alpine Edge was a packaging mistake which caused the "export: fatal: unable to exec /etc/s6/init/init-stage1: Permission denied" error that @timothydlister saw. This packaging issue was not present in s6-overlay for Alpine 3.13 (I only introduced the, now corrected, mistake in Edge).

As the original problem report for this ticket was observed on Debian then I don't believe the underlying issue is Alpine-specific.

andrewzah · 2021-03-19T13:54:38Z

This happens on debian, alpine, and centos for me. I build it from source, so I don't think it's a packaging issue.

dermotbradley · 2021-03-20T22:15:39Z

This happens on debian, alpine, and centos for me. I build it from source, so I don't think it's a packaging issue.

I found some time to look at the underlying issue and its not a packaging issue.

Using the reproduction repo of @b-m-f which is Ubuntu based I saw the same error. However the fix is simple - the "fix-mounted" file in that repo simply needs a newline added and it works! I also created an Alpine 3.13-based version of this "reproducer" and it failed in the same way until I added a newline to that file and then it also worked.

mustanggb · 2021-03-24T19:12:17Z

Think I just encountered this as well in docker with alpine 3.13 and s6-overlay 1.22.1.0

Dockerfile

FROM alpine:3.13

ADD https://github.com/just-containers/s6-overlay/releases/download/v1.22.1.0/s6-overlay-nobin.tar.gz /tmp/
RUN apk add --no-cache s6 s6-portable-utils && \
    tar -xzC / -f /tmp/s6-overlay-nobin.tar.gz && \
    rm /tmp/s6-overlay-nobin.tar.gz

ENTRYPOINT /init

Gets stuck on...

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...

Switching to alpine 3.12 and it works fine again.

EDIT:

Okay so it looks like this could be expected due to compatibility with dependencies, possibly execline.
So alpine 3.12 has execline 2.6.0.2, whereas alpine 3.13 has execline 2.7.0.0 it and looks like this doesn't work with either s6-overlay 1.22.1.0 (as I tried originally) or 2.1.0.0 (as packaged by @dermotbradley), but manually installing 2.2.0.3 and it does appear to work again (still testing).

@dermotbradley Maybe consider updating your s6-overlay package in 3.13 to 2.2.x.x

dermotbradley · 2021-03-25T02:20:23Z

@mustanggb

ADD https://github.com/just-containers/s6-overlay/releases/download/v1.22.1.0/s6-overlay-nobin.tar.gz /tmp/

You used this repo's "nobin" tarfile which only contains the s6-overlay specific files. If using this file fails but then using the same version of the "amd64" tarfile (obviously not then using "apk add" for the s6/s6-portable-utils packages) from this repo does work then that points to a version compatibility issue with the OS' (in this case Alpine's) versions of s6/execline/etc packages.

@dermotbradley Maybe consider updating your s6-overlay package in 3.13 to 2.2.x.x

I have replied to the Alpine gitlab issue you raised about this issue. I don't want to fill up this repo's issue with Alpine-specific discussions so we can talk further about it in that Gitlab issue.

Fundamentally when execline 2.7.0.0 came it out it changed some behaviour that then had to be fixed in s6-overlay (#317, #319), then when execline 2.8.0.0 came out it also changed some behaviour that required other s6-overlay changes (#335).

In general there is always likely to be some sort of time delay from whenever newer versions of s6 utilities are released and then when s6-overlay is updated to handle any changes (if needed).

cnt0 · 2021-03-25T04:00:58Z

Fundamentally when execline 2.7.0.0 came it out it changed some behaviour that then had to be fixed in s6-overlay

ah yes. Looks like this comment describes the exact problem I faced. This is the commit which fixes that. Guys, can you please reference such important issues in commit messages? It would've been so much easier to get the full picture in this case,,,

pvizeli · 2021-03-26T11:14:03Z

I have the same issue on 2.2.x.x like:
https://github.com/b-m-f/s6-overlay-bug-reproduction

I use alpine/debian/ubuntu with the tarfile from this repository:
https://github.com/home-assistant/docker-base

jprjr · 2021-03-26T12:00:44Z

Hi all, I think there's a lot of comments in this issue that may be specific to alpine's package of s6-overlay. I think @b-m-f provided an example that narrows the issue down. I'm pretty sure the core issue is how execline-2.7.0.0 changed handling non-existant and empty files on the forstdin program, and fix-attrs needs to be updated to handle that. Please give me some time and I'll address it when I can.

…

On March 26, 2021 7:14:21 AM EDT, Pascal Vizeli ***@***.***> wrote: I have the same issue on 2.2.x.x like: https://github.com/b-m-f/s6-overlay-bug-reproduction I use alpine/debian/ubuntu with the tarfile from this repository: https://github.com/home-assistant/docker-base -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #329 (comment)

-- Sent from my Android device with K-9 Mail. Please excuse my brevity.

jprjr · 2021-03-26T13:18:39Z

Here's some notes

fix-attrs has two places that uses forstdin.

There's a chunk that tests if a file is a directory, calls s6-ls, then loops over the contents of that -

s6-overlay/builder/overlay-rootfs/usr/bin/fix-attrs

Line 17 in 51467be

forbacktickx -0 subfile

forbacktickx is really just pipeline { stuff } forstdin

If something is an empty directory, s6-ls returns no output.

Before execline 2.7.0.0, forstdin would accept empty input and just not run the loop. Now, the input is empty, it exits 1.

The other place is

s6-overlay/builder/overlay-rootfs/usr/bin/fix-attrs

Line 32 in 51467be

forstdin -d"\n" -- line

- this is where it reads the contents of a file from the fix-attrs.d.

Previously, if a file did not end in a newline character (like in the repo @b-m-f created), forstdin would still return the line. Now, if the file does not end in a newline character, forstdin exits 1.

jprjr · 2021-04-10T17:24:25Z

I've been reviewing this, and I think the only real fix is to rewrite fix-attrs from scratch. That difference in behavior with the latest execline makes updating fix-attrs particularly difficult.

In most other cases, I was able to replace forstdin with elglob and loop over that. But fix-attrs has the feature of traversing hidden files, so elglob just won't really work. I don't know if I can write a glob pattern that will match regular files and hidden files, while also excluding the . and .. entries. s6-ls can do it, but then we're back at the original problem of empty directories - s6-ls will return empty output, so forstdin returns 1.

I think the better solution is to just write a custom program in C and include it as a static binary.

Upstream development appears to have stopped several months ago. Recent s6-overlay versions do not work correctly with recent execline versions (which are separately packaged for Alpine by skarnet). For more information see just-containers/s6-overlay#329 Closes #12547. If/when upstream resolves compatibility with general s6/execline packages then I will restart maintaining this package. For now the only solution for end-users is to download and use upstream's arch-specific binary tarfiles at https://github.com/just-containers/s6-overlay/releases which contain versions of s6/execline binaries that upstream has tested with s6-overlay.

Replaces forstdin with custom fork that allows for emtpy files and lines missing the newline. See #329

jprjr · 2021-11-23T22:49:45Z

Hi all, I believe I've come up with a fix for this and could use help testing.

I've made a fork of forstdin that re-enables some of the old behavior (reading in 0 bytes of input is fine, missing a final newline is also fine), and made a branch of s6-overlay that uses the fork.

Here is a n example Dockerfile for installing the from the latest build off the issue-329 branch:

FROM ubuntu
RUN apt-get update && apt-get install -y unzip curl

RUN curl -R -L -o /tmp/dist.zip \
  https://nightly.link/just-containers/s6-overlay/workflows/all/issue-329/dist.zip

RUN cd /tmp && unzip dist.zip && chmod +x s6-overlay-amd64-installer && /tmp/s6-overlay-amd64-installer /
ENTRYPOINT ["/init"]

If anybody out there can try this out and see if it fixes their issue, that would be a huge help!

ByJacob · 2021-12-11T16:13:50Z

Works for me. Use newest php:apache for base.

v2.2.0.3

app_1  | [s6-init] making user provided files available at /var/run/s6/etc...exited 0.
app_1  | [s6-init] ensuring user provided files have correct perms...exited 0.
app_1  | [fix-attrs.d] applying ownership & permissions fixes...
app_1  | [fix-attrs.d] 01-fix-index.php: applying... 
app_1  | [fix-attrs.d] 01-fix-index.php: exited 1.
app_1  | [fix-attrs.d] 02-fix-www-catalog: applying... 
app_1  | [fix-attrs.d] 02-fix-www-catalog: exited 1.
app_1  | [fix-attrs.d] done.
app_1  | [cont-init.d] executing container initialization scripts...
app_1  | [cont-init.d] done.
app_1  | [services.d] starting services
app_1  | [services.d] done.

issue-329 version

app_1  | [s6-init] making user provided files available at /var/run/s6/etc...exited 0.
app_1  | [s6-init] ensuring user provided files have correct perms...exited 0.
app_1  | [fix-attrs.d] applying ownership & permissions fixes...
app_1  | [fix-attrs.d] 01-fix-index.php: applying... 
app_1  | [fix-attrs.d] 01-fix-index.php: exited 0.
app_1  | [fix-attrs.d] 02-fix-www-catalog: applying... 
app_1  | [fix-attrs.d] 02-fix-www-catalog: exited 0.
app_1  | [fix-attrs.d] done.
app_1  | [cont-init.d] executing container initialization scripts...
app_1  | [cont-init.d] done.
app_1  | [services.d] starting services
app_1  | [services.d] done.

file 01-fix-index.php

/var/www/html/index.php true www-data 0600 0700

file 02-fix-www-catalog

/var/www/html true www-data:www-data 0644 0755

But when have bad file (example 01, wrong username) and use variable S6_BEHAVIOUR_IF_STAGE2_FAILS=2 execution continues

app_1  | [s6-init] making user provided files available at /var/run/s6/etc...exited 0.
app_1  | [s6-init] ensuring user provided files have correct perms...exited 0.
app_1  | [fix-attrs.d] applying ownership & permissions fixes...
app_1  | [fix-attrs.d] 01-fix-index.php: applying... 
app_1  | s6-envuidgid: fatal: unknown user: www-data2
app_1  | [fix-attrs.d] 01-fix-index.php: exited 1.
app_1  | [fix-attrs.d] 02-fix-www-catalog: applying... 
app_1  | [fix-attrs.d] 02-fix-www-catalog: exited 0.
app_1  | [fix-attrs.d] done.
app_1  | [cont-init.d] executing container initialization scripts...
app_1  | [cont-init.d] done.
app_1  | [services.d] starting services
app_1  | [services.d] done.

…erlay#329 Signed-off-by: Adam Warner <me@adamwarner.co.uk>

skarnet · 2022-01-20T10:37:11Z

Version 3.0.0.0 of s6-overlay is out, which should hopefully fix all these outstanding issues.
Please note that fix-attrs is deprecated; it's difficult to make work with USER containers, and a much better policy is to set appropriate ownership and permissions from outside the container, at the time when your filesystems are mounted or in your Dockerfile. It is still supported for now, though; I hope the new version of s6-overlay will work for you.
Closing this; please reopen if not fixed.

dermotbradley mentioned this issue Mar 13, 2021

Source tarfile has only some scripts executable and only some dirs in overlay-rootfs #334

Closed

elrido mentioned this issue Aug 8, 2021

edge image fails to build due to s6-overlay being broken PrivateBin/docker-nginx-fpm-alpine#57

Closed

jprjr mentioned this issue Sep 27, 2021

Terminating a Docker container with 1 process takes > 10 sec just-containers/socklog-overlay#8

Open

jprjr added a commit that referenced this issue Nov 23, 2021

Use new justc-forstdin in fix-attrs

d1ae72f

Replaces forstdin with custom fork that allows for emtpy files and lines missing the newline. See #329

jprjr added a commit that referenced this issue Nov 23, 2021

Use new justc-forstdin in fix-attrs

28bd01d

Replaces forstdin with custom fork that allows for emtpy files and lines missing the newline. See #329

jprjr added a commit that referenced this issue Nov 23, 2021

Use new justc-forstdin in fix-attrs

4876dc9

Replaces forstdin with custom fork that allows for emtpy files and lines missing the newline. See #329

PromoFaux added a commit to edgd1er/docker-pi-hole that referenced this issue Jan 17, 2022

while I'm in here - drop S6 overlay version per just-containers/s6-ov…

eed2035

…erlay#329 Signed-off-by: Adam Warner <me@adamwarner.co.uk>

skarnet closed this as completed Jan 20, 2022

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fix-attrs broken in v2.2.0.1 #329

fix-attrs broken in v2.2.0.1 #329

b-m-f commented Feb 14, 2021

b-m-f commented Feb 14, 2021 •

edited

jprjr commented Feb 15, 2021

b-m-f commented Feb 16, 2021 •

edited

rakheshster commented Feb 21, 2021

andrewzah commented Mar 11, 2021

timothydlister commented Mar 12, 2021 •

edited

dermotbradley commented Mar 12, 2021 via email

timothydlister commented Mar 12, 2021

dermotbradley commented Mar 12, 2021 via email

dermotbradley commented Mar 13, 2021

cnt0 commented Mar 18, 2021

dermotbradley commented Mar 19, 2021 •

edited

andrewzah commented Mar 19, 2021

dermotbradley commented Mar 20, 2021

mustanggb commented Mar 24, 2021 •

edited

dermotbradley commented Mar 25, 2021

cnt0 commented Mar 25, 2021 •

edited

pvizeli commented Mar 26, 2021

jprjr commented Mar 26, 2021 via email

jprjr commented Mar 26, 2021

jprjr commented Apr 10, 2021 •

edited

jprjr commented Nov 23, 2021

ByJacob commented Dec 11, 2021 •

edited

skarnet commented Jan 20, 2022

fix-attrs broken in v2.2.0.1 #329

fix-attrs broken in v2.2.0.1 #329

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b-m-f commented Feb 14, 2021

b-m-f commented Feb 14, 2021 • edited

jprjr commented Feb 15, 2021

b-m-f commented Feb 16, 2021 • edited

rakheshster commented Feb 21, 2021

andrewzah commented Mar 11, 2021

timothydlister commented Mar 12, 2021 • edited

dermotbradley commented Mar 12, 2021 via email

timothydlister commented Mar 12, 2021

dermotbradley commented Mar 12, 2021 via email

dermotbradley commented Mar 13, 2021

cnt0 commented Mar 18, 2021

dermotbradley commented Mar 19, 2021 • edited

andrewzah commented Mar 19, 2021

dermotbradley commented Mar 20, 2021

mustanggb commented Mar 24, 2021 • edited

dermotbradley commented Mar 25, 2021

cnt0 commented Mar 25, 2021 • edited

pvizeli commented Mar 26, 2021

jprjr commented Mar 26, 2021 via email

jprjr commented Mar 26, 2021

jprjr commented Apr 10, 2021 • edited

jprjr commented Nov 23, 2021

ByJacob commented Dec 11, 2021 • edited

skarnet commented Jan 20, 2022

b-m-f commented Feb 14, 2021 •

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b-m-f commented Feb 16, 2021 •

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