Bug #18867: Must upgrade Docker to support containers with libc 2.33 - Arvados

Actions

Copy link

Bug #18867

closed

Must upgrade Docker to support containers with libc 2.33

Added by Peter Amstutz almost 3 years ago. Updated almost 3 years ago.

Status:

Resolved

Priority:

Normal

Assigned To:

Ward Vandewege

Category:

Docker

Target version:

2022-03-30 Sprint

Start date:

03/16/2022

Due date:

% Done:

100%

Estimated time:

(Total: 0.00 h)

Story points:

Release:

Arvados 2.4.0

Release relationship:

Auto

Description

The effect is

2022-03-15T15:07:57.132119688Z stderr ERROR: R_HOME ('/usr/lib/R') not found

This appears to be due to the bug reported here:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005906

The gist is:

Container has glibc 2.33
When checking if a file or directory is executable, the new glibc uses a different system call than it used to
This system call is not on the list of permitted system calls inside Docker containers, so it gets a "operation not permitted" error
Because it returns an error, it thinks the directory doesn't exist (although it does)
As a result, R refuses to start, with a very misleading error message

This is reportedly fixed since Docker 20.10

This means we will need to upgrade to Docker 20.10 or later everywhere.

Subtasks 1 (0 open — 1 closed)

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Status changed from New to In Progress

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Description updated (diff)

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Subject changed from Upgrade Docker to support containers with libc 2.33 to Must upgrade Docker to support containers with libc 2.33

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Assigned To set to Ward Vandewege

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Target version changed from 2022-03-16 sprint to 2022-03-30 Sprint

Actions

Copy link

Updated by Ward Vandewege almost 3 years ago

Ready for review at 0059c1f8145f14432c464929c67f0cc2bee89e10 on branch 18867-compute-image-new-minimum-docker-version

I built images for ce8i5 and tordo. I tested the tordo image by running the CWL hasher against it, cf. https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-fzp65jk7mjq2vw6

Actions

Copy link

Updated by Peter Amstutz almost 3 years ago

Ward Vandewege wrote:

Ready for review at 0059c1f8145f14432c464929c67f0cc2bee89e10 on branch 18867-compute-image-new-minimum-docker-version

I built images for ce8i5 and tordo. I tested the tordo image by running the CWL hasher against it, cf. https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-fzp65jk7mjq2vw6

I suggest parameterizing the docker version, something like

dockerversion=5:20.10.13~3-0
$SUDO apt-get ~~yq --no-install-recommends install docker-ce=${dockerversion}~$family~~$distro

The rest LGTM!

Actions

Copy link

Updated by Ward Vandewege almost 3 years ago

Peter Amstutz wrote:

Ward Vandewege wrote:

Ready for review at 0059c1f8145f14432c464929c67f0cc2bee89e10 on branch 18867-compute-image-new-minimum-docker-version

I built images for ce8i5 and tordo. I tested the tordo image by running the CWL hasher against it, cf. https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-fzp65jk7mjq2vw6

I suggest parameterizing the docker version, something like

dockerversion=5:20.10.13~3-0
$SUDO apt-get ~~yq --no-install-recommends install docker-ce=${dockerversion}~$family~~$distro

The rest LGTM!

Thanks, merged with that change.

Actions

Copy link