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Bug #18867

closed

Must upgrade Docker to support containers with libc 2.33

Added by Peter Amstutz 11 months ago. Updated 10 months ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
Docker
Target version:
Start date:
03/16/2022
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-
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:

  1. Container has glibc 2.33
  2. When checking if a file or directory is executable, the new glibc uses a different system call than it used to
  3. This system call is not on the list of permitted system calls inside Docker containers, so it gets a "operation not permitted" error
  4. Because it returns an error, it thinks the directory doesn't exist (although it does)
  5. 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 open1 closed)

Task #18876: Review 18867-compute-image-new-minimum-docker-versionResolvedPeter Amstutz03/16/2022

Actions
Actions #1

Updated by Peter Amstutz 11 months ago

  • Status changed from New to In Progress
Actions #2

Updated by Peter Amstutz 11 months ago

  • Description updated (diff)
Actions #3

Updated by Peter Amstutz 11 months 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 #4

Updated by Peter Amstutz 11 months ago

  • Assigned To set to Ward Vandewege
Actions #5

Updated by Peter Amstutz 11 months ago

  • Target version changed from 2022-03-16 sprint to 2022-03-30 Sprint
Actions #6

Updated by Ward Vandewege 11 months 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 #7

Updated by Peter Amstutz 11 months 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 #8

Updated by Ward Vandewege 11 months 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 #9

Updated by Ward Vandewege 11 months ago

  • Status changed from In Progress to Resolved
Actions #10

Updated by Peter Amstutz 10 months ago

  • Release set to 46
Actions

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