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

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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:

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)

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Updated by Peter Amstutz 11 months ago

Status changed from New to In Progress

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Updated by Peter Amstutz 11 months ago

Description updated (diff)

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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

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Updated by Peter Amstutz 11 months ago

Assigned To set to Ward Vandewege

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Updated by Peter Amstutz 11 months ago

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

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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

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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!

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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.

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