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Bug #18867

closed

Must upgrade Docker to support containers with libc 2.33

Added by Peter Amstutz about 2 years ago. Updated about 2 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Ward Vandewege
Category:
Docker
Target version:
2022-03-30 Sprint
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:

  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 open — 1 closed)

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