Singularity pull fails

Dear Mindboggle Team

When we run:
singularity pull docker://nipy/mindboggle

Centos 7.5
Singularity compiled from source, version: 2.5.1-dist

We get an error:
Exploding layer: sha256:d06d6aefef13bd321bd94db90c1a2a3efb460276ea693ff2eccc467b43029566.tar.gz
WARNING: Warning handling tar header: (null)
ERROR : Error handling tar header: (null)
ABORT : Retval = 255
Cleaning up…
ERROR: pulling container failed!

A colleague has confirmed the same error on a separate cluster running Scientific Linux 6.7

Other Docker-based images pull into singularity fine, and we have previously successfully pulled the Mindboggle image into Singularity: it just appears that it is no longer working. Any advice gratefully received.

Best wishes,


i can reproduce this error on centos 7 with singularity version 2.5.1. however, this works with singularity version 2.4.5-HEAD.gde77554. something must have changed between these two releases that broke this. a docker whiteout file bugfix was introduced in 2.5 so perhaps the issue is related to that.

this seems more like a singularity issue than a mindboggle issue.

by the way, the preferred command to pull singularity is singularity build. so in mindboggle’s case:

$ singularity build mindboggle.sqsh docker://nipy/mindboggle

Coming back to this. I raised an issue with Singularity at:

It appears that the issue is with “__MACOSX” metadata files within the tar file, and how libarchive handles them (or not). Given that I haven’t had an issue with this with any other Docker images being pulled/built in Singularity, and can’t see that this is a wider issue for Singularity users, I’m reluctant to do a special build of Singularity with a particular version of libarchive just to handle this. Would it be possible, for future Mindboggle image builds / pushes to exclude these OS-specific files please?

Just to confirm, this is fixed via:

Thanks to all involved