GUI application error under Singularity

[hola]

Hello,

I'm starting to work with Singularity and still don't know all the details, so this may be something obvious, but I couldn't find the answer on my own. I am trying to use the gnuplot container built with this description file:

BootStrap: docker
From: ubuntu:latest

%post
   sed -i '/xenial.*universe/s/^#//g' /etc/apt/sources.list
   apt-get -y update
   apt-get -y install gnuplot xorg flashplugin-installer

I want to use it in both a CentOS 6 and a CentOS 7 host. In CentOS 7 everything goes well. However in CentOS 6 I get:

ERROR  : No valid /bin/sh in container

ABORT  : Retval = 255

And similar messages, with versions 2.6.0, 2.4.6 and 2.2.1 of Singularity. This lack of /bin/sh is something I have seen when creating other containers, not just for this gnuplot. In the CentOS 7 host I used just version 2.6.0 of Singularity and it worked with no problem. Maybe I did something wrong when creating the containers for the older versions of Singularity, 2.4.6 and 2.2.1, but I couldn't find documentation for these versions, only for 2.5 and 2.6. It seems the build command doesn't exist in these older versions, and maybe I'm using "create" wrongly.

Has anybody experienced something similar?

Thank you!

[Jafaruddin Lie]

Hi Hola
Do you have a %runscript section in your recipe?
Check this section: http://singularity.lbl.gov/docs-run#defining-the-runscript

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[hola]

Hi,

Thanks for your answer. I also tried that. Still the problem persists with CentOS 6 hosts. With Singularity 2.2.1 and the create command it builds the image, but when I try to run it, still says:

ERROR  : Container does not have a valid /bin/sh

ABORT  : Retval = 255

But when I try with Singularity 2.4.6 or 2.6.0, the build fails, saying:

User defined %runscript found! Taking priority.
Running post scriptlet
FATAL: kernel too old
ABORT: Aborting with RETVAL=255

I had already seen these kernel too old messages in CentOS 6 hosts.

Thanks!

[Dave Godlove]

Hey there, 

Sorry to hear that you are running into trouble.

Before attempting to answer your question it is my duty to point out that only the latest open source version of Singularity is officially supported.  The versions of Singularity that you are listing above have several high and medium severity security issues and should be removed.  Check these release notes for details.

https://github.com/singularityware/singularity/releases

In older versions of Singularity (prior to 2.4) Singularity had a bootstrap command.  One needed to first create an empty ext3 image file of a particular size and then bootstrap the definition file into the ext3 image.  This 2 step process was combined into the build command which does things a little differently under the hood and yields a squashfs image instead.

Here is some info:

http://singularity.lbl.gov/archive/docs/v2-2/docs-bootstrap

And here is where you can find older docs.

http://singularity.lbl.gov/archive/

Hope that helps!

Dave

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sylabs.io