Singularity version 3.2.1

[Luca.Capello]

Hi there,

@Pablo.Strasser

I discovered that now singularity is available without module load.
[…]
However this version is not available with module load.

Indeed, the rpmpkg:singularity was there since 2019-03-13, IIRC simply because the module:Singularity/2.4.2 was not compatible with CentOS 7:

1. you offered us to test CentOS 7 with Singularity (cf. WIP: Migrate Baobab to CentOS7 - #2 by Pablo.Strasser )
2. indeed module:Singularity/2.4.5 was added to Baobab only after, on 2019-04-19

Would it be possible to have this singularity version added as module by having the conflicting environment variable removed?

For sure, as a remainder the idea is to have as much software as possible via module , and not rpmpkg .

Secondly, a dependency of singularity 3.2.1 is missing

[strassp6@login2 ~]$ singularity build pytorch2.simg docker://nvcr.io/nvidia/pytorch:19.07-py3
[…]
INFO: Creating SIF file…
FATAL: While performing build: While searching for mksquashfs: exec: “mksquashfs”: executable file not found in $PATH

A google search show a package called squashfs-tools ( https://centos.pkgs.org/7/centos-x86_64/squashfs-tools-4.3-0.21.gitaae0aff4.el7.x86_64.rpm.html ).

rpmpkg:squashfs-tools is installed since you reported the first issue back on 2019-05-08 (cf. Problem on login node 2 for building singularity images - #2 by Luca.Capello ), the problem is that the mksqausfhs binary is installed in a privileged PATH:

[root@login2 ~]# which mksquashfs 
/usr/sbin/mksquashfs
[root@login2 ~]# 

It is the duty of Singularity (and not the package manager nor the system administrator) to allow using a tool which is privileged. Indeed, the module:Singularity/2.4.5 allows building images as an unprivileged user:

1. your docker://pytorch:latest (cf. Issue with GPU on CentOS7 - #3 by Pablo.Strasser ):

capello@login2:~$ module load GCC/5.4.0-2.26
capello@login2:~$ module laod Singularity/2.4.5
capello@login2:~$ singularity build pytorch_pablostrasser.simg docker://pablostrasser/pytorch:latest
[...]
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
Building Singularity image...
Singularity container built: pytorch_pablostrasser.simg
Cleaning up...
capello@login2:~$ 

2. one from the official Singularity documentation (cf. http://singularity.lbl.gov/docs-build-container#downloading-a-existing-container-from-singularity-hub ):

capello@login2:~$ singularity build lolcow.simg shub://GodloveD/lolcow
Cache folder set to /home/users/c/capello/.singularity/shub
Progress |===================================| 100.0% 
Building from local image: /home/users/c/capello/.singularity/shub/GodloveD-lolcow-master-latest.simg
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
Building Singularity image...
Singularity container built: lolcow.simg
Cleaning up...
capello@login2:~$ 

Please stick to module:Singularity/2.4.5 , I will remove the rpmpkg:singularity soon and start checking how to build a more recent version with module , despite upstream supporting only up to version 2.4.2 (cf. Redirecting... ).

Thx, bye,
Luca