[Gate-users] trying to use docker image with singularity

[Antoine Migeon]

Sorry, I just realized that I was using "run" instead of "exec".


With "run" without args, get an error and return to shell :

$ singularity run gate-8.1.p01.simg

ERROR  : Could not write to 
/soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime: Too 
many levels of symbolic links

==> return to shell


With "exec" the container works with only a startup error:

$ singularity exec gate-8.1.p01.simg Gate


ERROR  : Could not write to 
/soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime: Too 
many levels of symbolic links
[G4]
[G4] **************************************************************
[G4]  Geant4 version Name: geant4-10-04-patch-02 (25-May-2018)
[G4]                        Copyright : Geant4 Collaboration
[G4]                       References : NIM A 506 (2003), 250-303
[G4]                                  : IEEE-TNS 53 (2006), 270-278
[G4]                                  : NIM A 835 (2016), 186-225
[G4]                              WWW : http://geant4.org/
[G4] **************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0]
[Core-0] *************************************************
[Core-0]  GATE version 8.1.p01 (April 2018)
[Core-0]  Copyright : OpenGATE Collaboration
[Core-0]  Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0]  Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0]  Reference : Med. Phys. 41(6)    (2014)
[Core-0]  http://www.opengatecollaboration.org
[Core-0] *************************************************
[Core-0]
[Core-0] You are using Geant4 version 10.4.2
PreInit> exit
Graphics systems deleted.
Visualization Manager deleting...


I will try to test if Gate is working properly.

Antoine

Le 29/11/2018 à 09:04, Antoine Migeon a écrit :
>
> Hello,
>
> I'm trying to run the docker image with singularity. (from 
> https://hub.docker.com/r/opengatecollaboration/gate/ )
>
> First I get lots of warnings about tar header when pulling, maybe a 
> docker bug :
>
>
> # singularity build gate-8.1.p01.simg gate-8.1.p01.def
> ...
> Exploding layer: 
> sha256:dd37e1562ee37ac6950dadfa2c248a9862b2bc9fe4460938796dfd86094b0de1.tar.gz
> ...
> ...
> WARNING: Warning handling tar header: Can't create 
> 'var/lib/yum/yumdb/z/bc54415c0894da0ffcc88e978d9c2ad82a7798fd-zlib-devel-1.2.7-17.el7-x86_64/command_line'
> ...
> Exploding layer: 
> sha256:8eb0dc0cfbb26adc62fc641165771fd5a546f9b6b04f3320e4dee63755f92fb2.tar.gz
> ...
> Building Singularity image...
> ...
>
> ==> build OK with warnings
>
>
> When I run image :
>
> # singularity run gate-8.1.p01.simg bash
> ERROR  : Could not write to 
> /soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime: 
> Too many levels of symbolic links
> /usr/bin/bash: /usr/bin/bash: cannot execute binary file
>
>
> Did anyone try to run the docker image with singularity?
>
> Is there a docker recipe file that I could adapt to singularity?
>
>
> Antoine
>
> -- 
> Antoine Migeon
>
> Centre de Calcul et Messageries
> Direction du Numérique
> Université de Bourgogne
>
>
>
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> Gate-users at lists.opengatecollaboration.org
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