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<p>Sorry, I just realized that I was using "run" instead of "exec".</p>
<p><br>
</p>
<p>With "run" without args, get an error and return to shell :</p>
<p><tt>$ singularity run
gate-8.1.p01.simg
</tt></p>
<p><tt>ERROR : Could not write to
/soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime:
Too many levels of symbolic links</tt><tt><br>
</tt><br>
==> return to shell<br>
</p>
<p><br>
</p>
<p>With "exec" the container works with only a startup error:</p>
<p><tt>$ singularity exec gate-8.1.p01.simg Gate</tt></p>
<p><tt> </tt><tt><br>
</tt><tt>ERROR : Could not write to
/soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime:
Too many levels of symbolic links</tt><tt><br>
</tt><tt>[G4] </tt><tt><br>
</tt><tt>[G4]
**************************************************************</tt><tt><br>
</tt><tt>[G4] Geant4 version Name: geant4-10-04-patch-02
(25-May-2018)</tt><tt><br>
</tt><tt>[G4] Copyright : Geant4
Collaboration</tt><tt><br>
</tt><tt>[G4] References : NIM A 506 (2003),
250-303</tt><tt><br>
</tt><tt>[G4] : IEEE-TNS 53
(2006), 270-278</tt><tt><br>
</tt><tt>[G4] : NIM A 835 (2016),
186-225</tt><tt><br>
</tt><tt>[G4] WWW :
<a class="moz-txt-link-freetext" href="http://geant4.org/">http://geant4.org/</a></tt><tt><br>
</tt><tt>[G4]
**************************************************************</tt><tt><br>
</tt><tt>[G4] </tt><tt><br>
</tt><tt>[Core-0] Initialization of geometry</tt><tt><br>
</tt><tt>[Core-0] Initialization of physics</tt><tt><br>
</tt><tt>[Core-0] Initialization of actors</tt><tt><br>
</tt><tt>[Core-0] </tt><tt><br>
</tt><tt>[Core-0]
*************************************************</tt><tt><br>
</tt><tt>[Core-0] GATE version 8.1.p01 (April 2018)</tt><tt><br>
</tt><tt>[Core-0] Copyright : OpenGATE Collaboration</tt><tt><br>
</tt><tt>[Core-0] Reference : Phys. Med. Biol. 49 (2004)
4543-4561</tt><tt><br>
</tt><tt>[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901</tt><tt><br>
</tt><tt>[Core-0] Reference : Med. Phys. 41(6) (2014)</tt><tt><br>
</tt><tt>[Core-0] <a class="moz-txt-link-freetext" href="http://www.opengatecollaboration.org">http://www.opengatecollaboration.org</a> </tt><tt><br>
</tt><tt>[Core-0]
*************************************************</tt><tt><br>
</tt><tt>[Core-0] </tt><tt><br>
</tt><tt>[Core-0] You are using Geant4 version 10.4.2</tt><tt><br>
</tt><tt>PreInit> exit</tt><tt><br>
</tt><tt>Graphics systems deleted.</tt><tt><br>
</tt><tt>Visualization Manager deleting...</tt><tt><br>
</tt><br>
<br>
I will try to test if Gate is working properly.<br>
</p>
<p>Antoine<br>
</p>
<div class="moz-cite-prefix">Le 29/11/2018 à 09:04, Antoine Migeon a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:15761c1c-0262-c576-bec3-7abd9ee77697@u-bourgogne.fr">
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charset=iso-8859-15">
<p>Hello,</p>
<p>I'm trying to run the docker image with singularity. (from <a
class="moz-txt-link-freetext"
href="https://hub.docker.com/r/opengatecollaboration/gate/"
moz-do-not-send="true">https://hub.docker.com/r/opengatecollaboration/gate/</a>
)<br>
</p>
<p>First I get lots of warnings about tar header when pulling,
maybe a docker bug : <br>
</p>
<tt><br>
# singularity build gate-8.1.p01.simg gate-8.1.p01.def<br>
...</tt><br>
<tt>Exploding layer:
sha256:dd37e1562ee37ac6950dadfa2c248a9862b2bc9fe4460938796dfd86094b0de1.tar.gz<br>
...<br>
... </tt><tt><br>
</tt><tt>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'</tt><tt><br>
</tt><tt>...<br>
Exploding layer:
sha256:8eb0dc0cfbb26adc62fc641165771fd5a546f9b6b04f3320e4dee63755f92fb2.tar.gz<br>
...<br>
Building Singularity image...<br>
...<br>
<br>
==> build OK with warnings<br>
</tt>
<p><br>
</p>
<p>When I run image :</p>
<p># singularity run gate-8.1.p01.simg
bash
<br>
ERROR : Could not write to
/soft/c7/singularity/2.6.0/var/singularity/mnt/final/etc/localtime:
Too many levels of symbolic links<br>
/usr/bin/bash: /usr/bin/bash: cannot execute binary file<br>
<br>
</p>
<p><br>
</p>
<p>Did anyone try to run the docker image with singularity?<br>
<br>
Is there a docker recipe file that I could adapt to singularity?<br>
</p>
<p><br>
</p>
<p>Antoine<br>
</p>
<pre class="moz-signature" cols="72">--
Antoine Migeon
Centre de Calcul et Messageries
Direction du Numérique
Université de Bourgogne
</pre>
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