Message boards : ATLAS application : Guide for building everything from sources to run native ATLAS on Debian 9 (Stretch)
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bronco

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Message 36283 - Posted: 6 Aug 2018, 16:51:20 UTC - in response to Message 36277.  

Yes, it works. Thanks :)
$ singularity --version
2.6.0-HEAD.579c4150
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gyllic

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Message 36456 - Posted: 16 Aug 2018, 9:29:46 UTC - in response to Message 36277.  

If you confirm this works we can ask gyllic to update his instructions.
Is there a way to edit a few months old post? Othwise i will make a new post called "... Version 2".

I have built the singularity binaries from the current github master branch (which is the development branch) and tried to run the native ATLAS task with it. Unfortunately it did not work, here is the link: https://lhcathome.cern.ch/lhcathome/result.php?resultid=205038477. It says that singularity is not working.

First, the output of
singularity --version
is
singularity version 3.0.0-master.c033e898


To test if singularity is working I tried to execute the same command as the ATLAS_run_atlas_2.54 script, i.e.:
singularity exec -B /cvmfs %s hostname"%sin_image
which is "translated":
singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img hostname

The output is:
FATAL   [U=1000,P=20383]   SContainer()                  exec /.singularity.d/actions/exec failed: no such file or directory

To test if my singulariy setup is working i have build a new image with the command:
singularity build hello.img shub://vsoch/singularity-hello-world:latest

and tested it with:
singularity exec hello.img cat /etc/lsb-release

which returns:
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.3 LTS"

while I am on a debian machine. This indicates, at least in my opinion, that the singularity setup is working.

But I am still not sure why the ATLAS tasks are not working. Is there a problem with my singularity setup, is the singularity image used for ATLAS only compatible with singularity version < 3.x, is it a code problem within singularity, or something completely different?
Maybe a more advanced user with more knowledge can give an answer?
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David Cameron
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Message 36480 - Posted: 17 Aug 2018, 13:28:13 UTC - in response to Message 36456.  

Since singularity 3 is a complete rewrite it could be that the command line options have changed. In addition it's still under active development so probably not guaranteed that the latest master will work.

So for now I would recommend that people only use version 2.x. Once version 3 is more stable we can look into whether any changes are necessary on our side.
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gyllic

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Message 36703 - Posted: 13 Sep 2018, 22:14:29 UTC - in response to Message 36480.  
Last modified: 13 Sep 2018, 22:27:43 UTC

Since singularity 3 is a complete rewrite it could be that the command line options have changed. In addition it's still under active development so probably not guaranteed that the latest master will work.

So for now I would recommend that people only use version 2.x. Once version 3 is more stable we can look into whether any changes are necessary on our side.
Today I tested the latest github master branch version of singularity (with some of the current pull requests added manually) and now the native ATLAS tasks are running without any problem (tested on the dev-project site) with singularity 3.0.0 (alpha). See here: https://lhcathomedev.cern.ch/lhcathome-dev/result.php?resultid=2394056
So probably there won't be any changes needed in the ATLAS setup (at least to the current dev-project version) in order to run the native app with singularity 3.

Once singularity 3.0 is in beta, I will post an updated version of this guide in order to consider the changes since the original post.
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Message boards : ATLAS application : Guide for building everything from sources to run native ATLAS on Debian 9 (Stretch)


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