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Aurum
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Message 44810 - Posted: 24 Apr 2021, 20:41:53 UTC

It seems odd that CERN is sending me an image for a different operating system???
[2021-04-24 13:21:36] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname

Why send a CENTOS7 image to a Ubuntu computer???
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Message 44811 - Posted: 25 Apr 2021, 0:35:28 UTC - in response to Message 44810.  
Last modified: 25 Apr 2021, 0:37:00 UTC

Why send a CENTOS7 image to a Ubuntu computer???
Don't know. But here is my most recent Stderr output from a successful native ATLAS if you want to look at it.
https://lhcathome.cern.ch/lhcathome/result.php?resultid=314961081

Note that you have CVMFS working properly, so it must be a singularity problem.
Unfortunately, that covers a lot of ground.

PS - what do you get when you run "singularity --version"?
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Aurum
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Message 44812 - Posted: 25 Apr 2021, 7:04:36 UTC - in response to Message 44811.  

what do you get when you run "singularity --version"?

$ singularity --version
Command 'singularity' not found, but can be installed with:
sudo apt install singularity
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computezrmle
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Message 44813 - Posted: 25 Apr 2021, 8:22:08 UTC - in response to Message 44810.  

It seems odd that CERN is sending me an image for a different operating system???
[2021-04-24 13:21:36] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname

Why send a CENTOS7 image to a Ubuntu computer???

ATLAS scientific apps are developed to run within a well defined Centos environment.
A snapshot of this environment forms the singularity container.

On a (nearly arbitrary) host system running singularity this container can be executed independent from the host's original environment.
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Message 44815 - Posted: 25 Apr 2021, 10:05:28 UTC

I can't get it to install. Fails here:
root@Rig-48:/usr/local/bin/singularity# ./mconfig && \
>     make -C builddir && \
>     make -C builddir install
Configuring for project `singularity' with languages: C, Golang
=> running pre-basechecks project specific checks ...
=> running base system checks ...
 checking: host C compiler... cc
 checking: host C++ compiler... c++
 checking: host Go compiler (at least version 1.13)... not found!
mconfig: could not complete configuration
Even though
aurum@Rig-48:~$ go version
go version go1.16.3 linux/amd64
I don't have the foggiest idea what to try now. Any suggestions??? TIA
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Message 44816 - Posted: 25 Apr 2021, 10:53:47 UTC

Tried running an ATLAS WU but it failed at about 1%:
[2021-04-25 03:37:21] Using singularity image /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img
[2021-04-25 03:37:21] Checking for singularity binary...
[2021-04-25 03:37:21] Singularity is not installed, using version from CVMFS
[2021-04-25 03:37:21] Checking singularity works with /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img hostname
[2021-04-25 03:37:24] INFO: Converting SIF file to temporary sandbox... Rig-48 INFO: Cleaning up image...
[2021-04-25 03:37:24] Singularity works
[2021-04-25 03:37:24] Starting ATLAS job with PandaID=5037675747
[2021-04-25 03:37:24] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/2 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img sh start_atlas.sh
[2021-04-25 03:37:26] Job failed
[2021-04-25 03:37:26] INFO:    Converting SIF file to temporary sandbox...
[2021-04-25 03:37:26] INFO:    Cleaning up image...
[2021-04-25 03:37:26] FATAL:   container creation failed: hook function for tag prelayer returns error: failed to create /var/lib/alternatives directory: mkdir /var/lib/alternatives: read-only file system
[2021-04-25 03:37:26] ./runtime_log.err
[2021-04-25 03:37:26] ./runtime_log
03:47:26 (4413): run_atlas exited; CPU time 17.180037
03:47:26 (4413): app exit status: 0x1
03:47:26 (4413): called boinc_finish(195)
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Message 44817 - Posted: 25 Apr 2021, 11:01:52 UTC - in response to Message 44815.  

Singularity requires at least go 1.13.
On my OpenSuse systems go 1.16 also didn't work but 1.14 worked fine.
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Message 44818 - Posted: 25 Apr 2021, 15:02:12 UTC - in response to Message 44817.  

On my OpenSuse systems go 1.16 also didn't work but 1.14 worked fine.

That must be it. I have go version 1.15.2, which works fine.

Maybe he can figure out how to uninstall one version and get another.
It is always an adventure with singularity. You learn something each time, whether you want to or not.
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Message 44819 - Posted: 25 Apr 2021, 21:05:12 UTC - in response to Message 44818.  
Last modified: 25 Apr 2021, 21:09:49 UTC

I have go version 1.15.2, which works fine.
You read mind, I was wondering which Go version you used. I've tried Go 1.16.3, 1.14.15 and 1.14.1. None of them worked.
I also downgraded Singularity from 3.7.3 to 3.6.4 that you used. Still fails.
And all this time wasted just because a muon did a dance.

The release notes indicate that Singularity has been upgraded to fix security issues. It's a shame that CERN is so far behind.

Maybe he can figure out how to uninstall one version and get another.
"If you anticipate needing to remove Singularity, it might be easier to install it in a custom directory using the --prefix option to mconfig. In that case Singularity can be uninstalled simply by deleting the parent directory."
https://sylabs.io/guides/3.7/admin-guide/installation.html#remove-an-old-version
I just deleted my Singularity folder although in rereading the Sylabs instructions that may not have been sufficient.
My notes show last year's installation used the --prefix option:
sudo mkdir /usr/local/bin/singularity ; /
cd /usr/local/bin/singularity ; /
sudo wget https://github.com/hpcng/singularity/releases/tag/v3.7.3/singularity-3.7.3.tar.gz ; /
tar xvf singularity-3.7.3.tar.gz ; /
sudo apt install libarchive-dev ; /
./configure --prefix=/usr/local ; /
make ; /
sudo make install
This year's instructions say:
cd /usr/local/bin
export VERSION=3.6.4 && # adjust this as necessary \
    sudo wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
    sudo tar -xzf singularity-${VERSION}.tar.gz
cd /usr/local/bin/singularity
sudo -s 
./mconfig && \
    make -C builddir && \
    make -C builddir install
I added cd /usr/local/bin so it wasn't installed in my Home directory as the CERN instructions specify.
I would be willing to try a fresh install on a new-build computer that has never been tainted by an LHC@home attachment. But the ambiguity and contradictions have overwhelmed me.
https://lhcathome.cern.ch/lhcathome/result.php?resultid=315423475
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Message 44820 - Posted: 26 Apr 2021, 2:02:52 UTC - in response to Message 44819.  
Last modified: 26 Apr 2021, 2:04:58 UTC

I would be willing to try a fresh install on a new-build computer that has never been tainted by an LHC@home attachment. But the ambiguity and contradictions have overwhelmed me.

You are very brave to have made it this far. Most people haven't.
But if I ever need to install it on another machine, I may get stuck too.
It is not a great inducement for new users.
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Message 44821 - Posted: 26 Apr 2021, 2:36:00 UTC - in response to Message 44820.  

Greetings All

Just thought I would advise that am running Linux Mint 20.1, and completed 3 Native Atlas workunits (2 x with a HITS file - Valid but also 1 of my workunits lost the net connection and failed on HITS)

This machine is also running

Go version - go1.16.2

Singularity version - 3.7.2+10

Followed the instructions as per the following forum post, especially the section on Build and install singularity:

https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=4840

Also found some hints on the homepages if I came across a hiccup
CernVM https://cvmfs.readthedocs.io/en/stable/cpt-quickstart.html
GO https://golang.org/doc/install

Regards
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