Message boards : ATLAS application : Native Atlas Guide
Message board moderation

To post messages, you must log in.

AuthorMessage
Ryan Munro

Send message
Joined: 17 Aug 17
Posts: 25
Credit: 1,498,911
RAC: 4,802
Message 47038 - Posted: 22 Jul 2022, 11:36:55 UTC

Does anyone have an up-to-date guide at all? I tried following this one https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=4840 but kept getting errors, when I try and run the tasks they fail with a computational error.
I have CMVFS setup and the Theory tasks are running fine.

Thanks
ID: 47038 · Report as offensive     Reply Quote
computezrmle
Volunteer moderator
Volunteer developer
Volunteer tester
Avatar

Send message
Joined: 15 Jun 08
Posts: 2100
Credit: 162,794,886
RAC: 118,497
Message 47039 - Posted: 22 Jul 2022, 12:28:33 UTC - in response to Message 47038.  

Perhaps it's just a minor issue.
A logfile might be helpful but so far even errors are not yet reported.

Meanwhile you may post the output of:
cvmfs_config probe
cvmfs_config stat


And you may check whether Singularity (-> now called Apptainer) is installed.
ID: 47039 · Report as offensive     Reply Quote
Ryan Munro

Send message
Joined: 17 Aug 17
Posts: 25
Credit: 1,498,911
RAC: 4,802
Message 47040 - Posted: 22 Jul 2022, 13:11:47 UTC - in response to Message 47039.  

I don't think I have Singularity / Apptainer installed, is there a guide to doing so?
ID: 47040 · Report as offensive     Reply Quote
computezrmle
Volunteer moderator
Volunteer developer
Volunteer tester
Avatar

Send message
Joined: 15 Jun 08
Posts: 2100
Credit: 162,794,886
RAC: 118,497
Message 47041 - Posted: 22 Jul 2022, 13:37:26 UTC - in response to Message 47040.  

Your Linux distribution may provide an installation package.
If so, it should be enough to
- install it
- add the user running BOINC to the apptainer group
- log out and login that user (or reboot)


More information can be found here:
https://github.com/apptainer/apptainer
ID: 47041 · Report as offensive     Reply Quote
Ryan Munro

Send message
Joined: 17 Aug 17
Posts: 25
Credit: 1,498,911
RAC: 4,802
Message 47042 - Posted: 22 Jul 2022, 13:58:35 UTC

Found the guide here : https://apptainer.org/docs/admin/main/installation.html

WU is running a lot longer than it did before so I think I am good now, oddly the CPU and memory usage is minimum, is that normal?
ID: 47042 · Report as offensive     Reply Quote
computezrmle
Volunteer moderator
Volunteer developer
Volunteer tester
Avatar

Send message
Joined: 15 Jun 08
Posts: 2100
Credit: 162,794,886
RAC: 118,497
Message 47043 - Posted: 22 Jul 2022, 14:30:08 UTC - in response to Message 47042.  

Check the stderr.txt in the "slots" directory your task is running in.

It should end with something like:
[2022-07-22 10:08:58] Set ATHENA_PROC_NUMBER=2
[2022-07-22 10:08:58] Starting ATLAS job with PandaID=5533113941
[2022-07-22 10:08:58] Running command: /usr/bin/singularity exec --pwd /home/boinc3/BOINC_ATLAS/slots/0 -B /cvmfs,/home /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7 sh start_atlas.sh


After a few minutes (be patient) there should also be a subdirectory like "PanDA_Pilot-5533113941" and lots of other files.
ID: 47043 · Report as offensive     Reply Quote
Ryan Munro

Send message
Joined: 17 Aug 17
Posts: 25
Credit: 1,498,911
RAC: 4,802
Message 47044 - Posted: 22 Jul 2022, 15:20:55 UTC - in response to Message 47043.  

Second one is maxing the CPU now, odd that the first one didnt
ID: 47044 · Report as offensive     Reply Quote
maeax

Send message
Joined: 2 May 07
Posts: 1668
Credit: 97,116,982
RAC: 303,468
Message 47045 - Posted: 22 Jul 2022, 16:14:43 UTC - in response to Message 47044.  

This is over the day possible with some Tasks.
When a Atlas-Task is running over half a day, and no single Core using, something went wrong.
You can delete this Task. Have also up to five Tasks a day.
ID: 47045 · Report as offensive     Reply Quote
David Cameron
Project administrator
Project developer
Project scientist

Send message
Joined: 13 May 14
Posts: 378
Credit: 14,383,714
RAC: 6,327
Message 47060 - Posted: 3 Aug 2022, 9:24:46 UTC

The steps required to run native ATLAS depend heavily on the OS you are using, so it's hard to provide a single guide that works for everyone. But there are instructions available for specific platforms, eg Ubuntu 20.04.

The options for running ATLAS Linux are listed in this post: https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=5630&postid=44620#44620

I see now that all your tasks are successfully completing so feel free to share what you had to do to make it work :)
ID: 47060 · Report as offensive     Reply Quote
Aurum
Avatar

Send message
Joined: 12 Jun 18
Posts: 116
Credit: 39,222,833
RAC: 2,193
Message 47396 - Posted: 21 Oct 2022, 9:34:07 UTC - in response to Message 47038.  
Last modified: 21 Oct 2022, 9:35:10 UTC

Does anyone have an up-to-date guide at all? I tried following this one https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=4840 but kept getting errors, when I try and run the tasks they fail with a computational error.
I have CMVFS setup and the Theory tasks are running fine.
Thanks
After some trial 'n error this is what works for me for native ATLAS & Theory apps running Linux Mint 20.3:
sudo apt install runc
sudo apt install docker.io -y
sudo docker pull cvmfs/service
wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb
sudo dpkg -i cvmfs-release-latest_all.deb
rm -f cvmfs-release-latest_all.deb
sudo apt-get update
sudo apt-get install cvmfs -y
sudo wget https://lhcathome.cern.ch/lhcathome/download/default.local -O /etc/cvmfs/default.local
Open /etc/cvmfs/ as root:
In /etc/cvmfs/default.local add "single":
------------------------------------------------------ start of default.conf ------------------------------------------------
CVMFS_CLIENT_PROFILE=single
------------------------------------------------------ end of default.conf ------------------------------------------------
Edit /etc/cvmfs/default.local to this:
------------------------------------------------------ start of default.local ------------------------------------------------
# Must be set: the repositories required for ATLAS/Theory
# If "CVMFS_DEFAULT_DOMAIN" is set to "cern.ch" like in /etc/cvmfs/default.d/50-cern.conf simple names 
will expand to FQRNs, e.g. atlas -> atlas.cern.ch
CVMFS_REPOSITORIES="atlas,atlas-condb,grid,cernvm-prod,sft,alice"

# Must be set to ensure openhtc.io is used:
CVMFS_USE_CDN=yes

CVMFS_HTTP_PROXY="auto;DIRECT"

# Additional options
CVMFS_KCACHE_TIMEOUT=2
CVMFS_MAX_RETRIES=3
------------------------------------------------------ end of default.local ------------------------------------------------
sudo cvmfs_config setup
sudo cvmfs_config reload  (May not be needed but it doesn't hurt.)
cvmfs_config probe
If the probe fails, try to restart autofs with:
sudo systemctl restart autofs

ID: 47396 · Report as offensive     Reply Quote

Message boards : ATLAS application : Native Atlas Guide


©2022 CERN