Message boards :
ATLAS application :
native_mt app on Ubuntu 18.08
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Send message Joined: 8 May 17 Posts: 13 Credit: 38,288,392 RAC: 35,049 |
Anyone got native ATLAS app to run on Ubuntu 18.04 LTS ? I have a Ryzen machine running this OS and am trying to get it to crunch. cvmfs is installed and singularity 2.5.2 as well. Still tasks fail after about 10 minutes... Looking at the logs, it fails at this step: check singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img hostname Yet manually running that command it seems fine: boinc@boinc-ab350m:/var/lib/boinc/slots$ singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img host Any idea? Host link: https://lhcathome.cern.ch/lhcathome/show_host_detail.php?hostid=10510464 Example of failed task: https://lhcathome.cern.ch/lhcathome/result.php?resultid=205978265 |
Send message Joined: 13 Apr 18 Posts: 443 Credit: 8,438,885 RAC: 0 |
There were problems but that didn't start until version 3. Versions 2.6.0 and 2.5.1 are working fine for me. Your version 2.5.2 should be OK and in fact it runs when typed at the command line. I was going to say it might be an execute permission problem but then noticed the command prompt suggests you're maybe logged in as the boinc user. |
Send message Joined: 15 Jun 08 Posts: 2410 Credit: 225,984,010 RAC: 125,712 |
You may try a "cvmfs_config wipecache" and a "cvmfs_config probe". If the last command prints errors, post them here. Beside that you are running a 12-core setup which will try to allocate roughly 24 GB of RAM. Not a good idea on a 16 GB computer. You may limit the #cores per task via the project's webpage or a local app_config.xml. A 2-core setup should be a good starting point on this computer. |
Send message Joined: 8 May 17 Posts: 13 Credit: 38,288,392 RAC: 35,049 |
I ran both commands; they complete correctly. Good catch with the thread number, I've lowered it to 4 for now. Digging some more into system logs, I've found these errors Aug 28 18:22:12 boinc-ab350m Singularity: action-suid (U=1000,P=19539)> Home directory is not owned by calling user: /home/boinc Aug 28 18:22:12 boinc-ab350m Singularity: action-suid (U=1000,P=19539)> Retval = 255 yet boinc@boinc-ab350m:/var/lib/boinc/slots$ ls -ld /home/boinc/ drwxr-xr-x 8 boinc boinc 23 Aug 28 19:25 /home/boinc/ I've also tried what is listed under http://opensciencegrid.org/docs/worker-node/install-singularity/#validating-singularity and it looks ok boinc@boinc-ab350m:/var/lib/boinc/slots$ singularity exec --contain --ipc --pid \ > --home $PWD:/srv \ > --bind /cvmfs \ > /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo:el6 \ > ps -ef WARNING: Container does not have an exec helper script, calling 'ps' directly UID PID PPID C STIME TTY TIME CMD boinc 1 0 0 17:32 ? 00:00:00 ps -ef |
Send message Joined: 13 Apr 18 Posts: 443 Credit: 8,438,885 RAC: 0 |
Home directory is not owned by calling user: /home/boinc That rings a bell. It looks like maybe you made the same mistake I made a while ago. Did you use gyllic's directions for building BOINC, CVMFS and singularity and later install BOINC from repos without removing the prior BOINC installation? I did and IIRC the above message turned up. After much frustration trying to sort out the permissions and ownerships I gave up and reinstalled the OS. |
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