Message boards :
ATLAS application :
Native Atlas: "Output file missing"
Message board moderation
Author | Message |
---|---|
Send message Joined: 7 May 17 Posts: 16 Credit: 1,456,154 RAC: 0 |
Running Mint 19.1 Somehow I seem to have cvmfs reporting it is running OK. Having had issues with Singularity when trying to use the Debian guide I thought I would try the version in the Mint repository. End result is that with an app_config running 8 * 4t each with 3300MB allocated on 32t 32GB rig, all seems well for 15 Mins or so then computation error and log showing "Output file missing" I am guessing that this is a permissions issue so I am hoping one of you knows a quick fix Meanwhile I found https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=4396&postid=34494 which seems like my next try if you think I should start over. Thoughts anyone? |
Send message Joined: 9 Jan 15 Posts: 151 Credit: 431,596,822 RAC: 0 |
This is not SLC6, need to run with Singularity.... Checking Singularity... Singularity is installed copy /var/lib/boinc-client/slots/5/shared/input.tar.gz copy /var/lib/boinc-client/slots/5/shared/copy_2LbbWw copy /var/lib/boinc-client/slots/5/shared/ATLAS.root_0 copy /var/lib/boinc-client/slots/5/shared/RTE.tar.gz copy /var/lib/boinc-client/slots/5/shared/start_atlas.sh export ATHENA_PROC_NUMBER=2;start atlas job with Testing the function of Singularity... check singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img hostname Singularity isnt working... Looks like Singularity is broken. Did you use version 2.4.2? That guide should work and 2.4.2 been great for my host. |
Send message Joined: 14 Jan 10 Posts: 1268 Credit: 8,421,616 RAC: 2,139 |
...running 8 * 4t each with 3300MB allocated......I think your system is overloaded even when you have 32GB RAM. For ATLAS-native you need 1900MB of RAM for each worker=thread. 8 * 4 * 1900 > 32GB. |
Send message Joined: 7 May 17 Posts: 16 Credit: 1,456,154 RAC: 0 |
still playing with singularity The thread at https://lhcathome.cern.ch/lhcathome/forum_thread.php?id=4875&postid=37372#37372 seems to suggest that native Atlas requires 2100MB + 300MB*nCPUs. Hence the 3300 chosen |
Send message Joined: 15 Jun 08 Posts: 2386 Credit: 222,874,851 RAC: 137,170 |
Sure you did not only install CVMFS but it is also configured correctly? Do you get this output when you run "cvmfs_config probe"? Probing /cvmfs/atlas.cern.ch... OK Probing /cvmfs/atlas-condb.cern.ch... OK Probing /cvmfs/grid.cern.ch... OK Probing /cvmfs/cernvm-prod.cern.ch... OK It's just that it makes no sense to check for a singularity error if CVMFS is not working since singularity needs files from the CVMFS repository. |
Send message Joined: 7 May 17 Posts: 16 Credit: 1,456,154 RAC: 0 |
$ cvmfs_config probe Probing /cvmfs/atlas.cern.ch... OK Probing /cvmfs/atlas-condb.cern.ch... OK Probing /cvmfs/grid.cern.ch... OK ~$ One less than you ? This is after reinstall ...not attached to LHC yet if that matterrs |
Send message Joined: 15 Jun 08 Posts: 2386 Credit: 222,874,851 RAC: 137,170 |
Your's is OK if you only run ATLAS. cernvm-prod is only necessary for Theory native. Accidentally left it in the list. Could you run the suggested test command: singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/images/singularity/x86_64-slc6.img hostname This should print your hostname. If you don't want to post it here, just confirm that it is the command's output. |
Send message Joined: 7 May 17 Posts: 16 Credit: 1,456,154 RAC: 0 |
Hmmm not right now. When following the guide I mentioned in my first post re: Singularity, it all falls apart after that slightly modified download is unzipped into the /home/username folder. I have been looking around for what and where to cd to in order to "./configure --prefix=/usr/local" |
Send message Joined: 22 Mar 17 Posts: 55 Credit: 10,223,976 RAC: 2,477 |
Hmmm not right now. Singularity install: sudo wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list sudo apt-get install -y singularity-container And a singularity --version will return the version if installed correctly. |
Send message Joined: 7 May 17 Posts: 16 Credit: 1,456,154 RAC: 0 |
Now having installed singularity using : sudo wget -O- http://neuro.debian.net/lists/bionic.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list (I am on Mint 19.1 so Bionic on Ubuntu) Version shows fine The answer to your question is yes It is an older version but....... Am currently running another 8 and progress so far even after a couple of re-starts is beyond where I was before having reached 25% in around 45 mins on a pair of E5-2670's BoincTasks is reporting cpu just now @ 237% but it is climbing so maybe when I watch an undisturbed run it will improve |
©2024 CERN