Hi Simon, Thank you, that's worked like a charm. Regards, Roden ________________________________ From: gridpp-dirac-users-bounces@imperial.ac.uk <gridpp-dirac-users-bounces@imperial.ac.uk> on behalf of Simon Fayer <simon.fayer05@imperial.ac.uk> Sent: 02 August 2022 14:30 To: gridpp-dirac-users <gridpp-dirac-users@imperial.ac.uk> Subject: Re: [Gridpp-Dirac-Users] Singularity issues after the upgrade [was: The DIRAC upgrade has finished] Hi Roden, Your files are being included correctly in the sandbox (you can verify this by downloading an input sandbox via the web UI, or dirac-wms-job-get-input command). The error is generated from when you start your singularity container inside the job. The new version of DIRAC includes its own version of singularity which is given precedence over any locally available versions (this is a side-effect of the DIRAC environment change). The new singularity behaviour is that on start-up it changes the current directory (CWD) to $HOME, but your scripts are almost always in some kind of site/job-specific scratch directory. E.g.: Your script might be in /scratch/jobid/myscript.sh, but if you run "singularity <args> ./myscript.sh", it'll try to run it from /home/batchuser/myscript.sh instead: Hence the no such file or directory error. Can you please try adding this flag to your singularity options? -H "$(pwd):/home" This will set the home directory for the container to be simply "/home" inside the container, the CWD will be set to /home and this will contain the current scratch directory from outside the container. This should then work exactly as it used to, please let us know if it doesn't or you find any other issues. For debugging jobs, you can run them on your local node with the UI sourced: This gives an almost identical environment to running on the grid now (which is one of the advantages of the new environment set-up). Regards, Simon On Tue, Aug 02, 2022 at 12:21:05PM +0000, Derveni, Roden wrote:
Hi Daniela,
I've noticed I'm unable to direct my jobs to files in my sandbox after the update. A test job that I ran before the UI update now fails, as it's unable to find the file in my sandbox - although it is uploaded.
When directing it, I originally used (which worked) "foo bar ./file_in_sandbox.sh args"
Which produces an error log with: FATAL: stat /home/pltcom01/file_in_sandbox.sh: no such file or directory
As a test, uploading this file to cvmfs and directing it to the cvmfs version instead works successfully.
Is it possible that the environment leakage is causing this problem? Or is there a change to the UI to use the sandbox?
Many thanks, Roden
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