issues running larsoft in lxplus

[nilaybostan]

Here: https://dune.github.io/computing-basics-larsoft/04-intro-art-larsoft/index.html#running-at-cern, some typos should be corrected:

1. The Apptainer command should be changed to:
   /cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --shell=/bin/bash
   -B /cvmfs,/afs,/opt,/run/user,/etc/hostname,/etc/krb5.conf --ipc --pid
   /cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest

(there's no space in front of the -B in the link version, it creates a problem)

2. In addition, for users who rely on a text editor, the “make a fcl file” section might cause problems, since a text editor cannot be opened inside the Apptainer. Maybe the “make a fcl file” part could be placed before the CERN apptainer variant section.

3. export DUNELAR_VERSION=v10_00_04 should be updated with export DUNELAR_VERSION=v10_07_00d00

4. In the link, the first command for running larsoft says to use: lar -n 1 -c tmpgen.fcl -o gen.root So, I think the first line just after CERN Apptainer variant, Make a fcl file, should be changed to Make a fcl file, named tmpgen.fcl.

5. After 'A VNC session will be much faster...', a tutorial on how to use VNC on dunegpvm could be added.

BONUS: (note that: Also here, https://dune.github.io/computing-basics/sl7_setup#cern, CERN Apptainer command should be changed with this: /cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --shell=/bin/bash
-B /cvmfs,/afs,/opt,/run/user,/etc/hostname,/etc/krb5.conf --ipc --pid
/cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest)

The form in the link gives the issue.

Thank you for your consideration,
Nilay

[hschellman]

I was able to get emacs to work in the container (at least the final one)

[hschellman]

But I believe I have fixed the rest of the problems - and added a method for making tmpgen.fcl without an editor.

We are actively avoiding telling people how to use VNC's as they keep leaving processes open which slowly kills the vms. We're working on a solution with the system people.

[nilaybostan]

Hi Heidi — thank you. Everything seems fine now, except for the Apptainer command in the larsoft tutorial. It still gives me an issue,

but the one here is correct: https://dune.github.io/computing-basics/sl7_setup#cern-apptainer

I think the Apptainer command in this page: https://dune.github.io/computing-basics-larsoft/04-intro-art-larsoft/index.html#running-at-cern should be updated to match the one in https://dune.github.io/computing-basics/sl7_setup#cern-apptainer

In larsoft one gives me the following:

[nbostan@lxplus9106 ~]$ /cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --she
ll=/bin/bash
-B /cvmfs,/afs,/opt,/run/user,/etc/hostname,/etc/krb5.conf --ipc --pid
/cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest
Error for command "shell": unknown flag: --she

but this one: https://dune.github.io/computing-basics-larsoft/04-intro-art-larsoft/index.html#running-at-cern gives me the fine:

[nbostan@lxplus9106 ~]$ /cvmfs/oasis.opensciencegrid.org/mis/apptainer/current/bin/apptainer shell --shell=/bin/bash -B /cvmfs,/afs,/opt,/run/user,/etc/hostname --ipc --pid /cvmfs/singularity.opensciencegrid.org/fermilab/fnal-dev-sl7:latest
Apptainer>

Could you please correct this again? After this, everything will be ok.

Thank you.