Execute as_run in container from outside

zweideh

Hello dear community,

I would like to start script-based calculations from outside the Singularity container.

My current workflow looks like this:

./salome_meca-lgpl-2022.1.0-1-20221225-scibian-9 --command bash -c “source /home/vboxuser/coding/profile.sh && as_run --test forma01a”

I get the following response:

vboxuser@UbuntuCodeAster:~/containers$ ./salome_meca-lgpl-2022.1.0-1-20221225-scibian-9 --command bash -c "source /home/vboxuser/coding/profile.sh && as_run --test forma01a"
not exist: /etc/krb5.conf
INFO: Could not find any nv files on this host!
/home/vboxuser/coding/profile.sh: ligne 67: module : commande introuvable
singularity exit code: 127

I seem to be doing something wrong, but I can't figure out what it is.

StanislavPavlica

Hello zweideh,

try:
./salome_meca-lgpl-2022.1.0-1-20221225-scibian-9 -- shell -- as_run --test forma01a
Unfortunately test case in 2022 container end by error - insufficient memory.

In 2024 container it is running OK:
./salome_meca-lgpl-2024.1.0-1-20240327-scibian-11 -- shell -- as_run --test forma01a

Inside a directory where I put a project files (d1.comm d1.med d1.export) it is working:
~/salome_meca-lgpl-2022.1.0-1-20221225-scibian-9 -- shell -- as_run ./d1.export

Stano

zweideh

Hi Stano,

Thanks for your reply! That worked.

My main goal is to start a calculation from a Python script outside the container. I couldn't get it to work with the command above.

Or does it have to be called via the container?
singularity exec ...

zweideh

mf

zweideh

Hello,

you mean like this, put it in a whatever.py?

import subprocess
cmd = "./salome_meca-lgpl-2024.1.0-1-20240327-scibian-11 -- shell -- as_run --test forma01a"
subprocess.run(cmd, shell=True, check=True)

Just one way to launch any shell/bash command from Python,

Mario.

StanislavPavlica

Hello zweideh,

salome_meca-lgpl-2024.1.0-1-20240327-scibian-11 is a python script

If I run:
./salome_meca-lgpl-2024.1.0-1-20240327-scibian-11 -- shell -- as_run --test forma01a

this script prepares environment and at the end call singularity with command:

singularity exec --nv --bind /etc/krb5.conf:/etc/krb5.conf --bind /etc/ssl/certs:/etc/ssl/certs --bind /run/user/1002:/run/user/1002 --bind /tmp:/opt/salome_meca/V2024.1.0_scibian_univ/prerequisites/Cea_archive-9120/BINARIES-DB11/SALOME/USERS --bind /home/stano/.config/aster/salome_meca-lgpl-2024/.mozilla:/home/stano/.mozilla --bind /home/stano/.config/aster/salome_meca-lgpl-2024/.config:/home/stano/.config --bind /home/stano/.config/aster/salome_meca-lgpl-2024/.gnome:/home/stano/.gnome --bind /home/stano/.config/aster/salome_meca-lgpl-2024/.local:/home/stano/.local --bind /tmp:/local00/tmp /home/stano/salome_meca-lgpl-2024.1.0-1-20240327-scibian-11.sif /opt/salome_meca/salome_meca shell -- as_run --test forma01a

My Python knowledge is small, I don't now how to call Python script from another Python script.

Stano