Dear Qunex Team,
Description:
What I am trying to do is to enter the qunex container interactively (as it helps with testing out certain parameters). In versions of Qunex (prior to 1.0.0) I used to be able to do this with (using Singularity 3.7.1):
Call:
singularity run -e -B /path/to/folder/ /path/to/qunex/
However, with newer versions starting from 1.0.0 I only get “Singularity >” as the output as opposed to the usual Qunex output, and paths cannot be found for any of the qunex commands. I tried building/entering Qunex with newer versions of Singularity (4.2) which did not make a difference. I would appreciate it if you could please let me know what you think the issue might be. I should also mention that if I run commands with qunex_container script then everything seems to be fine. Thanks!
Deniz
Hi Deniz,
Welcome to the QuNex forum!
Yes, we noticed that the behavior of interactive container entrance is slightly different depending on the version of Singularity. For example, on my system, the command call you listed above works fine.
What happens in your case is that you enter the container successfully, however QuNex environment does not get sourced. There are a couple of ways to fix this.
- Try using singularity shell:
singularity shell -e -B /path/to/folder/ /path/to/qunex/
- Bash is the default container shell, try specifying that explicitly
singularity run -e -B /path/to/folder/ /path/to/qunex/ bash # or /bin/bash
- Source the environment manually once inside the container
singularity run -e -B /path/to/folder/ /path/to/qunex/
# when inside, run
source /opt/qunex/env/qunex_environment.sh
Best, Jure
Dear Jure,
Thanks a lot for your quick reply. Though “singularity shell/run” did not work, manually sourcing the environment seems to have solved the problem. Thanks again!
Best,
Deniz
Hi,
Glad it helped. Yes, this is the “bulletproof” option, but it unfortunately requires an additional command to be executed.
Best, Jure