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apptainer: use shell instead of bash #129

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Mar 26, 2024
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apptainer: use shell instead of bash #129

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8 changes: 4 additions & 4 deletions bih-cluster/docs/how-to/software/apptainer.md
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Expand Up @@ -39,7 +39,7 @@ The following guide gives a quick dive into using docker images with apptainer.
Run a bash in a docker image:

```bash
host:~$ apptainer bash docker://godlovedc/lolcow
host:~$ apptainer shell docker://godlovedc/lolcow
```

Run a command in a docker image:
Expand All @@ -51,7 +51,7 @@ host:~$ apptainer exec docker://godlovedc/lolcow echo "hello, hello!"
Run a bash in a docker image, enable access to the cuda driver (--nv) and mount a path (--bind or -B):

```bash
host:~$ apptainer bash --nv --bind /path_on_host/:/path_inside_container/ docker://godlovedc/lolcow
host:~$ apptainer shell --nv --bind /path_on_host/:/path_inside_container/ docker://godlovedc/lolcow
```

## Some Caveats and Notes
Expand All @@ -65,7 +65,7 @@ host:~$ apptainer bash --nv --bind /path_on_host/:/path_inside_container/ docker

- Environment variables can be provided by setting them in the bash and adding the prefix `APPTAINERENV_`:
```bash
host:~$ APPTAINERENV_HELLO=123 apptainer bash docker://godlovedc/lolcow echo $HELLO
host:~$ APPTAINERENV_HELLO=123 apptainer shell docker://godlovedc/lolcow echo $HELLO
```
- Calling `apptainer shell` or `apptainer exec` uses as cwd the host callers cwd not the one set in the Dockerfile.
One can change this by setting `--pwd`.
Expand All @@ -84,7 +84,7 @@ host:~$ apptainer run docker://godlovedc/lolcow
or to open a shell inside the image

```bash
host:~$ apptainer bash docker://godlovedc/lolcow
host:~$ apptainer shell docker://godlovedc/lolcow
```

Furthermore, similar to docker, one can pull (and convert) remote image with the following call:
Expand Down