csc-training · rkronberg · Nov 4, 2024 · Nov 1, 2024 · Nov 1, 2024
diff --git a/part-2/containers/apptainer-tutorial-part2.md b/part-2/containers/apptainer-tutorial-part2.md
@@ -1,184 +1,205 @@
----
-layout: default
-title: Apptainer tutorial 2
-parent: 10. Containers and Apptainer
-grand_parent: Part 2
-nav_order: 3
-has_children: false
-has_toc: false
-permalink: /hands-on/singularity/singularity-tutorial_part2.html
----
-
-# Apptainer tutorial, part 2
-
-## Using files
-
-💬 Apptainer containers have their own internal file system that is separated
-from the host file system.
-
-- The internal file system is always read-only when the container is run with
-  normal user privileges.
-
-💭 In most real use cases you might want to access the host file system to read
-and write files.
-
-- To do this, you must bind a writable directory on the host file system to the
-- internal file system of the container.
-
-💡 This is done using the command line argument `--bind` (or `-B`). The basic
-syntax is `--bind /path/inside/host:/path/inside/container`.
-
-💭 Some remarks:  
-- The bind path does not need to exist inside the container – it is created if
-  necessary.  
-- More than one bind pair can be specified.  
-- The option is available for all run methods described in the previous
-  tutorial.  
-
-1. To run these exercises on Puhti, use `sinteractive` or open a compute node
-   shell in the [Puhti web interface](https://www.puhti.csc.fi):
-
-   ```bash
-   sinteractive --account <project>  # replace <project> with your CSC project, e.g. project_2001234
-   ```
-
-2. Try listing the contents of your project directory (edit the path as needed)
-   from inside the container without `--bind`:
-
-   ```bash
-   export SCRATCH=/scratch/<project>/$USER  # replace <project> with your CSC project, e.g. project_2001234
-   apptainer exec tutorial.sif ls $SCRATCH
-   ```
-
-3. The container cannot see the host directory, so you will get a
-   `No such file or directory` error.
-4. Try binding the host directory `/scratch` to the directory `/scratch` inside
-   the container:
-
-   ```bash
-   apptainer exec --bind $SCRATCH:/scratch tutorial.sif ls /scratch
-   # or
-   apptainer exec --bind /scratch:/scratch tutorial.sif ls $SCRATCH
-   ```
-
-5. This time, the host directory is linked to the container directory and the
-   command shows what the container sees inside `/scratch`.
-
-   💡 You can use `--bind` to set the container, for example, to find input
-   data or configuration files from a certain directory.
-
-6. Bind the host directory specified in `$SCRATCH` to a directory called
-   `/input`:
-
-   ```bash
-   apptainer exec --bind $SCRATCH:/input tutorial.sif ls /input
-   ```
-
-### Using the `apptainer_wrapper` script
-
-1. If you use the wrapper script `apptainer_wrapper`, it will automatically
-   take care of the most common bind use cases.
-2. You just need to set a `$SING_IMAGE` environment variable to point to the
-   correct Apptainer image file:
-
-   ```bash
-   export SING_IMAGE=$PWD/tutorial.sif
-   apptainer_wrapper exec ls $SCRATCH
-   ```
-
-   💡 Note that the image file name is not needed in the `apptainer_wrapper`
-   command since `$SING_IMAGE` is set.
-
-   ‼️ Since some modules set `$SING_IMAGE` when loaded, it is a good idea to
-   start with `module purge` to make sure the correct image is used if you plan
-   to use `apptainer_wrapper`.
-
-## Environment variables
-
-💬 Some software may require environment variables to be set, e.g., to point to
-some reference data or a configuration file.
-
-💬 Most environment variables set on the host are inherited by the container.
-
-☝🏻 Sometimes this may be undesired, in which case the command line option
-`--cleanenv` can be used to prevent the host environment from being inherited
-by the container.
-
-💬 To set an environment variable specifically inside the container, you can
-set an environment variable `$APPTAINERENV_XXX` (where `XXX` is the variable
-name) on the host before invoking the container.
-
-1. Set some test variables:
-
-   ```bash
-   export TEST1="value1"
-   export APPTAINERENV_TEST2="value2"
-   ```
-
-2. Compare the outputs of:
-
-   ```bash
-   env | grep TEST
-   apptainer exec tutorial.sif env | grep TEST
-   apptainer exec --cleanenv tutorial.sif env | grep TEST
-   ```
-
-   - The first command is run on the host and we see `$TEST1` and
-     `$APPTAINERENV_TEST2`.
-   - The second command is run inside the container and we see `$TEST1`
-     (inherited from the host) and `$TEST2` (specifically set inside the
-     container by setting `$APPTAINERENV_TEST2` on the host).
-   - The third command is also run inside the container, but this time we
-     omitted the host environment variables so we only see `$TEST2`.
-
-1. Note that any command-line variables on the host are substituted by their
-   values when passed to the container:
-
-   ```bash
-   apptainer exec tutorial.sif echo $TEST1
-   apptainer exec tutorial.sif echo $TEST2
-   ```
-
-   - The first line prints the value set on the host.
-   - The second line results in an empty output because a variable called
-     `$TEST2` has not been set on host. It was `APPTAINERENV_TEST2="value2"`,
-     remember?
-
-## Exploring containers
-
-💬 Our test container includes the program `hello2`, but it has not been added
-to the `$PATH` variable.
-
-1. One way to find it is to try running `find` inside the container:
-
-   ```bash
-   apptainer exec tutorial.sif find / -type f -name "hello2" 2>/dev/null
-   ```
-
-2. You can now run it by providing the full path:
-
-   ```bash
-   apptainer exec tutorial.sif /found/me/hello2
-   ```
-
-3. Or you could add it to `$PATH` inside the container:
-
-   ```bash
-   export APPTAINERENV_PREPEND_PATH=/found/me
-   apptainer exec tutorial.sif hello2
-   ```
-
-💡 If you can't locate the desired binary with `find`, you can always use
-`apptainer shell` to explore the container.
-
-## More information
-
-💬 This tutorial is meant as a brief introduction to get you started.
-
-☝🏻 When searching online for instructions, pay attention that the instructions
-are for the same version of Apptainer as you are using. There has been some
-command syntax changes etc. between versions, so older instructions may not
-work as is. Also note that Apptainer was formerly known as Singularity.
-
-💡 For more detailed instructions, see the official
-[Apptainer documentation](https://apptainer.org/docs/user/latest/).
+---
+layout: default
+title: Apptainer tutorial 2
+parent: 10. Containers and Apptainer
+grand_parent: Part 2
+nav_order: 3
+has_children: false
+has_toc: false
+permalink: /hands-on/singularity/singularity-tutorial_part2.html
+---
+
+# Apptainer tutorial, part 2
+
+## Using files
+
+💬 Apptainer containers have their own internal file system that is separated
+from the host file system.
+
+- The internal file system is always read-only when the container is run with
+  normal user privileges.
+
+💭 In most real use cases you might want to access the host file system to read
+and write files.
+
+- To do this, you must bind a writable directory on the host file system to the
+- internal file system of the container.
+
+💡 This is done using the command line argument `--bind` (or `-B`). The basic
+syntax is `--bind /path/inside/host:/path/inside/container`.
+
+💭 Some remarks:  
+- The bind path does not need to exist inside the container – it is created if
+  necessary.  
+- More than one bind pair can be specified.  
+- The option is available for all run methods described in the previous
+  tutorial.  
+
+1. To run these exercises on Puhti, use `sinteractive` or open a compute node
+   shell in the [Puhti web interface](https://www.puhti.csc.fi):
+
+   ```bash
+   sinteractive --account <project>  # replace <project> with your CSC project, e.g. project_2001234
+   ```
+
+2. Try listing the contents of your project's `/projappl` directory (edit the path as needed)
+   from inside the container without `--bind`:
+
+   ```bash
+   apptainer exec tutorial.sif ls /projappl/<project> # replace <project> with your CSC project, e.g. project_2001234
+   ```
+
+3. The container cannot see the host directory, so you will get a
+   `No such file or directory` error.
+
+4. Try binding the host directory `/projappl` to the directory `/projappl` inside
+   the container:
+
+   ```bash
+   apptainer exec --bind /projappl:/projappl tutorial.sif ls /projappl/<project> # replace <project> with your CSC project, e.g. project_2001234
+   ```
+
+5. This time, the host directory is linked to the container directory and the
+   command shows what the container sees inside `/projappl`.
+
+   If the path is same in both host and container, you can simplify the
+   command a bit. This does the same as the above command:
+
+   ```bash
+   apptainer exec --bind /projappl tutorial.sif ls /projappl/<project> # replace <project> with your CSC project, e.g. project_2001234 
+   ```
+
+   💡 You can use `--bind` to set the container, for example, to find input
+   data or configuration files from a certain directory.
+
+6. Bind a host directory in `/scratch` to a directory called `/input` indide
+the container:
+
+   ```bash
+   apptainer exec --bind /scratch/<project>:/input tutorial.sif ls /input # replace <project> with your CSC project, e.g. project_2001234
+   ```
+
+### Using the `apptainer_wrapper` script
+
+1. If you use the wrapper script `apptainer_wrapper`, it will automatically
+   take care of the most common bind use cases.
+
+2. You just need to set a `$SING_IMAGE` environment variable to point to the
+   correct Apptainer image file:
+
+   ```bash
+   export SING_IMAGE=$PWD/tutorial.sif
+   apptainer_wrapper exec ls /projappl/<project> # replace <project> with your CSC project, e.g. project_2001234
+   ```
+
+   💡 Note that the image file name is not needed in the `apptainer_wrapper`
+   command since `$SING_IMAGE` is set.
+
+   ‼️ Since some modules set `$SING_IMAGE` when loaded, it is a good idea to
+   start with `module purge` to make sure the correct image is used if you plan
+   to use `apptainer_wrapper`.
+
+## Environment variables
+
+💬 Some software may require environment variables to be set, e.g., to point to
+some reference data or a configuration file.
+
+💬 Most environment variables set on the host are inherited by the container.
+
+☝🏻 Sometimes this may be undesired, in which case the command line option
+`--cleanenv` can be used to prevent the host environment from being inherited
+by the container.
+
+💬 To set an environment variable specifically inside the container, you can
+set an environment variable `$APPTAINERENV_XXX` (where `XXX` is the variable
+name) on the host before invoking the container.
+
+1. Set some test variables:
+
+   ```bash
+   export TEST1="value1"
+   export APPTAINERENV_TEST2="value2"
+   ```
+
+2. Compare the outputs of:
+
+   ```bash
+   env | grep TEST
+   apptainer exec tutorial.sif env | grep TEST
+   apptainer exec --cleanenv tutorial.sif env | grep TEST
+   ```
+
+   - Command `env` lists all set environment variables.
+   - The first command is run on the host and we see `$TEST1` and
+     `$APPTAINERENV_TEST2`.
+   - The second command is run inside the container and we see `$TEST1`
+     (inherited from the host) and `$TEST2` (specifically set inside the
+     container by setting `$APPTAINERENV_TEST2` on the host).
+   - The third command is also run inside the container, but this time we
+     omitted the host environment variables so we only see `$TEST2`.
+
+3. Note that any command-line variables on the host are substituted by their
+   values when passed to the container:
+
+   ```bash
+   apptainer exec tutorial.sif echo $TEST1
+   apptainer exec tutorial.sif echo $TEST2
+   ```
+
+   - The first line prints the value set on the host.
+   - The second line results in an empty output because a variable called
+     `$TEST2` has not been set on host. It was `APPTAINERENV_TEST2="value2"`,
+     remember?
+
+4. If you need to pass environment variables to a container, in most cases it 
+   easiest just to set them on host. If this is not possible, you need to make
+   sure thay variable names instead of their values are passed on to the 
+   container, e.g:
+
+   ```bash
+   apptainer exec tutorial.sif bash -c 'echo $TEST2'   
+   ```
+
+  In this example we run `bash` shell inside the container and user the `-c` 
+  option to give commands to run as a string. Since the string is encased in 
+  single quotes, any variables are passed literally instead of being 
+  substituted for their values.
+
+## Exploring containers
+
+💬 Our test container includes the program `hello2`, but it has not been added
+to the `$PATH` variable.
+
+1. One way to find it is to try running `find` inside the container:
+
+   ```bash
+   apptainer exec tutorial.sif find / -type f -name "hello2" 2>/dev/null
+   ```
+
+2. You can now run it by providing the full path:
+
+   ```bash
+   apptainer exec tutorial.sif /found/me/hello2
+   ```
+
+3. Or you could add it to `$PATH` inside the container:
+
+   ```bash
+   export APPTAINERENV_PREPEND_PATH=/found/me
+   apptainer exec tutorial.sif hello2
+   ```
+
+💡 If you can't locate the desired binary with `find`, you can always use
+`apptainer shell` to explore the container.
+
+## More information
+
+💬 This tutorial is meant as a brief introduction to get you started.
+
+☝🏻 When searching online for instructions, pay attention that the instructions
+are for the same version of Apptainer as you are using. There has been some
+command syntax changes etc. between versions, so older instructions may not
+work as is. Also note that Apptainer was formerly known as Singularity.
+
+💡 For more detailed instructions, see the official
+[Apptainer documentation](https://apptainer.org/docs/user/latest/).