fMRIPrep Bootcamp | Day 1

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.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-04-containers/">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 20%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-04-containers/
</a>

## Containers

Chris Markiewicz <<code>markiewicz@stanford.edu</code>>

Oscar Esteban <<code>phd@oscaresteban.es</code>>
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<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0; height: 20px; padding-top: 6px;" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
 Day 1 :: Containers

]

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# Outlook

.right-column3.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-04-containers/">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-04-containers/
</a>
]

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.large[

* What are containers and why researchers care?

* Docker

* Apptainer

]]

???

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.boxed-content[
.large.center[
# What are containers?
]
.large.center.gray-text[Why do we care?]
]

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.boxed-content[
.large[
*A container is a unit of software that packages code with its required dependencies in order to run in an isolated, controlled environment.
This allows you to run an application in a way that is predictable, repeatable, and without the uncertainty of inconsistent code execution 
across diverse development and production environments.
A container will always start up and run code the same way, regardless of what machine it exists on.*
]
.large.center.gray-text[https://www.digitalocean.com/community/conceptual-articles/introduction-to-containers]
]

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.boxed-content[
.large[
*A container is a unit of software that packages code with its required dependencies in order to run in an isolated, controlled environment.
This allows you to run an application in a way that is predictable, repeatable, and without the uncertainty of inconsistent code execution 
across diverse development and production environments.
A container will always start up and run code the same way, regardless of what machine it exists on.*
]
.large.center.gray-text[https://www.digitalocean.com/community/conceptual-articles/introduction-to-containers]
]

---
count:false

.boxed-content[
.large[
*A container is a unit of software that packages code with its required dependencies in order to run in an isolated, controlled environment.
This allows you to run an application in a way that is predictable, repeatable, and without the uncertainty of inconsistent code execution 
across diverse development and production environments.
A container will always start up and run code the same way, regardless of what machine it exists on.*
]
.large.center.gray-text[https://www.digitalocean.com/community/conceptual-articles/introduction-to-containers]
]

---

# Isn't this the same as virtual machines?

.boxed-content[
<figure style="width: 100%">
![:img containers-vs-vms, 100%](https://wac-cdn.atlassian.com/dam/jcr:92adde69-f728-4cfc-8bab-ba391c25ae58/SWTM-2060_Diagram_Containers_VirtualMachines_v03.png?cdnVersion=2218)
<figcaption>From <a href="https://www.atlassian.com/microservices/cloud-computing/containers-vs-vms">the Atlassian documentation</a></figcaption>
</figure>
]

---

.boxed-content[
.large.center[
# Docker]
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# First contact with docker

.boxed-content.pad-top[
<div class="asciicast" id="636539" data-src="images/docker-hello-world.cast"></div>
]

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# Container Images

.boxed-content.pad-top[
.no-bullet[
* .large[ Images are software bundles]
 * .larger[when executed become containers]

* .large[ Images are made of layers]
 * .larger[each layer encapsulates a set of filesystem changes]
 * .larger[layers are akin to software deployment steps]

* .large[ Layers are **unmutable**]
 * .larger[except for a R/W layer that is added on top by the container runtime]

* .large[ Layers are described in the `Dockerfile`]
 * .larger[The `Dockerfile` establishes the instructions to create an image]
 * .larger[The `Dockerfile` is some sort of recipe]

]
]

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# Building an image: docker/whalesay

## 1 The `Dockerfile`

.boxed-content[
```Dockerfile
# Containers are generally bootstrapped from an existing OS image
# Alpine Linux is a Linux distribution very small and simple
# It's special in that it is not based on the GNU Core Utilities
FROM alpine

# Our container will need perl
RUN apk add --no-cache perl

# Copy the original 'cowsay' program into one layer
COPY cowsay /usr/local/bin/cowsay

# Ensure permissions
RUN chmod a+rx /usr/local/bin/cowsay

# Copy the replacement of the cow asciiart with a whale
COPY docker.cow /usr/local/share/cows/default.cow

# Instruct the runtime to execute the new program
ENTRYPOINT ["/usr/local/bin/cowsay"]
```
]

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# Building an image: docker/whalesay

## 2 The `cowsay` script

.boxed-content[

Because it is a very long perl script, we just download it:

```bash
$ curl https://raw.githubusercontent.com/docker/whalesay/master/cowsay -o cowsay
```
]

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# Building an image: docker/whalesay

## 3 The replacement for the cow (`docker.cow`)

.boxed-content[
``` Perl
##
## Docker Cow
##
$the_cow = <<EOC;
 $thoughts
 $thoughts
 $thoughts
EOC
$the_cow .= <<'EOC';
 ## .
 ## ## ## ==
 ## ## ## ## ## ===
 /"""""""""""""""""\___/ ===
 { / ===-
 \______ O __/
 \ \ __/
 \____\_______/

EOC
```
]
---

# Building an image: docker/whalesay

## 4 Build it

.boxed-content[
```bash
$ docker build -t oesteban/whalesay .
```
]

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# Building the image

.boxed-content.pad-top[
<div class="asciicast" id="636540" data-src="images/docker-build.cast"></div>
]

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# Docker images and the *Docker Hub*

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.no-bullet[
* .large[Images can be distributed through **registries**.]
   * .larger[*Docker*'s official registry is called *Docker Hub*]
   * .larger[Thanks to *Docker Hub* we could fetch and execute the `hello-world` image]
   * .larger[Website: [hub.docker.com](https://hub.docker.com/)]

* .large[Let's download two interesting images:]
  * .larger[*MRIQC*]
    ``` Bash
    docker pull nipreps/mriqc:latest
    ```
  * .larger[*fMRIPrep*]
    ``` Bash
    docker pull nipreps/fmriprep:24.1.0rc0
    ```
]
]

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# Fetching images & the R/W runtime layer

.boxed-content.pad-top[
<div class="asciicast" id="636541" data-src="images/docker-pull.cast"></div>
]

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# Docker is not generally available at HPC systems

.boxed-content.pad-top[
<div class="asciicast" id="636542" data-src="images/apptainer-pull.cast"></div>
]

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# Pulling *MRIQC*'s image on the cluster

.boxed-content.pad-top[
<div class="asciicast" id="636543" data-src="images/apptainer-mriqc-pull.cast"></div>
]

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.boxed-content[
.large.center[
# Exercise
]
.large.center.gray-text[Pull **docker://nipreps/fmriprep:24.1.0rc0** on the cluster]
]