block_3_session_1_terminology_n_context.qmd

---
title: "Hacking for Science"
subtitle: "Block 3, Session 1: A Glimpse of DevOps"
author: "Matt Bannert ([@whatsgoodio](https://twitter.com/whatsgoodio))"
format: revealjs
chalkboard: true
echo: true
footer: "Hacking for Science by Dr. Matthias Bannert is licensed under [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/?ref=chooser-v1)"
---

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font-size:.5em;
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## [review](https://rse-book.github.io/stack-developer-toolkit.html) {.center}



## Today's Goals {.center}


- Catch a Glimpse of Development and Operations
- Terminology & Context
- Get an idea of apt infrastructure for team projects



## {.center}

![](img/server-thinking.jpg){fig-align="center"}

## {.center}

![](img/listen.jpg){fig-align="center"}


## {.center}

![](img/cloud.png){fig-align="center"}


## {.center}

![](img/inefficient.png){fig-align="center"}




## Resources -- <br> And What to Look For ... {.center}


## Size {.center}



## {.center}

![](img/overkill.png){fig-align="center"}


## {.center}

![](img/overload.jpg){fig-align="center"}



## Persistency

![](img/quit_py.png){fig-align="center"}

![](img/quit_r.png){fig-align="center"}


## Availability & Exposure {.center}



## Data Science Webserver Example

![](img/server-setup1.jpg){fig-align="center"}

## 

![](img/server-setup2.jpg){fig-align="center"}


## Data Science Webserver Example

![](img/server-setup3.jpg){fig-align="center"}

## Common Servers

```{r, echo=FALSE}
library(dplyr)
library(kableExtra)
tri <- tribble(
  ~ name, ~ "common ports", ~ description ,
  "Apache", "80, 443", "Basic Webserver",
  "nginx", "80, 443", "Webserver, Reverse Proxy",
  "Postgres", "5432", "Database",
  "RStudio Server", "8787", "RStudio made available through a web browser",
  "Shiny Server", "3838", "A webserver for shiny apps"
)

kable(tri)


```


## Reproducibility {.center}

![](img/version_error.png)



# Hosting Options





## {.center}

>Do not forget that hosting requires a development strategy. 


## On Premise (in house)

- [ETH Gitlab](https://gitlab.ethz.ch/)
- [Gitea](https://gitea.io/en-us/)
- [shiny server](https://rstudio.com/products/shiny/shiny-server/)


## SaaS (software as a service) {.center}


## SaaS (software as a service) / Serverless


:::: {.columns}


::: {.column width="40%" .smaller}


### Examples

- [Overleaf](https://www.overleaf.com/)
- [shinyapps.io](https://www.shinyapps.io/)
- [Google NLP](https://cloud.google.com/natural-language/#demo)


:::

::: {.column width="60%" .smaller}


### Advantages

- Hassle free (Hosting)
- Onboarding of non-hackers easier
- transparent pricing models


### Disadvantages



- Blackbox
- Vendor Lock-in depending on pricing model and software
- Relatively Expensive per Unit

:::

::::


## The Cloud {.center}


## Common Cloud Products


### Basic VMs

e.g., Google Compute Engine, Microsoft Azure Cloud VMs


### Single Purpose Environments

Docker hosts, e.g., Google Kubernetes Engine, Azure Kubernetes Service (AKS)


### Ready Made Services

AI & machine learning products, e.g., Google Cloud AutoML, SQL Cloud Hosting



# Containers - Building Blocks of Modern Infrastructure


## {.center}

>A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another

*--docker.com, what is a container ?*


## Excursion: Docker in one Slide

- single purpose, application focused virtualization
- **images: blueprints** for **containers**
- **Registries**: store images
- Docker files are text based configs from which images are created.
- Images can be stacked, so we can build on existing images
- Docker containers run on a Docker Host / Docker Desktop or in Docker Cluster like Docker Swarm or Kubernetes.



## A Basic Docker File: R with Postgres Driver

```sh
FROM rocker/r-ver:4.2.0 as deps
RUN apt-get update && apt-get install -y \
libpq-dev \
libcurl4-openssl-dev \
libxml2-dev \
libssl1.0-dev \
libssh-dev
```

Start and log into the container... 

```sh
# start the container in the background
docker run -it -d  --name pgr_container pgr

# log into the running container, use bash
docker exec -it pgr_container /bin/bash
```

<!--
a docker solution without docker desktop
https://www.viget.com/articles/how-to-use-docker-on-os-x-the-missing-guide/
-->



## What Is Docker Good for? {.center}


## Test Stack, Conserve Setups {.center} 

e.g., [PostgreSQL version on docker hub](https://hub.docker.com/_/postgres) 


## Run Applications w/o Side Effects {.center}


## Develop @home, Run in the Cloud {.center}



## Two Docker Based Examples {.center}



## Shiny Server {.center}

```
 docker run --rm -p 1234:3838 rocker/shiny

```
  
  
## Postgres Server  
  
```
docker run --rm  --name pg-docker -e POSTGRES_PASSWORD=postgres -d -p 1111:5432 
-v local/path:/var/lib/postgresql/data  postgres:11

```

-d: run as daemon, i.e., terminal window available

-e: pass on an environment parameter, in this case a password 

-p: port forwarding: host port:docker port

-v: Mount for persistent storage


(!): To make the two containers talk to each other, [consider docker compose](https://rse-book.github.io/infrastructure.html#docker-compose-manage-multiple-containers).