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<!DOCTYPE html>
<html>
<head>
<title>Title</title>
<meta charset="utf-8">
<link rel="stylesheet" type="text/css" href="slides.css">
</head>
<body>
<textarea id="source">
class: center, middle
# Docker for Cluster Computing in Python
.affiliations[
]
---
# Outline
.middlebelowheader[
### Distributed ML with joblib and dask/distributed
### A quick intro to Docker
### Cluster orchestration with Docker and Kubernetes
]
---
class: center, middle, bgheader
background-image: url(images/racks.jpeg)
background-size: cover
# Distributed ML with joblib and dask/distributed
---
class: singleimg
# A cluster for sklearn
.middlebelowheader[
]
---
# Demo
.middlebelowheader[
https://github.com/ogrisel/docker-distributed
Have a look a the notebooks in the `examples` folder.
.center[
<iframe width="420" height="315"
src="https://www.youtube.com/embed/6mKNSEQ0FIQ"
frameborder="0" allowfullscreen></iframe>
https://youtu.be/6mKNSEQ0FIQ
]
]
---
class: center, middle, bgheader
background-image: url(images/container_terminal.jpeg)
background-size: cover
# What is Docker?
---
# Docker is:
.middlebelowheader[
### Not a virtual machine system
### Linux container + Layered file-system + Abstract network
### It can run in a VM (or not)
]
---
class: singleimg
# VM vs Container
.middlebelowheader[
]
---
# Why is docker nicer than VMs
.middlebelowheader[
### Less overhead: isolation vs virtualization
### Layered FS: incremental diffs + common base images
### Nice command line based UX
### Simple reproducible builds and deployment
]
---
class: singleimg
# Docker architecture
.middlebelowheader[
]
---
# Some use cases
.middlebelowheader[
### Host applications / services efficiently
### Fast developer environment setup
### Flexible build / Continuous Integration
### Quickly provision a compute cluster
### Reproducible science
]
---
# Getting started with Docker
.middlebelowheader[
https://docs.docker.com/engine/installation/
### Windows: daemon in Linux with Hyper-V or Virtualbox
### OSX: daemon in Linux with xhyve or Virtualbox
### Linux: daemon on host without VM
### Cross-platform docker client binary
]
---
class: medium
# Running in a container
```
$ docker run python:3.5 python -c "print(40 + 2)"
```
---
class: medium
# Running in a container
```
$ docker run `python:3.5` python -c "print(40 + 2)"
```
---
class: medium
# Running in a container
```
$ docker run python:3.5 `python -c "print(40 + 2)"`
```
---
class: medium
# Running in a container
```
$ docker run `--rm` python:3.5 python -c "print(40 + 2)"
```
---
class: medium
# Running in a container
```
$ docker run --rm python:3.5 python -c "print(40 + 2)"
Unable to find image 'python:3.5' locally
latest: Pulling from library/python
357ea8c3d80b: Already exists
52befadefd24: Pull complete
3c0732d5313c: Pull complete
ceb711c7e301: Downloading [=========> ] 90.27 MB/129.7 MB
4211bb537697: Download complete
71f9074c0739: Download complete
3e5349707036: Download complete
```
---
class: medium
# Running in a container
```
$ docker run --rm python:3.5 python -c "print(40 + 2)"
Unable to find image 'python:3.5' locally
latest: Pulling from library/python
357ea8c3d80b: Already exists
52befadefd24: Pull complete
3c0732d5313c: Pull complete
ceb711c7e301: Pull complete
4211bb537697: Pull complete
71f9074c0739: Pull complete
3e5349707036: Pull complete
Digest: sha256:a755ad5a30b2[...]
Status: Downloaded newer image for python:3.5
42
```
---
class: medium
# Running in a container
```
$ docker run --rm python:3.5 python -c "print(40 + 2)"
Unable to find image 'python:3.5' locally
latest: Pulling from library/python
357ea8c3d80b: Already exists
52befadefd24: Pull complete
3c0732d5313c: Pull complete
ceb711c7e301: Pull complete
4211bb537697: Pull complete
71f9074c0739: Pull complete
3e5349707036: Pull complete
Digest: sha256:a755ad5a30b2[...]
Status: Downloaded newer image for python:3.5
42
$ docker run --rm python:3.5 python -c "print(40 + 3)"
43
```
---
class: medium
# Interactive sessions
```
$ docker run --rm -ti python:3.5 bash
root@10d2dfedb935:/#
```
---
class: medium
# Interactive sessions
```
$ docker run --rm -ti python:3.5 bash
root@10d2dfedb935:/# ps
PID TTY TIME CMD
1 ? 00:00:00 bash
8 ? 00:00:00 ps
root@10d2dfedb935:/#
```
---
class: medium
# Interactive sessions
```
$ docker run --rm -ti python:3.5 bash
root@10d2dfedb935:/# ps
PID TTY TIME CMD
1 ? 00:00:00 bash
8 ? 00:00:00 ps
root@10d2dfedb935:/# python
Python 3.5.2 (default, Aug 9 2016, 20:58:38)
[GCC 4.9.2] on linux
>>>
```
---
class: medium
# Interactive sessions
```
$ docker run --rm -ti python:3.5 bash
root@10d2dfedb935:/# ps
PID TTY TIME CMD
1 ? 00:00:00 bash
8 ? 00:00:00 ps
root@10d2dfedb935:/# python
Python 3.5.2 (default, Aug 9 2016, 20:58:38)
[GCC 4.9.2] on linux
>>> 40 + 2
42
```
---
class: medium
# Interactive sessions
```
$ docker run --rm -ti python:3.5 bash
root@10d2dfedb935:/# ps
PID TTY TIME CMD
1 ? 00:00:00 bash
8 ? 00:00:00 ps
root@10d2dfedb935:/# python
Python 3.5.2 (default, Aug 9 2016, 20:58:38)
[GCC 4.9.2] on linux
>>> 40 + 2
42
>>> ^D
root@10d2dfedb935:/# exit
```
---
class: medium
# A real-life example
```
$ cd bokeh/bokeyjs
$ npm install -g gulp
$ gulp build
[Bunch or errors caused by a broken nodejs install]
```
---
class: medium
# A real-life example
```
$ cd bokeh
$ docker run --rm --volume $PWD:/io node \
bash -c "cd /io/bokehjs && npm install -g gulp && gulp build"
```
---
class: medium
# A real-life example
```
$ cd bokeh
$ docker run --rm `--volume $PWD:/io` node \
bash -c "`cd /io/bokehjs` && npm install -g gulp && gulp build"
```
---
class: medium
# A real-life example
```
$ cd bokeh
$ docker run --rm --volume $PWD:/io node \
bash -c "cd /io/bokehjs && npm install -g gulp && gulp build"
npm info it worked if it ends with ok
npm info using [email protected]
npm info using [email protected]
npm info attempt registry request try #1 at 12:45:51 PM
npm http request GET https://registry.npmjs.org/gulp
[...] # Download the Internet
[13:03:42] Finished 'build' after 10 s
*$ ls bokehjs/node_modules | wc -l
*604
```
---
class: center, middle, bgheader
background-image: url(images/lego-painter.jpeg)
background-size: cover
# Building an image
---
class: middle, medium
```
$ git clone https://github.com/ogrisel/docker-distributed
$ ls docker-distributed
docker-compose.yml
*Dockerfile
examples
kubernetes
README.md
*requirements.txt
```
---
class: middle, medium
```
$ git clone https://github.com/ogrisel/docker-distributed
$ ls docker-distributed
docker-compose.yml
Dockerfile
*examples
kubernetes
README.md
requirements.txt
```
---
class: middle, medium
```
$ git clone https://github.com/ogrisel/docker-distributed
$ ls docker-distributed
*docker-compose.yml
Dockerfile
examples
*kubernetes
README.md
requirements.txt
```
---
class: middle
```dockerfile
FROM debian:jessie
MAINTAINER Olivier Grisel <[email protected]>
RUN apt-get update -yqq && apt-get install -yqq wget bzip2 git \
&& rm -rf /var/lib/apt/lists/*
# Configure environment
ENV LC_ALL=C.UTF-8 LANG=C.UTF-8
RUN mkdir /work
WORKDIR /work
# Install Python 3 from miniconda
RUN wget -O miniconda.sh \
https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash miniconda.sh -b -p /work/miniconda \
&& rm miniconda.sh
ENV PATH="/work/bin:/work/miniconda/bin:$PATH"
RUN conda install -y \
pip \
notebook \
pandas \
scikit-learn \
&& conda clean -tipsy
# Install the master branch of distributed and dask
COPY requirements.txt .
RUN pip install -r requirements.txt && rm -rf ~/.cache/pip/
# Add the example notebooks
COPY examples .
```
---
class: medium
# docker build
```
$ docker build -t ogrisel/distributed .
Sending build context to Docker daemon 178.2 kB
Step 1 : FROM debian:jessie
---> 1b01529cc499
Step 2 : MAINTAINER Olivier Grisel <[email protected]>
---> Using cache
---> 37887ee139f1
Step 3 : RUN apt-get update -yqq && apt-get install -yqq wget [...]
---> Using cache
---> 3c2b8caccb80
[...]
```
---
class: medium
# docker build & docker push
```
$ docker build -t ogrisel/distributed .
Sending build context to Docker daemon 178.2 kB
Step 1 : FROM debian:jessie
---> 1b01529cc499
Step 2 : MAINTAINER Olivier Grisel <[email protected]>
---> Using cache
---> 37887ee139f1
Step 3 : RUN apt-get update -yqq && apt-get install -yqq wget [...]
---> Using cache
---> 3c2b8caccb80
[...]
$ docker run --rm ogrisel/distributed \
python -c "import sklearn; print(sklearn.__version__)"
0.17.1
$ docker push ogrisel/distributed
```
---
class: center, middle, bgheader
background-image: url(images/orchestra.jpeg)
background-size: cover
# Orchestration
---
# Orchestration tools
.middlebelowheader[
<div style="display: flex">
<div style="width: 50%; padding: 1em">
<p><img height="50px" src="images/docker-logo.png" /></p>
<p>
<strong>Docker Swarm</strong> and Docker Compose
</p>
</div>
<div style="width: 50%; padding: 1em">
<p><img height="50px" src="images/kubernetes-logo.png" /></p>
<p>
<strong>Kubernetes</strong>
</p>
</div>
</div>
<div style="margin: 1em auto; width: 400px">
<p><img height="50px" src="images/dcos-logo.png" /></p>
<p>
<strong>DC/OS</strong> and Mesos
</p>
</div>
]
---
class: medium
# Kubernetes and GKE
```
$ gcloud config set compute/zone europe-west1-d
$ gcloud container clusters create cluster-1 \
--num-nodes 3 \
--machine-type n1-highcpu-32 \
--scopes bigquery,storage-rw \
--wait
Creating cluster cluster-1...done.
Created [https://container.googleapis.com/v1/.../cluster-1].
kubeconfig entry generated for cluster-1.
NAME ZONE ... MACHINE_TYPE NUM_NODES STATUS
cluster-1 europe-west1-d ... n1-highcpu-32 3 RUNNING
```
--
```
$ gcloud container clusters get-credentials cluster-1
Fetching cluster endpoint and auth data.
kubeconfig entry generated for cluster-1.
```
---
class: medium
# Kubernetes and GKE
```
$ git clone https://github.com/ogrisel/docker-distributed
$ cd docker-distributed
$ kubectl create -f kubernetes/
service "dscheduler" created
service "dscheduler-status" created
replicationcontroller "dscheduler" created
replicationcontroller "dworker" created
service "jupyter-notebook" created
replicationcontroller "jupyter-notebook" created
```
--
```
$ kubectl get services
NAME CLUSTER-IP EXTERNAL-IP PORT(S)
dscheduler 10.115.249.189 <none> 8786/TCP,9786/TCP
dscheduler-status 10.115.244.201 130.211.50.206 8787/TCP
jupyter-notebook 10.115.254.255 146.148.114.90 80/TCP
kubernetes 10.115.240.1 <none> 443/TCP
```
---
class: medium
# distributed-worker.yml
```yaml
apiVersion: v1
kind: ReplicationController
metadata:
name: dworker-controller
spec:
replicas: 3
selector:
name: dworker
template:
metadata:
labels:
name: dworker
spec:
containers:
- name: dworker
image: ogrisel/distributed:latest
args: ["dask-worker", "dscheduler:8786"]
```
---
# Conclusion
.middlebelowheader[
### Docker is a useful developer tool
### Containers make cluster setup reproducible and cloud agnostic
### Docker Swarm vs Kubernetes vs Mesos: learn any one and understand others
]
---
# Thank you
.middlebelowheader[
<div style="display: flex">
<div style="width: 50%; padding: 1em">
<p><img height="35px" src="images/carina-logo.svg" /></p>
<p>
<strong>Rackspace</strong> for free cloud resources to support SciPy
projects and for helping the Python community in general.
</p>
</div>
<div style="width: 50%; padding: 1em">
<p><img height="35px" src="images/gcp-logo.png" /></p>
<p>
<strong>Google</strong> for GCP credits to test distributed Python with
Kubernetes.
</p>
</div>
</div>
<div style="margin: 1em auto; width: 400px">
<p><img height="50px" src="images/inria-logo.png" /></p>
<p>
<strong>Inria</strong> for supporting my work on scikit-learn and related
projects.
</p>
</div>
]
---
class: middle
# Thank you!
## Sample configuration:
- [github.com/ogrisel/docker-distributed](http://github.com/ogrisel/docker-distributed)
## Those slides:
- [ogrisel.github.io/decks/2016_euroscipy_docker](
http://ogrisel.github.io/decks/2016_euroscipy_docker)
---
class: small
# Image credits
- "Supermicro Storage" by Robert: https://flic.kr/p/e17qr3
- "smiiile!" by mooglet: https://flic.kr/p/am9zQe
- "Docker Architecture" https://docs.docker.com/engine/understanding-docker/
- "Container terminal" by Martin Abegglen: https://flic.kr/p/b7rw5D
- "Symphonic Orchestra and Choir of the WYD" by HazteOir.org:
https://flic.kr/p/c5B6Cd
</textarea>
<script src="../remark.min.js" type="text/javascript">
</script>
<script type="text/javascript">
var slideshow = remark.create({
highlightStyle: 'github',
highlightSpans: true,
highlightLines: true
});
</script>
</body>
</html>