CSCS-summer-school-2017

CSCS-ICS-DADSi Summer School: Accelerating Data Science with HPC, September 4 – 6, 2017

Preparation

Step 0: Install Docker

Follow instructions on the Docker website to install Docker (don't use brew, etc.).

Step 1: Get the Docker image

Prerequisite: you should have Docker installed. After you install Docker you should configure it via Preferences/Advances to allow the Docker image to use 8Gb of memory.

Start by pulling the anglican-infcomp image from the Docker hub:

docker pull gbaydin/anglican-infcomp

Beware: this can take some time (approximately 15 minutes over a fast LAN connection), so it might be a good idea to start pulling this image as soon as possible before the exercise sessions.

Optional: Install nvidia-docker

If you have CUDA available, you can also install a Docker engine supporting NVIDIA GPUs. This will significantly speed up the neural network training phase, although the exercises we will cover already run fast enough without this.

Please follow instructions at the nvidia-docker repository.

Step 2: Clone this repository

At a location of your choosing, run

git clone https://github.com/probprog/CSCS-summer-school-2017.git

to clone this repository containing the summer school exercises.

Step 3: Run the Docker container

Linux

First run

xhost +

to allow access to the X server from the Docker container (this is needed for one of the exercises where a GUI is used).

Then change into the folder and start an interactive Docker container by running:

cd CSCS-summer-school-2017
docker run --rm -it -p 31415:31415 -v $PWD:/workspace -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix gbaydin/anglican-infcomp

Mac

First you need to download and install XQuartz.

Then run

socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"

You may need to install socat if you can't run this command.

In a different terminal, change into the folder and start an interactive Docker container by running:

cd CSCS-summer-school-2017
xhost +
ip=$(ifconfig | grep "inet " | grep -Fv 127.0.0.1 | awk '{print $2}' )
docker run --rm -it -p 31415:31415 -v $PWD:/workspace -e DISPLAY=$ip:0 -v /tmp/.X11-unix:/tmp/.X11-unix gbaydin/anglican-infcomp

Windows 10

Install Docker and Git bash. In the toolbar click the Docker button and increase the memory it uses under the advanced tab to, ideally, 8GB.

Using Windows Powershell run bash then run ipconfig to get your machines ip address then run the following command with 999.999.999.999 replaced with your ip address

docker run --rm -it -p 31415:31415 -v ${PWD}:/workspace -e DISPLAY=999.999.999.999:0 -v /tmp/.X11-unix:/tmp/.X11-unix gbaydin/anglican-infcomp

In the docker window then run

lein gorilla :port 31415 :ip 0.0.0.0

Then open a browser and go to

http://127.0.0.1:31415/worksheet.html

On Windows the physics example program will not display X-windows contents correctly with these settings.

---

This will have started a new Docker container using the anglican-infcomp image that you pulled in the previous step.

In this command --rm indicates that the container will be removed when it exists, -it attaches an interactive terminal to the container, -p 31415:31415 sets up a port mapping for port 31415 that is used for the Gorilla REPL for Clojure, and -v $PWD:/workspace mounts your current folder CSCS-summer-school-2017 as /workspace within the container. The flags -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix set up the X server access that is needed for one of the exercises using GUI.

If you want to run with GPU support, replace docker with nvidia-docker in the above command.

Exercises

Exercise 1: Probabilistic programming in Anglican

In the Docker instance change directory into the first programming project

cd exercises/exercise-1-probprog

then start a Clojure browser-based repl (read evaluate print loop)

lein gorilla :port 31415 :ip 0.0.0.0

Open a web browser and browse to the first, introduction-to-functional-programming-and-Clojure, exercise workbook 01-clojure-overview.clj

We recommend going through the following 4 exercises in order. We recommend not completing the first exercise in its entirety, instead, just completing a reasonable percentage of it, enough to get the basics, and then to move to the Anglican hello world example. Use shift-enter to evaluate the current cell. Additional commands and help are available in the GUI tab in the upper right hand corner.

1. 02-clojure-exercises.clj
2. 01-hello-world.clj
3. 02-gaussian.clj
4. 03-physics.clj

There are more exercises available and also accessible through the workbook GUI tab in the upper right hand corner.

Note that these exercise links will not work if you choose a different port than 31415, however, regardless of port choice the exercise workbooks will be available by name from the GUI tab. If they do not work at all this suggests a problem in your setup and help should be sought from the presenters in the first instance.

Important: Online Anglican documentation

Anglican documentation is available online, as are a number of helpful and simple example programs.

Exercise 2: Deep learning in Pytorch

We will run a Jupyter Python notebook using the Docker container. Start by running (for Linux and Mac):

docker run --rm -it -p 8888:8888 -v $PWD:/workspace gbaydin/anglican-infcomp jupyter notebook --ip 0.0.0.0 --no-browser --allow-root

On Windows, please replace -v $PWD:/workspace with -v %cd%:/workspace if you are using the command line (cmd) or with -v ${PWD}:/workspace if you are using the PowerShell.

This will start a Jupyter server inside the Docker container. In the terminal, you should see a line such as the following, telling you that the server is running and ready to accept connections:

[I 20:09:17.270 NotebookApp] The Jupyter Notebook is running at: http://0.0.0.0:8888/

Depending on the terminal you use, you can either right click on the link http://0.0.0.0:8888/ to open it in a web browser or just directly type it into the address bar a web browser. On Windows, please use the link http://localhost:8888/ instead.

You should now see a web browser window such as this:

Enter cscs as the password to authenticate.

Now please navigate to the exercise worksheets by clicking on exercises and then exercise-2-pytorch.

Now click on CSCS-summer-school-2017-exercise-2.ipynb to start the exercise notebook.

Exercise 3: Inference Compilation

In the Docker instance change directory into the third programming project

cd exercises/exercise-3-inference-compilation

tmux

Then start a tmux session which will let you switch between several programs in the same terminal (this will be needed to run the probabilistic program and the neural network at the same time):

tmux

Once inside a tmux session, you can:

• Split panes: Control + b and "
• Switch between panes: Control + b and <arrow key>
• Exit using exit command
• Detach the current session: Control + b and d

Once detached, you can re-attach to a detached session using tmux attach.

The Captcha worksheet

Create a new tmux session from the exercises/exercise-3-inference-compilation folder by running tmux and split the session to two panes using Control + b and ". In one of the panes, start a Clojure browser-based repl

lein gorilla :port 31415 :ip 0.0.0.0

Open a web browser and browse to the Captcha exercise in src/worksheets/captcha.clj (solutions are here and follow the instructions.

When you work through the notebook, there will be a point in which you will switch to the other tmux pane using Control + b and <arrow key> to start training the neural network.

Downloading the pre-trained compilation artifact

For the solutions worksheet to work, you will need to download a pre-trained artifact for the Captcha probabilistic program from here into the exercises/exercise-3-inference-compilation/resources/ folder.