This template is the first in a series of tutorials that will guide you through the process of creating a cookbook and running it on TACC systems. From simple ones that run a command to more complex ones that run a Python using conda or a Jupyter Notebook.

Requirements

• A GitHub account
• TACC account. If you don't have one, you can request one here
• To access TACC systems, you should have an allocation
  • You can see your allocations here
  • If you don't have an allocation, you can request one here

Template Overview

This template creates a simple cookbook that will run a job on a TACC cluster using two parameters/arguments, Greeting and Target, and obtain the output via a UI, saving it to a file named out.txt.

How does it work?

1. app.json file: contains the definition of the Tapis application, including the application's name, description, Docker image, input files, and advanced options.
2. Dockerfile: a Docker image is built from the Dockerfile. The Docker image defines the runtime environment for the application and the files that will be used by the application.
3. run.sh: contains all the commands that will be executed on the TACC cluster.

Job run script

The run.sh file is used to run the commands.

#!/bin/bash

Greeting=$1
Target=$2

FULL_GREETING="${Greeting} ${Target}. My name is ${_tapisJobOwner}"
echo "$FULL_GREETING"

echo $FULL_GREETING > $_tapisExecSystemOutputDir/out.txt

The run.sh script receives two parameters, Greeting and Target, and uses them to create a message that will be saved to a file named out.txt.

Also, the script uses the _tapisExecSystemOutputDir variable, which contains the path where the application writes the output files.

Create your Cookbook

Create a new repository

1. Click on the "Use this template" button to create a new repository
2. Fill in the form with the information for your new repository

Build the Docker image

You can skip this step if you don't want to build the Docker image yourself. You can use the Docker image from the Docker Hub.

1. Clone the repository
2. Build the Docker image using the command below

docker build -t cookbook-python .

3. Push the Docker image to a container registry

docker tag cookbook-python <your-registry>/cookbook-python
docker push <your-registry>/cookbook-python

Modify the app.json file

Each app has a unique id and description. So, you should change these fields to match your app's name and description.

1. Download the app.json file
2. Change the values id and description fields with the name and description as you wish.
3. If you built the Docker image, change the containerImage field with the image name you used.

Create a New Application on the Cookbook UI

1. Go to Cookbook UI
2. Click on the "Create Application" button
3. Fill in the form with the information from your app.json file
4. Click "Create Application"
5. A new application will be created, and you will be redirected to the application's page

Run your Cookbook

1. Go to the application's page on the Cookbook UI, if you are not already there
2. Click on the "Run" button on the right side of the page. This will open the Portal UI
3. Select the parameters for your job

Check the Output

1. After the job finishes, you can check the output by clicking on the "Output location" link on the job's page
2. You will be redirected to the output location, where you can see the output files generated by the job
3. Click on a file to see its content. In this case, the file is named out.txt

Next templates

• Running a command
• Running a Python script using conda
• Running a Jupyter Notebook

Authors

William Mobley - [email protected] Maximiliano Osorio