monai2021bootcamp-aws-instructions

These setup instructions describe how to access the AWS accounts for the third day of the MONAI MICCAI Bootcamp 2021. Each account will be shared by two users and every user will launch a dedicated GPU-based SageMaker notebook instance to work on the ML challenges.

Accessing your AWS account

Go to https://dashboard.eventengine.run/login and enter the event hash you have received via email and click on Accept Terms & Login:

On the next page, click on Email One-Time Password (OTP):

Enter the email address, which you used when you registered for the bootcamp. Using another email address won't allow you to access your temporary AWS account.

In the next window, click on AWS Console:

Another window will open. Please click on Open AWS Console:

Congratulations, you have accessed your AWS account, which you will use for the rest of the day. Now, we need to make sure to launch your own Jupyter server.

Launching your pre-configured SageMaker Notebook instance

In the search bar on the top, please type "service catalog" and click on Service Catalog in the search result list:

In Service Catalog, click on Bootcamp Notebook:

Click on Launch product:

Enter your specific notebook name into the Provisioned product name field and the NotebookInstanceName field. Remember, two users will share the same AWS account. Therefore, we recommend using a naming schema like notebook-[firstnamelastname]. The name must start with a letter (A-Z, a-z) or number (0-9) and can include hyphens (-), but not spaces. After that, click on Launch product at the bottom of the page (The launch button is not shown in the screenshot below). This will launch your pre-configured GPU-based SageMaker Jupyter notebook server in the background.

After that, you will see a notification on the top of the page that your notebook is being launched:

Now, we can leave Service Catalog.In the search bar at the top, enter "sagemaker" and click on SageMaker in the search result list:

In the SageMaker Console, click on Notebook instances in the left sidebar:

In the list of notebook instances, you will see the instance you just started via service catalog. If your instance is not yet in status "InService", just wait 1-2 minutes until the server was completely launched. Click on Open Jupyter Lab, which will open your Jupyter Lab environment in a separate tab.

Downloading the bootcamp notebooks

In Jupyter Lab, click on File > New > Terminal. We will now git clone the notebooks for today's challenge day.

In the terminal, type cd SageMaker and press Enter. Then type git clone https://github.com/Project-MONAI/MONAIBootcamp2021 and press Enter again. After that, you will be able to navigate to the notebooks you just downloaded via the file browser on the left:

Congratulations! You are now ready to get started. The NVIDIA team will share specific information on the notebooks for the Bootcamp Challenge Day you will use today later during our intro session. But please, keep on reading the last section below.

Launching Juypter notebooks

Important: When selecting and launching a notebook, you will be asked to select your preferred kernel. Please make sure to always select the conda_pytorch-latest_p36 kernel:

Have fun today and good luck with the mini challenges!

IMPORTANT: The notebooks were just updated on 07:45AM PT / 10:45AM ET / 4:45PM CEST

If you downloaded the notebooks before, please make sure to run the following instructions:

In Jupyter Lab, click on File > New > Terminal. In the terminal, type cd SageMaker and press Enter.
Then type git pull https://github.com/Project-MONAI/MONAIBootcamp2021 and press Enter again.

Additional resources for another day

Below, we also added the links to the recourses, which were mentioned in the AWS on MONAI session on Day 2.

Misc

MONAI dataset (Medical Segmentation Decathlon) on the Registry of Open Data: https://registry.opendata.aws/msd/

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