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The JEDI web applications, https://experiments.jcsda.org and https://skylab.jcsda.org, run on two individual AWS EC2 instances in the jscda-noaa account in us-east-1. They are voila applications running on port 8866 on an nginx web server on ports 80/443. The web apps are simply python notebooks in the diag-plots repository with r2d2-client as the only JCSDA dependency. These packages are located in /home/ubuntu. A python virtual environment located in /home/ubuntu/venv_web_app is used to install the required python packages and execute the voila application as a service.

...

For activating the web app's virtual environment in /home/ubuntu/venv_web_app and exporting R2D2's environmental variables for the client's configuration, execute source /home/ubuntu/setup.sh. 

Code Block
languageshell
title/home/ubuntu/setup.sh
#!/bin/bash
  
source /home/ubuntu/venv_web_app/bin/activate

export R2D2_USER=r2d2-web-app
export R2D2_HOST=aws-us-east-1
export R2D2_COMPILER=unknown
export R2D2_API_KEY=6a8bacf2-d6ae-11f0-9286-06d3b1fbe489
export R2D2_LOG_LEVEL=SILENT

...

The Nginx configuration files are located at /etc/nginx/sites-enabled/experiments.jcsda.org and /etc/nginx/sites-enabled/skylab.jcsda.org. Be sure to replace the word "experiments" with "skylab" for the other web app's file. 

Code Block
title/etc/nginx/sites-enabled/experiments.jcsda.org
server {
    server_name experiments.jcsda.org;
    proxy_buffering off;
    location / {
            proxy_pass http://localhost:8866;
            proxy_set_header Host $host;
            proxy_set_header X-Real-IP $remote_addr;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

            proxy_http_version 1.1;
            proxy_set_header Upgrade $http_upgrade;
            proxy_set_header Connection "upgrade";
            proxy_read_timeout 86400;
    }
    client_max_body_size 100M;
    error_log /var/log/nginx/error.log;

    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/experiments.jcsda.org/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/experiments.jcsda.org/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
}

server {
    if ($host = experiments.jcsda.org) {
        return 301 https://$host$request_uri;
    } # managed by Certbot

    listen 80;
    server_name experiments.jcsda.org;
    return 301 https://$host$request_uri;
    # return 404; # managed by Certbot
}

...

The Voila configuration files are located at /usr/lib/systemd/system/voila.service. 

Code Block
title/usr/lib/systemd/system/voila.service
[Unit]
Description=Voila

[Service]
Type=simple
PIDFile=/run/voila.pid
ExecStart=/home/ubuntu/venv_web_app/bin/python3.10 -m voila --no-browser --show_traceback=False diag-plots/src/jedi_data_viewer/skylab_data_viewer.ipynb
User=ubuntu
WorkingDirectory=/home/ubuntu/
Restart=always
RestartSec=10

[Install]
WantedBy=multi-user.target

...

  1. Log into the AWS Console in us-east-1 using the jcsda-noaa account.
  2. Navigate to the EC2 Instance dashboard.
  3. Click the checkbox next to "skylab.jcsda.org" or "experiments.jcsda.org" depending on which site is down. 
  4. Click the drop down arrow next to "Instance state" in the top bar and select "Reboot instance". This might take some time to stop and start. Once it says running again, verify the website is reachable and try to connect to the instance via ssh as the ubuntu user.
  5. If those fail, then you will need to stop/start the instance. That will change the public IP address so more steps will need to be taken in order to update with the new IP. Proceed to steps
    6. 5
  6. 6-X.
  7. Under "Instance state" click on "Stop instance" to shut it down. If this takes longer then a few minutes, do a "Force stop instance".
  8. Start the instance again, click "Instance state" and "Start instance". After it is back running, try to connect to the instance via ssh as the ubuntu user.
  9. Copy the new  “Public IPv4 address” and navigate to the Route 53 dashboard. Click "Hosted zones" then "jcsda.org". Scroll down to experiments.jcsda.org or skylab.jcsda.org and click "Edit record". Paste the new IP where the old one is and click "Save".
  10. Try loading the web page. If it still does not load, try with a different browser. If that does not load then you will need to restart services, so proceed with steps 9-X.
  11. Log back into the instance as user ubuntu via ssh. 

  12. Restart the following services and run:

    Code Block
    sudo systemctl restart nginx.service
sudo systemclt daemon-reload
sudo systemclt restart voila.service
  13. Verify the website is back up and running.

Update diag-plots

Updating the certificate

The certificate should be automatically updated and managed via CertBot and Let's Encrypt. If you need to manually update the certificate you can follow this procedure.

...

Code Block
languageshell

Run:

...

sudo certbot --nginx

Launch new instance running Voila and NGINX

Instructions from https://docs.google.com/document/d/1vqK-qAxBGt_I9j6VG1SSLtPhQp89PzV4Y32yuWLWbUg/edit

Voila documentation: https://voila.readthedocs.io/en/stable/deploy.html#running-voila-on-a-private-server

WARNING: These instructions are very old and some steps might be outdated or simply not correct for the current web apps. 

Start a new EC2 instance using the console:

  1. From https://console.aws.amazon.com/ec2/v2/home?region=us-east-1, click on the blue “Launch Instance” button
  2. Scroll down to Ubuntu Server 20.04 LTS (HVM), SSD Volume Type and click the blue “Select” button Note: The user name is ubuntu, unlike other EC2 instance, where the user name is ec2-user
  3. Select t2.large, and click “Next: Configure Instance Details”
  4. Keep the default options and click “Next: Add Storage” Note: An IAM role will need to be added to the instance in order to access private buckets. For Phase 0, the bucket that contains the pre-generated plots, jtd.jcsda, is public.
  5. Update the size to 50GB, and click “Next: Add Tags”. Note: It is good practice to add tags.
  6. Click “Next: Configure Security Groups”. 
  7. Change the radio button to “Select an existing security group”, and select sg-023d069fd080b4c15, or “dashboard”, which allows global HTTP and HTTPS access, and SSH access from NCAR IP addresses.
  8. Click launch and a key pair popup will appear. Choose “Create a new key pair” unless you want to use an old one of yours.
  9. Find your new instance in the console and edit the name field.

Create nginx Service:

Installing Python 3.10 on Ubuntu 20.04

Updates to OS

Code Block
languageshell
sudo apt update
sudo apt upgrade
sudo apt install build-essential libssl-dev libffi-dev

Download, Build, and Test

Code Block
languageshell
wget https://www.python.org/ftp/python/3.10.19/Python-3.10.19.tgz
tar -xvf Python-3.10.19.tgz
cd Python-3.10.19
./configure --enable-optimizations --with-ensurepip=install
nproc
make -j 8 
sudo make altinstall
/usr/local/bin/python3.10 --version

Create Virtual Environment for the Web App

The following command line will create the virtual environment for each web app. 

Code Block
languageshell
cd~
/usr/local/bin/python3.10 -m venv venv_web_app

Troubleshooting

How to run the web apps on a locally

How to print to output from ipywidgets

Code Block
languagepython
import ipywidgets as widgets
out = widgets.Output(layout={'border': '1px solid black'})
display(out)

from jedi_data_viewer_experiments import JediDataViewerExperiments
jedi_data_viewer_experiments = JediDataViewerExperiments(out)

with self._out: print('My message here')

Web page fails to load

Issue: the web pages will fail to load/ timeout

Explanation: Each time the website is hit a new python kernel is opened and will stay open forever. Therefore, when the instance memory is full of these python kernels the page will go down.

Solution: Reboot the EC2 Instance (see procedure above)

Launch New Instance Running Voila and Nginx [OUTDATED]

Instructions from https://docs.google.com/document/d/1vqK-qAxBGt_I9j6VG1SSLtPhQp89PzV4Y32yuWLWbUg/edit

Voila documentation: https://voila.readthedocs.io/en/stable/deploy.html#running-voila-on-a-private-server

WARNING: These instructions are very old and some steps might be outdated or simply not correct for the current web apps. 

Start a new EC2 instance using the console:

  1. From https://console.aws.amazon.com/ec2/v2/home?region=us-east-1, click on the blue “Launch Instance” button
  2. Scroll down to Ubuntu Server 20.04 LTS (HVM), SSD Volume Type and click the blue “Select” button Note: The user name is ubuntu, unlike other EC2 instance, where the user name is ec2-user
  3. Select t2.large, and click “Next: Configure Instance Details”
  4. Keep the default options and click “Next: Add Storage” Note: An IAM role will need to be added to the instance in order to access private buckets. For Phase 0, the bucket that contains the pre-generated plots, jtd.jcsda, is public.
  5. Update the size to 50GB, and click “Next: Add Tags”. Note: It is good practice to add tags.
  6. Click “Next: Configure Security Groups”. 
  7. Change the radio button to “Select an existing security group”, and select sg-023d069fd080b4c15, or “dashboard”, which allows global HTTP and HTTPS access, and SSH access from NCAR IP addresses.
  8. Click launch and a key pair popup will appear. Choose “Create a new key pair” unless you want to use an old one of yours.
  9. Find your new instance in the console and edit the name field.

Create nginx Service:

  1. SSH into the instance (Select instance from console, click the Connect button, copy and paste the example ssh line into your computer’s terminal). Make sure you’re on the NCAR VPN since you’ve set up the security group.

  2. Install nginx (enter in SSH’d terminal):

    Code Block
    sudo apt install nginx
sudo systemctl status nginx

     

  3. Connect {website_name}.jcsda.org to IPv4 on Route 53. (Go to https://console.aws.amazon.com/route53/v2/hostedzones#ListRecordSets/Z1F2XBLX8SOJLO, click create record, name it, keep the type as “A” and enter the instance’s public IPv4 as the Value)

  4. Create the file /etc/nginx/sites-enabled/{website_name}.jcsda.org with the following content:

    Code Block
    server {
    listen 80;
    server_name {website_name}.jcsda.org
  5. SSH into the instance (Select instance from console, click the Connect button, copy and paste the example ssh line into your computer’s terminal). Make sure you’re on the NCAR VPN since you’ve set up the security group.

  6. Install nginx (enter in SSH’d terminal):

    Code Block
    sudo apt install nginx
sudo systemctl status nginx

     

  7. Connect {website_name}.jcsda.org to IPv4 on Route 53. (Go to https://console.aws.amazon.com/route53/v2/hostedzones#ListRecordSets/Z1F2XBLX8SOJLO, click create record, name it, keep the type as “A” and enter the instance’s public IPv4 as the Value)

  8. Create the file /etc/nginx/sites-enabled/{website_name}.jcsda.org with the following content:

    Code Block
    server {
    listen 80;
    server_name {website_name}.jcsda.org;
    proxy_buffering off;
    location / {
            proxy_pass http://localhost:8866;
            proxy_set_header Host $host;
            proxy_set_header X-Real-IP $remote_addr;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

            proxy_http_version 1.1;
            proxy_set_header Upgrade $http_upgrade;
            proxy_set_header Connection "upgrade";
            proxy_read_timeout 86400;
    }

    client_max_body_size 100M;
    error_log /var/log/nginx/error.log;
}

     

  9. Enable and start the nginx service.

    Code Block
    sudo systemctl enable nginx.service
sudo systemctl start nginx.service


  10. Install pip

    Code Block
    sudo apt update && sudo apt install python3-pip

     

...

  1. Create /usr/lib/systemd/system/voila.service with the contents:

    Code Block
    [Unit]
Description=Voila

[Service]
Type=simple
PIDFile=/run/voila.pid
ExecStart=voila --no-browser --show_traceback=False jtd/voila/app.ipynb
User=ubuntu
WorkingDirectory=/home/ubuntu/
Restart=always
RestartSec=10

[Install]
WantedBy=multi-user.target

     

  2. Enable and start the voila.service:

    Code Block
    sudo systemctl enable voila.service
sudo systemctl start voila.service

     

  3. Restart nginx

    Code Block
    sudo systemctl restart nginx.service

     

    4. Enable access to https:

    Code Block
    sudo snap install core; sudo snap refresh core
sudo snap install --classic certbot
sudo ln -s /snap/bin/certbot /usr/bin/certbot
sudo certbot --nginx
  4. Check access on https://{website_name}.jcsda.org, it should be up and running

Troubleshooting

How to run the web apps on a locally

How to print to output from ipywidgets

import ipywidgets as widgets
out = widgets.Output(layout={'border': '1px solid black'})
display(out)

from jedi_data_viewer_experiments import JediDataViewerExperiments
jedi_data_viewer_experiments = JediDataViewerExperiments(out)

with self._out: print("")

Web page fails to load

Issue: the web pages will fail to load/ timeout

Explanation: Each time the website is hit a new python kernel is opened and will stay open forever. Therefore, when the instance memory is full of these python kernels the page will go down.

...

  1. -user.target

     

  2. Enable and start the voila.service:

    Code Block
    sudo systemctl enable voila.service
sudo systemctl start voila.service

     

  3. Restart nginx

    Code Block
    sudo systemctl restart nginx.service

     

  4. Enable access to https:

    Code Block
    sudo snap install core; sudo snap refresh core
sudo snap install --classic certbot
sudo ln -s /snap/bin/certbot /usr/bin/certbot
sudo certbot --nginx


  5. Check access on https://{website_name}.jcsda.org, it should be up and running