Successfully Deploying and Scaling Shiny Apps with ShinyProxy, Traefik and Docker Swarm

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Desk of Contents

Introduction

When you seek for R Shiny apps deployment and landed on this submit, chances are high you might be like me – an information scientist who simply wish to construct an honest app to host a dashboard or a prediction mannequin with out happening to the rabbit gap of DevOps or the frontend/backend improvement. Don’t fear, that is simply the factor you want and I promise nothing under is just too sophisticated. You’ll be able to in all probability undergo the next tutorial in half an hour. Now. let’s begin.

On this submit, we’ll construct a scalable, production-grade Shiny app powered by ShinyProxy and Docker Swarm and use Traefik to deal with the SSL certificates (which provides you the little padlock in entrance of your area identify), reverse proxy (for routing visitors from the 80 and 443 ports to your Shiny app and different locations if wanted) and cargo balancing.

Docker Swarm Architecture

If you’re not conversant in ShinyProxy and surprise why you must use it over the opposite choices, I’ve written one other submit titled
Deploying R Shiny apps utilizing ShinyProxy on Home windows 10 that explains it in additional element. When you haven’t used Docker know-how earlier than, it is usually a good suggestion to take a look at that submit first. Within the curiosity of house, I received’t cowl too many particulars concerning Docker on this tutorial.

Docker Swarm vs customary Docker containers

You in all probability surprise why you want Docker Swarm relatively than simply utilizing docker-compose to deploy containers, notably in the event you solely have one server/node/occasion. Docker Captain Bret Fisher defined it nicely
right here. I summarised a few key advantages of Docker Swarm under:

  • Docker Swarm is totally supported by Docker Engine, which implies 1) it solely takes a single line of command to create a Swarm and a couple of) it saves you time to manually set up docker-compose, which isn’t obtainable in the usual Docker Engine.
  • You’re future-proofed. If you wish to change into highly-available and scale out your app, you received’t want to begin from scratch. Once more, with Docker Swarm, it’s only a few instructions away from including extra nodes.
  • docker-compose is simply designed for improvement, not manufacturing, because it lacks a few necessary options out-of-the-box: 1) dealing with secret (that shops your keys and passwords securely) 2) auto-recovery of providers, 3) rollbacks and 4) healtchecks. The final one is especially essential for manufacturing.
  • You’ll be able to do rolling replace with Docker Swarm, which implies no downtime to your app.
  • Lastly, in case you are already utilizing docker-compose.yml file, it’s only a couple tweaks away to make it Docker Swarm pleasant!

Docker Swarm vs Kubernetes

When it comes to container orchestration instruments, Kubernetes is extra well-liked. It covers virtually all of the use circumstances and could be extra versatile than Docker Swarm. Plus, many distributors undertake the ‘Kubernetes first’ help technique and a few clouds even handle/deploy Kubernetes for you. Nonetheless, I’d nonetheless argue that Docker Swarm is enough for 80% of the use circumstances and method a lot simpler to arrange. This implies you may have your app working in hours relatively than days!

Traefik vs Nginx

If in case you have learn my earlier submit
Securing and monitoring ShinyProxy deployment of R Shiny apps, you could surprise why I switched away from Nginx to Traefik. That is primarily as a result of ease of arrange. Nginx settings can find yourself in big config maps which are onerous to learn and handle. This isn’t a difficulty with Traefik, which lets you use Docker labels to handle configs. We’ll see this later within the tutorial.

Stipulations

To be able to undergo the tutorial, you want not less than one server with the next specs:

  • Ubuntu Server 18.04 LTS LTS (though different variations might also work)
  • Minimal 1 GiB of reminiscence
  • Minimal Eight GB of storage
  • Set up Docker Engine

If in case you have an AWS Free Tier account, a free t2.micro occasion can be high quality. Nonetheless, I’d suggest you go for one thing with 2 GiB of reminiscence (e.g. t3a.small) in the event you additionally wish to check out the monitoring/managing instruments (e.g. Swarmpit, Grafana, and so on.) talked about later on this tutorial. My expertise is that ShinyProxy makes use of about 200-300 MiB of reminiscence and the demo Shiny app makes use of about 100 MiB. On high of that, in the event you depend the Traefik stack, you in all probability don’t have sufficient remaining reminiscence for the extra providers.

You additionally have to set the related ports so the Swarm nodes can talk with one another and permit visitors to your app. It’s best to use the AWS Safety Group (or equal from different Clouds) for simple setup and administration. Beneath are the particular settings:

SHOW AWS safety group settings

Swarm Supervisor Safety Group (Inbound Guidelines):

TYPE PROTOCOL PORTS SOURCE
Customized TCP Rule TCP 2377 Swarm managers and employees
Customized TCP Rule TCP 7946 Swarm managers and employees
Customized UDP Rule UDP 7946 Swarm managers and employees
Customized UDP Rule UDP 4789 Swarm managers and employees
Customized Protocol 50 all Swarm managers and employees
SSH TCP 22 Your ip
HTTP TCP 80 Wherever
HTTPS TCP 443 Wherever

Swarm Employee Safety Group (Inbound Guidelines):

TYPE PROTOCOL PORTS SOURCE
Customized TCP Rule TCP 7946 Swarm managers and employees
Customized UDP Rule UDP 7946 Swarm managers and employees
Customized UDP Rule UDP 4789 Swarm managers and employees
Customized Protocol 50 all Swarm managers and employees
SSH TCP 22 Your ip

We’ll first arrange a supervisor node. Upon getting launched the occasion with the related ports opened, we’ll set up Docker Engine utilizing the setup script.

curl -fsSL https://get.docker.com -o get-docker.sh
sh get-docker.sh

After putting in Docker, I’d recommend that you just add your consumer to the ‘docker’ group in order that you possibly can use Docker as a non-root consumer.

sudo usermod -aG docker ubuntu

And don’t neglect the logout and again in for this transformation to take impact. Then you must be capable of run docker instructions with out utilizing sudo.

Organising Docker Swarm

As talked about, you simply want one line of command to provoke a Docker Swarm, as it’s constructed into the usual Docker Engine.

docker swarm init

You will note one thing like this:

Swarm initialized: present node (xxxx) is now a supervisor.

We then have to get the be part of token for managers and employees.

docker swarm join-token employee
docker swarm join-token supervisor

Word down the be part of instructions. So as to add nodes to the present Swarm as a supervisor or employee, you merely have to launch one other occasion, set up Docker Engine and run the be part of instructions. Nonetheless, we don’t have to set them up for now.

Organising domains to your app and system dashboards

Let’s say you personal the area instance.com and also you wish to use the subdomain app.instance.com to your app. It is advisable to create the next DNS information to your app and Traefik dashboard:

RECORD TYPE NAME VALUE
A app.instance.com IP of your Swarm Grasp occasion
A traefik.sys.app.instance.com IP of your Swarm Grasp occasion

Organising Traefik stack

Our subsequent activity is to arrange the proxy/load balancer Traefik.
Docker Swarm Rocks has an exquisite tutorial for it. I’ve summarised the important thing steps right here. First, we have to create an overlay community shared with Traefik and permit nodes on the Swarm to speak with one another. Word that that is totally different from the host-specific networks we create utilizing the default bridge driver, which solely permits networking between containers in a single server. The overlay community sits on high of (overlays) the host-specific networks and permits containers related to it to speak securely when encryption is enabled.

docker community create --driver=overlay traefik-public

Get the Swarm node ID of this node and retailer it in an atmosphere variable.

export NODE_ID=$(docker information -f '{{.Swarm.NodeID}}')

Create a tag on this node, in order that Traefik is all the time deployed to the identical node and makes use of the identical quantity.

docker node replace --label-add traefik-public.traefik-public-certificates=true $NODE_ID

Create an atmosphere variable together with your e-mail, for use for the technology of Let’s Encrypt certificates.

export EMAIL=admin@instance.com

Create an atmosphere variable with the area you wish to use for the Traefik dashboard. When you specified a special area identify earlier than, you want to replace the under code accordingly. You’ll entry the Traefik dashboard at this area.

export DOMAIN=traefik.sys.app.instance.com

Create an atmosphere variable with a username (you’ll use it for the HTTP Fundamental Auth for Traefik dashboard).

export USERNAME=admin

Create an atmosphere variable that shops the hashed password. Word that the under command will assist you to enter the password into an interactive immediate, which is safer simply typing into the shell (which shall be saved within the shell historical past).

export HASHED_PASSWORD=$(openssl passwd -apr1)

Verify when you have efficiently created a password:

echo $HASHED_PASSWORD

It is going to appear like:

$apr1$HOr/xJFw$uUY15r1qS.5AA2hk.ssda1

Now, let’s deploy the primary stack – Traefik. The writer at Docker Swarm Rocks did a tremendous job of constructing this course of as straightforward as doable. You merely have to obtain the yaml file.

curl -L dockerswarm.rocks/traefik.yml -o traefik.yml

If you wish to edit the yaml file, I’ve copied them under. Word that there are some helpful feedback inline that inform you what every a part of code does.

SHOW traefik.yml

model: '3.3'
providers:
traefik:
# Use the most recent Traefik picture
picture: traefik:v2.2
ports:
# Hear on port 80, default for HTTP, essential to redirect to HTTPS
- 80:80
# Hear on port 443, default for HTTPS
- 443:443
deploy:
placement:
constraints:
# Make the traefik service run solely on the node with this label
# because the node with it has the quantity for the certificates
- node.labels.traefik-public.traefik-public-certificates == true
labels:
# Allow Traefik for this service, to make it obtainable within the public community
- traefik.allow=true
# Use the traefik-public community (declared under)
- traefik.docker.community=traefik-public
# Use the customized label "traefik.constraint-label=traefik-public"
# This public Traefik will solely use providers with this label
# That method you may add different inner Traefik cases per stack if wanted
- traefik.constraint-label=traefik-public
# admin-auth middleware with HTTP Fundamental auth
# Utilizing the atmosphere variables USERNAME and HASHED_PASSWORD
- traefik.http.middlewares.admin-auth.basicauth.customers=${USERNAME?Variable not set}:${HASHED_PASSWORD?Variable not set}
# https-redirect middleware to redirect HTTP to HTTPS
# It may be re-used by different stacks in different Docker Compose information
- traefik.http.middlewares.https-redirect.redirectscheme.scheme=https
- traefik.http.middlewares.https-redirect.redirectscheme.everlasting=true
# traefik-http arrange solely to make use of the middleware to redirect to https
# Makes use of the atmosphere variable DOMAIN
- traefik.http.routers.traefik-public-http.rule=Host(`${DOMAIN?Variable not set}`)
- traefik.http.routers.traefik-public-http.entrypoints=http
- traefik.http.routers.traefik-public-http.middlewares=https-redirect
# traefik-https the precise router utilizing HTTPS
# Makes use of the atmosphere variable DOMAIN
- traefik.http.routers.traefik-public-https.rule=Host(`${DOMAIN?Variable not set}`)
- traefik.http.routers.traefik-public-https.entrypoints=https
- traefik.http.routers.traefik-public-https.tls=true
# Use the particular Traefik service api@inner with the net UI/Dashboard
- traefik.http.routers.traefik-public-https.service=api@inner
# Use the "le" (Let's Encrypt) resolver created under
- traefik.http.routers.traefik-public-https.tls.certresolver=le
# Allow HTTP Fundamental auth, utilizing the middleware created above
- traefik.http.routers.traefik-public-https.middlewares=admin-auth
# Outline the port within the Docker service to make use of
- traefik.http.providers.traefik-public.loadbalancer.server.port=8080
volumes:
# Add Docker as a mounted quantity, in order that Traefik can learn the labels of different providers
- /var/run/docker.sock:/var/run/docker.sock:ro
# Mount the quantity to retailer the certificates
- traefik-public-certificates:/certificates
command:
# Allow Docker in Traefik, in order that it reads labels from Docker providers
- --providers.docker
# Add a constraint to solely use providers with the label "traefik.constraint-label=traefik-public"
- --providers.docker.constraints=Label(`traefik.constraint-label`, `traefik-public`)
# Don't expose all Docker providers, solely those explicitly uncovered
- --providers.docker.exposedbydefault=false
# Allow Docker Swarm mode
- --providers.docker.swarmmode
# Create an entrypoint "http" listening on handle 80
- --entrypoints.http.handle=:80
# Create an entrypoint "https" listening on handle 80
- --entrypoints.https.handle=:443
# Create the certificates resolver "le" for Let's Encrypt, makes use of the atmosphere variable EMAIL
- --certificatesresolvers.le.acme.e-mail=${EMAIL?Variable not set}
# Retailer the Let's Encrypt certificates within the mounted quantity
- --certificatesresolvers.le.acme.storage=/certificates/acme.json
# Use the TLS Problem for Let's Encrypt
- --certificatesresolvers.le.acme.tlschallenge=true
# Allow the entry log, with HTTP requests
- --accesslog
# Allow the Traefik log, for configurations and errors
- --log
# Allow the Dashboard and API
- --api
networks:
# Use the general public community created to be shared between Traefik and
# every other service that must be publicly obtainable with HTTPS
- traefik-public
volumes:
# Create a quantity to retailer the certificates, there's a constraint to ensure
# Traefik is all the time deployed to the identical Docker node with the identical quantity containing
# the HTTPS certificates
traefik-public-certificates:
networks:
# Use the beforehand created public community "traefik-public", shared with different
# providers that have to be publicly obtainable through this Traefik
traefik-public:
exterior: true


When you’ve gotten the file in your server, cd to the file listing and use the next command to deploy a Docker Swarm stack.

docker stack deploy -c traefik.yml traefik

There is just one service on this stack. You’ll be able to examine the standing of this service utilizing:

docker service ls

You will note one thing like under:

ID NAME MODE REPLICAS IMAGE PORTS
moybzwb7mq15 traefik_traefik replicated 1/1 traefik:v2.2 *:80->80/tcp, *:443->443/tcp

It’s named as traefik_traefik as a result of it’s deployed right into a stack referred to as traefik and the service identify can be referred to as traefik. You’ll be able to customise them in the event you like. Additionally, observe that the REPLICAS variable exhibits you the variety of copy of this service. ‘1/1’ means we wish just one copy and there may be one up and working. You’ll be able to examine the log utilizing:

docker service logs traefik_traefik

A couple of minutes after deploying the stack, Traefik ought to arrange the SSL certificates to your website utilizing Let’ Encrypt. You could discover that is a lot simpler and cleaner than my earlier answer. Now, take a look at traefik.sys.instance.com. It’s best to see the Traefik dashboard (use the username and password you simply set to log in).

Traefik Dashboard 1

There are some key ideas, which I’ve summarised under:

  • Suppliers: Uncover the providers that dwell in your infrastructure (their IP, well being, …). We’re utilizing Docker right here.
  • Entrypoints: Hear for incoming visitors (ports, …). We’ve got the 80 and 443 open for HTTP and HTTPS visitors.
  • Routers: Analyse the requests (host, path, headers, SSL, …). At present, we solely route related to traefik.sys.app.instance.com. We are able to arrange different routers later.
  • Companies: Ahead the request to your providers (load balancing, …).
  • Middlewares: Might replace the request or make selections primarily based on the request (authentication, fee limiting, headers, …)

These have been created utilizing the instructions and labels within the traefik.yml file. For particulars, you could wish to examine the
official Traefik documentation.

Organising ShinyProxy stack

Let’s transfer on to arrange our principal ShinyProxy stack. Only a reminder that this stack consists of the ShinyProxy (acts like a container supervisor for Shiny apps) and your Shiny apps. First, clone
my GitHub repo:

git clone https://github.com/presstofan/shinyproxy-docker-swarm-demo.git

There are two necessary information that I wish to level out right here.

software.yml within the ‘software’ folder is the config file for ShinyProxy. I’ve already set it as much as work with Docker Swarm. I’ve added feedback within the file however simply wish to flag out a few issues:

  1. title could be modified to no matter you want.
  2. Please maintain the default port 8080 for ShinyProxy to make issues simpler.
  3. Word that the Utilization Statistics Monitoring part has been commented out. Please examine the non-obligatory sections under if you wish to set it up.
  4. To make the demo straightforward, it’s set to easy authentication. Nonetheless, I strongly advise you to vary to a stronger authentication in manufacturing. Once more, please examine the non-obligatory sections later on this tutorial the place I offered some steering to arrange the OpenID Join authentication with AWS Cognito.
  5. container-backend have to be set to ‘docker-swarm’ to make it appropriate with Swarm mode.
  6. Underneath specs, you may specify the Shiny apps you wish to serve. Right here I set it up to make use of a demo app euler from my Docker Hub repo. Please examine this submit for the way to construct a Shiny app picture to make use of in ShinyProxy.
SHOW software.yml

proxy:
title: My Superior Shiny Portal
port: 8080 # use Port 8080 for ShinyProxy
container-wait-time: 30000 # how lengthy ought to we look ahead to the container to spin up (30s as default as that is sufficient for our Shiny apps)
heartbeat-rate: 10000 # the consumer's browser will ship a heartbeat name each heartbeat-rate milliseconds (10s as default)
heartbeat-timeout: 60000 # if the server doesn't obtain a heartbeat for heartbeat-timeout milliseconds, the related proxy shall be launched (60s as default)
#### Set Up Utilization Statistics Monitoring
# usage-stats-url: http://influxdb:8086/write?db=shinyproxy_usagestats # use InfluxDB to retailer utilization statistics; could be in a special server
# usage-stats-username: xxxx # influxdb username if wanted
# usage-stats-password: xxxx # influxdb password if wanted
#### OpenID Join Authentication ####
# authentication: openid # use openid auth framework
# openid:
# roles-claim: cognito:teams # use the teams worth handed by AWS cognito to establish consumer teams
# auth-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/oauth2/authorize
# token-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/oauth2/token
# jwks-url: # https://cognito-idp.{area}.amazonaws.com/{userPoolId}/.well-known/jwks.json
# logout-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/logout?client_id={client_id}&logout_uri={your_host_url}
# client-id: # get this from AWS Cognito consumer pool administration web page
# client-secret: # get this from AWS Cognito consumer pool administration web page
#### Easy Authentication (for demo solely, do not use in manufacturing) ####
authentication: easy
admin-groups: admins
customers:
- identify: admin
password: admin
teams: admins
- identify: take a look at
password: take a look at
teams: admins
# Set the container backend: The container-backend could be certainly one of docker (default), docker-swarm or Kubernetes
container-backend: docker-swarm
docker:
internal-networking: true
# Beneath is a listing of Shiny apps and their config
specs:
- id: euler
display-name: Euler's quantity
container-cmd: ["R", "-e", "shiny::runApp('/root/euler')"]
container-image: presstofan/shiny-euler-app # this have to be changed with your individual Shiny app in manufacturing
access-groups: admins # give particular entry proper to a gaggle
container-network: sp-net
server:
useForwardHeaders: true # this is essential to make the AWS Cognito auth works
logging:
file:
shinyproxy.log


shinyproxy.yml is the docker-compose file that we’ll use to deploy the ShinyProxy stack. Once more, I’ve set it up for the tutorial however please observe that:

  1. There are two providers, shinyProxy after which demo Shiny app euler. You’ll be able to add extra Shiny apps to be served however don’t neglect to replace the software.yml file.
  2. The shinyProxy service is on two overlay networks, traefik-public and sp-net. You’ll be able to consider these are the frontend community and backend community to make sure higher safety. We might want to arrange the sp-net community shortly. euler and different Shiny apps solely have to be on the sp-net community, not exposing to the web straight.
  3. Much like the traefik service, we wish to solely place the shinyproxy service on Swarm Supervisor nodes. We’ll begin with just one duplicate.
  4. The labels part is the place we specify configuration values for Traefik. Docker labels don’t do something by themselves, however Traefik reads these so it is aware of the way to deal with containers. Word that this have to be service-level labels relatively than container-level (i.e. beneath the deploy tag). In a nutshell, the labels instruct Traefik to be careful for requests for a selected area (specified by the atmosphere variable APP_DOMAIN, which we’ll set shortly) and route the visitors to port 8080 of the shinyproxy service.
SHOW shinyproxy.yml

model: '3.3'
providers:
shinyproxy:
picture: presstofan/shinyproxy-example
# The labels part is the place you specify configuration values for Traefik.
# Docker labels don’t do something by themselves, however Traefik reads these so
# it is aware of the way to deal with containers.
ports:
- 8080
networks:
- traefik-public
- sp-net
deploy:
replicas: 1
restart_policy:
situation: on-failure
placement:
constraints:
- node.position==supervisor
labels:
- traefik.allow=true # allow traefik
- traefik.docker.community=traefik-public # put it in the identical community as traefik
- traefik.constraint-label=traefik-public # assign the identical label as traefik so it may be found
- traefik.http.routers.shinyproxy.rule=Host(`${APP_DOMAIN?Variable not set}`) # hearken to port 80 for request to APP_DOMAIN (use along with the road under)
- traefik.http.routers.shinyproxy.entrypoints=http
- traefik.http.middlewares.shinyproxy.redirectscheme.scheme=https # redirect visitors to https
- traefik.http.middlewares.shinyproxy.redirectscheme.everlasting=true # redirect visitors to https
- traefik.http.routers.shinyproxy-secured.rule=Host(`${APP_DOMAIN?Variable not set}`) # hearken to port 443 for request to APP_DOMAIN (use along with the road under)
- traefik.http.routers.shinyproxy-secured.entrypoints=https
- traefik.http.routers.shinyproxy-secured.tls.certresolver=le # use the Let's Encrypt certificates we arrange earlier
- traefik.http.providers.shinyproxy-secured.loadbalancer.server.port=8080 # ask Traefik to seek for port 8080 of the shinyproxy service container
volumes:
- ./software/software.yml:/decide/shinyproxy/software.yml
- /var/run/docker.sock:/var/run/docker.sock
euler:
picture: presstofan/shiny-euler-app
networks:
- sp-net
networks:
traefik-public:
exterior: true
sp-net:
exterior: true


After cloning the repo, cd into shinyproxy-docker-swarm-demo

cd shinyproxy-docker-swarm-demo/

Don’t neglect to arrange the atmosphere variable APP_DOMAIN. This needs to be the area of your app you arrange earlier together with your DNS supplier.

export APP_DOMAIN=app.instance.com

And arrange the overlay community sp-net:

docker community create --driver=overlay sp-net

Then, you may deploy the ShinyProxy stack.

docker stack deploy -c shinyproxy.yml shinyproxy

We are able to examine the standing of the service utilizing:

docker service ls

You will note the next providers (it might probably take a couple of minutes to obtain the pictures for the primary time):

ID NAME MODE REPLICAS IMAGE PORTS
llqkqa5fjymj shinyproxy_euler replicated 1/1 presstofan/shiny-euler-app:newest
dgiss3o277q2 shinyproxy_shinyproxy replicated 1/1 presstofan/shinyproxy-example:newest *:30000->8080/tcp
moybzwb7mq15 traefik_traefik replicated 1/1 traefik:v2.2 *:80->80/tcp, *:443->443/tcp

Give it a minute and examine app.instance.com and you will note the login display. Log in with the password you set in software.yml to see the demo app.

ShinyProxy

When you go to the Traefik dashboard, now you can discover the extra router, service and middleware associated to ShinyProxy.

Scaling your Swarm cluster

Now involves the attention-grabbing half. Let’s say in case your app is getting well-liked and also you wish to launch an extra server to share the workload. You’ll be able to simply add nodes to your Swarm.

First, we have to launch one other AWS occasion (or server from different Clouds). Repeat the steps above however this time we wish to use the safety group settings for Swarm Employees.

SHOW AWS safety group settings

Swarm Employee Safety Group (Inbound Guidelines):

TYPE PROTOCOL PORTS SOURCE
Customized TCP Rule TCP 7946 Swarm managers and employees
Customized UDP Rule UDP 7946 Swarm managers and employees
Customized UDP Rule UDP 4789 Swarm managers and employees
Customized Protocol 50 all Swarm managers and employees
SSH TCP 22 Your ip

SSH into the brand new occasion and set up Docker Engine as above. When that’s accomplished, we have to be part of the Swarm we arrange and the be part of token we obtained from the Supervisor node would come in useful. Run it within the new occasion. The token would appear like one thing under:

docker swarm be part of --token SWMTKN-1-xxxxxxxxxxxxxxxxxxx-xxxxxxxxxxxxxxx 172.x.x.x:2377

If profitable, you’d see the message ‘This node joined a swarm as a employee.’ When you now change to the Supervisor node shell and run:

docker node ls

You’ll see:

ID HOSTNAME STATUS AVAILABILITY MANAGER STATUS ENGINE VERSION
5b6py13brdoihrcct9oy68wpq * ip-172-31-49-53 Prepared Energetic Chief 19.03.10
3j3ecsf4fhz3cwhu98w5cv1bo ip-172-31-71-189 Prepared Energetic 19.03.10

Congratulations! You’ve simply created your two-node Swarm. Traefik and ShinyProxy solely get deployed on the Supervisor node as we instructed however the Shiny apps could be deployed to the Employee nodes. Docker because the load balancer will handle that routinely. You’ll be able to confirm this by launching the app and docker service ls the providers. The Shiny app is hosted by the brand new service sp-service-xxxxxx. You need to use docker service ps SERVICE to examine the node the service is on. Word that the primary time you deploy a service to a node it’ll take a while to obtain the pictures. However it received’t be an issue afterward because it ought to have the pictures within the cache. One other level I wish to point out is that you’ll have to launch the app with one other username created within the software.yml to see two Shiny providers. It’s because ShinyProxy assigns service/container by the consumer, not session. When a consumer indicators out, the service/container is eliminated.

ID NAME MODE REPLICAS IMAGE PORTS
llqkqa5fjymj shinyproxy_euler replicated 1/1 presstofan/shiny-euler-app:newest
dgiss3o277q2 shinyproxy_shinyproxy replicated 1/1 presstofan/shinyproxy-example:newest *:30000->8080/tcp
4y0yljabbwld sp-service-1d6329ff-1f03-47d5-a297-efd1d2e20f88 replicated 1/1 presstofan/shiny-euler-app
moybzwb7mq15 traefik_traefik replicated 1/1 traefik:v2.2 *:80->80/tcp, *:443->443/tcp

Selecting the variety of nodes

Listed here are some notes on selecting the variety of nodes. In concept, you may arrange a couple of Supervisor nodes (e.g. three and even 5). Nonetheless, the neighborhood version of Traefik received’t help distributed Let’s Encrypt certificates, that means that solely one of many node could be your gateway and your DNS have to level the area to that node. If you’re constructing a posh app that requires HA, you wish to examine
Traefik Enterprise Version. For a lot of use circumstances, making your major Supervisor node sufficiently highly effective (e.g. 2 GiB of reminiscence) and offload Shiny apps to the employees can be ok. There may be much less constraint in selecting the variety of employee nodes and the specs rely upon the app you serve.

Rebalancing nodes

While you add a brand new node to a Swarm or a node reconnects to the Swarm after a interval of unavailability, the Swarm doesn’t routinely give a workload to the idle node. Based on Docker, it is a design determination.

If the swarm periodically shifted duties to totally different nodes for the sake of steadiness, the shoppers utilizing these duties can be disrupted. The objective is to keep away from disrupting working providers for the sake of steadiness throughout the swarm. When new duties begin, or when a node with working duties turns into unavailable, these duties are given to much less busy nodes. The objective is eventual steadiness, with minimal disruption to the top consumer.

If wanted, we may pressure the nodes to rebalance through the use of the command under:

docker service replace --force

That is fairly useful when you have simply added or eliminated many nodes. Nonetheless, the replace causes the service duties to restart. Shopper purposes could also be disrupted.

(Optionally available) Monitoring Docker Swarm with Swarmpit

Your Supervisor node might have 2 GiB of reminiscence to deal with the extra monitoring stack.

Swarmpit gives easy and straightforward to make use of interface to your Docker Swarm cluster. You’ll be able to handle your stacks, providers, secrets and techniques, volumes, networks and so on. To set this up, we first have to create one other A report with our DNS supplier to level to the Supervisor node ip handle.

RECORD TYPE NAME VALUE
A swarmpit.sys.app.instance.com IP of your Swarm Grasp occasion

The method of deploying the Swarmpit stack is similar to how we deployed the Traefik stack.

Arrange the atmosphere variables:

export DOMAIN=swarmpit.sys.app.instance.com
export NODE_ID=$(docker information -f '{{.Swarm.NodeID}}')

Create a label on this node, in order that the CouchDB database utilized by Swarmpit is all the time deployed to the identical node and makes use of the prevailing quantity:

docker node replace --label-add swarmpit.db-data=true $NODE_ID

Create one other label on this node, in order that the Inflow database utilized by Swarmpit is all the time deployed to the identical node and makes use of the prevailing quantity:

docker node replace --label-add swarmpit.influx-data=true $NODE_ID

Obtain the swarmpit.yml

curl -L dockerswarm.rocks/swarmpit.yml -o swarmpit.yml

Or create one within the Supervisor node your self with the template under:

SHOW swarmpit.yml

model: '3.3'
providers:
app:
picture: swarmpit/swarmpit:newest
atmosphere:
- SWARMPIT_DB=http://db:5984
- SWARMPIT_INFLUXDB=http://influxdb:8086
volumes:
- /var/run/docker.sock:/var/run/docker.sock:ro
ports:
- 888:8080
networks:
- web
- traefik-public
deploy:
sources:
limits:
cpus: '0.50'
reminiscence: 1024M
reservations:
cpus: '0.25'
reminiscence: 512M
placement:
constraints:
- node.position == supervisor
labels:
- traefik.allow=true
- traefik.docker.community=traefik-public
- traefik.constraint-label=traefik-public
- traefik.http.routers.swarmpit-http.rule=Host(`${DOMAIN?Variable not set}`)
- traefik.http.routers.swarmpit-http.entrypoints=http
- traefik.http.routers.swarmpit-http.middlewares=https-redirect
- traefik.http.routers.swarmpit-https.rule=Host(`${DOMAIN?Variable not set}`)
- traefik.http.routers.swarmpit-https.entrypoints=https
- traefik.http.routers.swarmpit-https.tls=true
- traefik.http.routers.swarmpit-https.tls.certresolver=le
- traefik.http.providers.swarmpit.loadbalancer.server.port=8080
db:
picture: couchdb:2.3.0
volumes:
- db-data:/decide/couchdb/information
networks:
- web
deploy:
sources:
limits:
cpus: '0.30'
reminiscence: 512M
reservations:
cpus: '0.15'
reminiscence: 256M
placement:
constraints:
- node.labels.swarmpit.db-data == true
influxdb:
picture: influxdb:1.7
volumes:
- influx-data:/var/lib/influxdb
networks:
- web
deploy:
sources:
reservations:
cpus: '0.3'
reminiscence: 128M
limits:
cpus: '0.6'
reminiscence: 512M
placement:
constraints:
- node.labels.swarmpit.influx-data == true
agent:
picture: swarmpit/agent:newest
atmosphere:
- DOCKER_API_VERSION=1.35
volumes:
- /var/run/docker.sock:/var/run/docker.sock:ro
networks:
- web
deploy:
mode: world
sources:
limits:
cpus: '0.10'
reminiscence: 64M
reservations:
cpus: '0.05'
reminiscence: 32M
networks:
web:
driver: overlay
attachable: true
traefik-public:
exterior: true
volumes:
db-data:
driver: native
influx-data:
driver: native


When prepared, deploy the stack utilizing:

docker stack deploy -c swarmpit.yml swarmpit

Verify whether it is working:

docker stack ps swarmpit

It is going to present one thing like under:

ID NAME IMAGE NODE DESIRED STATE CURRENT STATE ERROR PORT
kkhasdfvce30 swarmpit_agent.ndasdfav5 swarmpit/agent:newest canine.instance.com Working Working Three minutes in the past
k8oasdfg70jm swarmpit_agent.i9asdfjps swarmpit/agent:newest cat.instance.com Working Working Three minutes in the past
kcvasdft0yzj swarmpit_agent.3jasdfd3k swarmpit/agent:newest snake.instance.com Working Working Three minutes in the past
9onasdfzopve swarmpit_agent.r6asdfb20 swarmpit/agent:newest snake.instance.com Working Working Three minutes in the past
fxoasdfwjrbj swarmpit_db.1 couchdb:2.3.Zero canine.instance.com Working Working Three minutes in the past
m4jasdf3369c swarmpit_app.1 swarmpit/swarmpit:newest cat.instance.com Working Working Three minutes in the past

Lastly, give it a minute or two and go to swarmpit.sys.app.instance.com to entry to the dashboard. You can be prompted to arrange the login first time you employ it.

Swarmpit

(Optionally available) Monitoring ShinyProxy with Grafana and InfluxDB

Your Supervisor node might have 2 GiB of reminiscence to deal with the extra monitoring stack.

ShinyProxy natively helps utilization statistics monitoring with
InfluxDB, a time-series database. What we have to do is to arrange the InfluxDB service and level ShinyProxy to it. We’ll then use a well known device
Grafana to visualise the information.

First, let’s create the A report together with your DNS supplier for internet hosting Grafana.

RECORD TYPE NAME VALUE
A grafana.sys.app.instance.com IP of your Swarm Grasp occasion

Then, go to the Supervisor node shell and navigate to the shinyproxy-docker-swarm-demo/software folder and open the software.yml file. Find and uncomment the next line:

 #### Set Up Utilization Statistics Monitoring
usage-stats-url: http://influxdb:8086/write?db=shinyproxy_usagestats # use InfluxDB to retailer utilization statistics; could be in a special server

This may inform ShinyProxy to ship the utilization statistics to port 8086 of a container referred to as influxdb on the identical Docker community. It additionally specifies the identify of the goal database shinyproxy_usagestats. Word that in the event you choose, you may launch one other occasion to host the InfluxDB. If that’s the case, the usage-stats-url must level to the brand new occasion. See my earlier tutorial for the way to arrange a
Monitoring Manchine.

ShinyProxy stack received’t be routinely up to date after altering the software.yml. We have to pressure it to restart the service.

docker service replace shinyproxy_shinyproxy --force

A minute later, the ShinyProxy service needs to be up once more with the brand new settings. You’ll be able to examine it by visiting app.instance.com.

Now, we have to create the InfluxDB-Grafana stack. Navigate to the shinyproxy-docker-swarm-demo folder and you can see a file referred to as usagestats.yml. You’ll be able to go away all of the settings as default.

SHOW usagestats.yml

model: '3.3'
providers:
grafana:
picture: grafana/grafana:7.0.1
ports:
- 3000
networks:
- traefik-public
atmosphere:
- GF_SECURITY_ADMIN_USER=${ADMIN_USER:-admin}
- GF_SECURITY_ADMIN_PASSWORD=${ADMIN_PASSWORD:-admin}
- GF_USERS_ALLOW_SIGN_UP=false
deploy:
mode: replicated
replicas: 1
placement:
constraints:
- node.position == supervisor
sources:
limits:
reminiscence: 128M
reservations:
reminiscence: 64M
labels:
- traefik.allow=true
- traefik.docker.community=traefik-public
- traefik.constraint-label=traefik-public
- traefik.http.routers.grafana.rule=Host(`${GRAFANA_DOMAIN?Variable not set}`)
- traefik.http.routers.grafana.entrypoints=http
- traefik.http.middlewares.grafana.redirectscheme.scheme=https
- traefik.http.middlewares.grafana.redirectscheme.everlasting=true
- traefik.http.routers.grafana-secured.rule=Host(`${GRAFANA_DOMAIN?Variable not set}`)
- traefik.http.routers.grafana-secured.entrypoints=https
- traefik.http.routers.grafana-secured.tls.certresolver=le
- traefik.http.providers.grafana-secured.loadbalancer.server.port=3000
volumes:
- grafana:/var/lib/grafana
influxdb:
picture: influxdb:1.8.0
ports:
- 8086
networks:
- traefik-public
- sp-net
deploy:
sources:
reservations:
cpus: '0.3'
reminiscence: 128M
limits:
cpus: '0.6'
reminiscence: 512M
placement:
constraints:
- node.position==supervisor
atmosphere:
INFLUXDB_DB: shinyproxy_usagestats # this have to match the database laid out in software.yml
# INFLUXDB_ADMIN_USER: admin
# INFLUXDB_ADMIN_PASSWORD: admin
# INFLUXDB_HTTP_AUTH_ENABLED: "true" # have to delete quantity if change the database atmosphere
volumes:
- influxdb:/var/lib/influxdb
networks:
traefik-public:
exterior: true
sp-net:
exterior: true
volumes:
grafana:
influxdb:


Create an atmosphere variable referred to as GRAFANA_DOMAIN and assign it to the brand new subdomain you simply created.

export GRAFANA_DOMAIN=grafana.sys.app.instance.com

Launch the Usagestats stack with:

docker stack deploy -c usagestats.yml usagestats

Look forward to a minute and examine the service.

docker service ps usagestats_grafana
docker service ps usagestats_influxdb

And go to grafana.sys.app.instance.com, you will note the login web page. While you log in for the primary time, it’ll immediate you to vary your password. The default password and username are each admin.

Grafana Login

Upon getting signed in, click on on the configuration image on the left and choose Knowledge Supply. When prompted, select InfluxDB.

Grafana Data Source

Beneath is the information supply settings. The naked minimal settings we have to specify is the Title, URL and Database. URL ought to level to InfluxDB, adopted by the 8086 port. On this case, it needs to be ‘http://influxdb:8086’ (or modify it to level to your monitor occasion in the event you set it up individually). Then we might want to put shinyproxy_usagestats for Database.

Grafana Database Settings

As soon as it’s accomplished, click on the Save & Take a look at button on the finish of the web page and you will note a message saying ‘Knowledge supply is workin’.

The subsequent step is to construct the dashboards to visualise the information. To take action, hover on the ‘Plus’ image after which click on ‘Dashboard’. A dashboard comprises a number of panels and every panel consists of the question half and the visualisation half. We’ll begin by clicking ‘Add Question’. Beneath is the panel editor. It features a question builder that lets you get began. There’s a easy question to observe the login within the instance. You may also change to the question textual content enhancing mode, which is extra versatile for my part. There isn’t a lot info recorded by ShinyProxy however you’ve gotten the fundamental info resembling login, sign-out, begin and cease apps. Extra sophisticated queries could be constructed to point out the variety of customers in the intervening time, how lengthy every of them makes use of the apps and and so on. With a little bit learn on the InfluxDB syntax, you must be capable of do it.

Grafana Dashboard ShinyProxy

(Optionally available) Organising AWS Cognito

The tutorial makes use of the easy authentication methodology offered by ShinyProxy, which retailer usernames and passwords in plain textual content within the software.yml. That is hardly a good selection for manufacturing. ShinyProxy natively helps many of the well-liked authentication framework. You’ll be able to examine
right here for particulars. When you determine to make use of AWS Cognito for authentication (which I extremely suggest), you’ll need to arrange a Cognito Person Pool upfront. That is comparatively simple and the official information could be discovered
right here. Step 1 and a couple of within the information are important for this tutorial. Upon getting set the consumer pool, you’ll need to do a few issues:

  1. Take a observe of your Pool Id, which follows the format Pool {area}_{id} (e.g. us-east-1_XXXXXXXXX). From right here, it’s also possible to get the area of your consumer pool, which shall be helpful later.
  2. Create a take a look at consumer account for your self beneath the Customers and teams tab. Create a gaggle referred to as admins and assign the take a look at account to that group.
  3. Create an App shopper referred to as ‘shiny-simulator-test’ (or a reputation of your alternative). Word down the App shopper id and App shopper secret.
  4. Underneath the App integration/App shopper settings, examine Cognito Person Pool because the Enabled Id Suppliers. You may also use different Id suppliers resembling Fb or Google however I received’t cowl them right here.
  5. On the identical web page, set the Callback URL(s) to ‘https://{your_domain}/login/oauth2/code/shinyproxy’ and the Signal out URL(s) to ‘https://{your_domain}’. Within the tutorial, I’ll use ‘app.instance.com’ as a placeholder.
  6. Once more, on the identical web page, beneath OAuth 2.0, examine Authorization code grant, Implicit grant for Allowed OAuth Flows after which examine every little thing apart from cellphone for Allowed OAuth Scopes.
  7. On the App integration/Area identify, set the Area prefix of your alternative and observe down the entire Amazon Cognito area. That is the area identify of the sign-in web page customers shall be redirected to once they go to your web site. You’ve a alternative of establishing your individual area for the sign-in web page.

Then you want to change the next elements of the software.yml, commenting/deleting the Easy Authentication part and uncommenting the OpenID Join Authentication part. You have to the data above. This step is error-prone as I continuously discover myself mistyping the url or setting values. It might be simpler in the event you fork my GitHub repo and put together the settings regionally earlier than importing it to your Supervisor node.

 #### OpenID Join Authentication ####
# authentication: openid # use openid auth framework
# openid:
roles-claim: cognito:teams # use the teams worth handed by AWS cognito to establish consumer teams
auth-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/oauth2/authorize
token-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/oauth2/token
jwks-url: # https://cognito-idp.{area}.amazonaws.com/{userPoolId}/.well-known/jwks.json
logout-url: # https://{cognito_domain_prefix}.auth.{area}.amazoncognito.com/logout?client_id={client_id}&logout_uri={your_host_url}
client-id: # get this from AWS Cognito consumer pool administration web page
client-secret: # get this from AWS Cognito consumer pool administration web page
#### Easy Authentication (for demo solely, do not use in manufacturing) ####
# authentication: easy
# admin-groups: admins
# customers:
# - identify: admin
# password: admin
# teams: admins
# - identify: take a look at
# password: take a look at
# teams: admins

Don’t neglect to pressure the service to restart to make the settings take impact.

docker service replace shinyproxy_shinyproxy --force

Subsequent Steps

That concludes this tutorial. We should always have a scalable Shiny app served by ShinyProxy with a secured host and monitoring functionality. Utilizing Docker Swarm and Traefik makes our lives a lot simpler and the deployment needs to be future-proofed. One factor that’s good to have is the power to elastically scale the app. This proofs to be a non-trivial activity and I’ll discover in future posts.

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