Introduction

We deployed a shiny-app that demonstrate acmt-network. Note that the geocoder and mapper sends data to openstreetmap and is not private.

This also implements a few functionalities that would otherwise not achievable without shiny-server pro. Multiple Docker containers, each hosting the same shiny-app, are created to parallel shiny-app serving. Connection time out and load-balancing over the containers are also enabled using HAProxy.

Below describes the steps for future reference.

Install the app for acmt-network

0. screen -r run_acmt_network
1. Download acmt-network with git clone https://github.com/2533245542/acmt-network.git.
2. cd acmt-network
3. Open vim src/app/Dockerfile. Uncomment the following lines of code.

#RUN R -e "install.packages(c('shiny', 'shinythemes', 'tidygeocoder'))"
#RUN yes | apt-get install gdebi-core
#RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.16.958-amd64.deb
#RUN yes | gdebi shiny-server-1.5.16.958-amd64.deb
#RUN git clone https://github.com/2533245542/acmt-shiny.git /srv/shiny-server/acmt_shiny
#RUN sed -i '2s/.*/run_as rstudio;/' /etc/shiny-server/shiny-server.conf
#RUN sed -i '17s#.*#path <- "http://172.17.0.1:5000/latlong?"#' /home/rstudio/workspace/GeocoderACMT.R
#RUN sed -i '49s#.*#acs_columns_url <- "http://172.17.0.1:7000/ACSColumns.csv"#' /home/rstudio/workspace/GeocoderACMT.R
#CMD shiny-server

4. Run acmt-network with docker compose -f docker-compose.yml -f docker-compose.shiny.yml up --build in this screen and put the screen to background.

5. Try these websites: acmt.csde.washington.edu acmt.csde.washington.edu:8000/acmt_shiny acmt.csde.washington.edu:8000 acmt.csde.washington.edu:8000/sample-apps/hello/

Note that the terminal has to be remained open for serving the app (but not if the sys rebbot and auto start-up launch is enabled).

schedule daily system reboot and launch acmt-shiny at system start-up

Run crontab -e and add the below lines to the end of the file, save.

00 1 * * * sudo shutdown -r
@reboot cd /home/wzhou87/deploy/acmt-network;docker compose -f docker-compose.yml -f docker-compose.shiny.yml up --build

The first line schedules a system reboot daily at 1am; the second runs acmt-shiny at start-up

enable connection time out and load balancing

Add to the end of the file

backend shiny_backend
       mode http
       balance leastconn
       timeout connect 300s
       timeout client 300s
       timeout server 300s # the one that decides the time out
       server shiny_backend_1   127.0.0.1:8000
       server shiny_backend_2   127.0.0.1:8080
       server shiny_backend_3   127.0.0.1:8081
       server shiny_backend_4   127.0.0.1:8082
       server shiny_backend_5   127.0.0.1:8083

other commands

see log

cd /var/log/shiny-server

make a port open

systemctl stop shiny-server

nginx

nginx -s reload vim /etc/nginx/nginx.conf nginx -s stop

docker images and containers operation

stop all running containers

docker stop $(docker ps -aq)

remove all containers

docker rm $(docker ps -aq)

remove an image

docker rmi acmt-network_app

remove a container

docker stop acmt-network-app-1
docker rm acmt-network-app-1
docker stop acmt-network-app1-1
docker rm acmt-network-app1-1

enter a running container

docker exec -it acmt-network-app-1 /bin/bash

haproxy

start proxy with sudo service haproxy start, start app with docker compose up --build, 8080 does not work when accessing with http://acmt.csde.washington.edu:8080/acmt_shiny, 443 also not work when accessing with http://acmt.csde.washington.edu:443 stop proxy with sudo service haproxy stop, start app with docker compose up --build, 8080 works when accessing with http://acmt.csde.washington.edu:8080/acmt_shiny, 443 not work when accesing with http://acmt.csde.washington.edu:443, start proxy, 8000 and 8080 still works, 443 still not work sudo systemctl reload haproxy

sudo service haproxy stop;sudo service haproxy start

miscelanous

Restart the app after a server shutdown

1. screen -S run_acmt_network
2. run systemctl stop shiny-server to close port 8000 if opened previously
3. in acmt-network, run docker compose up --build

Uninstall the app on the server

docker system prune -a --volumes --force since this is the only Docker process we run on the server.

Start the app for testing

In global.R, set acmt_network_path <- "../local_acmt_network_development/local_acmt_network_v0.0.10/" to the path to the location of the ACMT source files.

In acmt-shiny, do

library(shiny)
runApp()

Install acmt-shiny directly on the server

0. Install prerequisites following acmt-network/src/app/Dockerfile (tidyverse, libudunits2-dev, libgdal-dev, R -e "install.packages(c('geosphere', 'lwgeom', 'raster', 'sf', 'tidycensus', 'tigris', 'units', 'USAboundaries', 'reshape2', 'rgeos', 'osrm', 'leaflet'))", R -e "install.packages(c('shiny', 'shinythemes', 'tidygeocoder'))", gdebi-core, shiny-server)
1. download acmt-shiny with sudo git clone https://github.com/2533245542/acmt-shiny.git /srv/shiny-server/acmt_shiny
2. download acmt-network with git clone https://github.com/2533245542/acmt-network.git ~/direct_deploy/acmt_network
3. vim acmt_network/src/app/workspace/GeocoderACMT.R, set enable_connection_to_docker_network to FALSE and comment out

        download.file(url = "http://sandbox.idre.ucla.edu/mapshare/data/usa/other/spcszn83.zip", destfile = "ACMT/spcszn83.zip")
        unzip("ACMT/spcszn83.zip", exdir="ACMT")
        download.file(url = "https://www2.census.gov/geo/tiger/GENZ2017/shp/cb_2017_us_county_500k.zip", destfile = "ACMT/cb_2017_us_county_500k.zip")
        unzip("ACMT/cb_2017_us_county_500k.zip", exdir="ACMT")

4. sudo vim /srv/shiny-server/acmt_shiny/global.R to set the path to ~/direct_deploy/acmt_network/src/app/workspace
5. sudo vim /etc/shiny-server/shiny-server.conf to set run_as wzhou87 and listen 8000.
6. run shiny-server to start the shiny server.