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Mateo Garcia edited this page Jul 20, 2018 · 47 revisions

This document describes different steps to install a euglena lab server

Repository

Install Ubuntu 18.04 LTS

Create an account with username mserver

Add a root account

sudo passwd root

Log in as root

su

Change /etc/passwd and replace 1000 for mserver to 2000 (both instances -- the user ID and the group ID)

Change /etc/group and replace 1000 for mserver to 2000

Change ownership of all files belonging to the user:

find / -uid 1000 -exec chown -h 2000 {} +
find / -gid 1000 -exec chgrp -h 2000 {} +

(Don't fear 'Operation not permitted' warnings for processes, i.e. /proc...)

Logout and relogin into shell. (If you receive 'who are you' warnings, reboot the machine.)

git clone git@github.com:hirklab/euglenalab.git
cd euglenalab/
git submodule init
git submodule update --recursive

You will likely need to generate an SSH key and add it to your GitHub account under Settings for the above to work.

Configure

cp deployment.js.sample deployment.js
cp .env.default .env

Update deployment.js and .env for IPs, Database and Execute. Then:

sudo ./setup_iptables.sh

If you lose Internet access after the above, reboot the machine.

Virtual Environment (Optional)

sudo apt-get update

sudo easy_install --upgrade pip
sudo apt-get install python-pip python-dev build-essential 
sudo apt-get install autoconf libtool nasm yasm cmake libav-tools
sudo apt-get install libjpeg8-dev imagemagick libv4l-dev libavcodec-dev libswscale-dev libkrb5-dev cmake
sudo pip install --upgrade pip 
sudo pip install --upgrade virtualenv 
sudo pip install --upgrade virtualenv virtualenvwrapper
echo "export WORKON_HOME=~/.virtualenv" >> ~/.bashrc
echo ". /usr/local/bin/virtualenvwrapper.sh" >> ~/.bashrc
mkdir -p ~/.virtualenv     
source ~/.bashrc
mkvirtualenv euglenalab

pip install nodeenv xlsxwriter numpy 
nodeenv -p
workon euglenalab

Shared

cd shared/
npm install
cd ..

Connect to Production Server (only needed if storage server is not local to same machine)

ssh-copy-id mserver@euglena.stanford.edu

Database [Host Server]

Stores all tables for user details, experiments, live experiments in queue

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927
echo "deb http://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.2.list
sudo apt-get update
sudo apt-get install -y mongodb-org
sudo service mongod start

mkdir db
scp mserver@euglena.stanford.edu:tmp/dump/master.tar.gz db/
cd db
tar xvzf master.tar.gz
mongorestore -d dev ./master
cd ..

Webserver [Host Server]

Main Server which interacts with user frontend to authenticate and run experiments

Setup processing data links for file download and video display

cd ~/euglenalab/server/public/media/finalBpuDataLinks
ln -sf ~/finalBpuData ./

cd ~/euglenalab/server
./install.sh
./run.sh
cd ..

If the forever command is not found, you may need to install it globally:

sudo npm install forever -g

BPU Controller [Host Server]

Middleware between webserver and BPUs which

  • controls which BPU should handle the next experiment
  • maintains queue for all the experiments
  • routes all user commands for experiments to BPUs from webserver

Executing controller

cd controller
npm install
./run.sh
cd ..

Processing Server [Host Server]

It executes multiple processing nodes to ingest all the images recorded for the experiment and process them into a movie and multiple data files for later analysis.

cd processing
./build.sh

Link OpenCV to virtualenv

cd ~/.virtualenv/euglenalab/lib/python2.7/site-packages/
ln -s /usr/local/lib/python2.7/site-packages/cv2.so cv2.so

Build GoLang

sudo apt install golang
echo 'export GOPATH=$HOME/go' >> ~/.bashrc
echo 'export PATH=${PATH}:${GOPATH}/bin' >> ~/.bashrc
source ~/.bashrc
go get gopkg.in/mgo.v2

If using virtual environment:

workon euglenalab

Execute

./run.sh

Storage Setup [Host Server]

sudo apt-get install nfs-common nfs-kernel-server
sudo nano /etc/exports

Add below

/home/mserver/bpuEuglenaData_forMounting 192.168.1.100/24(rw,async,no_wdelay,crossmnt,no_root_squash,insecure_locks,sec=sys,anonuid=1025,anongid=100)

Create a directory /home/mserver/bpuEuglenaData_forMounting

Execute

sudo service nfs-kernel-server start
sudo exportfs

This should show the below

/home/mserver/bpuEuglenaData_forMounting
	192.168.1.100/24

BPU Setup [BPU]

Hostname and IP Setup

Change /etc/hosts to reflect IP for Eug-X

Change /etc/hostname to name for eug-X

Change /etc/network/interfaces to reflect IP for Eug-X

Filesystem

sudo raspi-config

Choose Expand the filesystem

Choose Enable Camera

If camera is not working, execute

sudo modprobe bcm2835-v4l2

Add below to /etc/modules-load.d/modules.conf

bcm2835-v4l2

Execute

sudo reboot
cd euglenalab-github/setupBpuScripts/

Make change for auto-mounting

sudo nano /etc/fstab
192.168.1.100:/home/mserver/bpuEuglenaData_forMounting /mnt/bpuEuglenaData nfs rw,nosuid,nolock        0       0
    sudo reboot

Following command does the same operation for once. Changes do NOT persist reboot

Mount

   sudo mount 192.168.1.100:/home/mserver/bpuEuglenaData_forMounting /mnt/bpuEuglenaData -v

Set Folder Permissions

sudo chown -R pi:bpudata /mnt/bpuEuglenaData/
sudo chmod -R 775 /mnt/bpuEuglenaData/

Start Streamer

./mountAndStartImageStreamer.sh

Start Server

cd ../bpu
./initLeds.sh
./startBpu.sh

(You can also start the above scripts in the background by running ./run_bpu.sh.)

Know Public IP

curl http://ipecho.net/plain

Database config [Host Server]

Add BPU to mongoDB via mongoBooster. Specifically, add to the BPU table.

Make sure BPU is in the list in ./shared/mainConfig.js and

Shared Storage [Host Server + Synology NAS server]

Network Configuration [Host Server]

  1. Open the RV325 Gigabit Dual WAN VPN Router (using Opera browser) [https://192.168.1.1/default.htm]

  2. On the left menu click setup --> Port Address Translation PAT

  3. Click on 'Service Management...' tab below the Port Address Translation Table

  4. Click on 'Add' to add a device (e.g. CameraN). Set the external port value to (20000+(N*5)), and internal port value to 8080 for CameraN. Then click 'Save'.

  5. Click on 'Add' tab below the Port Address Translation Table and select the new device you included (e.g. CameraN). Set the 'Name or IP Address' value to the static BPU IP you used for your BPU. Select 'Enable' option.

Firewall Controller Setup [Host Server]

  1. Open the Firewall application
  2. Set the following values: a. Profile: Public b. Status: ON c. Incoming: Allow d. Outgoing: Allow
  3. Click on the '+' under 'Rules' and select 'Advanced' tab
  4. Set the following values: a. Name: EugN b. Insert: N+1 (for a new BPU) c. Policy: Allow d. Direction: Out e. Interface: All Interfaces f. Log: Do Not Log g. Protocol: Both h. From: 192.168.1.(200+(N*5)) 8080 i. To: 171.65.102.104 20000+(N)
  5. Click 'Add'

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