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Cloud server

These are internal notes from Jeroen on how I set up the public cloud server. These are not official instructions! They are specific to my setup. Consult the PDF server manual for general instructions

Setup opencpu-server

New linode server with Ubuntu 16.04. To enable apparmor, change kernel to GRUB2 which boots the official Ubuntu kernel.

sudo apt-get update
sudo apt-get dist-upgrade

# Add user (interactive)
sudo adduser jeroen
sudo visudo

# Change hostname
sudo echo "dev.opencpu.org" > /etc/hostname

Now reboot. Then login as jeroen

sudo apt-get install byobu software-properties-common
sudo add-apt-repository ppa:opencpu/opencpu-2.2 && sudo apt-get update
sudo apt-get install opencpu-server

# test it
curl http://localhost/ocpu/info

Setup mail server relay

sudo apt-get install postfix libsasl2-modules

Then edit the file /etc/postfix/sasl_passwd and add a (replace PASSWORD with plaintext password):

smtp.mailgun.org [email protected]:PASSWORD

Then run:

sudo postmap /etc/postfix/sasl_passwd
sudo chmod 0600 /etc/postfix/sasl_passwd /etc/postfix/sasl_passwd.db

Now edit /etc/postfix/main.cf and set:

# Set by Jeroen
relayhost = smtp.mailgun.org

# At the end if the fuke
smtp_sasl_auth_enable = yes
smtp_sasl_password_maps = hash:/etc/postfix/sasl_passwd
smtp_sasl_security_options = noanonymous

And then run sudo service postfix restart

Copy apps from old server

When upgrading R it may be easier to reinstall all apps using this script.

When using the same version of R, we can just copy the installed files:

sudo -i
cd /usr/local/lib/opencpu
rsync -avz -e ssh [email protected]:/usr/local/lib/opencpu/apps .

Setup nginx cache server

New server. Run:

sudo add-apt-repository ppa:opencpu/opencpu-dev 
sudo apt-get update
sudo apt-get install opencpu-cache

Setup HTTPS

sudo apt-get install certbot
sudo certbot certonly --manual -d *.ocpu.io -d *.opencpu.org

And follow the steps. To auto-renew, add a sudo (root) crontab:

0 0 1 * * /usr/bin/certbot renew

Configure the back-end server ip address:

# Update opencpu server
sudo vi /etc/nginx/conf.d/opencpu.conf

# Also set rstudio back-end server
sudo vi /etc/nginx/opencpu.d/rstudio.conf

Enable the ocpu.io site

sudo ln -s /usr/lib/opencpu/ocpu.io/ocpu-io /etc/nginx/sites-available/ocpu-io
sudo /usr/lib/opencpu/scripts/nginx_ensite ocpu-io
sudo /usr/lib/opencpu/scripts/nginx_ensite opencpu-homepage

Now also update the cert in the main site (default uses snakeoil):

sudo vi /etc/nginx/sites-available/opencpu

And restart

sudo service nginx restart

Optionally you can limit connections of the backend from only nginx

sudo vi /etc/apache2/sites-enabled/opencpu

Insert the IP address where it says require local, e.g. require ip 123.123.123.123. Also make sure to close port 80.

Update DNS

Update DNS records for:

  • ocpu.io
  • dev.opencpu.org
  • dev1.opencpu.org

In Linode control panel under 'Remote access' you can set the 'Reverse DNS'.

Enable RSPM

Edit /etc/opencpu/Rprofile and add:

options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))

Making Java Work

Arggh, Java. I think we always jdk:

sudo apt-get install openjdk-8-jdk
sudo R CMD javareconf

However rApache doesn't read javaconf. The easiest workaround is just

sudo ln -s /usr/lib/jvm/default-java/jre/lib/amd64/server/libjvm.so /usr/lib/

That should allow for loading the rJava package. But there is more. The JVM has a memory allocation bug which require you set rlimit.as in /etc/opencpu/server.conf far boven the required amount of memory.

Make TensorFlow work

See here. I ran this as root:

sudo apt-get install python3-pip python3-dev python3-virtualenv 
sudo pip3 install --upgrade tensorflow h5py