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deploying-rap3-with-azure

Ampersand in Ordina's cloud

In early 2017 the need arose for an Ampersand implementation in Ordina's cloud, to let young professionals get acquainted with Ampersand. We chose to implement RAP3 in Azure, because Ordina has an Azure subscription. RAP3 is the same environment that our students use at the Open Universiteit, so the maintainance of RAP3 can be reused for both target audiences.

This chapter is an account of the installation process. It is an example for those who want to deploy Ampersand by hand.
I suppose this is useless, because we can now deploy Ampersand automatically, using docker. But I cannot exclude there are reasons for doing this.

  1. It documents the installation we made for Ordina.
    We want maintenance of RAP3 to be transferrable to other persons, so we need to document the choices made and the reasons for making them.

  2. It contains all information needed to make a deployment script for automated deployment.
    We want to automate deployment, so that RAP3 will always be up to date with the most recent stable release of Ampersand.

Each step in the installation process gets a separate section in this text. It is not necessary to do them in the given order.dir

1. Setting up the virtual machine​

I needed an Azure account to enter the Azure portal and install a server for Ampersand. I got my account from Ordina, using the Azure subscription named 'Ordina TC - RT O Pega - Learning'. Azure offers preconfigured installations to kick-start a virtual machine. I picked LAMP by Bitnami.

The following settings were (or will be) made:

server nameWolfram
type VM-diskHDD
OSUbuntu 14.04.5
configurationBitnami LAMP 5.6.27-0
documentationhttps://docs.bitnami.com/azure/infrastructure/lamp
Admin user nameampersandadmin
verification typepassword (Stef Joosten knows the password)
Resource group (in Azure)Ampersand
location (in Azure)Western Europe
Size4 core, 8 GB, 8 disks, Max. IOP's 8x500
Inbound port: HTTPTCP/80
Inbound port: HTTPSTCP/443
Inbound port: SSHTCP/22
Inbound port: SFTPTCP/22
Public IP-adres52.174.4.78
PHP version (RAP3 requires PHP version 5.6 or higher)5.6.27
{APPDIR}= the directory into which the RAP3 files will be deployed/home/bitnami/htdocs
{APPACC}= the account under which the RAP3 application will run (the apache account, i.e. ${APACHE_RUN_USER} c.q. ${APACHE_RUN_GROUP} as defined in apache2.conf)daemon (this name is set in /opt/bitnami/apache2/conf/original/httpd.conf)
{APPHOST} = the URI of the machine that hosts the RAP3 application (e.g. 'mydomain.org', or 'rap3.mydomain.org')
{APPPORT} = the port at which the Apache server will be listening80
{APPURI} = the URI at which the RAP3 application will be accessible for browsers (e.g. 'mydomain.org/RAP3', or 'RAP3.mydomain.org')
{APPURL} = the full name for calling the application (e.g. https://mydomain.org:8080/RAP3', or [https://RAP3.mydomain.org\](https://RAP3.mydomain.org%29\)

I have been able to access this machine through SSH, using the Admin user name and password. I have verified the PHP-version by using the command php --version. In the sequel, I will refer to this machine as "the server".

TODO: make sure that {APPHOST} can be found by DNS.

I have verified that that any applicable firewalls allow traffic on port 80 {APPPORT} by browsing from outside the network to 52.174.4.78 (the public IP-address).

2. Getting MySQL and phpMyAdmin to work​

To run RAP3 requires Apache and MySQL. Both are already installed on the server. However, you need the database administrator password to set it up for Ampersand. This step requires a server, so you must have finished section 1 successfully.

To get into phpMyAdmin can only be done in localhost. This requires an SSH-tunnel into the server. The instruction is found on https://docs.bitnami.com/azure/components/phpmyadmin. I got it done using PuTTY as my SSH-client. Upon success, you can log in to phpMyAdmin in your browser using http://127.0.0.1:8888/phpmyadmin (case sensitive!)

Instructions on how to find the initial password for phpMyAdmin are found on https://docs.bitnami.com/azure/faq/#find_credentials. Since Bitnami-documentation on the web describes different ways to obtain the phpMyAdmin root password and only one of them works, I had a hard time getting the right password. I found it in the diagnostic data for startup, as described in the abovementioned link. When installing the virtual machine, DO NOT switch off the diagnostics for startup, because you will not get the log that contains the root-password.

After logging into phpMyAdmin as root, I created a user called 'ampersand' with password 'ampersand' and host 'localhost', in compliance with the defaults used in the Ampersand compiler. I have issued limited authorizations:

![](/assets/MySQL authorization.png)

3. Uploading and running RAP3​

To run RAP3, the web-application must be installed on /home/bitnami/htdocs. This step requires sections 1 and 2 to be finished successfully. It also requires you to have a complete RAP3 web-application available for uploading to the server. If you don't have that web-application, you need to build it. Upon completion of step 8 you will have built that web-application by yourself.

To upload RAP3, I followed the instructions on https://docs.bitnami.com/azure/faq/#how-to-upload-files-to-the-server-with-sftp to upload the RAP3 web-application from my laptop onto the server. I put it on /home/bitnami/htdocs, which is the location of web-applications on this particular configuration. (On vanilla Linux this would be on /var/www, I guess). This screenshot shows the situation after the transfer:![](/assets/Filezilla with RAP3.png)

To allow the computer to upload files and write logs if needed, you must make daemon the owner of these files, because that user represents the Apache server.

sudo chown -R daemon /opt/bitnami/apache2/htdocs/RAP3/

Remark: This is not the way to go. The best practice is to tell Apache2 to behave as ampersandadmin. That way, in case of problems Apache can only "destroy" RAP3-stuff, rather than wreck the entire system because he is "daemon".

You can test whether this is successful by browsing to 52.174.4.78/RAP3/

It should show:

![](/assets/initial RAP3 screen.png)

Because the Apache server needs to write files and create directories, it is necessary that it has a shell. I checked this in the file /etc/passwd. This file contains a line that starts with daemon, which is the user of the Apache server.

daemon❌1:1:daemon:/usr/sbin:/bin/bash

If the last part of that line reads/bin/bash, you know that Apache can execute shell commands. (I discovered this while solving a Slim Application Error, saying that mkdir()fails, which was caused by Apache not having a shell at its disposal.)

Now you are done.

If you need to restart the apache server for whatever reason, here is the command:

sudo /opt/bitnami/ctlscript.sh restart apache

If there are problems, check the Apache server:

4. Filling and updating the Git repository with Ampersand files and Ampersand models​

To build an Ampersand-compiler, we need the Ampersand source files, which reside in a GitHub repository. We can download these source files on a fresh server, so this step merely requires section 1 to be finished successfully. The RAP3 source files reside in a GitHub repository as well, so we'll just clone both repositories into the server.

Git comes preconfigured in Bitnami's LAMP configuration.

First time: make Git repositories​

I have used Git on the command line to get the Ampersand source code and the Ampersand model repository cloned onto the server.

I have created /home/ampersandadmin/git for storing the local clones. Here is what I did:

mkdir ~/git

cd ~/git

git clone https://github.com/AmpersandTarski/Ampersand

git clone https://github.com/AmpersandTarski/Ampersand-models

Now you are done. The directory /home/ampersandadmin/git/Ampersand contains the source code of the Ampersand compiler. The directory /home/ampersandadmin/git/Ampersand-models contains the source code of the Ampersand models.

To verify that the Ampersand clone has succeeded and that you are in the development branch, navigate to ~/git/Ampersand and ask for the Git status:

bitnami@Wolfram:~/git/Ampersand$ git status

On branch development

Your branch is up-to-date with 'origin/development'.

nothing to commit, working directory clean

You can do the same in the Ampersand-models directory. There you must verify that you are in the master branch:

bitnami@Wolfram:~/git/Ampersand$ cd ../Ampersand-models/

bitnami@Wolfram:~/git/Ampersand-models$ git status

On branch master

Your branch is up-to-date with 'origin/master'.

nothing to commit, working directory clean

Subsequent use: update Git repositories​

To update RAP3 to a new version, I have pulled the sources from the Github repository into the git-repository on Wolfram:

cd ~/git/Ampersand-models/
git pull

This works, because a pull action does a fetch automatically. To update the Ampersand compiler to to a new version, I have pulled the sources from the Github repository into the git-repository on Wolfram:

cd ~/git/Ampersand/
git pull

5. Installing Haskell​

In order to build an Ampersand-compiler, we need a Haskell installation. This can be done on a clean machine, so this step merely requires section 1 to be finished successfully.

I have used Haskell stack for installing Haskell. First I installed stack by following the instructions on the internet for a generic Linux installation:

bitnami@Wolfram:~$ sudo apt-get update

bitnami@Wolfram:~$ curl -sSL https://get.haskellstack.org/ | sh

Stack works. It is installed to /usr/local/bin/stack.

Stack gives a warning about the PATH:

WARNING: '/home/ampersandadmin/.local/bin' is not on your PATH.

For best results, please add it to the beginning of PATH in your profile.

Haskell puts the binaries it produces on ~/.local/bin/. For this reason I have added this directory to the $PATH variable by changing the file ~/.profile. In this file I edited:

# set PATH so it includes user's private bin if it exists

if [ -d "$HOME/.local/bin" ] ; then

PATH="$HOME/.local/bin:$PATH"

fi

6. Creating an Ampersand-compiler​

To generate RAP3 we need an Ampersand-compiler. The RAP3 user will also use that compiler. For both reasons, we need a working Ampersand compiler on the server. This step requires sections 4 and 5 to be finished successfully.

Having the source code of the Ampersand-compiler on the system, I created an executable by running stack install. Here is what I did:

cd ~/git/Ampersand

stack setup

stack install

A 1-core machine with 1.75GB memory has been shown too small to build the Ampersand-compiler. In that case, stack install does not show any progress. It got stuck without any hints about what is wrong. It did succeed on a 4-core 8GB configuration (A4).

7. Installing LaTeX and GraphViz​

When the RAP3-user generates documentation, RAP3 will call on pdflatex, neato and dot. For this purpose we must install LaTeX and GraphViz. This can be done on a fresh server, so this step only requires section 1 to be finished successfully.

For generating pictures, Ampersand needs the commands dot and neato. For that purpose I installed:

bitnami@Wolfram:~$ sudo apt-get install graphviz

That worked.

As RAP3 lets the user generate documentation, Ampersand needs the command pdflatex . For that purpose I followed the instructions on https://www.tug.org/texlive/quickinstall.html.

Here is what I did to install texlive:

  1. I decided to Install TeX Live over the Internet.
  2. I downloaded install-tl-unx.tar.gz to my home directory /home/ampersandadmin. This gave me the archive file.
  3. I unpacked the archive saying tar -zxvf install-tl-unx.tar.gz. This resulted in a directory install-tl-20170411.
  4. Then I changed to the new directory by saying: cd install-tl-20170411.
  5. I then ran ./install-tl. (Somehow it didn't work without ./ up front).
  6. In install-tl, I selected options abcfgkvwXIKPS (by running command C) to get a not-too-large installation that does everything Ampersand needs. After selection I returned to the main menu by command R. By the way, this can be done using a profile file, which is useful for unattended installation.
  7. Then I ran the installer by running command I. That took a while (about an hour or so).
  8. I updated the file /home/ampersandadmin/.profile to prepend "/usr/local/texlive/2016/bin/x86_64-linux" to the PATH, so that the shell can find the required binaries.
  9. I ran a test to see whether all packages for TeX Live are present. They weren't. When running the test, pdflatex provides the name of a missing package, e.g. "! LaTeX Error: File `glossaries.sty' not found." I used tlmgr install glossaries to install the missing package. I did that for each missing package.
  10. The directories used by TeX Live are:

TEXDIR (the main TeX directory):

/usr/local/texlive/2016

TEXMFLOCAL (directory for site-wide local files):

/usr/local/texlive/texmf-local

TEXMFSYSVAR (directory for variable and automatically generated data):

/usr/local/texlive/2016/texmf-var

TEXMFSYSCONFIG (directory for local config):

/usr/local/texlive/2016/texmf-config

TEXMFVAR (personal directory for variable and automatically generated data):

~/.texlive2016/texmf-var

TEXMFCONFIG (personal directory for local config):

~/.texlive2016/texmf-config

TEXMFHOME (directory for user-specific files):

~/texmf

The easier way seems to be:

bitnami@Wolfram:~$ sudo apt-get install texlive

However, that did not work. On internet, apt-get install texliveis discouraged because it results in outdated latex stuff.

8. Installing SmartGit (a nice-to-have)​

For looking into the local Git repository, it is nice to have a Git-client installed. This step requires section 1 to be finished successfully.

When updates of Ampersand are being deployed, this is done via GitHub. For this reason it is convenient to have a Git-client on this machine. Sourcetree, however, does not work on Linux. So I installed Smartgit:

bitnami@Wolfram:~$  sudo add-apt-repository ppa:eugenesan/ppa

bitnami@Wolfram:~$  sudo apt-get update

bitnami@Wolfram:~$  sudo apt-get install smartgit

I have not yet figured out how to run Smartgit. I presume to have to make a graphical terminal tunnel of some sort to run it.

9. Local Settings​

To inspect and change the local settings, you need the file localsettings.php on directory ~/git/Ampersand-models/RAP3/include. This step requires section 4 to be finished successfully. This file contains comments that guide you to use the correct settings in a development situation and in a production situation. Read the file and follow the instructions it contains, especially when making the transition from development to production.

Logging can be switched on and off (or tuned) in your localsettings.php file.

I have made a file called localSettingsAzure.php, to use for copying the right settings just after RAP3 has been updated from GitHub. The localSettings.php in GitHUb is of course not the one needed in Wolfram.

10. Generating the RAP3 application​

To generate the code of the RAP3 web-application, you need to run the Ampersand compiler on the RAP3 source code. So, this step requires sections 4 and 6 to be finished successfully.

It requires to execute the following commands:

 cd ~/git/Ampersand-models/
git pull
cd ~/git/Ampersand-models/RAP3/
sudo chown -R bitnami /home/bitnami/htdocs/RAP3
ampersand --meta-tables --add-semantic-metamodel -p/home/bitnami/htdocs/RAP3 RAP3.adl --verbose
sudo chown -R bitnami /home/bitnami/htdocs/RAP3
sudo chmod -R g+w /home/bitnami/htdocs/RAP3
sudo cp ./include/localSettingsAzure.php /home/bitnami/htdocs/RAP3/localSettings.php

Generating RAP3 takes a while. If everything works out, the compiler terminates with the message: "Finished processing your model." Whenever I want to monitor progress, I have appended --verbose to the ampersand command, to get information about intermediate results. I used the chgrp and chmod commands to allow the Apache server write access to the RAP3 directory. Generating everything first to a new directory, RAP, keeps the downtime between updates low for the user. Before compiling RAP3, I checked the version and the current branch of the RAP3 source code:

cd ~/git/Ampersand-models/
git status

If, for whatever reason, you want to delete earlier versions of the deployed RAP3-code, use this command:

sudo rm -rfd /home/bitnami/htdocs/RAP3

11. Last minute changes before going to production​

  1. In the source code of RAP3, in the file SIAM_importer.adl:
    1. disable "RAP3_LoginForDevelopment.ifc", to prevent users from seeing
    2. enable "RAP3_LoginForProduction.ifc"
    3. disable "../SIAM/SIAM_AutoLoginAccount.adl"
  2. Edit the file /home/ampersandadmin/git/RAP3/include/localSettingsAzure.php and follow instructions in it. Make sure to copy it to /home/bitnami/htdocs/RAP3/localSettings.php before going live.

12. Security measures​

The following measures have to be taken. Currently, they are not in effect.

  1. SSH configuration: prevent that outside users log in as daemon (nor as root) (see for example [http://serverfault.com/questions/285800/how-to-disable-ssh-login-with-password-for-some-users\](http://serverfault.com/questions/285800/how-to-disable-ssh-login-with-password-for-some-users%29\)
  2. Apache: see https://httpd.apache.org/docs/trunk/misc/security_tips.html
  3. HTTPS-cookies need a flag "Secure", "HHTP-only", and "Samesite". This needs to be addressed in the application code; not in the deployment.

13. Troubleshooting​

13.1 When reinstalling the database ...​

A symptom of installation problems with the database is excessive waiting for a reponse, while "Hello, world!" is in the browser screen. It does take a while, because all rules must be checked. However, anything over 10 minutes is excessive.

If the browser shows messages in this process, check whether a database exists in the first place. (See step 2 for instructions). If there is no database, check the file /home/bitnami/htdocs/RAP/localSettings.php

Check the database credentials (dbUser, dbHost, dbPassword) are set to the correct values in the local settings. Do not set dbName. Make sure that Config::set('productionEnv', 'global', false) is set to enable reinstallation of the database.
Be sure to set it back to true after a new database is made.

31.2 Deadlock on all signals table​

At some point in time, while Stef and Han were accessing RAP3 in different sessions, we got a timeout (See this issue). While unsure what the exact problem is, we guessed that the all_sessions table could cause this problem.

After googleing around, I decided that it might be a good idea to increase the timeout value. So I added the following line into the file /opt/bitnami/mysql/my.cnf :

innodb_lock_wait_timeout=600

Also, because we do not know what is going on, I decided to enable the logging of deadlocks:

innodb print all deadlocks = ON