Common Setup

Introduction

This document is the first section of three explaining how to install the CBRAIN platform:

Common Setup -> BrainPortal Setup -> Bourreau Setup

For a general overview of these documents, please refer to the section, "Overview of installation process", in the Setup Guide.

This particular document explains how to install the UNIX environment and files common to both the BrainPortal Rails and Bourreau Rails applications.

This document describes the initial installation steps for either:

A personal CBRAIN server for development by an individual programmer, or
A production server for multiple users.

It is assumed that the person reading this document is a reasonably competent UNIX user and familiar with command-line environments, as well as typical system administration concepts such as libraries, packages, filesystem paths, networking and environment variables.

All commands shown in this guide use the bash command-line interpreter.

1. About the platform

CBRAIN is a Ruby on Rails application at its core. You can find out more about Ruby (the programming language) and Ruby on Rails (the web-based framework) online here: rubyonrails.org

The two Rails applications

There are in fact two distinct types of Rails applications in a typical CBRAIN installation:

A BrainPortal application, which provides the CBRAIN web frontend and most of the other capabilities of the platform.
A Bourreau application, which is a simpler, lighter Rails application that is deployed on each of the supercomputer servers and receives commands from the BrainPortal application.

The three Rails environments

In Rails, there are development and test environments that are mostly used by individual programmers working on an application. For CBRAIN, this usually consists of a single BrainPortal application running locally and a single Bourreau application running alongside. In this case the Bourreau application appears to be on a supercomputer server even though it is likely just running on the programmer's own desktop computer. Information about customizing these environments can be found in the document on Development Hints.

A production environment usually consists of a set of multiple instances of the BrainPortal application running on the main web server and a single Bourreau application running separately on each of the supercomputer clusters that are available to users. Information about deploying a production environment can be found in the document on Production Hints.

As a side note, Bourreau (pronounced "Boo-Row") is the French word for an executioner (the profession) and its plural is Bourreaux (pronounced exactly the same way, since the "x" is silent).

2. System requirements

Before installing CBRAIN, make sure that the system meets the following basic requirements.

i. Supported operating systems

CBRAIN has been developed and deployed successfully on two major classes of operating systems:

Mac OS X, versions named Snow Leopard all the way to Mavericks (and it would probably work on later versions too).
Linux, in particular the CentOS and Ubuntu distributions.

With a few adjustments to the following instructions, CBRAIN can likely be deployed on many other flavors of Linux or other UNIX operating systems.

ii. OpenSSH

OpenSSH is normally installed on the aforementioned operating systems. If you are using Linux and it has not been installed, use the local package manager to install it or ask the system administrator to do so.

iii. MySQL (or MariaDB)

Access to a MySQL server is necessary. You can either install your own MySQL server or use one already available. It is necessary to have on the server:

A standard user account (do not use the root account!).
A database with full write access. This database must also be blank, meaning that it exists (with any name that you choose) but there are NO TABLES in it yet.

It is outside the scope of this guide to describe the steps necessary to set up such a system. But there is plenty of documentation online explaining how to install a MySQL server, create an account, and create a database on it. Nevertheless, the basic steps for setting up a MySQL administrator account (assuming we are creating a database for a development environment) are as follows:

create database cbrain_dev;
create user     'cbrain'@'localhost' identified by 'oh-oh-this-is-a-pw';
grant all on cbrain_dev.* to 'cbrain'@'localhost';

Note that the database is never accessed from any other machine than the one where the BrainPortal is installed; all the other resources that need to access it within the CBRAIN system do so using SSH tunnels. This is a convenient security feature, as it means the database server never has to be directly exposed to the outside world. More information about the communication infrastructure can be found in the CBRAIN Communications document.

A note about MariaDB: the CBRAIN developers have never tested CBRAIN on MariaDB, but are quite confident that it would work perfectly well with it too.

iv. Xcode for Mac OS X

If Mac OS X is used for development, then it is necessary to install Xcode. A typical Macintosh computer does not come with any development tools and so they must be installed separately. Xcode is free and provided by Apple as a download.

3. Software installation

CBRAIN is a complex piece of Ruby software, but its installation is made much simpler by the use of a few excellent external applications.

i. RVM

RVM (Ruby Version Manager) is an all-in-one solution for installing and managing Ruby interpreters and Ruby libraries packaged as gems. The instructions for installing RVM with a UNIX account can be found on the web site. We recommend setting up a plain RVM environment without installing any other components right away: the RVM documentation proposes an all-in-one installation of RVM, Ruby and Rails, but here we set them up separately.

The steps are as follows:

Install RVM itself

cd $HOME
# See the RVM home page to double-check the following command!
# You will likely need to install a PGP key first.
# See https://rvm.io
\curl -sSL https://get.rvm.io | bash -s stable
# Follow the RVM instructions...

Log out, and then log back in (to start a new shell session) and verify that RVM is installed:
```
rvm info
```

A report shows the version of RVM that is installed and possibly other system information. If instead the message rvm: command not found is shown, then either you did not log out or RVM was not installed properly.

ii. Ruby

It is important to consider which version of Ruby to install. CBRAIN has been tested and deployed on many Ruby versions including Ruby 2.2.0. This is the version that is currently recommended (minor upgrades to this version are fine too). Ruby versions before 2.0 may not work well.

In the following steps, RVM is used to install Ruby.

rvm install 2.4.1

This is often a step where problems occur; to install Ruby there are several system libraries and packages that must also be installed and RVM attempts to install them. If you are using a system where you do not have administrative privileges, ask the sysadmin to do this for you. Once these packages are installed, try installing Ruby again a second time.

Once Ruby is installed, use the following commands for RVM to use it as a default whenever you connect:

rvm use 2.4.1
rvm --default 2.4.1

You can run 'rvm info' again to make sure this version is selected.

iii. CBRAIN code base

Next extract the CBRAIN code base to the location where you plan to deploy it. The easiest way to do this is to clone the repository directly from GitHub.

cd $HOME      # or anywhere else you prefer
git clone https://github.com/aces/cbrain.git

This creates a directory called 'cbrain' with all of the files for the two Rails applications, in subdirectories named BrainPortal and Bourreau.

iv. Gems

Ruby Gems are convenient packages for Ruby libraries and applications. A consequence of installing Ruby with RVM, as described above, is that you should now have access to a utility called 'bundler' which provides a nice front-end to installing and encapsulating a bunch of Ruby gems. If 'bundler' is not installed (you can check with 'which bundle') then you can install it with:

gem install bundler --no-ri --no-rdoc

At this point the steps are different, depending on which of the following components you want to install:

The BrainPortal application (the web frontend),
The Bourreau (the execution server side application), or
Both

If you want to install the BrainPortal application, run the bundler from its directory and all the required Ruby Gems are installed. Carry out the following steps:

cd cbrain/BrainPortal   # make sure you are IN BrainPortal/ !
bundle install          # note: the command is 'bundle' without a 'r'

In the same way, if you want to install the Bourreau application, run the bundler from its directory:

cd cbrain/Bourreau      # make sure you are IN Bourreau/ !
bundle install          # note: the command is 'bundle' without a 'r'

The BrainPortal and Bourreau side each has a particular set of gems that they require, with some gems common to both. There are several gems that require compilation of custom code and this is where most installation problems occur. Often it is simply a matter of installing some development libraries on the system.

Here is a table of libraries that are often required:

CentOS package name	Ubuntu package name
mysql-devel	libmysqlclient-dev
MariaDB-devel	libmariadbclient-dev
libxml2	libxml2
libxml2-devel	libxml2-dev
libxslt	libxslt
libyaml-devel	libyaml-dev

There is one more step, once all of the gems are installed. Because of a tiny bug in the install process of the gem 'sys-proctable', it is necessary to use the following procedure:

Find out where the gem has been installed by the bundler.
Go to that directory.
Run the command 'rake install' (which modifies or copies a file, but may also give error messages, which can be safely ignored):

  bundle show sys-proctable
  (copy the directory shown)
  cd /to/that/directory
  rake install

v. Plugins installation

Some components of CBRAIN can be installed separately. They are distributed in plugins packages; the structure of these packages is described in the Plugins Structure document, but for the moment we only install the default components that come with the base CBRAIN installation. If there are other third-party plugins packages that you want to use, extract them under 'BrainPortal/cbrain_plugins' first (even if right now you plan to install only a Bourreau).

Installing the plugins packages requires running a rake task.

For a BrainPortal:

cd BrainPortal
rake cbrain:plugins:install:all

For a Bourreau:

cd Bourreau
rake cbrain:plugins:install:all

The base CBRAIN distribution comes with a plugins package already extracted, called "cbrain-plugins-base", which contains some simple Userfile and CbrainTask definitions. A CBRAIN installation would probably not work at all without this package.

This rake task can be run many times without causing any problems.

4. Moving on

At this point most of the basic files and programs needed to configure either the BrainPortal or Bourreau application are in place.

If you are installing a BrainPortal application, then follow the instructions in the BrainPortal Setup document.
If you have already set up a BrainPortal and are ready to install a Bourreau (there can be more than one for each BrainPortal), then follow the instructions in the Bourreau Setup document.

5. Additional help

Refer to the Troubleshooting and FAQ documents for general information and hints about common issues. If these documents do not provide answers to your questions, then you might consider contacting us. Our contact information is at the bottom of the Home page.

Note: Original author of this document is Pierre Rioux

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