Installation¶
If you would like to contribute to Dallinger, please follow these alternative install instructions.
Installation Options¶
Dallinger is tested with Ubuntu 14.04 LTS, 16.04 LTS, 18.04 LTS and Mac OS X locally. We do not recommended running Dallinger with Microsoft Windows, however if you do, running Ubuntu in a virtual machine is the recommend method. You can also read about what is possible with using Dallinger with Docker here.
Using Dallinger with Docker¶
Docker is a containerization tool used for developing isolated software environments. Read more about using Dallinger with Docker here.
Install Python¶
Dallinger is written in the language Python. For it to work, you will need to have Python 2.7 installed, or alternatively Python 3.6 or higher. Python 3 is the preferred option. You can check what version of Python you have by running:
python --version
You will also need to have pip installed. It is included in some of the later versions of Python 3, but not all. (pip is a package manager for Python packages, or modules if you like.)
Mac OS X¶
Using Homebrew will install the latest version of Python and pip by default.
brew install python
This will install the latest Python3 and pip3.
You can also use the preinstalled Python in Mac OS X, currently Python 2.7 as of writing.
If you installed Python 3 with Homebrew, you should now be able to run the python3 command from the terminal.
If the command cannot be found, check the Homebrew installation log to see
if there were any errors. Sometimes there are problems symlinking Python 3 to
the python3 command. If this is the case for you, look here for clues to assist you.
With the preinstalled Python in Mac OS X, you will need to install pip yourself. You can use:
sudo easy_install pip
Should that not work for whatever reason, you can search here for more clues.
Ubuntu¶
Ubuntu 18.04 LTS ships with Python 3.6.
Ubuntu 16.04 LTS ships with Python 3.5, while Ubuntu 14.04 LTS ships with Python 3.4. In case you are using these distribution of Ubuntu, you can use dallinger with Python 2.7 or upgrade to the latest Python 3.x on your own.
(All three of these Ubuntu versions also provide a version of Python 2.7)
If you do not have Python 3 installed, you can install it from the Python website.
Also make sure you have the python headers installed. The python-dev package contains the header files you need to build Python extensions appropriate to the Python version you will be using. You will also need to install pip.
If using Python 2.7.x:
sudo apt-get install python-dev
sudo apt install -y python-pip
If using Python 3.x:
sudo apt-get install python3-dev
sudo apt install -y python3-pip
Anaconda¶
conda install python
Install Postgresql¶
Mac OS X¶
On Mac OS X, we recommend installing using Homebrew:
brew install postgresql
Postgresql can then be started and stopped using:
brew services start postgresql
brew services stop postgresql
Ubuntu¶
The lowest version of Postgresql that Dallinger v5 supports is 9.4.
This is fine for Ubuntu 18.04 LTS and 16.04 LTS as they ship with Postgresql 10.4 and 9.5 respectively, however Ubuntu 14.04 LTS ships with Postgresql 9.3
Postgres can be installed using the following instructions:
Ubuntu 18.04 LTS:
sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib
To run postgres, use the following command:
sudo service postgresql start
After that you’ll need to run the following commands
sudo sed /etc/postgresql/10/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/10/main/postgresql.conf'
sudo service postgresql reload
Ubuntu 16.04 LTS:
sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib
To run postgres, use the following command:
service postgresql start
After that you’ll need to run the following commands
sudo sed /etc/postgresql/9.5/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/9.5/main/postgresql.conf'
sudo service postgresql reload
Ubuntu 14.04 LTS:
Create the file /etc/apt/sources.list.d/pgdg.list and add a line for the repository:
sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list'
Import the repository signing key, update the package lists and install postgresql:
wget -q https://www.postgresql.org/media/keys/ACCC4CF8.asc -O - | sudo apt-key add -
sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib
To run postgres, use the following command:
sudo service postgresql start
After that you’ll need to run the following commands
sudo sed /etc/postgresql/10/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/10/main/postgresql.conf'
sudo service postgresql reload
Create the databases¶
Mac OS X¶
After installing Postgres, you will need to create two databases: one for your experiments to use, and a second to support importing saved experiments. It is recommended that you also create a database user.
Naviagate to a terminal and type:
createuser -P dallinger --createdb
(Password: dallinger)
createdb -O dallinger dallinger
createdb -O dallinger dallinger-import
The first command will create a user named dallinger and prompt you for a
password. The second and third command will create the dallinger and
dallinger-import databases, setting the newly created user as the owner.
You can optionally inspect your databases by entering psql dallinger.
Inside psql you can use commands to see the roles and database tables:
\du
\l
To quit:
\q
If you get an error like the following:
createuser: could not connect to database postgres: could not connect to server:
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
then postgres is not running. Start postgres as described in the Install Postgresql section above.
Ubuntu¶
Make sure that postgres is running. Switch to the postgres user:
sudo -u postgres -i
Run the following commands:
createuser -P dallinger --createdb
(Password: dallinger)
createdb -O dallinger dallinger
createdb -O dallinger dallinger-import
exit
The second command will create a user named dallinger and prompt you for a
password. The third and fourth commands will create the dallinger and dallinger-import databases, setting
the newly created user as the owner.
Finally restart postgresql:
sudo service postgresql reload
Install Heroku¶
To run experiments locally or on the internet, you will need the Heroku Command Line Interface installed, version 3.28.0 or better. If you want to launch experiments on the internet, then you will also need a Heroku.com account, however this is not needed for local debugging.
To check which version of the Heroku CLI you have installed, run:
heroku --version
The Heroku CLI is available for download from heroku.com.
Install Redis¶
Debugging experiments requires you to have Redis installed and the Redis server running.
Install Git¶
Dallinger uses Git, a distributed version control system, for version control of its code. If you do not have it installed, you can install it as follows:
Mac OS X¶
brew install git
Ubuntu¶
sudo apt install git
Set up a virtual environment¶
Note
If you are using Anaconda, ignore this virtualenv
section; use conda to create your virtual environment. Or, see the
special Anaconda installation instructions.
Why use virtualenv?
Virtualenv solves a very specific problem: it allows multiple Python projects that have different (and often conflicting) requirements, to coexist on the same computer. If you want to understand this in detail, you can read more about it here.
Now let’s set up a virtual environment by running the following commands:
Mac OS X¶
If using Python 2.7 and pip:
pip install virtualenv
pip install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
export VIRTUALENVWRAPPER_PYTHON=$(which python)
source $(which virtualenvwrapper.sh)
If using Python 3.x and pip3 (Python 3.7 in this example):
pip3 install virtualenv
pip3 install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)
source $(which virtualenvwrapper.sh)
Now create the virtual environment using:
mkvirtualenv dlgr_env --python <specify_your_python_path_here>
Examples:
Using homebrew installed Python 3.7:
mkvirtualenv dlgr_env --python /usr/local/bin/python3.7
Using Python 2.7:
mkvirtualenv dlgr_env --python /usr/bin/python
Virtualenvwrapper provides an easy way to switch between virtual environments
by simply typing: workon [virtual environment name].
The technical details:
These commands use pip/pip3, the Python package manager, to install two
packages virtualenv and virtualenvwrapper. They set up an
environmental variable named WORKON_HOME with a string that gives a
path to a subfolder of your home directory (~) called Envs,
which the next command (mkdir) then makes according to the path
described in $WORKON_HOME (recursively, due to the -p flag).
That is where your environments will be stored. The source command
will run the command that follows, which in this case locates the
virtualenvwrapper.sh shell script, the contents of which are beyond
the scope of this setup tutorial. If you want to know what it does, a
more in depth description can be found on the documentation site for virtualenvwrapper.
Finally, the mkvirtualenv makes your first virtual environment which
you’ve named dlgr_env. We have explicitly passed it the location of the Python
that the virtualenv should use. This Python has been mapped to the python
command inside the virtual environment.
The how-to:
In the future, you can work on your virtual environment by running: Python 2.7
export VIRTUALENVWRAPPER_PYTHON=$(which python)
source $(which virtualenvwrapper.sh)
workon dlgr_env
Python 3.x
export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)
source $(which virtualenvwrapper.sh)
workon dlgr_env
NB: To stop working in the virtual environment, run deactivate. To
list all available virtual environments, run workon with no
arguments.
If you plan to do a lot of work with Dallinger, you can make your shell
execute the virtualenvwrapper.sh script everytime you open a terminal. To
do that type:
Python 2.7
echo "export VIRTUALENVWRAPPER_PYTHON=$(which python)" >> ~/.bash_profile
echo "source $(which virtualenvwrapper.sh)" >> ~/.bash_profile
Python 3.x
echo "export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)" >> ~/.bash_profile
echo "source $(which virtualenvwrapper.sh)" >> ~/.bash_profile
From then on, you only need to use the workon command before starting.
Ubuntu¶
sudo pip install virtualenv
sudo pip install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/local/bin/virtualenvwrapper.sh
Now create the virtualenv using the mkvirtualenv command as follows:
If you are using Python 3 that is part of your Ubuntu installation (16.04 or 18.04):
mkvirtualenv dlgr_env --python /usr/bin/python3
If you are using Python 2 that is part of your Ubuntu installation:
mkvirtualenv dlgr_env --python /usr/bin/python
If you are using another Python version (eg. custom installed Python 3.x on Ubuntu 14.04):
mkvirtualenv dlgr_env --python <specify_your_python_path_here>
Virtualenvwrapper provides an easy way to switch between virtual environments
by simply typing: workon [virtual environment name].
The technical details:
These commands use pip, the Python package manager, to install two
packages virtualenv and virtualenvwrapper. They set up an
environmental variable named WORKON_HOME with a string that gives a
path to a subfolder of your home directory (~) called Envs,
which the next command (mkdir) then makes according to the path
described in $WORKON_HOME (recursively, due to the -p flag).
That is where your environments will be stored. The source command
will run the command that follows, which in this case locates the
virtualenvwrapper.sh shell script, the contents of which are beyond
the scope of this setup tutorial. If you want to know what it does, a
more in depth description can be found on the documentation site for virtualenvwrapper.
Finally, the mkvirtualenv makes your first virtual environment which
you’ve named dlgr_env. We have explicitly passed it the location of the Python
that the virtualenv should use. This Python has been mapped to the python
command inside the virtual environment.
The how-to:
In the future, you can work on your virtual environment by running:
source /usr/local/bin/virtualenvwrapper.sh
workon dlgr_env
NB: To stop working in the virtual environment, run deactivate. To
list all available virtual environments, run workon with no
arguments.
If you plan to do a lot of work with Dallinger, you can make your shell
execute the virtualenvwrapper.sh script everytime you open a terminal. To
do that:
echo "source /usr/local/bin/virtualenvwrapper.sh" >> ~/.bashrc
From then on, you only need to use the workon command before starting.
Install Dallinger¶
Install Dallinger from the terminal by running
pip install dallinger[data]
Test that your installation works by running:
dallinger --version
If you use Anaconda, installing Dallinger probably failed. The problem is
that you need to install bindings for the psycopg2 package (it helps
Python play nicely with Postgres) and you must use conda for conda to
know where to look for the links. You do this with:
conda install psycopg2
Then, try the above installation commands. They should work now, meaning you can move on.
Next, you’ll need access keys for AWS, Heroku, etc..