Installation
RAIL is actually distributed as several software packages. However, depending on your use case it is likely that you will be working directly with one of the packages.
Some of the RAIL algorithms have dependencies that are sensitive to out-of-date code versions, therefore it is strongly recommended that you create a new dedicated virtual environment for RAIL to avoid problems with pip/conda failing to update some packages that you have previously installed during installation of RAIL. Also, having multiple version of RAIL in your path can cause difficult to diagnose problems, so we encourage you to make sure that you don’t have an existing version of RAIL installed in your .local area or in your base conda environment.
Installation Options
There are several ways you might choose to install RAIL.
Exploration Installation: install all of the RAIL algorithms and explore RAIL using a series of demonstration jupyter notebooks.
Production Installation: install all of the RAIL algorithms in an existing conda environment.
Algorithm Installation install a single RAIL algorithm in an existing conda environment.
Developer Installation: install all of RAIL algorithms from source in “editable” mode.
Note
In the following instructions you will see the use of both pip
and conda
.
We have found that conda
is particularly good at creating virtual environments
and installing packages that have compiled libraries. Thus we prefer it over
pip
and venv
for those purposes.
Additionally, we use pip
to build and install RAIL code from source because
conda
does not provide that functionality.
Tip
Throughout the installation documentation we make reference to conda
as
a tool to create a RAIL virtual environment and install compiled dependencies
we acknowledge that it can be potentially very slow. Using mamba
can be
significantly faster, but it is not as widely adopted in the community.
If you would like to experiment with mamba
it can be installed with
conda install mamba -n base -c conda-forge
. The mamba
documentation
is here.
Exploration Installation
Here we will be installing the source code from rail to access all of the demonstration notebooks, and use that to install all of the other algorithms.
We have included an environment.yml
that makes it easy to create a virtual
environment named “[env]” that uses conda to install some packages that have
compiled libraries.
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda env create -f environment.yml -n [env] # or mamba env create, which is much faster
conda activate [env]
pip install -e .[dev]
If for some reason the pip install .[dev]
fails (e.g.,because of a problem
in building the dependencies for one of the algorithms) you can run a more
fault-tolerant installation using a rail script:
pip install -e .
rail install --package-file rail_packages.yml
At that point you should be able to run the demonstration notebooks, e.g.;
jupyter-notebook examples/estimation_examples/RAIL_estimation_demo.ipynb
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda env create -f environment.yml -n [env] # or mamba env create, which is much faster
conda activate [env]
pip install -e '.[dev]'
If for some reason the pip install '.[dev]'
fails (e.g.,because of a
problem in building the dependencies for one of the algorithms) you can run
a more fault-tolerant installation using a rail script:
pip install -e .
rail install --package-file rail_packages.yml
At that point you should be able to run the demonstration notebooks, e.g.;
jupyter-notebook examples/estimation_examples/RAIL_estimation_demo.ipynb
Production Installation
Here we will be installing all of the RAIL algorithms into an existing virtual
environment “[env]”. To do this we recommend that you install rail
from source,
to be sure to get the latest version of the conda-reqs.txt
file.
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda activate [env]
conda install -n [env] -c conda-forge --file conda-reqs.txt # or mamba install, which is much faster
pip install .[algos]
Again, if for some reason the pip install .[algos]
fails (e.g.,because
of a problem in building the dependencies for one of the algorithms) you
can run a more fault-tolerant installation using a rail script:
pip install .
rail install --package-file rail_packages.yml
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda activate [env]
conda install -n [env] -c conda-forge --file conda-reqs.txt # or mamba install, which is much faster
pip install '.[algos]'
Again, if for some reason the pip install ‘.[algos]’ fails (e.g.,because of a problem in building the dependencies for one of the algorithms) you can run a more fault-tolerant installation using a rail script:
pip install .
rail install --package-file rail_packages.yml
Algorithm Installation
Here we will be installing a single RAIL algorithm (e.g., rail_som
) into an
existing virtual environment “[env]”.
conda activate [env]
pip install pz-rail-som # (note the name change)
Again, if for some reason that fails because of conflicting dependencies,
then adding the dependencies with compiled libraries via conda might fix
the issue. We have included conda-reqs.txt
file in each RAIL algorithm’s
repository to specify the dependencies of that algorithm that might best
be installed using conda.
git clone https://github.com/LSSTDESC/rail_som.git
cd rail_som
conda install -n [env] -c conda-forge --file conda-reqs.txt
pip install -e .
conda activate [env]
pip install pz-rail-som # (note the name change)
Again, if for some reason that fails because of conflicting dependencies,
then adding the dependencies with compiled libraries via conda might fix
the issue. We have included conda-reqs.txt
file in each RAIL algorithm’s
repository to specify the dependencies of that algorithm that might best
be installed using conda.
git clone https://github.com/LSSTDESC/rail_som.git
cd rail_som
conda install -n [env] -c conda-forge --file conda-reqs.txt
pip install -e .
Developer Installation
Here we will be installing the source code from rail to access all of the demonstration notebooks, and using that to install all of the other algorithms.
We have included an environment.yml
that makes it easy to create a virtual
environment named “[env]” that uses conda to install some packages that have
compiled libraries.
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda env create -f environment.yml -n [env] # or mamba env create, which is much faster
conda activate [env]
pip install -e .
rail clone-source --package-file rail_packages.yml
rail install --package-file rail_packages.yml --from-source
git clone https://github.com/LSSTDESC/rail.git
cd rail
conda env create -f environment.yml -n [env] # or mamba env create, which is much faster
conda activate [env]
pip install -e .
rail clone-source --package-file rail_packages.yml
rail install --package-file rail_packages.yml --from-source
RAIL Command Line Utility
RAIL provides a command line utility to help with installation and maintenance of RAIL.
The command line utility is called rail
.
You can see the available commands by running rail --help
.
The most useful commands are:
rail install
: install RAIL packages from pypi or from source.rail update-source
: update RAIL packages from source.
Tip
To update all your rail packages, in the current environment, use:
rail update-source --package-file rail_packages.yml
from the root of rail.
RAIL packages
Depending on how you want to use RAIL you will be installing one or more RAIL packages. So, first let’s clarify the RAIL packages structure.
rail_base (pz-rail-base on pypi): includes the RAIL base classes and some very simple example algorithms that do not include any dependencies beyond numpy and scipy.
rail_<algorithm> (for now this includes rail_delight, rail_bpz and rail_flexzboost) (pz-rail-<algorithm> on pypi): these are small packages that split out algorithms that do have complicated dependencies. They are all independent of each other, but each one does depend on RAIL.
rail_pipelines (pz-rail-pipelines on pypi): is the package where we develop data analysis pipelines that use the various algorithms.
rail_hub (pz-rail-hub on pypi): is the umbrella package that pulls together RAIL and the various rail_<algorithm> packages.
Note that the various RAIL packages all populate the rail namespace in python. I.e., in python you will be importing from rail or rail.pipelines or rail.estimation.algos, not rail_<alogrithm> or rail_pipelines.
Installing any of the RAIL packages should automatically install all of the dependent RAIL packages. However, in some cases you might find that you explicitly need to modify the source code in more than one package, in which case you will want to install multiple packages from source.
In every RAIL package we have included an environment.yml that makes it easy to create a conda environment named “[name-for-your-env]” that uses conda to install some packages that have compiled libraries we have found that it is easier to install with conda.
conda env create -f environment.yml -n [name-for-your-env]
Where you have replaced [name-for-your-env] with whatever name you wish to use, e.g. rail. (This is in fact the default, and you will get it if you leave off the -n [name-for-your-env] You can then run the command
conda activate [name-for-your-env]
To activate this environment. We are now ready to install RAIL.
Now you need to decide which RAIL packages to install and if you want to install from source, or just install the packages.
If you want to add the conda environment that you are about to create as a kernel that you can use in a Jupyter notebook, see the Adding your kernel to jupyter section further down on this page.
Installing with pip
All you have to do is:
pip install <package>
Installing from source
To install RAIL from source, you will Clone this repo to your local workspace. Specifically:
git clone https://github.com/LSSTDESC/RAIL.git # (or whichever packages you need)
cd RAIL
pip install -e .[all] # (or pip install -e '.[all]' if you are using zsh, note the single quotes).
If you only want to install the dependencies for a specific piece of RAIL, you
can change the install option. E.g. to install only the dependencies for the
Creation Module or the Estimation Module, run pip install .[creation]
or
pip install .[estimation]
respectively.
For other install options, look at the keys for the extras_require
dictionary
at the top of setup.py
.
Algorithm / architecture specific issues
Installing Delight
For Delight you should be able to just do:
pip install pz-rail-delight
For Delight you should be able to just do:
pip install pz-rail-delight
However, the particular estimator Delight
is built with Cython
and uses openmp
. Mac has dropped native support for openmp
, which will likely cause problems when trying to run the DelightEstimator
estimation code in RAIL. See the notes below for instructions on installing Delight if you wish to use this particular estimator.
If you are installing RAIL on a Mac, as noted above the DelightEstimator
estimator requires that your machine’s gcc
be set up to work with openmp
. If you are installing on a Mac and do not plan on using DelightEstimator
, then you can simply install RAIL with pip install .[base]
rather than pip install .[all]
, which will skip the Delight package. If you are on a Mac and do expect to run DelightEstimator
, then follow the instructions here to install Delight before running pip install .[all]
.
Installing FlexZBoost
For FlexZBoost, you should be able to just do
pip install pz-rail-flexzboost
But if you run into problems you might need to:
install
xgboost
with the commandpip install xgboost==0.90.0
install FlexCode with
pip install FlexCode[all]
Installing bpz_lite
For bpz_lite, you should be able to just do
pip install pz-rail-bpz
But if you run into problems you might need to:
cd to a directory where you wish to clone the DESC_BPZ package and run
git clone https://github.com/LSSTDESC/DESC_BPZ.git
cd to the DESC_BPZ directory and run
python setup.py install
(add--user
if you are on a shared system such as NERSC)try
pip install pz-rail-bpz
again.
Using GPU-optimization for pzflow
Note that the Creation Module depends on pzflow, which has an optional GPU-compatible installation. For instructions, see the pzflow Github repo.
On some systems that are slightly out of date, e.g. an older version of python’s
setuptools
, there can be some problems installing packages hosted on GitHub
rather than PyPi.
We recommend that you update your system; however, some users have still reported
problems with installation of subpackages necessary for flexzboost
and bpz_lite
.
If this occurs, try the following procedure:
Once you have installed RAIL, you can import the package (via import rail
)
in any of your scripts and notebooks.
For examples demonstrating how to use the different pieces, see the notebooks in
the examples/
directory.
Adding your kernel to jupyter
If you want to use the kernel that you have just created to run RAIL example demos,
then you may need to explicitly add an ipython kernel.
You may need to first install ipykernel with conda install ipykernel
.
You can then add your kernel with the following command, making sure that you
have the conda environment that you wish to add activated.
From your environment, execute the command:
python -m ipykernel install --user --name [name_to_call_new_kernel]
(you may or may not need to prepend sudo
depending on your permissions).
When you next start up Jupyter you should see a kernel with your new name as an
option, including using the Jupyter interface at NERSC.