NBODYKIT: A Massively Parallel, Large-Scale Structure Toolkit, Other Cosmology Tools and Products
Posted: Fri Nov 09, 2018 2:39 pm
NBODYKIT is an open source project written in Python that provides a set of state-of-the-art, large-scale structure algorithms useful in the analysis of cosmological datasets from N-body simulations and observational surveys. All algorithms are massively parallel and run using the Message Passing Interface (MPI). You can dive straight and deploy NbodyKit in an interactive environment containing Jupyter Notebooks (see The Cookbook Recipes) available to users via the BinderHub service (see also BinderHub and JupyterHub with Kubernetes ), by just clicking the "launch binder" button at https://nbodykit.readthedocs.io/en/latest/index.html to get started.
NbodyKit has tons of modules and functionalities available here. See the The Cookbook and the API Reference for a quick start.
NbodyKit is compatible with Python versions 2.7, 3.5, and 3.6, and the source code is publicly available on https://github.com/bccp/nbodykit. NbodyKit has pre-built binaries and all of its dependencies available via Anaconda distribution that are compatible with Linux and macOS platforms. To avoid dependency conflicts, it is recommended to install nbodykit into a fresh virtual environment, achieved with the following commands:
If you need Jupyter Notebook, you can install it using Python’s package manager, pip or Anaconda.
If using pip, first, ensure that you have the latest pip (older versions may have trouble with some dependencies):
pip3 install --upgrade pip
Then install the Jupyter Notebook using:
pip3 install jupyter
Use pip instead of pip3 if using Python 2.x.
You can then launch Jupyter Notebook as:
$jupyter notebook
If you get an error AttributeError: type object 'IOLoop' has no attribute 'initialized', just do the following:
See reasons here.
After launching the notebook, follow instructions displayed in the Terminal:
"Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
http://localhost:8888/?token=c5a1a49859 ... 023a07b14a"
See also Interactive Parallel Computing with IPython -ipyparallel
NbodyKit has tons of modules and functionalities available here. See the The Cookbook and the API Reference for a quick start.
NbodyKit is compatible with Python versions 2.7, 3.5, and 3.6, and the source code is publicly available on https://github.com/bccp/nbodykit. NbodyKit has pre-built binaries and all of its dependencies available via Anaconda distribution that are compatible with Linux and macOS platforms. To avoid dependency conflicts, it is recommended to install nbodykit into a fresh virtual environment, achieved with the following commands:
- $ conda create --name nbodykit-env python=3 # or use python=2 for python 2.7*
- $ source activate nbodykit-env
- $ conda install -c bccp nbodykit
If you need Jupyter Notebook, you can install it using Python’s package manager, pip or Anaconda.
If using pip, first, ensure that you have the latest pip (older versions may have trouble with some dependencies):
pip3 install --upgrade pip
Then install the Jupyter Notebook using:
pip3 install jupyter
Use pip instead of pip3 if using Python 2.x.
You can then launch Jupyter Notebook as:
$jupyter notebook
If you get an error AttributeError: type object 'IOLoop' has no attribute 'initialized', just do the following:
- $pip uninstall tornado //Successfully uninstalled tornado-5.1
- $pip install tornado==4.5.3
See reasons here.
After launching the notebook, follow instructions displayed in the Terminal:
"Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
http://localhost:8888/?token=c5a1a49859 ... 023a07b14a"
See also Interactive Parallel Computing with IPython -ipyparallel