NBODYKIT: A Massively Parallel, Large-Scale Structure Toolkit, Other Cosmology Tools and Products

User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#1

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:

  1. $ conda create --name nbodykit-env python=3 # or use python=2 for python 2.7*
  2. $ source activate nbodykit-env
  3. $ 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:

  1. $pip uninstall tornado //Successfully uninstalled tornado-5.1
  2. $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
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#2

Here is another useful cosmological code:

CAMB (Code for Anisotropies in the Microwave Background), a cosmology code for calculating CMB, lensing, galaxy count, dark-age 21cm power spectra, matter power spectra and transfer functions, see Demos. The main code is written in Python with numerical calculations implemented efficiently in Python-wrapped modern Fortran. The code includes other general utility function for cosmological calculations. You can git clone it up from its GitHub repository -- CAMB.

You can run the power spectra calculations on Binder (see also gke.mybinder.org):

https://notebooks.gesis.org/binder/jupy ... demo.ipynb
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#3

0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#4

LensPix: Fast MPI full sky transforms for HEALPix

https://cosmologist.info/lenspix/
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#5

Here is another useful astronomical software, DS9:
http://ds9.si.edu/site/Home.html
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#8

Haslam 408 MHz all-sky map with filtering and strong sources removed, and Haslam 408 MHz all-sky map with no filtering -- Legacy Archive for Microwave Background Data Analysis (LAMBDA) Data Products

Foreground - Haslam 408 MHz

Haslam 408 MHz


See also Haslam 408 MHz All-Sky Map

An improved source-subtracted and destriped Haslam 408 MHz all-sky map

http://www.jb.man.ac.uk/research/cosmos/haslam_map/

Max Planck Institute for Radio Astronomy (MPIfR ) Survey Sampler website

http://www3.mpifr-bonn.mpg.de/survey.html
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#9

This wiki site maintained by the European Space Agency (ESA) contains 2015 CMB spectra and likelihood code, and description of various CMB measurements likelihood and power spectra.

The 2015 Explanatory Supplement is contained in this location.

The latest Planck Legacy Explanatory Supplement contains the descriptions of all the Planck products, including the 2013, 2015 and 2018 data releases. Previous instances of the Explanatory Supplement (2013 and 2015), including this one, are not fully up-to-date and have been discontinued during 2018.

The up-to-date link is associated to the famous Planck papers:

Planck 2013 results. XVI. Cosmological parameters

Planck 2013 results. XVI. Cosmological parameters

We present the first results based on Planck measurements of the CMB temperature and lensing-potential power spectra. The Planck spectra at high multipoles are extremely well described by the standard spatially-flat six-parameter LCDM cosmology. In this model Planck data determine the cosmological parameters to high precision. We find a low value of the Hubble constant, H0=67.3+/-1.2 km/s/Mpc and a high value of the matter density parameter, Omega_m=0.315+/-0.017 (+/-1 sigma errors) in excellent agreement with constraints from baryon acoustic oscillation (BAO) surveys. Including curvature, we find that the Universe is consistent with spatial flatness to percent-level precision using Planck CMB data alone. We present results from an analysis of extensions to the standard cosmology, using astrophysical data sets in addition to Planck and high-resolution CMB data. None of these models are favoured significantly over standard LCDM. The deviation of the scalar spectral index from unity is insensitive to the addition of tensor modes and to changes in the matter content of the Universe. We find a 95% upper limit of r<0.11 on the tensor-to-scalar ratio. There is no evidence for additional neutrino-like relativistic particles. Using BAO and CMB data, we find N_eff=3.30+/-0.27 for the effective number of relativistic degrees of freedom, and an upper limit of 0.23 eV for the summed neutrino mass. Our results are in excellent agreement with big bang nucleosynthesis and the standard value of N_eff=3.046. We find no evidence for dynamical dark energy. Despite the success of the standard LCDM model, this cosmology does not provide a good fit to the CMB power spectrum at low multipoles, as noted previously by the WMAP team. While not of decisive significance, this is an anomaly in an otherwise self-consistent analysis of the Planck temperature data.


Planck 2015 results. XIII. Cosmological parameters

Planck 2015 results. XIII. Cosmological parameters

We present results based on full-mission Planck observations of temperature and polarization anisotropies of the CMB. These data are consistent with the six-parameter inflationary LCDM cosmology. From the Planck temperature and lensing data, for this cosmology we find a Hubble constant, H0= (67.8 +/- 0.9) km/s/Mpc, a matter density parameter Omega_m = 0.308 +/- 0.012 and a scalar spectral index with n_s = 0.968 +/- 0.006. (We quote 68% errors on measured parameters and 95% limits on other parameters.) Combined with Planck temperature and lensing data, Planck LFI polarization measurements lead to a reionization optical depth of tau = 0.066 +/- 0.016. Combining Planck with other astrophysical data we find N_ eff = 3.15 +/- 0.23 for the effective number of relativistic degrees of freedom and the sum of neutrino masses is constrained to < 0.23 eV. Spatial curvature is found to be |Omega_K| < 0.005. For LCDM we find a limit on the tensor-to-scalar ratio of r <0.11 consistent with the B-mode constraints from an analysis of BICEP2, Keck Array, and Planck (BKP) data. Adding the BKP data leads to a tighter constraint of r < 0.09. We find no evidence for isocurvature perturbations or cosmic defects. The equation of state of dark energy is constrained to w = -1.006 +/- 0.045. Standard big bang nucleosynthesis predictions for the Planck LCDM cosmology are in excellent agreement with observations. We investigate annihilating dark matter and deviations from standard recombination, finding no evidence for new physics. The Planck results for base LCDM are in agreement with BAO data and with the JLA SNe sample. However the amplitude of the fluctuations is found to be higher than inferred from rich cluster counts and weak gravitational lensing. Apart from these tensions, the base LCDM cosmology provides an excellent description of the Planck CMB observations and many other astrophysical data sets.


Planck 2018 results. VI. Cosmological parameters

Planck 2018 results. VI. Cosmological parameters

We present cosmological parameter results from the final full-mission Planck measurements of the CMB anisotropies. We find good consistency with the standard spatially-flat 6-parameter ΛCDM cosmology having a power-law spectrum of adiabatic scalar perturbations (denoted "base ΛCDM" in this paper), from polarization, temperature, and lensing, separately and in combination. A combined analysis gives dark matter density Ωch2=0.120±0.001, baryon density Ωbh2=0.0224±0.0001, scalar spectral index ns=0.965±0.004, and optical depth τ=0.054±0.007 (in this abstract we quote 68% confidence regions on measured parameters and 95% on upper limits). The angular acoustic scale is measured to 0.03% precision, with 100θ=1.0411±0.0003. These results are only weakly dependent on the cosmological model and remain stable, with somewhat increased errors, in many commonly considered extensions. Assuming the base-ΛCDM cosmology, the inferred late-Universe parameters are: Hubble constant H0=(67.4±0.5)km/s/Mpc; matter density parameter Ωm=0.315±0.007; and matter fluctuation amplitude σ8=0.811±0.006. We find no compelling evidence for extensions to the base-ΛCDM model. Combining with BAO we constrain the effective extra relativistic degrees of freedom to be Neff=2.99±0.17, and the neutrino mass is tightly constrained to mν<0.12eV. The CMB spectra continue to prefer higher lensing amplitudes than predicted in base -ΛCDM at over 2σ, which pulls some parameters that affect the lensing amplitude away from the base-ΛCDM model; however, this is not supported by the lensing reconstruction or (in models that also change the background geometry) BAO data. (Abridged)
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
User avatar
Eli
Senior Expert Member
Reactions: 189
Posts: 5950
Joined: 10 years ago
Location: Tanzania
Contact:

#10

FastICA: a fast algorithm for Independent Component Analysis

https://scikit-learn.org/stable/modules ... stICA.html

Test Jupyter notebook yourself.
0
TSSFL -- A Creative Journey Towards Infinite Possibilities!
Post Reply
  • Similar Topics
    Replies
    Views
    Last post

Return to “Astronomy, Astrophysics & Cosmology”

  • Information
  • Who is online

    Users browsing this forum: No registered users and 0 guests