Calculates analytic cosmological radiative transfer solutions in simplified geometries.
Project description
Description
Rabacus is a Python package for performing analytic radiative transfer calculations in simple geometries relevant to cosmology and astrophysics. It also contains tools to calculate cosmological quantities such as the power spectrum and mass function.
Prerequisites
The Rabacus package requires three other Python packages and a fortran compiler,
Numpy (version 1.7 or later)
Fortran compiler in your path.
Installing prerequisites with pip
A simple way to install Python packages is using the package manager pip. To check if you have pip installed on your system, type pip at the command line,
pip
If this produces usage instructions then congratulations, you have pip installed. If not, instructions for installing pip can be found here. To check if the python packages are installed on your system, attempt to import them from the python command prompt,
>>> import scipy >>> import numpy as np >>> import quantities as pq
If any of these import commands produce an error message you will need to install the proper software before installing Rabacus. Once you have access to pip, you can install any missing prerequisites using the following commands,
sudo pip install scipy sudo pip install numpy sudo pip install quantities
If you do not have root access on your system you can pass the --user flag which will install the packages into a hidden folder called .local in your home directory,
pip install --user scipy pip install --user numpy pip install --user quantities
Installing prerequisites on Debian (Ubuntu)
On Debian based systems (such as Ubuntu) you may prefer to install these prerequisites using the APT tool,
sudo apt-get install python-scipy python-numpy python-quantities
To increase the speed of execution, much of Rabacus is written in Fortran 90 and then wrapped using the f2py tool that is part of numpy. For the installation to be successful, a fortran compiler must be in your executable path. If you don’t already have one, I recommend the gnu fortran compiler gfortran. On Debian based systems (such as Ubuntu) you can install this compiler using the APT tool,
sudo apt-get install gfortran
Installation
With the prequisites installed on your system, you are ready to install the Rabacus package itself.
Setting F90 environment variable
Rabacus makes use of OpenMP directives in the Fortran code base and so we have to make sure the code is compiled correctly. In order to do this, you have to let the build system know what Fortran 90 compiler you are going to be using. The simplest way to do this is to set the environment variable F90 before following the installation instructions below. Rabacus has been tested with the intel compiler and the gnu gfortran compiler. For other compilers you will have to follow the Manual Install instructions below.
To use the gfortran compiler, type the following at the command line (in Bash)
export F90=gfortran
To use the intel compiler set
export F90=ifort
Single command install
If you have made the appropriate sacrifices to the computer gods, you should be able to install an OpenMP enabled version of Rabacus with a single comand line call to pip,
sudo pip install rabacus
As was the case for the prerequisites, if you do not have root access on your system you can pass the --user flag which will install Rabacus into a hidden folder called .local in your home directory,
pip install --user rabacus
If the last two lines printed to the screen are,
Successfully installed rabacus Cleaning up...
then congratulations you have a working copy of Rabacus. To double check, begin an ipython session and attempt an import,
import rabacus as ra
Packages installed with pip can be uninstalled in the same way,
pip uninstall rabacus
Manual install
If the above process fails for any reason we can always download Rabacus and manually invoke the setup script. The first step is to download and untar the Rabacus tar.gz file from the PyPI site (https://pypi.python.org/pypi/rabacus) and change into the main Rabacus directory,
gunzip rabacus-x.x.x.tar.gz tar xvf rabacus-x.x.x.tar cd rabacus-x.x.x
Now we have direct access to the setup.py file which gives us a lot more freedom but it comes at the cost of slightly more complexity. First it’s a good idea to see which fortran compilers are detected on your machine. The following command will list all of the fortan compilers found on your system and all the compilers available for your system but not found.
f2py -c --help-fcompiler
For example on my machine I get the following,
Fortran compilers found: --fcompiler=gnu95 GNU Fortran 95 compiler (4.8.1-10) --fcompiler=intelem Intel Fortran Compiler for 64-bit apps (14.0.2.144) Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=gnu GNU Fortran 77 compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pathf95 PathScale Fortran Compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler
Now we decide which of the fortran compilers to use and which flags to pass the build command. Suppose you wanted to use the Intel compiler. Edit the setup.py file such that the variable f90_flags is a list of compile flags and omp_lib is a list containing the linking flags. For example,
f90_flags = ["-openmp", "-fPIC", "-xHost", "-O3", "-ipo",
"-funroll-loops", "-heap-arrays", "-mcmodel=medium"]
omp_lib = ["-liomp5"]
These variables are already defined near the top of the setup.py file and will need to be overwritten. Once this is done, we give the build command to the setup.py script,
python setup.py build --fcompiler=intelem
After the package is built, give the install command to actually install it,
sudo python setup.py install --record rabacus_install_files.txt
The last part of the command is to allow for easy uninstall. This process just involves deleting all installed files which will be listed in the file rabacus_install_files.txt. This can be accomplished using the following command,
cat rabacus_install_files.txt | xargs sudo rm -rf
The install can also be done locally for those without root permission on their system by passing the --user flag to the install command,
python setup.py install --user --record rabacus_install_files.txt
Note that if you previously did an install of Rabacus that required the sudo command you will likely need to delete the rabacus.egg-info directory and some directories inside the build directory as they will need to be modified but will be owned by root. If you are only doing a local install then this shoudn’t be necessary. This procedure should work for any fortran compiler supported by f2py (i.e. any compiler in the list returned when using the --help-fcompiler flag.
Testing install
Detailed examples of using rabacus are available by following the link to the users guide below. However, we present a short example with the expected output below as a way to quickly test that a new installation has basic functionality. We first import rabacus and then create an object that gives access to the meta galactic radiation background described in Haardt & Madau 2012. Finally, we ask for the photo-heating rate of He I at a redshift of 3.0.
import rabacus as ra hm12 = ra.HM12_Photorates_Table() z = 3.0 print hm12.He1h(z)
The expected output from a working rabacus installation is given below. Note that there may be differences in the last significant figure due to different processor architectures.
3.39163517433e-12 eV/s
Project URLs
documentation (http://pythonhosted.org//rabacus)
version control (https://bitbucket.org/galtay/rabacus)
