3ML brings together multiple instrument and fitting software packages into a common framework. Thus, installing all the pieces can be a bit of a task for the user. In order to make this a less painless process, we have packaged most of the external dependencies into conda (see below). However, if you want more control over your install, 3ML is available on PyPI via pip. If you have issues with the installs, first check that you have properly installed all the external dependencies that you plan on using. Are their libraries accessible on you system’s standard paths? If you think that you have everything setup properly and the install does not work for you, please submit an issue and we will do our best to find a solution.
Conda is a platform independent package manager. It allows to install 3ML (and a lot of other software) without the need to compile anything, and in a completely separate environment from your system and your system python.
If you don’t know Conda¶
If you are not familiar with conda, install 3ML with the automatic script which will take care of everything:
Download the script from here
Run the script with
bash install_3ML.sh. If you plan to use XSPEC models use
bash install_3ML.sh --with-xspec.
The script will install 3ML and then create a
threeML_init.shscript and a
threeML_init.cshscript. Source the former if you are using Bash (
source threeML_init.sh) and the second one if you are using Csh/Tcsh (
If you already know Conda¶
If you are familiar with Conda and you already have it installed, you can install 3ML by creating an environment with:
conda create --name threeML -c conda-forge python=3.7 numpy scipy matplotlib
then activating your environment and installing 3ML as:
conda activate threeML conda install -c conda-forge -c threeml astromodels threeml
Finally, if you also need XSPEC models you can install them by running:
conda install -c xspecmodels xspec-modelsonly
If you would like to install 3ML and astromodels on their own and have more control over which dependencies you would like to use. Please to the following
It is highly recommended you work within a python virtual environment to keep you base python clean
pip install astromodels
pip install threeml
If you need to build other dependencies such as pagmo, multinest, XSPEC, etc., it is recommended you do this before installing astromodels!
A docker with the complete 3ML environment and all dependencies can be installed with
docker pull threeml/notebook:latest
which will install a docker taht can be launched with
docker run -it --rm -p 8888:8888 -v $PWD:/workdir -w /workdir threeml/notebook
which will launch a notebook server that can operate on the current directory. The notebooks and be accessed by typing
localhost:8888 in your browser.
You need to set up packages such as AERIE (for HAWC), or the Fermi Science Tools, before running the script, otherwise some of the functionalities will not work.
AERIE for HAWC: make sure that this works before running the script:
> liff-PointSourceExpectation --version INFO [CommandLineConfigurator.cc, ParseCommandLine:137]: liff-PointSourceExpectation Aerie version: 2.04.00 Build type: Debug
If it doesn’t, you need to set up the HAWC environment (refer to the appropriate documentation)
Fermi Science Tools for Fermi/LAT analysis: make sure that this works:
> gtirfs ... P8R2_TRANSIENT100_V6::EDISP0 P8R2_TRANSIENT100_V6::EDISP1 ...
If it doesn’t, you need to configure and set up the Fermi Science Tools.
ROOT: ROOT is not required by 3ML, but it provides the Minuit2 minimizer which can be used in 3ML. If you have ROOT, make sure that this works before running the script:
> root-config --version 5.34/36
Install from source (advanced)¶
Remove any previous installation you might have with:
> pip uninstall threeML > pip uninstall astromodels > pip uninstall cthreeML
> pip install numpy scipy ipython astropy numba cython > pip install git+https://github.com/threeML/threeml.git > pip install git+https://github.com/threeML/astromodels.git --upgrade
In order to use the HAWC plugin, you will also need to install cthreeML (run this after setting up the HAWC environment):
> pip install git+https://github.com/threeML/cthreeML.git
NOTE: If you do not have permission to install packages in your current python environment, you can still install the packages by adding the
--useroption at the end of each
Tips for Mac users¶
The following paths need to be added to you DYLD_LIBRARY path if you have FORTRAN installed via these package managers:
Please inform us if you have problems related to your FORTRAN distribution.