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The Nuclear Multimessenger Astronomy (NMMA) framework

The Nuclear Multimessenger Astronomy (NMMA) framework#

nmma is a fully featured, Bayesian multi-messenger pipeline targeting joint analyses of gravitational-wave and electromagnetic data (focusing on the optical). Using bilby as the back-end, the software is capable of sampling these data sets using a variety of samplers. It uses chiral effective field theory based neutron star equation of states when performing inference, and is also capable of estimating the Hubble Constant.

Instructions For NMMA Installation#

For science users#

If you are a science user and want to use NMMA for your analysis, you can install NMMA using conda as follows:

conda create --name nmma_env python=3.10
conda install -c conda-forge nmma

If you have an issue, such as Solving environment: failed with initial frozen solve, an option could be:

conda create --name nmma_env python=3.10
conda install mamba -c conda-forge
mamba install nmma -c conda-forge

If you are a developer or you want to build NMMA from source, please refer to the developer section below.

Note

The above may not work for arm64 Macs; see specifc instructions below.

For developers and contributors#

The steps highlighted below are primarily for Linux systems and Windows users are advised to use WSL (preferrably Ubuntu 20.04) for smooth installation. Ubuntu 20.04 is available for free download on Microsoft Store.

Installing Anaconda3

On your Linux/WSL terminal, run the following commands to install anaconda (replace 5.3.1 by the latest version):

wget https://repo.anaconda.com/archive/Anaconda3-5.3.1-Linux-x86_64.sh
bash Anaconda3-5.3.1-Linux-x86_64.sh

(For 32-bit installation, skip the \_64 in both commands)

Note

If you already have Anaconda3 installed, please make sure that it is updated to the latest version using conda update –all. Also check that you do not have multiple versions of Python installed in usr/lib/ directory as it can cause version conflicts while installing dependencies.

Now do:

conda update --all

Cloning the NMMA repository

Fork the NMMA repository: NMMA Github Repo

Note that we link above to the main branch, but suggest making changes on your own fork (please also see our contributing guide). Now, after forking, run the following command to clone the repository into your currently directory (by default, in your home directory):

git clone https://github.com/your_github_username/nmma

Change directory to the nmma folder:

cd nmma

Create a new environment using this command (environment name is nmma_env in this case):

conda create --name nmma_env python=3.10
conda activate nmma_env

Note

If this gives an error like: CommandNotFoundError: Your shell has not been properly configured to use 'conda activate', then run:

source ~/anaconda3/etc/profile.d/conda.sh

then proceed with conda activate nmma_env.

Get the latest pip version

pip install --upgrade pip

Check python and pip version like this:

python --version
pip --version

Python 3.9 and above and Pip 21.2 and above is ideal for this installation. It is recommended to update these for your installation.

Install mpi4py:

conda install mpi4py

Warning

We discourage installing mpi4py with pip. The installation does not work properly due to issues with MPI header files, etc.

Install parallel-bilby:

conda install -c conda-forge parallel-bilby

Note

Installing parallel-bilby takes quite some time. Please be patient. If you encounter any errors, please check the parallel-bilby installation guide for more details.

Note

For those installing on WSL with pip, you may encounter an issue with installing parallel-bilby due to a dependency on python-ligo-lw. This can be resolved by installing gcc with the following command:

sudo apt-get install gcc

and attempting to install parallel-bilby again.

Install pymultinest (note this line may not work for arm64 Macs; see specifc instructions below)

conda install -c conda-forge pymultinest

Warning

In case an error comes up during an NMMA analysis of the form:

ERROR: Could not load MultiNest library "libmultinest.so"
ERROR: You have to build it first
ERROR: and point the LD_LIBRARY_PATH environment variable to it!

Then, for using the PyMultinest library, it is required to get and compile the Multinest library separately. Instructions for the same are given here:

https://johannesbuchner.github.io/PyMultiNest/install.html

Use the commands below to install the dependencies given in requirements.txt file which are necessary for NMMA:

pip install .

Note

There is an issue pip installing pyfftw on arm64 Mac systems; see the dedicated section below for a solution. If any package appeared to have an issue installing, you can first check by attempting to install it again using pip:

pip install importlib_resources
pip install  extinction
pip install dill
pip install multiprocess
pip install lalsuite
pip install python-ligo-lw
pip install sncosmo
pip install scikit-learn
pip install joblib
conda install -c conda-forge p-tqdm

Note

If everything has gone smoothly, all of these above mentioned “pip install something” commands will show that the requirements have already been satisfied. Otherwise, these will cover the dependencies if not covered by pip install .. Also, if running pip install . shows something on the lines of “cannot cythonize without cython”, do:

conda install -c anaconda cython==0.29.24
pip install

For arm64 Macs#

Follow the instructions above, but with the following modifications:

Install C compiler and cmake:

conda install -c conda-forge c-compiler
brew install cmake

Known arm64 Mac issues

  1. For arm64 Macs (e.g. M1, M2), there is an issue installing pyfftw with pip (see pyFFTW/pyFFTW#349). To address, first try running

    conda install -c conda-forge pyfftw

    If this completes successfully, re-run any failed installations and continue. Otherwise, use Homebrew to run

    brew install fftw

    then add the following lines to your .zprofile or .bash_profile:

    export PATH="/opt/homebrew/bin:$PATH"
export DYLD_LIBRARY_PATH=/opt/homebrew/opt/fftw/lib
export LDFLAGS="-Wl,-S,-rpath,/opt/homebrew/opt/fftw/lib -L/opt/homebrew/opt/fftw/lib"
export CFLAGS="-Wno-implicit-function-declaration -I/opt/homebrew/opt/fftw/include"

    Close and reopen your terminal and run

    pip install pyfftw

    You may then need to rerun pip install -r requirements.txt to complete the dependency installations.

    Tip

    FFTW installation can also be attempted using conda as follows

    conda install -c conda-forge fftw
DYLD_LIBRARY_PATH=$HOME/anaconda3/envs/nmma_env
pip install pyfftw

    Replace DYLD_LIBRARY path by your NMMA virtual environment path if it is not same as give here

  2. The osx-arm64 conda-forge channel does not include pymultinest. Running pip install -r requirements.txt should have installed pymultinest, but you will still need to install and compile Multinest from the source. Within the nmma directory, run:

    git clone https://github.com/JohannesBuchner/MultiNest
cd MultiNest/build
cmake ..
make

    Next, add the following lines to your .zprofile or .bash_profile:

    export LD_LIBRARY_PATH=$HOME/nmma/MultiNest/lib:$LD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=$HOME/nmma/MultiNest/lib:$DYLD_LIBRARY_PATH

    Note

    Modify these paths as appropriate for the location of your MultiNest installation. You can also combine the DYLD_LIBRARY_PATH lines for MultiNest and fftw (above) into a single line

  3. There are also issues with tensorflow and arm64 Macs. If using tensorflow, install it with the following commands:

    pip install tensorflow-macos
pip install tensorflow-metal

First Test for NMMA

Run the following commands:

ipython
import nmma
import nmma.em.analysis
import nmma.eos.create_injection

Tip

(Okay, last one!): if everything is ok, it’s the end of the installation. But in case it shows that such-and-such modules are absent, feel free to install those modules by visiting their anaconda documentation and install those with their given commands. In case modules like afterglowpy and dust_extinction are needed, don’t hesitate to do it with pip (normally it shouldn’t happen), but some modules may not install correctly in case of disturbance.

Please pay special attention to the import nmma.em.analysis and make sure that it does not generate any errors.

Unfortunately, due to the web of package requirements that NMMA depends on, running setup.py does not typically finish without errors the first time through. Experience has shown that in the vast majority of cases, simply pinning versions such as:

pip install astropy==4.3.1

and then trying again is sufficient for completion of the installation. This instruction file will likely cover the issues you might face during your installation. However, please open issues on GitHub if there appear to be unresolvable conflicts.

Building custom lalsuite from source#

If you want to install a custom lalsuite version (e.g. with a certain GW template model), then lalsuite needs to be build from scratch. This requires setting up the conda environment through conda-forge

conda create -c conda-forge --prefix=YOUR_PREFIX python=3.9
conda activate YOUR_PREFIX

and then installing mpi4py first before installing the required packages for the build process (here the second line):

conda install mpi4py
conda install -c conda-forge "astropy>=1.1.1" autoconf automake bc cfitsio doxygen fftw freezegun c-compiler gsl h5py hdf5 healpy "help2man>=1.37" "ldas-tools-framecpp<3.0.0a0" "libframel<9.0.0a0" ligo-gracedb ligo-segments "lscsoft-glue>=2.0.0" make matplotlib-base metaio "mpmath>=1.0.0" numpy pillow "pkg-config>=0.18.0" pytest "scipy>=0.9.0" six "swig>=3.0.10" zlib

When this is done, you can proceed installing nmma as above (i.e. via requirements.txt etc.) but note that from the dependencies lalsuite is then installed via pip. This installation needs to be removed

pip uninstall lalsuite

Then the build process for the custom lalsuite can be started

cd YOUR_CUSTOM_LALSUITE
./00boot
./configure --prefix=YOUR_PREFIX --disable-all-lal --enable-swig-python  --enable-lalsimulation --enable-lalframe
make; make install

It might happen that in the course of this some packages will be downgraded. You can just update them afterwards to a sufficient version, e.g.

pip install astropy>=5.2.2

Installation on expanse and other cluster resources#

When installation on cluster resources, it is common that all modules required for installing NMMA out of the box are not available. However, most will make it possible to import the required modules (most commonly, these are software like gfortran or mpi).

For example, on XSEDE’s Expanse cluster, one can start a terminal session with:

module load sdsc
module load openmpi

and follow the instructions above.

Note

If module load openmpi does not execute directly and it asks for dependencies, one can proceed with:

module load sdsc
module load cpu/0.15.4
module load gcc/9.2.0
module load openmpi/4.1.1

Internetless Clusters#

Some cluster resources may not have access to the internet or could block some forms of data transfer. This will cause some difficulties with certain packages and will require some fixes to how NMMA interacts with them and changes to how you call some commands in NMMA. This can also affect how you install NMMA on the cluster. Because the cluster is in some way restricted, it may be that the conda install nmma -c conda-forge or the pip install nmma commands don’t work. Thus to install NMMA, you will need to install from the source. To begin, you will want to copy the NMMA repository from your local to the cluster using an scp or rsync commmand because likely the git commands will fail. Once NMMA is downloaded to the cluster, navigate to the main directory and run

pip install -r requirements.txt
pip install .

and check that the installation was successful by running the first check for NMMA given above. After installation, the next most likely difference is how NMMA uses the trained kilonova models during any form of EM analysis. When running any analysis that requires the use of the trained grid of models you will need to add the –local-only flag to the analysis command. For example,

lightcurve-analysis \
     --model LANLTP2 \
     --svd-path svdmodels/ \
     --filters ztfg,ztfi,ztfr \
     --ztf-sampling \
     --ztf-uncertainties \
     --ztf-ToO 180 \
     --local-only \
     --interpolation-type tensorflow \
     --outdir outdir/TP2_ztf \
     --label TP2_ztf \
     --prior priors/LANL2022.prior \
     --tmin 0. \
     --tmax 14 \
     --dt 0.1 \
     --error-budget 1 \
     --nlive 1024 \

Matplotlib fonts#

On new Linux installations, we sometimes come across the warning: findfont: Font family ['Times New Roman'] not found. Falling back to DejaVu Sans. If you do prefer to use ‘Times New Roman’ for all of your plotting needs, you can install msttcorefonts with:

sudo apt install msttcorefonts -qq

After removing the matplotlib cache:

rm ~/.cache/matplotlib -rf

Beautiful fonts should be yours.

Contributing#

nmma is released under the MIT license. We encourage you to modify it, reuse it, and contribute changes back for the benefit of others. We follow standard open source development practices: changes are submitted as pull requests and, once they pass the test suite, reviewed by the team before inclusion. Please also see our contributing guide.

User Guide#

Contents