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Install and run Cobaya+SOLikeT

Preferred Way: Using the provided conda environment

We have provided a conda environment defined in soliket-tests.yml which provides easy set up of a virtual envrinoment with all the dependencies installed in order to run SOLikeT and its tests on multiple platforms (explicitly tested for ubuntu and MacOS-11):

$ conda env create --file soliket-tests.yml

You can then install the latest released version of SOLikeT from PyPI into this environment:

$ conda activate soliket-tests
$ pip install soliket

Installing in editable mode for development

If you wish to actively develop the code you can instead install the in-development version of SOLikeT from the github repository in editable mode:

$ git clone https://github.com/simonsobs/soliket
$ cd soliket
$ pip install -e .

Optional: Install CosmoPower

In order to use the CosmoPower Theories within SOLikeT you will need to additionally install CosmoPower (and with it tensorflow, which is rather heavy and hence left out of the default installation).

Unless using an M1 Mac this should be easily achievable with:

$ pip install cosmopower

If you wish to install it using your own system tools (including new M1 Mac) some useful information is provided below.

Harder Way: Preparing your own environment

CREATE VIRTUAL CONDA ENV TO RUN COBAYA Based on cobaya documentation.

$ sudo apt update && sudo apt install gcc gfortran g++ openmpi-bin openmpi-common libopenmpi-dev libopenblas-base liblapack3 liblapack-dev make
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
$ bash miniconda.sh -b -p $HOME/miniconda
$ export PATH="$HOME/miniconda/bin:$PATH"
$ conda config --set always_yes yes --set changeps1 no
$ conda create -q -n cobaya-env python=3.7 scipy matplotlib cython PyYAML pytest pytest-forked flaky
$ source activate cobaya-env
$ pip install mpi4py

INSTALL COBAYA

$ pip install cobaya
$ sudo apt install libcfitsio-bin libcfitsio-dev
$ cobaya-install cosmo --packages-path cobaya_packages

INSTALL SOLIKET

$ conda install -c conda-forge compilers pyccl
$ git clone https://github.com/simonsobs/soliket
$ cd soliket
$ pip install -e .

At NERSC

Based on Perlmutter. Note: you may want to run cobaya in the SCRATCH directory (see thread here).

Build mpi4py in your custom conda environment Based on NERSC documentation.

module load python
conda create -n soliket-tests python numpy
conda activate soliket-tests
module swap PrgEnv-${PE_ENV,,} PrgEnv-gnu
MPICC="cc -shared" pip install --force-reinstall --no-cache-dir --no-binary=mpi4py mpi4py

Load fftw, gsl and cmake (WOULD BE NEEDED BY PYCCL)

module load cray-fftw
module load gsl
module load cmake

Please, make sure to load cmake as your last command, so that the path to cmake bin is prepended to your PATH (see this issue).

Install additional requirements and soliket

pip install pytest-cov make swig
git clone https://github.com/simonsobs/soliket
cd soliket
pip install -e .

BONUS: install cosmopower (optional) cosmopower is not automatically installed (see above). However, if you want to use this option, do the following:

pip install cosmopower
cobaya-install planck_2018_highl_plik.TTTEEE_lite_native

Test soliket

pytest -v soliket

Run soliket

Create your job script following cobaya docs.

NOTE: Any time you log in to a new perlmutter shell, remember to always load the relevant modules (in particular, those needed for pyccl). A good option is to create an alias in your bashrc with all the relevant commands.

Please, don't hesitate to open issues and/or be in touch with us, should you find any problems. Many thanks to Luca Pagano, Serena Giardiello, Massimiliano Lattanzi, Pablo Lemos, +++

On M1 Mac

There is an issue with installing tensorflow (needed for cosmopower) on M1 Mac that is likely to be solved in the future. For the moment, if you want to couple SOLikeT to cosmopower, please follow this guidance:

  1. Download latest miniconda installer (e.g., here: Download Conda environment) and properly rename it (e.g., -> miniconda.sh)
  2. Install miniconda and tensor flow-deps
bash ~/miniconda.sh -b -p $HOME/miniconda
source ~/miniconda/bin/activate
conda install -c apple tensorflow-deps
  1. git clone soliket and create your virtual env
git clone https://github.com/simonsobs/soliket
cd soliket
conda env create -n my_env -f soliket-tests.yml
conda activate my_env
  1. Install tensorflow-macos and metal with correct versioning
pip install tensorflow-macos
pip install tensorflow-metal
  1. Download and install cosmopower manually
git clone https://github.com/alessiospuriomancini/cosmopower
cd cosmopower
pip install .
  1. Go back to soliket folder and install it
cd path/to/your/soliket
pip install -e .