This repository supports running a simulation-based/likelihood-free analysis based on forward-simulatios of KiDS-1000 cosmic shear within the CosmoSIS and GLASS frameworks that was used in the following analyses:
- Forward simulations and inference analysis: von Wietersheim-Kramsta et al. 2024
- Simulation-based inference pipeline: Lin et al. 2023
The repository is based on the master branch of KCAP module which can be found here.
The pipeline is built on CosmoSIS, albeit a modified version that is pip-installable and doesn't rely on environmental variables.
The KiDS-SBI repository integrates the Generator for Large Scale Structure environment (Tessore et al. 2023), which can be found here, into CosmoSIS.
In addition, the KiDS-SBI implements a new methodology to project 3D power spectra to 2D angular power spectra within the nonLimber module. This is achieved using the Levin method Levin 1994 and the code is available here.
Clone the repository:
git clone [email protected]:mwiet/kids_sbi.git
cd kids_sbi
It's strongly recommended to use some kind of encapsulated environment to install kids_sbi, e.g., using conda. Here we assume that there is a anaconda installation available, that we need MPI support, and that we're on a machine with up-to-date GCC compilers. Notes on installations on macOS and details on how to set up things manually are here.
On machines with module support (e.g., splinter, cuillin), load the anaconda and openmpi modules first:
module load anaconda
module load openmpi
If there's no automated way to load these modules, make sure conda and MPI executables (mpif90) are on your PATH. For instructions on how to set up your own conda installation, see Install conda. If you're using your own anaconda installation, don't load the module as well, as this just causes conflicts.
Now set up the conda environment using the provided conda_env.yaml file:
conda env create -f conda_env.yaml
This creates a kids_sbi_env environment that should have all the necessary dependencies. Activate the environment with source activate kids_sbi_env. NOTE: GLASS requires python >= 3.9
We need to install CAMB because we use the new python interface for it. If kcap is to be used on a local machine, pip install camb is all there is to do. On a heterogenous cluster like splinter or cuillin, we need to build CAMB ourselves, however. To do so, run
cd $MAIN_PATH
git clone --recursive [email protected]:cmbant/CAMB.git
cd $MAIN_PATH/CAMB
python setup.py build_cluster
python setup.py install
We also need to install GLASS:
cd $MAIN_PATH
git clone https://github.com/glass-dev/glass.git $MAIN_PATH/glass
cd $MAIN_PATH/glass
git checkout -b kids_sbi_stable 9af4d02
mv $MAIN_PATH/glass/lensing.py $MAIN_PATH/glass/lensing.py.bak
cp $MAIN_PATH/kids_sbi/glass/lensing.py $MAIN_PATH/glass/lensing.py
pip install -e .
Cosmology dependency:
cd $MAIN_PATH
git clone https://github.com/glass-dev/cosmology.git $MAIN_PATH/glass_cosmology
cd $MAIN_PATH/glass_cosmology
git checkout -b kids_sbi_stable 4c9052f
pip install -e .
CosmoSIS-GLASS interface:
cd $MAIN_PATH
git clone https://github.com/mwiet/glass-cosmosis.git $MAIN_PATH/glass-cosmosis
cd $MAIN_PATH/glass-cosmosis
pip install -e .
Next, we have to install the nonLimber module:
cd $MAIN_PATH
git clone https://github.com/rreischke/nonLimber_matter_shells.git $MAIN_PATH/nonLimber_matter_shells
cd $MAIN_PATH/nonLimber_matter_shells
pip install .
Finally, we also have to install SALMO:
cd $MAIN_PATH
git clone https://github.com/Linc-tw/salmo.git $MAIN_PATH/salmo
cd $MAIN_PATH/salmo/build
cmake ..
make
We can now build kids_sbi (which installs a standalone version of CosmoSIS):
cd $MAIN_PATH/kids_sbi
python build.py
To uninstall CosmoSIS (for example if you need to get the newest version), run pip uninstall cosmosis_standalone. To make a fresh installation of kids_sbi, run python build.py --clean.
The default macOS compilers are supported now but gfortran still needs to be installed. This can be done with homebrew by running brew install gcc. Note that gcc 9.2 seems to be incompatible with the PolyChord samplers included in cosmosis, so use a different version (e.g., 9.1).
If no MPI support is required, run python build.py --no-mpi.
Make sure conda and MPI are accessible (e.g., by running module load anaconda and module load openmpi) and that kcap_env is activated (source activate kcap_env).
To test that everything is working, run the tests (todo...) and some of the configs in runs/config:
mkdir runs/output
cosmosis runs/config/KV450_no_sys.ini
For MPI:
mpirun -n 4 cosmosis --mpi runs/config/KV450_no_sys.ini
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