Install HEALPix and PolSpice in a conda environment


October 14, 2020

Some notes on how to install HEALPix and PolSpice inside a conda environment, with some details about doing it at NERSC, but most of the tutorial is independent of that.

Setup the conda environment and the compilers

I assume here we are installing it into a custom conda environement the possibly contains all other cosmology packages, like healpy.

For example created with:

module load python
conda create -n pycmb python==3.7 healpy matplotlib ipykernel

When you activate the conda environment, the variable $CONDA_PREFIX is automatically set to the base folder of the environment, something like:


To make it simpler, I am using gcc and gfortran, if at NERSC run:

module load PrgEnv-gnu

if that fails, probably you need first to unload the Intel environment:

module unload PrgEnv-intel
module load PrgEnv-gnu

Install cfitsio

cfitsio is quite easy, better download the version included in healpy because it has a couple of fixes:

git clone
cd cfitsio

We want to install it into a dedicated folder, not the same lib folder of the conda environment, so that we don’t risk to have conflicts with the compiler libraries during the build process:

./configure --prefix=$CONDA_PREFIX/cfitsio
make -j8 shared install

Install HEALPix

HEALPix installs itself in the same folder where it is unpacked, and then modifies the bash profile to make things work. As we want to keep things isolated, let’s unpack the Healpix package into the conda environment folder, so it will be something like:



configure the C, the Fortran packages, the Fortran package requires libsharp, set everything to default except location of cfitsio where you need (notice lib at the end):


When the installer asks whether to modify .profile respond no. Now the installer will create some scripts in the ~/.healpix folder and modify .profile, we want to only activate HEALPix in our conda environment so we should modify .profile and remove the lines added by HEALPix.

Finally we can have HEALPix automatically activated when the conda environment is initialized (notice we need the script to end in .sh):

mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d
ln -s ~/.healpix/3_70_Linux/config ${CONDA_PREFIX}/etc/conda/activate.d/

Restart the conda environment, and try to run anafast to check that it works. If you are at NERSC, make sure that you are always loading the GNU programming environment by having:

module swap PrgEnv-intel PrgEnv-gnu

in .bashrc.ext.

Install PolSpice

Create a build folder inside the source folder and create a file with this content:

cmake .. -DCFITSIO=${CONDA_PREFIX}/cfitsio/lib -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_C_COMPILER=gcc


make -j8

This will put the spice executable into the ../bin folder, just copy it to the conda environment bin folder:

cd ..
cp bin/spice ${CONDA_PREFIX}/bin/

We can also copy the 2 python modules into the environment:

cp bin/ bin/ ${CONDA_PREFIX}/lib/python3.*/site-packages/

Check it works:

spice -usage

Uninstall PolSpice

rm ${CONDA_PREFIX}/bin/spice ${CONDA_PREFIX}/lib/python3.*/site-packages/ ${CONDA_PREFIX}/lib/python3.*/site-packages/