Setup a conda environment at NERSC


November 8, 2022

Obsolete: see the new version

NERSC recommends to use the “Global Common” to store Conda environments, because it is optimized to store lots of small files. Consider that it is mounted read-only on computing nodes. The filesystem is organized by groups, so choose one of your groups:


for example for me it is the cmb group.

mkdir -p /global/common/software/$GROUP/$USER/conda
cd ~
ln -s /global/common/software/$GROUP/$USER c

So we can access it quickly under ~/c.

Then we create a Conda environment with mamba, specifying the version of python and other packages:

export ENV=pycmb
module load python3 # it should load the latest Anaconda
mamba create --prefix /global/common/software/$GROUP/$USER/conda/$ENV python==3.10 numpy astropy matplotlib ipykernel numba  pytest toml cython scipy namaster -c conda-forge

We can also set that path for conda to automatically search into, this will pickup also future Conda environments on the same path:

conda config --append envs_dirs /global/common/software/$GROUP/$USER/conda

We do not want that long path in our prompt, so:

conda config --set env_prompt '({name}) '

So we can activate the environment specifying only the name:

conda activate $ENV

In order to use it also on Jupyter@NERSC you will need to register the kernel:

ipython kernel install --name $ENV --user

Tip for CMB people, make sure you build healpy from source to get the best performance on Spherical Harmonics Transforms:

CC=gcc CXX=g++ CFLAGS="-fPIC -O3 -march=native" CXXFLAGS="-fPIC -O3 -march=native" pip3 install --user --no-binary healpy --ignore-installed healpy