Micromamba

Micromamba#

  1. Download and Install micromamba

cd $WORKDIR
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
./bin/micromamba shell init -s bash  ./micromamba
source ~/.bashrc

Caution

WORKDIR should be a large storage, do not use the HOME directory for installation

On gricad , it could be /bettik/PROJECTS/PROJECT_NAME/USER_NAME

On ige-clusters, it could be /workdir/TEAM_NAME/USER_NAME or /workdir2/TEAM_NAME/USER_NAME

  1. Create an environment with python=3.10

micromamba create -n myenv python=3.10 -c conda-forge

  1. Activate the environment and install a package

micromamba activate myenv
micromamba install package_name -c conda-forge

Warning

In a submission job, you will probably add the following to activate your environment

. $WORKDIR/micromamba/etc/profile.d/micromamba.sh
OR
. $WORKDIR/micromamba/etc/profile.d/mamba.sh
and then 
micromamba activate myenv

Warning

On some clusters (for example Dahu), your micromamba process will likely be killed by the system when you try to install environments or packages, because it uses too much memory. In this case, log in to a computation node to perform such tasks.

Example 1: Create R environment and install R packages

# Create an environment with python=3.10
micromamba create -n Renv python=3.10 -c conda-forge

# Activate the environment
micromamba activate Renv

# Install R+ netcdf package
micromamba install r r-base r-essentials -c conda-forge
micromamba install r-ncdf4 -c conda-forge

Example 2: Create a ferret environment

# Create an environment with python=3.8 (needed for Gricad clusters to get the display)
micromamba create -n pyferret python=3.8  -c conda-forge pyferret ferret_datasets --yes

# Activate the environment
micromamba activate pyferret