Miniconda3

Miniconda is a free, miniature installation of Anaconda Distribution that includes only conda, Python, the packages they both depend on, and a small number of other useful packages.

Miniconda is useful to create your own conda environment in the /fs/agustina/USER folder. To do this, you can import your own yaml file and create the environment with the following commands:

Usage

module load miniconda3/3.12
mkdir -p /fs/agustina/$(whoami)/conda-env
$MINICONDA3_HOME/bin/conda-env create --prefix /fs/agustina/$(whoami)/conda-env/my-conda-env --file /fs/agustina/$(whoami)/conda-env/my-environment-file.yml
source $MINICONDA3_HOME/bin/activate /fs/agustina/$(whoami)/conda-env/my-conda-env

Once you have the environment ready and activated, you can more packages with pip install inside the environment, the you can create a bash script to launch the environment in agustina cluster:

Example script : test-miniconda.sh

#!/bin/bash

#SBATCH -o test-miniconda-infos%j.o
#SBATCH -p thin
#SBATCH -N 1

module load miniconda3/3.12

# activate environment
source $MINICONDA3_HOME/bin/activate /fs/agustina/$(whoami)/conda-env/my-conda-env

python -v

echo "done!!"

Submit with :

sbatch --account=your_project_ID test-miniconda.sh

**Base file: my-environment-file.yml **

name:
channels:
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - blas=1.0=mkl
  - bzip2=1.0.8=h5eee18b_6
  - ca-certificates=2024.9.24=h06a4308_0
  - expat=2.6.3=h6a678d5_0
  - intel-openmp=2023.1.0=hdb19cb5_46306
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libmpdec=4.0.0=h5eee18b_0
  - libstdcxx-ng=11.2.0=h1234567_1
  - libuuid=1.41.5=h5eee18b_0
  - mkl=2023.1.0=h213fc3f_46344
  - mkl-service=2.4.0=py313h5eee18b_1
  - mkl_fft=1.3.11=py313h5eee18b_0
  - mkl_random=1.2.8=py313h06d7b56_0
  - ncurses=6.4=h6a678d5_0
  - numpy=2.1.3=py313hf4aebb8_0
  - numpy-base=2.1.3=py313h3fc9231_0
  - openssl=3.0.15=h5eee18b_0
  - pip=24.2=py313h06a4308_0
  - python=3.13.0=hf623796_100_cp313
  - python_abi=3.13=0_cp313
  - readline=8.2=h5eee18b_0
  - setuptools=72.1.0=py313h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tbb=2021.8.0=hdb19cb5_0
  - tk=8.6.14=h39e8969_0
  - tzdata=2024b=h04d1e81_0
  - xz=5.4.6=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - alabaster==1.0.0
      - babel==2.16.0
      - certifi==2024.8.30
      - charset-normalizer==3.4.0
      - contourpy==1.3.1
      - cycler==0.12.1
      - docutils==0.21.2
      - fonttools==4.55.0
      - idna==3.10
      - imagesize==1.4.1
      - jinja2==3.1.4
      - kiwisolver==1.4.7
      - markupsafe==3.0.2
      - matplotlib==3.9.2
      - packaging==24.2
      - pillow==11.0.0
      - pygments==2.18.0
      - pyparsing==3.2.0
      - python-dateutil==2.9.0.post0
      - requests==2.32.3
      - scipy==1.14.1
      - six==1.16.0
      - snowballstemmer==2.2.0
      - sphinx==8.1.3
      - sphinxcontrib-applehelp==2.0.0
      - sphinxcontrib-devhelp==2.0.0
      - sphinxcontrib-htmlhelp==2.1.0
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==2.0.0
      - sphinxcontrib-serializinghtml==2.0.0
      - urllib3==2.2.3
      - wheel==0.38.1

More info :