Anaconda 2024

Anaconda 2024 is a free and open-source software distribution of the Python and R languages, used in data science and machine learning. It is aimed at simplifying the deployment and management of software packages.

WARNING: If you do not know how to create your own anaconda environment in agustina cluster, please read the instruction below, otherwise send and email with your request to agustina@bifi.es for further assistance.

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

Usage

module load anaconda/2024
mkdir -p /fs/agustina/$(whoami)/conda-env
$ANACONDA3_HOME/bin/conda-env create --prefix /fs/agustina/$(whoami)/conda-env/my-conda-env --file /fs/agustina/$(whoami)/conda-env/my-environment-file.yml
source $ANACONDA3_HOME/bin/activate /fs/agustina/$(whoami)/conda-env/my-conda-env

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

Example script : test-anaconda.sh

#!/bin/bash

#SBATCH -J test-anaconda
#SBATCH -o test-anaconda-%j.msg
#SBATCH -e test-anaconda-%j.err
#SBATCH -p thin
#SBATCH -N 1

module load anaconda/2024

# activate environment
source $ANACONDA3_HOME/bin/activate /fs/agustina/$(whoami)/conda-env/my-conda-env

python -v

echo "done!!"

Submit with :

sbatch --account=your_project_ID test-anaconda.sh

Base file: my-environment-file.yml

name: base
channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - archspec=0.2.3=pyhd8ed1ab_0
  - boltons=24.0.0=pyhd8ed1ab_0
  - brotli-python=1.1.0=py312h2ec8cdc_2
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.32.3=h4bc722e_0
  - ca-certificates=2024.8.30=hbcca054_0
  - certifi=2024.8.30=pyhd8ed1ab_0
  - cffi=1.17.1=py312h06ac9bb_0
  - charset-normalizer=3.4.0=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - conda=24.9.2=py312h7900ff3_0
  - conda-libmamba-solver=24.9.0=pyhd8ed1ab_0
  - conda-package-handling=2.4.0=pyh7900ff3_0
  - conda-package-streaming=0.11.0=pyhd8ed1ab_0
  - distro=1.9.0=pyhd8ed1ab_0
  - fmt=10.2.1=h00ab1b0_0
  - frozendict=2.4.6=py312h66e93f0_0
  - h2=4.1.0=pyhd8ed1ab_0
  - hpack=4.0.0=pyh9f0ad1d_0
  - hyperframe=6.0.1=pyhd8ed1ab_0
  - idna=3.10=pyhd8ed1ab_0
  - jsonpatch=1.33=pyhd8ed1ab_0
  - jsonpointer=3.0.0=py312h7900ff3_1
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.21.3=h659f571_0
  - ld_impl_linux-64=2.43=h712a8e2_2
  - libarchive=3.7.4=hfca40fe_0
  - libcurl=8.10.1=hbbe4b11_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=hd590300_2
  - libexpat=2.6.4=h5888daf_0
  - libffi=3.4.2=h7f98852_5
  - libgcc=14.2.0=h77fa898_1
  - libgcc-ng=14.2.0=h69a702a_1
  - libgomp=14.2.0=h77fa898_1
  - libiconv=1.17=hd590300_2
  - libmamba=1.5.9=h4cc3d14_0
  - libmambapy=1.5.9=py312h7fb9e8e_0
  - libnghttp2=1.64.0=h161d5f1_0
  - libnsl=2.0.1=hd590300_0
  - libsolv=0.7.30=h3509ff9_0
  - libsqlite=3.47.0=hadc24fc_1
  - libssh2=1.11.0=h0841786_0
  - libstdcxx=14.2.0=hc0a3c3a_1
  - libstdcxx-ng=14.2.0=h4852527_1
  - libuuid=2.38.1=h0b41bf4_0
  - libxcrypt=4.4.36=hd590300_1
  - libxml2=2.13.4=h064dc61_2
  - libzlib=1.3.1=hb9d3cd8_2
  - lz4-c=1.9.4=hcb278e6_0
  - lzo=2.10=hd590300_1001
  - mamba=1.5.9=py312h9460a1c_0
  - menuinst=2.2.0=py312h7900ff3_0
  - ncurses=6.5=he02047a_1
  - openssl=3.4.0=hb9d3cd8_0
  - packaging=24.2=pyhd8ed1ab_0
  - pip=24.3.1=pyh8b19718_0
  - platformdirs=4.3.6=pyhd8ed1ab_0
  - pluggy=1.5.0=pyhd8ed1ab_0
  - pybind11-abi=4=hd8ed1ab_3
  - pycosat=0.6.6=py312h98912ed_0
  - pycparser=2.22=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.12.7=hc5c86c4_0_cpython
  - python_abi=3.12=5_cp312
  - readline=8.2=h8228510_1
  - reproc=14.2.4.post0=hd590300_1
  - reproc-cpp=14.2.4.post0=h59595ed_1
  - requests=2.32.3=pyhd8ed1ab_0
  - ruamel.yaml=0.18.6=py312h66e93f0_1
  - ruamel.yaml.clib=0.2.8=py312h66e93f0_1
  - setuptools=75.3.0=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - tqdm=4.67.0=pyhd8ed1ab_0
  - truststore=0.10.0=pyhd8ed1ab_0
  - tzdata=2024b=hc8b5060_0
  - urllib3=2.2.3=pyhd8ed1ab_0
  - wheel=0.45.0=pyhd8ed1ab_0
  - xz=5.2.6=h166bdaf_0
  - yaml-cpp=0.8.0=h59595ed_0
  - zstandard=0.23.0=py312hef9b889_1
  - zstd=1.5.6=ha6fb4c9_0
prefix:

More info :