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Python environments


There is many python distributions on IPSL Mesocenter.

Avaible through modules, we recommand to use anaconda distribution for python:

# module avail python
---------------------- /etc/modulefiles/Products ----------------------
python/2.7-anaconda    python/2.7.6-canopy-1.3(default)  
python/2.7-anaconda44  python/3.4-anaconda3              
python/2.7-anaconda50  python/3.6-anaconda50             

----------- /net/nfs/tools/meso-sl6/modules-spack/Products ------------
python/3.8-anaconda  python/meso-3.8  python/meso-3.9  

Best choice now (2022) are

python/meso-3.9 python/meso-3.8 anaconda3-py/2021.05 anaconda3-py/2021.11

  • python/meso-3.9 full anaconda 2021.11 (python 3.9.7) with the following addition
    • basemap, basemap-data-hires, cartopy, xarray, netcdf4, dask-jobqueue, mpi4py
    • cdo, esmtools
    • pathlib pipenv, plotly, pydot, scikit-optimize, termcolor, virtualenv, zarr
    • pytorch-1.8.2-lts
  • python/meso-3.8 full anaconda 2021.05 (python 3.8.8) with the following addition
    • xarray, cartopy , mpi4py , netcdf4 , dask-jobqueue ,esmtools, pathlib
    • pipenv, plotly, pydot, scikit-optimize, termcolor, virtualenv, zarr
    • pytorch-1.8.2-lts

All packages I need are in the distribution

I just do for example : module load python/meso-3.9

To know the exact package list : conda list

I need to add some package and modify version of few package

First , I'm loading the module : module load python/conda-2021.05 to be able to add or modify or add package I need to clone the installation

conda create --name "Replace_by_your_proj_name" --clone="$(which python | xargs dirname)/.."

this command could take time , when it's finish, you need to activate your environment conda activate Replace_by_your_proj_name

the module load command and conda activate ) must be executed in each session to use your python environment ( interactive or batch )

SafetyError warning are normal because some libraries have been patched by us

I want to download my own conda

Warning , our System is very old and new conda distribution cannot be installed anymore

There is no fix for the installer himself
the last Installers Versions known to work are :


The actual one cannot be installed directly on Mesocenter :


I prefer small customized distribution managed by yaml file

Customized distribution is very good for production and could be reproduced on any computer any package version could be freezed in configuration file and package could be added by conda or pip
It's also a good solution if you need to distribute software to other user on other computer because you are sure they have the same environment and you just need to give them the yaml file

don't load any python module

download a miniconda distribution
wget ; bash ./

Welcome to Miniconda3 4.x.xx

In order to continue the installation process, please review the license
Please, press ENTER to continue
Miniconda End User License Agreement  

Do you accept the license terms? [yes|no]
[no] >>> **yes**

Miniconda3 will now be installed into this location: 

  - Press ENTER to confirm the location  
  - Press CTRL-C to abort the installation  
  - Or specify a different location below  

Unpacking payload ...
Collecting package metadata (current_repodata.json): done                                                                                                                   
Solving environment: done

## Package Plan ##

  environment location: /home/xxxxxx/miniconda3

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> **yes**
no change     /home/xxxxxx/miniconda3/condabin/conda
no change     /home/xxxxxx/miniconda3/bin/conda
no change     /home/xxxxxx/miniconda3/bin/conda-env
no change     /home/xxxxxx/miniconda3/bin/activate
no change     /home/xxxxxx/miniconda3/bin/deactivate
no change     /home/xxxxxx/miniconda3/etc/profile.d/
no change     /home/xxxxxx/miniconda3/etc/fish/conf.d/
no change     /home/xxxxxx/miniconda3/shell/condabin/Conda.psm1
no change     /home/xxxxxx/miniconda3/shell/condabin/conda-hook.ps1
no change     /home/xxxxxx/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh
no change     /home/xxxxxx/miniconda3/etc/profile.d/conda.csh
modified      /home/xxxxxx/.bashrc

==> For changes to take effect, close and re-open your current shell. <==

If you'd prefer that conda's base environment not be activated on startup, 
   set the auto_activate_base parameter to false: 

conda config --set auto_activate_base false

Thank you for installing Miniconda3!

[/home/xxxxxx/miniconda3] >>> 

if you do not answer yes to the last question you need to prepend in your path the directory of the conda command export PATH=/home/xxxxxx/miniconda3/bin:$PATH

create a yaml file like this sample

# name of my project virtualenv 
name: MyProj
# needed  anaconda channels 
   - defaults
   - conda-forge
   - mro
# package list to install via conda 
   - jupyterlab=0.35
   - matplotlib<3.1
   - pandas=0.24
   - python=3.7
   - scikit-learn=0.20
   - rake_nltk
   - beautifulsoup4
   - psycopg2=2.8
   - requests=2.21
   - pymongo=3.7
   - pytest
   - scikit-learn=0.20
   - scipy=1.2
   - seaborn=0.9
   - statsmodels=0.9
   - flake8
   - openpyxl=2.6
   - pip
# package list installed via pip 
   - pip:
       - pycryptodomex==3.8.1
       - pytest-mpl==0.10
       - pytest-cov==2.6.1

then launch the following command : conda env create -f MyProj.yml

Each time you need to use your distribution you have to do
source activate MyProj

and it is a good practice to exit properly when you are done working in this setting source deactivate MyProj