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README.md

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  • setup_venv_hdfml.sh 1.12 KiB
    #!/bin/bash
    # __author__ = Felix Kleinert
    # __date__  = '2020-04-06'
    
    # This script creates a virtual env which contains all modules which are not available via slrum/easybuild (see mlt_modules_hdfml.sh)
    # enter setting dir if called externally
    
    # $1 has to be an abs path to HPC_setup. If not provided, $PWD is used
    
    if [[ $1 != '' ]]; then
      cur=$1
    else
      cur=$PWD
    fi
    
    # load existing modules
    source ${cur}mlt_modules_hdfml.sh
    
    # create venv
    python3 -m venv ${cur}../venv_hdfml
    
    source ${cur}/../venv_hdfml/bin/activate
    
    # export path for side-packages 
    export PYTHONPATH=${cur}/../venv_hdfml/lib/python3.6/site-packages:${PYTHONPATH}
    
    pip install -r ${cur}/requirements_HDFML_additionals.txt
    pip install --ignore-installed matplotlib==3.2.0
    pip install --ignore-installed pandas==1.0.1
    pip install --ignore-installed statsmodels==0.11.1
    pip install --ignore-installed tabulate
    pip install -U typing_extensions
    # see wiki on hdfml for information oh h5py:
    # https://gitlab.version.fz-juelich.de/haf/Wiki/-/wikis/HDF-ML%20System
    
    export CC=mpicc
    export HDF5_MPI="ON"
    pip install --no-binary=h5py h5py
    pip install --ignore-installed netcdf4==1.5.4