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INSTALL_DEPENDENCIES.md

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Install the Required Dependencies

DART-PFLOTRAN interface requires multiple preinstalled packages. Here, I'll detail of how to install some of them.

Install Anaconda in Unix system through command-line

The installation of anaconda on Windows and Mac is straightforward. One can refer it from the official website. For unix systems (e.g., supercomputer), one might prefer the installation through command-line. The procedures are as follows:

  • Download the installable package by using curl in a specified location (make sure to replace the version with the one you prefer from the archive): 
    curl -O https://repo.continuum.io/archive/Anaconda3-2019.10-Linux-x86_64.sh
  • Install the package: 
    bash Anaconda3-2019.10-Linux-x86_64.sh

Create conda virtual environment and install the required packages

A more detailed document of conda environment is available at the doc. Here, I'll illustrate the procedures of installing the packages used in DART-PFLOTRAN:

  • Create a virtual environment (named as geosci) with python 3.7: 
    conda create --name geosci python=3.7
  • Config the conda package channel to conda-forge: 
    conda config --add channels conda-forge
conda config --set channel_priority strict
  • Install the required dependencies: 
    conda install numpy scipy pandas h5py f90nml matplotlib seaborn
conda install netcdf4 netcdf-fortran
conda install nco

Configure the environment variables for using netcdf-fortran

Note that one can also install netcdf-fortran through apt-get in unix systems. However, if sudo is not accessible, the netcdf and its fortran/python interface can be installed through conda. To allow the usage of netcdf fortran, we need to do some configuations as follows:

  • Check the locations of netcdf includedir/libdir and whether netcdf-fortran interace is installed by typing:

    nc-config --all

    , which gives us the following information if the netcdf-fortran is installed successfully:

    --has-fortran   -> yes
 --fc            -> /home/conda/feedstock_root/build_artifacts/netcdf-fortran_1571147053770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
 --fflags        -> /home/jian449/software/anaconda3/envs/geosci/include
 --flibs         -> -L/home/jian449/software/anaconda3/envs/geosci/lib
 --has-f90       -> TRUE
 --has-f03       -> FALSE

--prefix        -> /home/jian449/software/anaconda3/envs/geosci
--includedir    -> /home/jian449/software/anaconda3/envs/geosci/include
--libdir        -> /home/jian449/software/anaconda3/envs/geosci/lib
--version       -> netCDF 4.7.1

  • To make sure the linked library of netcdf-fortran is usable by a fortran compiler (e.g., gfortran), one can either add the libdir to LD_LIBRARY_PATH in your bash profile or add it in the specific conda environment. Obviously, the latter is preferable. To do that, follow the following procedures -- Enter your environment directory and create some subdirectories and files:

    cd $CONDA_PREFIX
mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh

    Edit ./etc/conda/activate.d/env_vars.sh as follows:

    #!/bin/sh

export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=/home/jian449/software/anaconda3/envs/geosci/lib:${LD_LIBRARY_PATH}

    Edit ./etc/conda/deactivate.d/env_vars.sh as follows:

    #!/bin/sh

export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}
unset OLD_LD_LIBRARY_PATH

  • To use it, do the following (replace gfortran with your own fortran compiler):

    gfortran [source_fortran_file] -o [target_file] -I/home/jian449/software/anaconda3/envs/geosci/include -lnetcdff