instructions.txt

=============
Linux Ubuntu:

1. Install netcdf and C and Fortran compilers on Linux Ubuntu (full howto: https://cloud-gc.readthedocs.io/en/stable/chapter04_developer-guide/install-basic.html)

    Update package metadata:

        $ sudo apt-get update

    Install GNU compiler:

        $ sudo apt-get install gcc gfortran

    Executables will be installed to /usr/bin/:

        $ which gcc gfortran
        /usr/bin/gcc
        /usr/bin/gfortran

    Check versions:

        $ gcc --version
        gcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609
        ...
        $ gfortran --version
        GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609
        ...


    Install netcdf

        $ sudo apt-get install libnetcdf-dev libnetcdff-dev

    Check NetCDF-C configuration:

        $ nc-config --all

        This netCDF 4.4.0 has been built with the following features:
        ...

    Check NetCDF-Fortran configuration:

        $ nf-config --all

        This netCDF-Fortran 4.4.3 has been built with the following features:
        ...
        --prefix    -> /usr
        --includedir-> /usr/include
        --version   -> netCDF-Fortran 4.4.3

    --includedir will be used to include this NetCDF library when compiling Fortran code.


2. Navigate to SOFTX-D-16-00023
    $ cd SOFTX-D-16-00023

   and modify NA and NI paths in EBM/src/Makefile and paths in EBM/preprocess/preprocess.sh according to the ones indicated by --includedir above.

3. Navigate to EBM/src/

    $ cd EBM/src/

   and compile the EBM code:
    
    $ make -f Makefile

   It might be necessary to remove the following line from Makefile if it hinders compiling (the line seems to be required for MacOS users)

    FC=gfortran -fallow-argument-mismatch

4. Give executable permissions to EBM program:

    $ chmod +x ebm.sh

5. Run the EBM program:

    $ ./ebm.sh


===========
MacOS

A. Install gfortran compiler using Homebrew: https://www.macinchem.org/reviews/cheminfo/cheminfoMacUpdate.php
 
B. Install netcdf using this command in the Terminal

    brew install netcdf

C. Modify paths in EBM/scr/Makefile and /preprocess/preprocess.sh (see pt 2. in Linux version)

D. At the beginning of Makefile add the following line

    FC=gfortran -fallow-argument-mismatch

E. Compile program and change permissions (see points 3., 4. in Linux version)

F. Run program

    EBM/src/ebm.sh 

============
Git-ignoring files:

In addition to .gitignore (which does not ignore existing, modified files) one can choose to ingore the two files with local paths, and all the files in EBM/output/directory by running the follwoging two commands:

    $ git update-index --assume-unchanged EBM/src/Makefile EBM/preprocess/preprocess.sh
    $ git ls-files -z EBM/output/ | xargs -0 git update-index --assume-unchanged

In order to revoke ignoring with the above method run:

    $ git update-index --no-assume-unchanged <file>

In order to override ignoring by .gitignore, change the local.gitignore content, or run:

    $ git add -f <file>