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leonfoks committed Oct 11, 2024
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3 changes: 1 addition & 2 deletions docs/_sources/content/getting_started/installation.rst.txt
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Expand Up @@ -15,8 +15,8 @@ If you require parallel file reading and writing, you will also need to install

If you need to install the parallel IO version of the code, we would recommend that you start with a clean install of Python. This makes it easier to determine whether you have installed and linked the correct version of the parallel HDF5 library.

There are two versions when installing GeoBIPy, a serial version, and a parallel version. Since GeoBIPy uses a Fortran backend for forward modelling frequency domain data, you will need to have a Fortran compiler installed. Make sure that the compiler can handle derived data types since I make use of object oriented programming in Fortran.

There are two versions when installing GeoBIPy, a serial version, and a parallel version. Since GeoBIPy uses a Fortran backend for forward modelling frequency domain data, you will need to have a Fortran compiler installed. Make sure that the compiler can handle derived data types since I make use of object oriented programming in Fortran.

Installing a serial version of GeoBIPy
======================================
Expand All @@ -28,7 +28,6 @@ You should then be able to import modules from geobipy. For this type of instal

**Side note:** Let's say you ran a production run on a parallel machine with MPI and parallel HDF capabilities. You generated all the results, copied them back to your local machine, and wish to make plots and images. You will only need to install the serial version of the code on your local machine to do this.


Installing a parallel version of GeoBIPy
========================================
Installing the parallel version of the code is a little trickier due to the dependencies necessary between the OpenMPI and/or HDF libraries, and how Python's mpi4py and h5py wrap around those.
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34 changes: 23 additions & 11 deletions docs/_sources/index.rst.txt
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.. geobipy documentation master file, created by
sphinx-quickstart on Fri Oct 11 10:02:08 2024.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
############################################################
Welcome to GeoBIPy: Geophysical Bayesian Inference in Python
############################################################

geobipy documentation
=====================
This package uses a Bayesian formulation and Markov chain Monte Carlo sampling methods to
derive posterior distributions of subsurface and measured data properties.
The current implementation is applied to time and frequency domain electromagnetic data.
Application outside of these data types is in development.

Add your content using ``reStructuredText`` syntax. See the
`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
documentation for details.
Currently there are two types of data that we have implemented; frequency domain electromagnetic data,
and time domain electromagnetic data.
The package comes with a frequency domain forward modeller, but it does not come with a time domain forward modeller.
See the section :ref:`Installing_time_domain_forward_modeller` for more information.

Using GeoBIPy on Yeti
~~~~~~~~~~~~~~~~~~~~~

There is no need to install GeoBIPy on Yeti.
Simply type "module load python/geobipy" for the serial version of the code, mainly used for plotting results,
or "module load python/pGeobipy" for a parallel enabled version.

`Codebase is here! <https://github.com/usgs/geobipy/>`_

.. toctree::
:maxdepth: 2
:caption: Contents:
:maxdepth: 2

content/getting_started/getting_started
content/api/api

166 changes: 80 additions & 86 deletions docs/content/getting_started/getting_started.html
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