diff --git a/docs/sphinx/source/build-the-docs.rst b/docs/sphinx/source/build-the-docs.rst index 952d040d..9a922153 100644 --- a/docs/sphinx/source/build-the-docs.rst +++ b/docs/sphinx/source/build-the-docs.rst @@ -3,8 +3,7 @@ Building the docs Dependencies to build the documentation: -* Sphinx -* sphinxcontrib.napoleon +* Sphinx >= 1.3 * sphinxcontrib.programoutput If you have the dependencies listed above, and you want to build the diff --git a/docs/sphinx/source/conf.py b/docs/sphinx/source/conf.py index 884ca83b..86677b69 100644 --- a/docs/sphinx/source/conf.py +++ b/docs/sphinx/source/conf.py @@ -45,7 +45,9 @@ # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. -needs_sphinx = '1.3' +needs_sphinx = '1.3' # so we have sphinx.ext.napoleon + # otherwise you could install and use + # sphinxcontrib.napoleon # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. diff --git a/docs/sphinx/source/environment-modules-notes.rst b/docs/sphinx/source/environment-modules-notes.rst index f911b428..83393562 100644 --- a/docs/sphinx/source/environment-modules-notes.rst +++ b/docs/sphinx/source/environment-modules-notes.rst @@ -1,6 +1,18 @@ Notes on building environment-modules ===================================== +Update 2015-10-05 +----------------- +Below are Mark Kness' notes on building and using ``environment-modules``. I +have since found lmod_ to be a slightly better documented and supported +alternative. + +- Bob Grant + +.. _lmod: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod + +Environment Modules +------------------- environment-modules is a tool, written with Tcl, that makes it convenient to switch environment settings. It is not required to use DistArray, but we find it useful in development. It is a difficult name to google. I had to build it diff --git a/docs/sphinx/source/getting-started.rst b/docs/sphinx/source/getting-started.rst index d84f974d..4551b16d 100644 --- a/docs/sphinx/source/getting-started.rst +++ b/docs/sphinx/source/getting-started.rst @@ -4,6 +4,7 @@ Getting Started To see some examples of what DistArray can do, check out our IPython notebooks on nbviewer (also in the ``examples`` directory of the DistArray source). -* `DistArray Features `_ +* `DistArray Features `_ * `Seismic Volume `_ * `Julia Set `_ +* `Gaussian Elimination `_ diff --git a/docs/sphinx/source/hdf5-notes.rst b/docs/sphinx/source/hdf5-notes.rst index e2096b14..7c0f17bb 100644 --- a/docs/sphinx/source/hdf5-notes.rst +++ b/docs/sphinx/source/hdf5-notes.rst @@ -1,6 +1,26 @@ Building HDF5 and h5py for DistArray ==================================== +If you want to use DistArray's parallel IO capabilities on HDF5 files, +parallel-enabled HDF5 and h5py installations are required. Unfortunately, +installing these can be somewhat of a pain. + +Update 2015-10-05 +----------------- + +The "Original Notes" below are pretty old at this point. Recently I have had +success installing a parallel-enabled HDF5 (1.8.15) using Homebrew on OS X:: + + $ brew install hdf5 --with-mpi + +The instructions for building ``h5py`` on top of a parallel hdf5 have also +changed, but are available +`here `_. + + +Original Notes +-------------- + These are notes from trying to build HDF5 1.8.12 and h5py 2.2.1 against mpi4py 1.3 and openmpi-1.6.5 on OS X 10.8.5. @@ -43,7 +63,7 @@ directory:: This gives me an error about "MPI Message" addressed here:: https://github.com/h5py/h5py/issues/401 - + After patching api_compat.h as suggested, it builds. One could also use the ``master`` version of h5py from GitHub instead of the latest release. diff --git a/docs/sphinx/source/history.rst b/docs/sphinx/source/history.rst index 700a8835..8b9da1fb 100644 --- a/docs/sphinx/source/history.rst +++ b/docs/sphinx/source/history.rst @@ -2,6 +2,5 @@ History ------- DistArray was started by Brian Granger in 2008 and is currently being developed -at Enthought by a team led by Kurt Smith, in partnership with Bill Spotz from -Sandia's (Py)Trilinos project and Brian Granger and Min RK from the IPython -project. +by Enthought in partnership with Bill Spotz from Sandia's (Py)Trilinos project +and Brian Granger and Min RK from the IPython project. diff --git a/docs/sphinx/source/installation.rst b/docs/sphinx/source/installation.rst index 3c4c599d..a3b03bd4 100644 --- a/docs/sphinx/source/installation.rst +++ b/docs/sphinx/source/installation.rst @@ -3,13 +3,13 @@ Installation DistArray requires the following Python libraries: -* `NumPy`_, -* `IPython`_, and -* `Mpi4Py`_. +* `numpy`_, +* `ipyparallel`_, and +* `mpi4py`_. -.. _NumPy: http://www.numpy.org -.. _IPython: http://ipython.org -.. _Mpi4Py: http://mpi4py.scipy.org +.. _numpy: http://www.numpy.org +.. _ipyparallel: https://github.com/ipython/ipyparallel +.. _mpi4py: http://mpi4py.scipy.org Optionally, DistArray can make use of: @@ -28,17 +28,27 @@ or:: pip install distarray +Experimental conda-quickstart +----------------------------- + +Alternatively, we have an experimental `conda-quickstart` script in the +``quickstart`` directory of the root of this source tree. Given an Anaconda +installation, this script will attempt to install create a conda environment +for you, installing MPI, mpi4py, and the above Python dependencies as +necessary. See ``README.rst`` in that directory for more information. + + Testing Your Installation ------------------------- To test your installation, you will first need to start an IPython.parallel -cluster with MPI enabled. The easist way is to use use the ``dacluster`` -command that comes with DistArray:: +cluster with MPI enabled. The easist way is to use the ``dacluster`` command +that comes with DistArray:: dacluster start See ``dacluster``'s help for more:: - + dacluster --help You should then be able to run all the tests from the DistArray source