Commit 703d56e4 authored by Radovan Bast's avatar Radovan Bast

pasting sources from 2013 installation guide

parents
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
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$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
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PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
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Dalton/LSDalton Installation Guide
==================================
This is the source code behind http://dalton-installation.readthedocs.org.
You are most welcome to contribute;
see http://dalton-installation.readthedocs.org/en/latest/doc/contributing.html.
# -*- coding: utf-8 -*-
#
# dalton-installation documentation build configuration file, created by
# sphinx-quickstart on Thu Jul 24 21:03:14 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys
import os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.todo',
'sphinx.ext.mathjax',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'dalton-installation'
copyright = u'2014, Dalton/LSDalton developers'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '2014.0'
# The full version, including alpha/beta/rc tags.
release = '2014.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'default'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'dalton-installation'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'dalton-installation.tex', u"Dalton/LSDalton Installation Guide",
u'Dalton/LSDalton developers', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'dalton-installation', u"Dalton/LSDalton Installation Guide",
[u'Dalton/LSDalton developers'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'dalton-installation', u"Dalton/LSDalton Installation Guide",
u'Dalton/LSDalton developers', 'dalton-installation', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
Installation instructions for system administrators
===================================================
Please read the other installation sections for details
but the installation procedure is basically this::
$ ./setup [--flags] --prefix=/full/install/path/
$ cd build
$ make [-jN]
$ ctest [-jN]
$ make install
This will install binaries, run scripts, the basis set library,
as well as tools into the install path.
Advise users to always set a suitable scratch directory::
$ export DALTON_TMPDIR=/full/path/scratch
Basis set directory
===================
The basis set directory is copied to the build directory
(and possibly install directory).
The ``dalton`` and ``lsdalton`` scripts will automatically
find them. You can define or append custom basis set directories
by exporting BASDIR::
export BASDIR='/somepath:/otherpath'
How you can contribute to this documentation
============================================
These pages are rendered using `RST/Sphinx <http://sphinx-doc.org/rest.html>`_ and served using
`Read the Docs <https://readthedocs.org>`_.
RST is a subset of Sphinx. Sphinx is RST with some extensions.
How to modify the webpages
--------------------------
The source code for this documentation is hosted on `GitHub <https://github.com/daltonprogram/installation>`_.
You need a `GitHub <https://github.com>`_ account to modify the sources.
With a GitHub account you have two possibilities to edit the sources:
* You write an email to bast at kth dot se and ask to be added as project team member. After that you can push
directly to https://github.com/daltonprogram/installation. Once you commit and push, a webhook
updates the documentation on http://dalton-installation.readthedocs.org/. This typically takes less than a minute.
* You fork https://github.com/daltonprogram/installation and submit your changes at some point via a pull request. This means
that your changes are not immediately visible but become so after a team member reviews your changes
with a mouse click thus integrating them to https://github.com/daltonprogram/installation.
**Note that the entire documentation including the entire documentation
source code is public.**
Do not publish sensitive information and harvestable email addresses.
How to locally test changes
---------------------------
You do not have to push to see and test your changes.
You can test them locally.
For this install python-sphinx and python-matplotlib.
Then build the pages with::
$ make html
Then point your browser to _build/html/index.html.
The style is not the same but the content is what you
would see after the git push.
Expert options
==============
Compiling in verbose mode
-------------------------
Sometimes you want to see the actual compiler flags and definitions when compiling the code::
$ make VERBOSE=1
How can I change optimization flags?
------------------------------------
You can turn optimization off (debug mode) like this::
$ ./setup --type=debug [other flags]
$ cd build
$ make
You can edit compiler flags in cmake/compilers/{FortranFlags.cmake, CFlags.cmake, CXXFlags.cmake}.
Alternatively you can edit compiler flags through ccmake::
$ cd build
$ ccmake ..
Basic installation
==================
General
-------
Dalton is configured using CMake, typically via the ``setup`` script,
and subsequently compiled using make or gmake.
The ``setup`` script is a useful front-end to CMake.
You need python to run ``setup``.
Basics
------
To see all options, run::
$ ./setup --help
The ``setup`` script does nothing else than creating the directory "build" and
calling CMake with appropriate environment variables and flags::
$ ./setup [--flags]
$ cd build
$ make
By default CMake builds out of source. This means that all object files and the
final binary are generated outside of the source directory. Typically the build
directory is called "build", but you can change the name of the build directory
(e.g. "build_gfortran")::
$ ./setup [--flags] build_gfortran
$ cd build_gfortran
$ make
By default we compile all targets (DALTON and LSDALTON). Instead of typing
``make``, you can restrict compilation to only ``dalton.x`` or ``lsdalton.x``
like this::
$ make dalton.x
$ make lsdalton.x
You can compile the code on several cores::
$ make -j4
Typical examples
----------------
In order to get familiar with the configuration setup, let us demonstrate
some typical configuration scenarios.
Configure for parallel compilation using MPI (make sure to properly export MPI
paths)::
$ ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx
There is a shortcut for it::
$ ./setup --mpi
Configure for sequential compilation using ifort/icc/icpc and link against parallel mkl::
$ ./setup --fc=ifort --cc=icc --cxx=icpc --mkl=parallel
Configure for sequential compilation using gfortran/gcc/g++::
$ ./setup --fc=gfortran --cc=gcc --cxx=g++
Parallel compilation on a Cray::
./setup --fc=ftn --cc=cc --cxx=CC --cray --mpi
Parallel compilation on a SGI using Intel compilers and MPT::
./setup --fc=ifort --cc=icc --cxx=icpc --sgi-mpt
You get the idea. The configuration is usually good at detecting math libraries
automatically, provided you export the proper environment variable ``MATH_ROOT``,
see :ref:`linking_to_math`.
What to do if CMake is not available or too old?
------------------------------------------------
If it is your machine and you have an Ubuntu or Debian-based distribution::
$ sudo apt-get install cmake
On Fedora::
$ sudo yum install cmake
Similar mechanisms exist for other distributions or
operating systems. Please consult Google.
If it is a cluster, please ask the Administrator to install/upgrade CMake.
If it is a cluster, but you prefer to install it yourself (it's easy):
1. Download the latest pre-compiled tarball from http://www.cmake.org/cmake/resources/software.html
2. Extract the tarball to, say, ~/cmake-2.8.11-Linux-i386
3. Set correct PATH variable
.. _linking_to_math:
Linking to math libraries
=========================
General
-------
Dalton requires BLAS and LAPACK libraries. Typically you will want to link to
external math (BLAS and LAPACK) libraries, for instance provided by MKL or
Atlas.
By default the CMake configuration script will automatically detect these libraries::
$ ./setup --blas=auto --lapack=auto # this is the default
if you define MATH_ROOT, for instance::
$ export MATH_ROOT='/opt/intel/mkl'
Do not use full path MATH_ROOT='/opt/intel/mkl/lib/ia32'. CMake will append the
correct paths depending on the processor and the default integer type. If the
MKL libraries that you want to use reside in
/opt/intel/mkl/10.0.3.020/lib/em64t, then MATH_ROOT is defined as::
$ export MATH_ROOT='/opt/intel/mkl/10.0.3.020'
Then::
$ ./setup [--flags]
$ cd build
$ make
Intel/MKL
---------
If you compile with Intel compilers and have the MKL library available, you
should use the --mkl flag which will automatically link to the MKL libraries
(in this case you do not have to set MATH_ROOT).
You have to specify whether you want to use the sequential or parallel
(threaded) MKL version. For a parallel Dalton runs you should probably link to
the sequential MKL::
$ ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --mkl=sequential
For a sequential compilation you may want to link to the parallel MKL::
$ ./setup --fc=ifort --cc=icc --cxx=icpc --mkl=parallel
The more general solution is to link to the parallel MKL and control the number
of threads using MKL environment variables.
Cray
----
Cray typically provides own optimized BLAS/LAPACK wrappers.
For this use the option --cray to disable automatic BLAS/LAPACK detection::
$ ./setup --fc=ftn --cc=cc --cxx=CC --cray
Explicitly specifying BLAS and LAPACK libraries
-----------------------------------------------
If automatic detection of math libraries fails for whatever reason, you can
always call the libraries explicitly like here::
$ ./setup --blas=/usr/lib/libblas.so --lapack=/usr/lib/liblapack.so
Alternatively you can use the --explicit-libs option. But in this case you should
disable BLAS/LAPACK detection::
$ ./setup --blas=none --lapack=none --explicit-libs="-L/usr/lib -lblas -llapack"
Builtin BLAS and LAPACK implementation
--------------------------------------
If no external BLAS and LAPACK libraries are available, you can use the builtin
implementation. However note that these are not optimized and you will sacrifice
performance. This should be the last resort if nothing else is available::
$ ./setup --blas=builtin --lapack=builtin
LSDALTON/ScaLAPACK/Intel/MKL
----------------------------
If you compile with Intel compilers and have the MKL library available, you
can chose to compile LSDALTON using the ScaLAPACK library provided by Intel.
In this case you should set the MATH_ROOT enviromental variable and use
the --scalapack flag which will automatically link to the MKL libraries.
You should not use the --mkl flag for this setup::
$ ./setup --fc=mpif90 --cc=mpicc --cxx=mpicxx --scalapack
Scratch directory
=================
DALTON and LSDALTON need a scratch directory to write temporary files.
Ideally this should be a fast-access disk.
You should always specify an explicit scratch directory with::