Add Readthedocs site (#29)

* Added Cray-DRC Support

* Set DRC variable only when available

* Removed Python Bindings from compilation

* Added drc info for clients without MPI

* Added const keyword to metadata API

* clang formatting

* Initial doc commit

* Remove python configuration from readthedocs

* Make attempting the python bindings dependent on having a python build

* Move policies from bindings out to main CMakeLists.txt

* Fixed bug that was stopping multi-node DHT updates

* Add a test with misaligned DHT updates vs writes

* Only subtract found elements that are in the server's index range

* When processing subs, consider hash segment overlap

* Remove duplicates in obj_desc list sent in reply to query_rpc

* Formatting

* Warning cleanup

* format fixes

* Added Cray-DRC Support

* Set DRC variable only when available

* Added drc info for clients without MPI

* Added const keyword to metadata API

* clang formatting

* Add dspaces_iput for non-blocking puts

* Adapt test_writer_server to iput option

* Formatting

* Make attempting the python bindings dependent on having a python build

* Move policies from bindings out to main CMakeLists.txt

* Add flag to suppress type mismatch error in gcc-10

* A little better handling of numpy includes

* Added missing init file

* Theme update

* Added theme deps

* index update test

* Add installation page

* Update index

* index update

* Fix of link

* Set wait on sub request before sending to server. Avoids notify coming back before the sub is reqdy.

* index additions

* Formatting

* Add first layer doc files

* Add finalize flag to requests

* Update test for new allocate flag

* Add allocate flag to dspaces_iput

* Free data buffer when finalizing put request

* Add check flag to dspaces_iput

* Initial doc commit

* Remove python configuration from readthedocs

* Theme update

* Added theme deps

* index update test

* Add installation page

* Update index

* index update

* Fix of link

* index additions

* Add first layer doc files

* Add installation instructions

* usage

* Usage

* usage

* usage

* usage

* Added namespace for cmake exports

* usage

* running.rst

* running

* api

* Configure make file for exmamples

* Updated example dataspaces.conf files

* Update example documentation

Co-authored-by: pradsubedi <[email protected]>
Co-authored-by: pradsubedi <[email protected]>
Co-authored-by: Philip Davis <[email protected]>

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: "3.7"
+   install:
+   - requirements: docs/requirements.txt

CMakeLists.txt

@@ -87,5 +87,11 @@ if(${ENABLE_TESTS})
   add_subdirectory(tests)
 endif(${ENABLE_TESTS})
 if(${ENABLE_EXAMPLES})
-  add_subdirectory(examples)
+    configure_file(
+        ${PROJECT_SOURCE_DIR}/examples/opts.mk.in
+        ${PROJECT_BINARY_DIR}/examples/opts.mk
+        @ONLY
+    )
+    file(GLOB EXAMPLE_DIRS ${PROJECT_SOURCE_DIR}/examples/ex*)
+    file(COPY ${PROJECT_SOURCE_DIR}/examples/Makefile ${EXAMPLE_DIRS} DESTINATION ${PROJECT_BINARY_DIR}/examples)
 endif(${ENABLE_EXAMPLES})

bindings/python/dspaces.py

@@ -1,4 +1,4 @@
-from dspaces_wrapper import *
+from dspaces.dspaces_wrapper import *
 import numpy as np
 
 class dspaces:

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = .build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

@@ -0,0 +1,4 @@
+DataSpaces API
+==============
+
+

docs/conf.py

@@ -0,0 +1,184 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = u'DataSpaces'
+copyright = u'2021, '
+author = u''
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u''
+
+
+# -- 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.coverage',
+    'sphinx.ext.ifconfig',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [u'.build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- 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 = 'renku'
+
+# 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 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'DataSpacesdoc'
+
+
+# -- 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': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (master_doc, 'DataSpaces.tex', u'DataSpaces Documentation',
+     u'Philip Davis', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'dataspaces', u'DataSpaces Documentation',
+     [author], 1)
+]
+
+
+# -- 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 = [
+    (master_doc, 'DataSpaces', u'DataSpaces Documentation',
+     author, 'DataSpaces', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True

docs/examples.rst

@@ -0,0 +1,2 @@
+DataSpaces Examples
+===================

docs/index.rst

@@ -0,0 +1,32 @@
+.. DataSpaces documentation master file, created by
+   sphinx-quickstart on Tue Sep 28 14:04:59 2021.
+
+Welcome to DataSpaces
+=====================
+
+DataSpaces is a communication library aimed at supporting interactions between large-scale scientific simulation, analysis, and visualization programs. 
+DataSpaces enables programs to write to and read from shared N-dimensional arrays without centralized query processing or indexing using low-latency RDMA transfers. 
+The result is highly-scalable data access between components of an HPC workflow. 
+DataSpaces can be used to tranfer data in *in-situ* workflows, such as coupled simulations and in-situ analysis workflows, 
+moving data through shared memory and RDMA tranfers, rather than using the file system.
+Like a shared file system, DataSpaces allow data readers to be decoupled from writers in both space in time.
+In other words, no sychronization of writers and readers is required, and readers may access data written by any process.
+
+
+Contents
+========
+
+.. toctree::
+
+   installation
+   usage
+   running
+   API
+   examples
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,42 @@
+Installing
+==========
+
+The easiest way to install DataSpaces is using `Spack <https://spack.readthedocs.io/en/latest/>`_. Spack is a package manager aimed at HPC and scientific computing.
+ Using Spack simplifies the installation of DataSpaces and its dependencies.
+
+Installing Spack
+----------------
+
+To install Spack, follow the getting started instructions found `here <https://spack.readthedocs.io/en/latest/getting_started.html>`_. 
+This will install the package manager, and make a large variety of packages available.
+
+Installing the DataSpaces repository
+------------------------------------
+
+The DataSpaces group maintains a repository for the DataSpaces spack package (and any relevant ancillary packages). This can be found `here <https://github.com/rdi2dspaces/dspaces-spack>`_. 
+In order to use this package, you will need to first install Spack using the above instructions.
+Once you have done this, you can load the DataSpaces package repository by doing the following:
+
+.. code-block:: console
+
+   git clone https://github.com/rdi2dspaces/dspaces-spack.git
+   spack repo add dspaces-spack
+
+Installing DataSpaces
+---------------------
+
+One the DataSpaces repository has been loaded, the dataspaces package can be installed with:
+
+.. code-block:: console
+
+   spack install dataspaces
+
+This will automatically install allDdataSpaces dependencies and the dataspaces package itself. 
+Once the package has been installed the command:
+
+.. code-block:: console
+
+   spack load dataspaces
+
+Configures the environment to use DataSpaces, adding the server binary's directory to `PATH`, any shared library paths to `LD_LIBRARY_PATH`, etc. 
+This simplifies building and running programs that use DataSpaces.

docs/requirements.txt

@@ -0,0 +1 @@
+renku-sphinx-theme

docs/running.rst

@@ -0,0 +1,57 @@
+How to Run
+==========
+
+Running the Server
+-----------------
+The DataSpaces server expects to find the `dataspaces.conf` file in its working directory. 
+The format of this file is a list of configuration values, one per line. 
+The possible values are as follows:
+
+`<variable> = <value>`, e.g.
+`num_apps = 1`
+
+`num_apps`: this value is the number of `dspaces_kill()` calls from clients that are needed to kill the server binary.
+
+`ndim`: number of dimensions for the default global data domain.
+
+`dims`: size of each dimension for the default global data domain.
+
+`max_versions`: maximum number of versions of a data object to be cached in DataSpaces servers.
+
+`hash_version`: the type of distributed hash table used. A value of `1` means that a Hilbert SFC is partitioned into continuous segments and distributed across the servers.
+ A value of `2` means the space is partitioned by repeating bisection along the longest domain.
+
+*NOTES* on what values to use
+
+The global dimensions have implications for performance. Data indexing will be partitioned evently across the global dimensions, 
+and so if data is only being writtent to a subset of the global dimensions there is a risk of unabalanced indexing load.
+Ideally, the data domain being written to will match the global dimensions as closely as possible. The default value set in
+`dataspaces.conf` is for convenience. The application can set this per variable with `dspaces_define_gdim()`.
+
+`hash_version = 1` has better locality in the most general case, and should be preferred unless the dimensions of the data 
+domain are not a power of two or the ratio of longest to shortest dimension is greater than two.
+
+`num_apps` should be set in conjunction with how `dspaces_kill()` is used in the application(s) using dataspaces. Generally, one rank
+of each application should call `dspaces_kill()`, and the number of process groups using dataspaces will be the same as `num_apps`. 
+Occasionally, it is not practical to have a client call `dspaces_kill()`, and the dataspaces repo provides a standalone binary `terminator` 
+to send a single `dspaces_kill()` and then exit.
+
+Bootstrapping communication
+---------------------------
+The server produces a bootstrap file during its init phase, `conf.ds`. This file must be read by the clients (or rank zero of the clients 
+if `dspaces_init_mpi()` is being used. This file provides the clients with enough information to make initial contact with the server and
+perform wire-up. In order to find this file, the server and client application must be run in the same working directory, or at last a symlink of `ds.conf` should be present.
+
+Environment variables
+---------------------
+There are a few environment variables that can be used to influence DataSpaces.
+
+`DSPACES_DEBUG` - enables substantial debug output for both clients and server.
+
+`DSPACES_DEFAULT_NUM_HANDLERS` - the number of request handling threads launched by the server (in addition to the main thread). Default: 4.
+ This value should be changed if it is likely to oversubscribe or underutilize the node the server is running on.
+
+ Running the server
+ ------------------
+
+The server binary, `dspaces_server`, takes a single argument: the listen_address. This is a Mercury-specific connection string (see Mercury documentation for details.) Common values are: `sockets` to use TCP for communication, `sm` for shared memory (if all clienta and server processes are on the same node) and `ofi+X` for RDMA, where `X` is `verbs`, `psm2`, or `cray` as is appropriate for the system fabric.