Added documentation

README.md

@@ -1,24 +1,12 @@
 # DELTA-FUSION (aDaptive rEaL Time Analysis of big fusion data)
 
-This project facilitates near real-time streaming analysis of big fusion data on HPC resources.
-
-
-This project implements a streaming analysis workflow. Data is streamed by a generator, using the new
-ADIOS2 WAN capabilities, to a processing facility. At the processing facility, the received data packets
-are analyzed and stored by a backend. Optional visualization can be attached by coupling to the backend.
-
-This repository is a loose collection of 
-* generators
-* processors
-* backends
-
-The implemented analysis routines are based on [https://www.github.com:minjunJchoi/fluctana](https://www.github.com:minjunJchoi/fluctana) refactored in cython and adapted as computational kernels
-
-Generators, processors, and backends read their configuration from a shared json file. The different
-implementations don't have a common syntax yet.
+Delta facilitates near real-time streaming analysis of big fusion data on
+remote HPC resources. It consists of multiple executables that send,
+receive, and process data on different machines. The picture below gives an 
+overview of Delta.
 
 Here is a diagram of the framework:
-![Delta Architecture](https://github.com/rkube/delta/blob/master/doc/delta_architecture.png "Delta Architecture")
+![Delta Architecture](https://github.com/rkube/delta/blob/master/docs/source/delta_arch_v02.png "Delta Architecture")
 
 # Implemented Workflows
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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 = 'Delta-fusion'
+copyright = '2020, R. Kube, R.M. Churchill, J. Choi, J. Wang'
+author = 'R. Kube, R.M. Churchill, J. Choi, J. Wang'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = []
+
+
+# -- 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 = 'alabaster'
+
+# 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']

docs/source/configuring.rst

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+***********************************
+Configuring data analysis workflows
+***********************************
+
+The behaviour of `Delta` is defined by a global configuration file
+
+

docs/source/index.rst

@@ -0,0 +1,46 @@
+.. Delta-fusion documentation master file, created by
+   sphinx-quickstart on Thu Oct 22 11:55:40 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Delta-fusion's documentation!
+========================================
+Delta facilitates near real-time streaming analysis of big fusion data on
+remote HPC resources. It consists of multiple executables that send,
+receive, and process data on different machines. The picture below gives an 
+overview of Delta.
+
+
+.. figure:: delta_arch_v02.png
+    :align: center
+
+    Target architecture of Delta 
+
+At the data generation site, a `generator` reads measurement data from file and stages
+it for streaming. The data stream is received by a `middleman` that forwards it 
+to the `processor`, which executes data analysis kernels on a supercomputer.
+The analysis results are stored and made available to web-clients by a separate
+webserver.
+
+This documentation describes the capabilities of `Delta`, how to configure it and
+how to launch distributed anaylsis workflows.
+
+
+Guide
+^^^^^
+
+
+.. toctree::
+   :maxdepth: 2
+
+   configuring
+   launching
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/launching.rst

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+*********************************************
+Launching data analysis workflows using Delta
+*********************************************
+
+
+
+
+1-node scenario
+###############
+In this scenario Delta will run on a single node only. This is the recommended way
+to test data analysis workflows.
+
+The commands below set up the environment on cori to start the processor:
+
+.. code-block:: shell
+
+    #!/bin/bash
+    module unload PrgEnv-cray PrgEnv-gnu PrgEnv-intel
+    module load PrgEnv-gnu
+    module unload craype-hugepages2M 
+    module unload python
+    module load python3
+    module use -a /global/cscratch1/sd/jyc/sw/modulefiles
+    module load adios2/devel
+    module load python_delta_comm
+
+    export OMP_NUM_CORES=4
+    export OMP_PROC_BIND=true
+    export OMP_PLACES=cores 
+
+    srun -n 16 -c 4 --cpu-bind=cores python -m mpi4py.futures processor.py --config configs/delta_config.json
+
+
+2-node scenario
+###############
+In this scenario, the `generator` streams data directly to the `proceessor`.
+
+The recommended way is to start the `processor` on cori. You may need to increase the
+timeout in the message queues to accomodate a longer wait for initial time chunks.
+After the processor has started, launch the generator on the KSTAR DTN:
+
+The commands below set up the environment on the KSTAR DTN to start the generator
+
+.. code-block:: shell
+
+    module use -a /home/choij/sw/spack/share/spack/modules/linux-centos7-haswell
+    module use -a /home/choij/sw/spack/share/spack/modules/linux-centos7-broadwell
+    module use -a /home/choij/sw/modulefiles
+
+    module load openmpi
+    module load zeromq adios2
+    module load python py-numpy py-mpi4py py-h5py py-scipy
+
+    mpirun -n 1 python generator.py --config configs/test_2node.json
+
+
+
+
+3-node scenario
+###############
+In this scenario the `generator` streams data to a `middleman` which forwards the
+packages to the `processor`.
+
+The recommended way is to start the `processor` first, then the `middleman`, and
+finally the `generator`.
+
+The commands below set up the environment on the NERSC DTN to start the middleman
+
+.. code-block:: shell
+
+    #!/bin/bash
+    module use -a /global/cscratch1/sd/jyc/dtn/sw/spack/share/spack/modules/linux-centos7-ivybridge
+    module load openmpi
+    module load zeromq
+    module load python py-numpy py-mpi4py py-h5py py-scipy py-matplotlib py-pyyaml
+    module use -a /global/cscratch1/sd/jyc/dtn/sw/modulefiles
+    module load adios2
+    module load python_delta_comm
+
+    python middleman.poy --config configs/test_3node.json