update README

Xtra-Computing · Nov 22, 2017 · 703b1f2 · 703b1f2
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diff --git a/Doxyfile b/Doxyfile
@@ -791,7 +791,8 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = ./include/thundersvm \
-                         ./src/thundersvm
+                         ./src/thundersvm \
+                         ./docs/index.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -983,7 +984,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = docs/index.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing

diff --git a/README.md b/README.md
@@ -1,13 +1,22 @@
+# ThunderSVM
 [![Build Status](https://travis-ci.org/zeyiwen/thundersvm.svg?branch=master)](https://travis-ci.org/zeyiwen/thundersvm)
 
-<div align="center"><img src="https://github.com/zeyiwen/thundersvm/raw/improve-doc/logo.png" width = "30%" height = "30%" align=left/>
+<div align="center">
+<img src="https://github.com/zeyiwen/thundersvm/raw/master/docs/_static/lang-logo.png" width="250" height="200" align=left/>
+<img src="https://github.com/zeyiwen/thundersvm/raw/master/docs/_static/overall.png" width="250" height="200" align=left/>
 </div>
 
-# Overview
+## Overview
 The mission of ThunderSVM is to help users easily and efficiently apply SVMs to solve problems. Some key features of ThunderSVM are as follows.
 * Support one-class, binary and multi-class SVM classification, SVM regression, and SVMs with probability outputs.
 * Have Python, R and Matlab interfaces.
 
+## Contents
+- [Getting Started](https://github.com/zeyiwen/thundersvm/tree/improve-doc#getting-started)
+- [Advanced](https://github.com/zeyiwen/thundersvm/tree/improve-doc#advanced)
+- [Working without GPUs](https://github.com/zeyiwen/thundersvm/tree/improve-doc#working-without-gpus)
+- [Documentations](http://thundersvm.readthedocs.io)
+- [API Reference (doxygen)](http://zeyiwen.github.io/thundersvm/)
 ## Getting Started
 ### Prerequisites
 * [CUDA](https://developer.nvidia.com/cuda-downloads)
@@ -27,13 +36,24 @@ mkdir build && cd build && cmake .. && make -j
 bin\thundersvm-train -c 100 -g 0.5 ../dataset/test_dataset.txt
 bin\thundersvm-predict ../dataset/test_dataset.txt test_dataset.model test_dataset.predict
 ```
-### Run Tests
+You will see `Accuracy = 0.98` after successful running.
+
+## Advanced
+## Working without GPUs
+If you don't have GPUs, ThunderSVM can work with CPU only.
+### Get Eigen Library
+ThunderSVM uses [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) for matrix calculation. To use Eigen, just 
+initialize the submodule. 
 ```bash
-make runtest
+# in thundersvm root directory
+git submodule init eigen && git submodule update
 ```
-
-## API
-[API Reference](http://zeyiwen.github.io/thundersvm/)
+### Build without GPUs
+```bash
+# in thundersvm root directory
+mkdir build && cd build && cmake -DUSE_CUDA=OFF -DUSE_EIGEN=ON .. && make -j
+```
+Now ThunderSVM will work solely on CPUs and does not rely on CUDA.
 ## TODO
 - integrate with interfaces