Merge pull request #201 from williamfgc/cleanup

Updating some documentation, removed a warning and h5 file name

ReadMe.md

@@ -15,9 +15,20 @@ Copyright.txt for more details.
 * source - Main ADIOS source
 * testing - Tests
 
+## Documentation
+Please find ADIOS2 software documentation online under the project GitHub wiki:
+[https://github.com/ornladios/ADIOS2/wiki](https://github.com/ornladios/ADIOS2/wiki)
+
+To generate Doxygen application programming interface (API) documentation see 
+instructions under: [doc/ReadMe.md](doc/ReadMe.md)  
+
 ## Getting Started
 
-ADIOS 2.0 uses CMake for it's build environment.  CMake expects projects to use "out-of-source" builds, which means keeping a separate build and source directory (different from autotools, which usually uses an in-source build). To build ADIOS:
+ADIOS 2.0.0.alpha uses CMake for its build environment.  CMake expects projects 
+to use "out-of-source" builds, which means keeping a separate build and source 
+directory (different from autotools, which usually uses an in-source build). 
+
+To build ADIOS:
 
 1. Clone the repository:
 		
@@ -35,17 +46,18 @@ ADIOS 2.0 uses CMake for it's build environment.  CMake expects projects to use
 	
 3. ***Configure the project with CMake***. The following options can be specified as `ON` or `OFF` with cmake's `-DVAR=VALUE` syntax, where VAR options are:
 
-	* `ADIOS_BUILD_SHARED_LIBS` - Build shared libraries (`OFF` for static)
-	* `ADIOS_BUILD_EXAMPLES   ` - Build examples
-	* `ADIOS_BUILD_TESTING    ` - Build test code
-	* `ADIOS_USE_MPI          ` - Enable MPI
-	* `ADIOS_USE_BZip2        ` - Enable [BZip2](http://www.bzip.org/) compression
-	* `ADIOS_USE_ZFP          ` - Enable [ZFP](https://github.com/LLNL/zfp) compression
-	* `ADIOS_USE_ADIOS1       ` - Enable the [ADIOS 1.x](https://www.olcf.ornl.gov/center-projects/adios/) engine
-	* `ADIOS_USE_DataMan      ` - Enable the DataMan engine for WAN transports
-	* `ADIOS_USE_Python       ` - Enable the Python bindings
+	* `ADIOS2_BUILD_SHARED_LIBS` - Build shared libraries (`OFF` for static)
+	* `ADIOS2_BUILD_EXAMPLES   ` - Build examples
+	* `ADIOS2_BUILD_TESTING    ` - Build test code
+	* `ADIOS2_USE_MPI          ` - Enable MPI
+	* `ADIOS2_USE_BZip2        ` - Enable [BZip2](http://www.bzip.org/) compression (not implemented)
+	* `ADIOS2_USE_ZFP          ` - Enable [ZFP](https://github.com/LLNL/zfp) compression (not implemented)
+	* `ADIOS2_USE_ADIOS1       ` - Enable the [ADIOS 1.x](https://www.olcf.ornl.gov/center-projects/adios/) engine
+	* `ADIOS2_USE_DataMan      ` - Enable the DataMan engine for WAN transports
+	* `ADIOS2_USE_Python       ` - Enable the Python bindings
 
-    ***Important, automatic discovery***: ADIOS 2.0 CMake has an AUTO discovery "ON" default option. If a certain     dependency is found in the system installation path (_e.g._ /usr/), not a custom one (_e.g._ /home , /opt ) it will turn on installation for that dependency automatically 
+    ***Important, automatic discovery***: ADIOS 2.0 CMake has an AUTO discovery "ON" default option. If a certain 
+    dependency is found in the system installation path (_e.g._ /usr/), not a custom one (_e.g._ /home , /opt ) it will turn on installation for that dependency automatically 
 
     In addition, the -DCMAKE_VAR frequent options can be selected:
 	    * `CMAKE_INSTALL_PREFIX   ` - Prefix location for installation with `make install`, default depends on system (_e.g._ /usr/local)
@@ -54,7 +66,7 @@ ADIOS 2.0 uses CMake for it's build environment.  CMake expects projects to use
 	Example:
 	```
 	$ cd build
-	$ cmake -DADIOS_USE_MPI=ON -DADIOS_USE_BZip2=ON -DCMAKE_BUILD_TYPE=Debug ../ADIOS2
+	$ cmake -DADIOS_USE_MPI=ON -DCMAKE_BUILD_TYPE=Debug ../ADIOS2
 	-- The C compiler identification is GNU 6.3.1
 	-- The CXX compiler identification is GNU 6.3.1
 	-- Check for working C compiler: /usr/bin/cc
@@ -83,7 +95,7 @@ ADIOS 2.0 uses CMake for it's build environment.  CMake expects projects to use
 	    Build Type:   Debug
 	    Testing: ON
 	    MPI:     OFF
-	    BZip2:   ON
+	    BZip2:   OFF
 	    ADIOS1:  OFF
 	    DataMan: OFF
 	
@@ -109,4 +121,5 @@ ADIOS 2.0 uses CMake for it's build environment.  CMake expects projects to use
 
 ## Developers
 
-To summit changes to ADIOS 2.0: please see the wiki https://github.com/ornladios/ADIOS2/wiki Contributing to ADIOS section, or the local [Contributors Guide](Contributing.md).
+To summit changes to ADIOS 2.0: please see the [wiki's](https://github.com/ornladios/ADIOS2/wiki)  
+Contributing to ADIOS section, or the local [Contributors Guide](Contributing.md).

examples/heatTransfer/ReadMe.md

+examples/heatTransfer
+
+Test that solves a 2D Poisson equation for temperature in homogeneous media
+using finite differences. This examples shows a straight-forward way to hook an
+application to the ADIOS2 library for its IO.
+
+
+1. read: illustrates an experimental Read API, uses adios1 underneath  
+
+2. write: illustrates the Write API, resulting binaries under build/bin require arguments  
+  
+    * adios1    
+    * adios2
+    * hdf5
+    * phdf5
\ No newline at end of file

examples/hello/README.md

@@ -2,20 +2,20 @@ examples/hello
 
 Provides tests and illustrates how to use very basic functionality in adios2
 
-* adios1Writer (ADIOS_USE_ADIOS1=ON)
-    1. Write BP format files using adios1 library through adios2 interface  
+1. adios1Writer (-DADIOS2_USE_ADIOS1=ON -DADIOS1_DIR=/adios1-location)  
+    * Write BP format files using adios1 library through adios2 interface    
 	
-* bpWriter
-    1. Write BP format files for one Variable
+1. bpWriter    
+    * Write BP format files for one Variable  
     
-* bpTimeWriter
-    1. Write BP format files for two Variables (one is timestep) using time aggregation
+1. bpTimeWriter
+    * Write BP format files for two Variables (one is timestep) using time aggregation   
     
-* datamanReader (to be deprecated, ADIOS_USE_DataMan=ON)
-    1. Read real-time WAN streams using dataman
+1. datamanReader (to be deprecated, ADIOS_USE_DataMan=ON)
+    * Read real-time WAN streams using dataman 
     
-* datamanWriter
-    1. Write real-time WAN streams using dataman 
+1. datamanWriter  
+    * Write real-time WAN streams using dataman    
     
-* hdf5Writer (ADIOS_USE_HDF5=ON)
-    1. Write HDF5 files using interoperability through the adios2 interface 
+1. hdf5Writer (-DADIOS_USE_HDF5=ON)  
+    * Write HDF5 files using interoperability through the adios2 interface    
\ No newline at end of file

examples/hello/hdf5Writer/helloHDF5Writer.cpp

@@ -45,7 +45,7 @@ int main(int argc, char *argv[])
             "bpFloats", {size * Nx}, {rank * Nx}, {Nx}, adios2::ConstantDims);
 
         /** Engine derived class, spawned to start IO operations */
-        auto hdf5Writer = hdf5IO.Open("myVector.bp", adios2::OpenMode::Write);
+        auto hdf5Writer = hdf5IO.Open("myVector.h5", adios2::OpenMode::Write);
 
         if (!hdf5Writer)
         {

examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp

@@ -38,7 +38,7 @@ int main(int argc, char *argv[])
             "bpFloats", {}, {}, {Nx}, adios2::ConstantDims);
 
         /** Engine derived class, spawned to start IO operations */
-        auto hdf5Writer = hdf5IO.Open("myVector.bp", adios2::OpenMode::Write);
+        auto hdf5Writer = hdf5IO.Open("myVector.h5", adios2::OpenMode::Write);
 
         if (!hdf5Writer)
         {

source/adios2/transform/compression/BZip2.h

@@ -2,7 +2,7 @@
  * Distributed under the OSI-approved Apache License, Version 2.0.  See
  * accompanying file Copyright.txt for details.
  *
- * BZip2.h
+ * BZip2.h not yet implemented
  *
  *  Created on: Oct 17, 2016
  *      Author: William F Godoy godoywf@ornl.gov