examples/hello/bpWriter working

To do:

BPReader examples and BP1Reader class

Pull request to Jason's branch

Added clang++ for MAC OS in buildDataMan.sh

Added -Wl,-rpath to Makefiles in DataMan examples
Added more variables to buildDataMan.sh

Other DataMan library dependencies must be in LD_LIBRARY_PATH

Added BP1Writer pgindex and metadata functionality. Need to hook it with
BPWriter engine 

Added complex support in ADIOS class and DataMan engine and example for
DataManWriter

Modified Makefile.libs and Makefiles in ./examples/hello/datamanReader
and ./examples/hello/datamanWriter

Need to set DATAMAN_LOC in those makefiles for local DataMan
installation.

Need to set DATAMAN_LOCATION in buildDataMan.sh for local DataMan
installation.

Run ./buildDataman.sh see contents for detailed info

Testing

see examples/hello/dataman and examples/hello/writer for working
examples

Run ./buildTest.sh to build and run Vis engine example

Corrected bugs in Group in GetDimensions functions

Corrected bug by including cmath in adiosFunctions.cpp

Removed helloWriter.cpp and helloDataMan.cpp, now using
helloDataMan_OOP.cpp and helloWriter_OOP.cpp

Prevented from compiling and running hello examples
Makefile in dataman needed to link with libpthread -lpthread

Tested memory leaks with valgrind for simple example
Verifying if variable index is written correctly

Added ./src/format/BP1Writer.cpp

To do:
Need to test for array index and payload write

Working on writing variables to bp format

Implemented and tested hello world for dataman:
examples/hello/data/helloDataMan_OOP.cpp

Updated README.md

Propagate GetType<T> in Group, Engine and Support classes

To do:

Test ./examples/hello/writer/helloWriter_OOP.cpp

BP1Writer: Continue working on functions to write data and metadata

Group: added Dims alias and SetDimensions function, so dimensions can be built from a Var List put in an std::initializer_list<Var>

Added a bool flag in Variable to know if it is a dimension


To do:
Allow for passing values at DefineVariable

rather than handlers

Group&, Method& and the polymorphic std::shared_ptr<Engine> will be
returned by DeclareGroup, DeclareMethod and Open.

Added Group functions DefineVariable to be a template
Now using adios::Var when creating a variable (still a variable name
string).

Uses more C++ OO + templates features

Compiled and tested with ./examples/hello/helloWriter_OOP.cpp , mpi and
no-mpi versions

Method class allows parameters
Removed Capsule Parameters (will be default or provided by Engine)

To do:
BP Format class

DataMan class implemented under include/engine/dataman and
src/engine/dataman

Implemented transport MdtmMan used by DataMan engine under
include/transport and src/transport. This will serve as the basis for
WAN transport

Modified Makefile to include DataMan paths

To do:

Create Format class and assign BP Format to it

Compile and test a Hello DataMan example

Run and tested helloWriter under examples/hello/writer
Fixed Makefile

Added example/hello/dataman with API examples
Changed mpidummy.h due to an error in Titan compilation with g++

First function argument should name the required:
Buffer type for AddCapsule, e.g. AddCapsule( "Heap", ... );
Transport method for AddTransport, e.g. AddTransport( "POSIX", ... );

This version compiles. 
Tested with 2 write APIs:

under examples/hello/singleBP
helloSingleBP.cpp -> using ADIOS single manager class from ADIOS.h
helloSingleBP.cpp -> using ADIOS objects from ADIOS_OO.h

both generate a .bp file using a POSIX transport

To do:
Test compilation in other platforms/compilers
Add coverage test cases
Add the NULL transport (does nothing)
Work on SingleBP engine to generate bp format
XML config file support (to be defined)

Introducing Engine

Defining Write API cases

Removed public directory

Working on Write function so CCapsule can write to its m_Buffer

Set include/transport/CDataMan.h and src/transport/CDataMan.cpp for
integration with DataMan TCP communication

Created examples/dataman/datamanNoXML.cpp for later testing of DataMan
transport method

Need to compare memcpy and insert performance for writing to a
vector<char> buffer

Modified CGroup.m_Variable to allow for Global Dimensions and Offsets
and const members at creation

Modified CGroup member functions to allow creating new Variables and
Attributes

Added a C-API test case ./examples/hello/C/helloFStream.c


To do:

Need to test C-API and new CGroup

Testing sending buffers from all to rank=0

Added files include/public/ADIOS_C.h, src/public/ADIOS_C.cpp (with
std::exception handling), examples/hello/helloADIOS_C.c (not yet tested)

Working on CFStream.cpp testing vector<char> as buffer

Need to define types supported for C++, C, Fortran

Need to defined XML specs


To do:

Test added file examples/hello/helloADIOS_C.c

Test class CFStream implementation assuming MPI