ChangeLog

2013-03-19 Jerry Chou
	* src/fq.*: add optional flag to call getData collectively or
	independently
	* src/queryProcessor.*: add optional flag to broadcast
	query results
	* src/indexBuilder.*: add optional flag to setData collectively or
	independently

2013-02-22 Jerry Chou
	* examples/queryIndex.cpp: allocate memory to coords
	* src/hdf5file.cpp: fix the maximum chunk size under multidimension
	size[0] = floor(FQ_MAX_CHUNK_SIZE/(totalSize/dim[0]));
	* add flag "-lm" for HDF5 in configure.ac
	* fix the bug when determining the mpi_max_iter
2013-02-13 John Wu
        * src/fq.h: replace the argument streaming with a void* to make it
	possible to pass an ADIOS read method to BPArrayIODriver

2013-02-13 John Wu
	* src/ArrayIODriver.h: change nextStepInStream to nextStep,
	this function can also be used in nonstreaming mode
	* src/queryProcessor.cpp, src/indexBuilder.cpp: use the new
	function to advance through steps

2013-02-12 John Wu
	* configure.ac: update to work with ADIOS 1.4.1 on ORNL machines
	* examples/BPread.cpp: add function doRead to limit the scope of
	queryProcessor (in order to properly close the open files before
	MPI_Finalize)
	* src/fqIndex.cpp: change function buildNew to consitently use
	ierr >= 0 instead of mixing with ierr > 0
	* src/queryProcessor.cpp: change all assignment of mpi_max_iter to
	get the value returned from getMpiMaxIter

2012-12-19 John Wu
        * src/const.h: add conditional macro to allow user to specify
	FQ_MAX_CHUNK_SIZE at compile time, change the default value to be
	10 million

2012-12-18 John Wu
	* src/fqColumn.cpp: change loadIndex to make use std::auto_ptr to
	free the temporary index objects in case they are not created
	completely (a problem noticed by Benson Ma)
	* src/queryParser.yy: add destructors to clean up after the
	intermediate objects (a problem noticed by Benson Ma)

2012-12-06 John Wu
	* src/fq.cpp:242 add test to supress the reporting of time to PE
	0 if the verbose level is less than 5 (to prevent massive number
	reporting of timing values)
	* examples/MagNullQueryIndex.cpp: add macro around MPI_Finalize to
	make it usable without MPI

2012-11-27 John Wu
	* src/hdf5file.h: remove ibis.h from the list of included files
	* src/const.h: change FQT_ERROR tp FQT_UNKNOWN, add FQT_UBYTE,
	FQT_SHORT, and FQT_USHORT
	* src/*.cpp: update files to deal with the newly added data types

2012-11-12 John Wu
	* runconfig: change version of ADIOS from 1.3.1 to 1.4.1 on hopper
	* configure.ac: when --without-hdf5 is specified, also turn off
	--enable-hdf5, cleanup the use of MXML_HOME, CXXCPFLAGS ->
	CXXCPPFLAGS, make use of adios_config
	* src/ArrayIODriver.h: add functions isStreaming, nextStepInStream
	* src/queryProcessor.cpp: in function recordRegions add code to
	deal with streaming data
	* src/BPArrayIODrive.h:894 change the initial value of sz from -1
	to 0
	* examples/BP*.cpp: remove variable fileModel

2012-11-09 John Wu
	* src/metadataMgr.h: remove unused variable varCount from the
	class
	* src/fqPart.h: add function getQuery to return a pointer to the
	mesh query object to be used by QueryProcessor::recordRegions
	* src/queryProcessor.h, src/queryProcessor.cpp: add fucntion
	QueryProcessor::recordRegions

2012-11-08 John Wu
	* src/fqVar.h: add functions VarInfo::copy, VarSpace::setOffsets,
	VarSpace::setCounts, VarSpace::setStrides, rename
	VarSpace::setName to VarSpace::setText (to match getText) -- this
	new functions are used to implement metadataMgr::findShortMatch

2012-11-07 John Wu
	* examples/*.cpp: add option -d to be an alias for option -f (for
	data file) (existing -d option changed to -x - for export)
	* src/metadataMgr.cpp: add function findShortMatch

2012-11-06 John Wu
	* src/fqPart.cpp: change createQuery to attempt to reuse the
	existing query tokens when the where clause is exactly the same

2012-11-04 John Wu
	* src/fqPart.h, src/fqPart.cpp: rename getHitPointCoords to
	getHitsAsPoints and getHitBoxCoords as getHitsAsBoxes, update
	their inline documentation, add function getHitsAsLines, change
	the order of coordinates in a bounding box to the same as FastBit
	meshQuery

2012-11-03 John Wu
	* src/fq.h, src/queryProcessor.h, src/indexBuilder.h: change the
	default verboseness level to be ibis::gVerbose just in case it has
	been set somewhere else (previous default value was 0, which
	resets the value to 0 if it has been set elsewhere)
	* src/ADIOS_Wrapper.h, src/ADIOS_Wrapper.cpp: change class
	BPCommon to be a singleton class for the sole purpose of invoking
	adios_init_noxml and adios_finalize (can not really use this
	option because adios_finalize needs to be called before
	MPI_Finalize)

2012-11-01 John Wu
	* src/const.h: change enum type DataModel to FileFormat
	* examples/buildIndex.cpp: allow multiple -name options to be used
	on one command line

2012-10-31 John Wu
	* src/BPArrayIODriver.cpp: modify composeFieldName to match
	composeFBIprefix, consolidate the naming operations to use
	composeFieldName only, remove function getFastBitADIOSVar (use
	getADIOSVar instead), remove makeVariableName (use
	composeFieldName instead), rename function composeFieldName to be
	indexFieldName, add function indexGroupName because each
	invocation of writeFastBitIndex needs a new ADIOS group with a
	different name, modify getGroupInfo to allow time to appear as any
	part of the group name
	* examples/BPqueryIndex.cpp: restore the code in do_query that
	extract the selected values
	* src/BPArrayIODriver.cpp: modify getADIOSVar to use the full
	variable name instead of just the last part

2012-10-30 John Wu
	* src/fqVar.h: check the sizes of arrays in setName
	* src/fqPart.cpp: in buildIndexes, only build indexes if the
	number of rows is more than 1024

2012-10-29 John Wu
	* src/BPArrayIODriver.cpp: rename composeGrpName to
	composeFBIprefix (FBI as a shorthand for FastBit Index), make
	consistent uses of the prefix in writing

2012-10-28 John Wu
	* configure.ac: check for the default path used by the procedure
	that automatically downloads FastBit (test the code on
	portnoy.lbl.gov)

2012-10-26 John Wu
	* configure.ac: add code to automatically download FastBit
	ibis1.3.3
	* src/*.cpp: minor clean up based on the warnings from PGI
	compilers
	* src/BPArrayIODrive.cpp: select correct ADIOS method depending on
	whether MPI is being used
	* src/ADIOS_Wrapper.h, src/ADIOS_Wrapper.cpp: avoid opening the
	file in read-only mode (i.e., avoid calling the function
	ADIOS_File::open) if ADIOS_File is not initialized with read-only
	mode

2012-10-25 John Wu
	* src/ADIOS_Wrapper.h, src/ADIOS_Wrapper.cpp: remove the argument
	readOnly from the constructor of ADIOS_File because the BP file is
	always open in read only mode (all write operations have to open
	the file in the write mode separately), check the nil pointers in
	the arguments to ADIOS_Var constructors

2012-10-24 John Wu
	* examples/BP*.cpp, examples/MagNull*.cpp: update for working
	without MPI
	* src/BPArrayIODriver.h, src/BPArrayIODriver.cpp: remove unused
	functions getFastBitGrpName, getFastBitVarName,
	getFastBitVariableInfo, rename makeFastBitGrpName to
	composeGrpName, makeFastBitFieldName to composeFieldName
	* src/fqVar.h: change VarSpace::getCounts and friends to return a
	constant reference to the underlying vectors instead of new
	vectors

2012-10-23 John Wu
	* src/BPArrayIODriver.cpp: clean up log messages
	* configure.ac: update for NOMPI build

2012-10-22 John Wu
	* configure.ac: add code to remove -O flags from CXXFLAGS and
	CFLAGS with --disable-xopt is specified
	* examples/histogram.cpp: clean up in-line documentation

2012-10-19 John Wu
	* src/fq.h, src/fq.cpp: update to match the new constructors of
	BPArrayIODriver
	* src/ADIOS_Wrapper.h, src/ADIOS_Wrapper.cpp,
	src/BPArrayIODriver.h, src/BPArrayIODriver.cpp: modification to
	work with ADIOS 1.4
	* examples/Makefile.am: add targets MagNullQueryIndex and
	MagNullQueryScan
	* examples/MagNull*.cpp, examples/BP*.cpp: update files so that
	they can be compiled (still need debugging)

2012-10-15 John Wu
	* src/Doxyfile: disable the generation of latex files

2012-10-09 Jerry Chou
	* src/queryProcessor.*, src/fqPart.*: change histogram type from
	uint64 to uint32
	* INSTALL: add note on how to compile seralized version on HOPPER

2012-10-05 John Wu
	* src/arrayIODriver.h, src/BPArrayIODrive.h: add indentation to
	the in-line documentation

2012-09-21 John Wu
	* configure.ac: change INCLUDE to AM_CPPFLAGS to satisfy autoconf
	1.12.4

2012-05-29 John Wu
	* src/indexBuilder.h: remove #include "hdf5file.h"
	* configure.ac: when --disable-parallel is specified, the default
	version of library has no MPI

2012-05-29 Seung Woo Son
	* src/pnetCDFfile.cpp: fix a bug during equalityQuery
	* configure.ac: add FQ_VERIFIED_PNETCDF condition for checking least
	requirement of FastQuery build

2012-05-10 John Wu
	* INSTALL, README: add note about source availbe from portal.nersc.gov
	* Makefile.am, src/Makefile.am, examples/Makefile.am: make sure
	'make dist' includes all necessary files to run the test scripts

2012-04-27 John Wu
	* COPYING: add official copyright notice (BSD with grant-back)

2012-02-27 Seung Woo Son
	* src/pnetCDFfile.cpp: modify createBitmapKeys(), createBitmapOffset(),
	and createBitmap() so that the bitmap, bitmapkeys, and bitmapoffsets
	are stored in a separate variable during each mpi iteration

2012-02-21 Seung Woo Son
	* src/pnetCDFfile.cpp: add/modify functions related to building indexes
	* src/fq.cpp: remove conditional initialization of mpi_comm

2012-02-18 John Wu
	* examples/Makefile.am: bypass libtool to avoid problems on hopper
	(Cray XE6), update rule nompi to make sure FQ_NOMPI is defined
	among the CXXFLAGS
	* *: replace leftover FQ_HAVE_MPIO with FQ_NOMPI (inverted)

2012-02-17 John Wu
	* src/fq.h: consolidate the detection of whether to report timing
	information to one static member variable of FastQuery class
	* src/Makefile.am: modify rule to remove libfastquery_nompi.la in
	'make clean', add call to NORMAL_INSTALL to install-exec-local

2012-02-17 Seung Woo Son
	* src/pnetCDFfile.cpp, src/pnetCDFfile.h: add pnetCDF support

2012-02-16 John Wu
	* configure.ac: remove FQ_HAVE_MPIO, replce with source code with
	FQ_NOMPI (to be passed through command line through
	CXXFLAGS/CFLAGS)
	* src/Makefile.am: add rules to build libfastquery_nompi.a
	* src/ADIOS_Wrapper.*, src/fq.cpp: reformat code to be less than
	80-character per line, fix error reported by gcc 3.4

2012-02-03 Jerry Chou
	* configure.ac: remove --enable-mpi, mpi library will always be
        checked. Add MPICH_HOME into default mpi path location.

2012-01-10 John Wu
	* configure.ac: check for CRAY_HDF5_DIR and CRAY_NETCDF_DIR when
	the corresponding options are enabled but package directories are
	not specified
	* src/hdf5file.cpp: change the 3rd argument to
	H5Pset_fapl_mpiposix and H5Pset_fapl_mpio from MPI_INFO_NULL to 0
	(they actually want the boolean value false to indicate we are not
	using gpfs, so a better solution is needed in the future)

2012-01-09 John Wu
	* configure.ac: clean up, restore FLAGS after failed compilation
	tests, add --with-szlib to specify szlib to be used with HDF5

2012-01-08 John Wu
	* configure.ac: only attempt to link with netCDF, HDF5 and BP if
	asked throught --enable-option or --with-option, declare error
	only if none of netCDF, HDF5 or BP is verified to exist

2012-01-07 John Wu
	* src/netCDFfile.cpp, src/hdf5file.cpp, src/queryProcessor.cpp:
	address warnings raised by GCC 4.2.1 on a MAC
	* configure.ac: attempt to compile a MPI program without any flags
	to see if it works (this should work on Cray machines using Cray's
	own compiler wrappers)

2012-01-06 John Wu
	* configure.ac: add tests for libmpi in addition to libmpich when
	checking for MPI

2011-12-13 John Wu
	* src/fpPart.cpp: update for FastBit version 1.2.6

/**** version0.8 ****/
2011-09-08 Jerry Chou
       *: fix examples/read.cpp to free file handler before MPI_Finalize
       *: fix the number of built variables in indexBuilder::buildIndexes()
2011-07-15 Jinoh Kim & Jerry Chou
       *: add BP driver
       *: add BP example code: BPread.cpp, BPbuildIndex.cpp BPqueryIndex.cpp
       *: fix read.cpp
2011-07-07 Jerry Chou
       *: add ibis::BYTE to fqIndex.cpp
       *: add -l option to examples/writeAttr.cpp
       *: add file description in README
       *: fix query syntax to include varPath
2011-06-03 Jerry Chou
       *: change the fastbit version to 1.2.3.4
       *: remove __curDatasetId and __curDatasetName from hdf5file.cpp and hdf5file.h
       *: add optimization and debug options to the configure.ac file
       *: allow varName to be the fullpath starting with '/' by modifying the MetadataMgr::getAllVariables()
       *: fix bug for chunking and unlimit dataset code in HDF5::__createDataset()
       *: fix bug for setting bitmapOffset and range in FQ_IndexBinned::write()
       *: fix bug by replacing constructor array_t(T*, start, offset) with array_t(T*, start, end) in FQ_IndexBinned::activate() and FQ_IndexUnbinned::activate()
       *: fix bug by replacing the word_t size from 4 bytes to sizeof(word_t)

/**** version0.7 ****/
2011-05-12 Jerry Chou
        *: checked in the initial set of files into SVN at nersc