hdf_archive Class Reference

class to handle hdf file More...

Collaboration diagram for hdf_archive:

Public Member Functions
template<class Comm = Communicate*>
	hdf_archive (Comm c, bool request_pio=false)
	constructor More...
	hdf_archive ()
	~hdf_archive ()
	destructor More...
bool	is_parallel () const
	return true if parallel i/o More...
bool	is_master () const
	return true if master in parallel i/o More...
hid_t	getFileID () const
	return file_id. should be only be used for connecting to old codes when porting More...
bool	create (const std::filesystem::path &fname, unsigned flags=H5F_ACC_TRUNC)
	create a file More...
bool	open (const std::filesystem::path &fname, unsigned flags=H5F_ACC_RDWR)
	open a file More...
void	close ()
	close all the open groups and file More...
void	flush ()
	flush a file More...
bool	closed ()
	return true if the file is closed More...
bool	is_group (const std::string &aname)
	check if aname is a group More...
bool	is_dataset (const std::string &aname)
	check if aname is a dataset More...
template<typename T >
bool	is_dataset_of_type (const std::string &aname)
	check if aname is a dataset of type T More...
hid_t	top () const
	return the top of the group stack More...
bool	open_groups ()
	check if any groups are open group stack will have entries if so More...
void	push (const std::string &gname, bool createit=true)
	push a group to the group stack More...
void	push (const hdf_path &gname, bool createit=true)
void	pop ()
std::string	group_path_as_string () const
	Return a string representation of the current group stack. More...
template<typename T >
bool	getShape (const std::string &aname, std::vector< int > &sizes_out)
	read the shape of multidimensional filespace from the group aname this function can be used to query dataset for preparing containers. More...
template<typename T >
bool	writeEntry (T &data, const std::string &aname)
	write the data to the group aname and return status use write() for inbuilt error checking More...
template<typename T >
void	write (T &data, const std::string &aname)
	write the data to the group aname and check status runtime error is issued on I/O error More...
template<typename T , typename IT , std::size_t RANK>
void	writeSlabReshaped (T &data, const std::array< IT, RANK > &shape, const std::string &aname)
	write the container data with a specific shape and check status More...
template<typename T , typename = std::enable_if_t<!std::is_const<T>::value>>
bool	readEntry (T &data, const std::string &aname)
	read the data from the group aname and return status use read() for inbuilt error checking More...
template<typename T , typename = std::enable_if_t<!std::is_const<T>::value>>
void	read (T &data, const std::string &aname)
	read the data from the group aname and check status runtime error is issued on I/O error More...
template<typename T , typename IT , std::size_t RANK, typename = std::enable_if_t<!std::is_const<T>::value>>
void	readSlabReshaped (T &data, const std::array< IT, RANK > &shape, const std::string &aname)
	read file dataset with a specific shape into a container and check status More...
template<typename T , typename IT , std::size_t RANK, typename = std::enable_if_t<!std::is_const<T>::value>>
void	readSlabSelection (T &data, const std::array< IT, RANK > &readSpec, const std::string &aname)
	read a portion of the data from the group aname and check status runtime error is issued on I/O error More...
void	unlink (const std::string &aname)

Private Types
enum	{ IS_PARALLEL = 0, IS_MASTER, NOIO }

Private Member Functions
void	set_access_plist (Communicate *comm, bool request_pio)
	set the access property More...
void	set_access_plist ()

Private Attributes
std::bitset< 4 >	Mode
	bitset of the io mode Mode[IS_PARALLEL] : true, if parallel Mode[IS_MASTER] : true, if the node is master Mode[NOIO] : true, if I/O is not performed More...
hid_t	file_id
	file id More...
hid_t	access_id
	access id More...
hid_t	xfer_plist
	transfer property More...
hid_t	lcpl_id
	Link creation property list identifier. More...
std::stack< hid_t >	group_id
	FILO to handle H5Group. More...
std::vector< std::string >	group_names
	Track group names corresponding to group_id. More...
std::string	possible_filename_
	Name of file that hdf_archive thinks is open. More...

Static Private Attributes
static const hid_t	is_closed = -1

Detailed Description

class to handle hdf file

Definition at line 51 of file hdf_archive.h.

Member Enumeration Documentation

anonymous enum

anonymous enum

private

Enumerator
IS_PARALLEL
IS_MASTER
NOIO

Definition at line 54 of file hdf_archive.h.

  {
    IS_PARALLEL = 0,
    IS_MASTER,
    NOIO
  };

Constructor & Destructor Documentation

hdf_archive() [1/2]

hdf_archive ( Comm  c, bool  request_pio = false  )

inline

constructor

Parameters

c	communicator
request_pio	turns on parallel I/O, if true and PHDF5 is available, hdf_archive is in parallel collective IO mode if true and PHDF5 is not available, hdf_archive is in master-only IO mode if false, hdf_archive is in independent IO mode

Definition at line 102 of file hdf_archive.h.

References hdf_error_suppression::enabled, and hdf_archive::set_access_plist().

      : file_id(is_closed), access_id(H5P_DEFAULT), xfer_plist(H5P_DEFAULT), lcpl_id(H5P_DEFAULT)
  {
    if (!hdf_error_suppression::enabled)
      throw std::runtime_error("HDF5 library warnings and errors not suppressed from output.\n");
    set_access_plist(c, request_pio);
  }

hdf_archive() [2/2]

hdf_archive ( )

inline

Definition at line 110 of file hdf_archive.h.

References hdf_error_suppression::enabled, and hdf_archive::set_access_plist().

                : file_id(is_closed), access_id(H5P_DEFAULT), xfer_plist(H5P_DEFAULT), lcpl_id(H5P_DEFAULT)
  {
    if (!hdf_error_suppression::enabled)
      throw std::runtime_error("HDF5 library warnings and errors not suppressed from output.\n");
    set_access_plist();
  }

~hdf_archive()

~hdf_archive

(

)

destructor

Definition at line 25 of file hdf_archive.cpp.

References hdf_archive::access_id, hdf_archive::close(), hdf_archive::lcpl_id, and hdf_archive::xfer_plist.

{
#if defined(ENABLE_PHDF5)
  if (xfer_plist != H5P_DEFAULT)
    H5Pclose(xfer_plist);
  if (access_id != H5P_DEFAULT)
    H5Pclose(access_id);
#endif
  if (lcpl_id != H5P_DEFAULT)
    H5Pclose(lcpl_id);
  close();
}

Member Function Documentation

close()

void close

(

)

close all the open groups and file

Definition at line 38 of file hdf_archive.cpp.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::group_names, and hdf_archive::is_closed.

Referenced by hdf_archive::create(), HybridRepSetReader< SA >::create_spline_set(), SplineSetReader< typename SA::SplineBase >::create_spline_set(), LCAOrbitalBuilder::createBasisSetH5(), QMCGaussianParserBase::createBasisSetWithHDF5(), QMCGaussianParserBase::createCenterH5(), QMCGaussianParserBase::createDeterminantSetWithHDF5(), QMCGaussianParserBase::createIonSet(), QMCGaussianParserBase::createMultiDeterminantSetCIHDF5(), QMCGaussianParserBase::createShellH5(), SplineSetReader< typename SA::SplineBase >::createSplineDataSpaceLookforDumpFile(), QMCGaussianParserBase::createSPOSetsH5(), HDFWalkerOutput::dump(), QMCGaussianParserBase::dump(), LCAOrbitalBuilder::EvalPeriodicImagePhaseFactors(), RMGParser::getCell(), LCAOHDFParser::getCell(), LCAOHDFParser::getGeometry(), LCAOHDFParser::getMO(), LCAOHDFParser::getSuperTwist(), EshdfFile::handleKpt(), LCAOrbitalBuilder::loadBasisSetFromH5(), LCAOSpinorBuilder::loadMO(), LCAOrbitalBuilder::loadMO(), main(), QMCFixedSampleLinearOptimizeBatched::one_shift_run(), hdf_archive::open(), SkParserHDF5::parse(), LCAOHDFParser::parse(), LCAOSpinorBuilder::putFromH5(), LCAOrbitalBuilder::putFromH5(), LCAOrbitalBuilder::putPBCFromH5(), RandomNumberControl::read_parallel(), RandomNumberControl::read_rank_0(), SlaterDetBuilder::readDetListH5(), EshdfFile::readKptGvecs(), QMCCostFunctionBase::reportParametersH5(), EstimatorManagerBase::stop(), TEST_CASE(), qmcplusplus::TEST_CASE(), OneBodyDensityMatricesTests< T >::testRegisterAndWrite(), RandomNumberControl::write_parallel(), RandomNumberControl::write_rank_0(), and hdf_archive::~hdf_archive().

{
  while (!group_id.empty())
  {
    hid_t gid = group_id.top();
    group_id.pop();
    group_names.pop_back();
    H5Gclose(gid);
  }
  if (file_id != is_closed)
    H5Fclose(file_id);
  file_id = is_closed;
}

closed()

bool closed ( )

inline

return true if the file is closed

Definition at line 153 of file hdf_archive.h.

References hdf_archive::file_id, and hdf_archive::is_closed.

{ return file_id == is_closed; }

create()

bool create	(	const std::filesystem::path &	fname,
		unsigned	flags = H5F_ACC_TRUNC
	)

create a file

Parameters

fname	name of hdf5 file
flags	i/o mode

Returns

true, if creation is successful

Definition at line 143 of file hdf_archive.cpp.

References hdf_archive::access_id, hdf_archive::close(), hdf_archive::file_id, hdf_archive::is_closed, hdf_archive::IS_MASTER, hdf_archive::IS_PARALLEL, hdf_archive::Mode, hdf_archive::NOIO, and hdf_archive::possible_filename_.

Referenced by HybridRepSetReader< SA >::create_spline_set(), SplineSetReader< typename SA::SplineBase >::create_spline_set(), HDFWalkerOutput::dump(), QMCGaussianParserBase::dump(), QMCFixedSampleLinearOptimizeBatched::one_shift_run(), QMCCostFunctionBase::reportParametersH5(), EstimatorManagerBase::start(), TEST_CASE(), qmcplusplus::TEST_CASE(), OneBodyDensityMatricesTests< T >::testRegisterAndWrite(), BranchIO< SFNB >::write(), RandomNumberControl::write(), and VariableSet::writeToHDF().

{
  possible_filename_ = fname;
  if (Mode[NOIO])
    return true;
  if (!(Mode[IS_PARALLEL] || Mode[IS_MASTER]))
    throw std::runtime_error("Only create file in parallel or by master but not every rank!");
  close();
  file_id = H5Fcreate(fname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, access_id);
  return file_id != is_closed;
}

flush()

void flush ( )

inline

flush a file

Definition at line 146 of file hdf_archive.h.

References hdf_archive::file_id, and hdf_archive::is_closed.

Referenced by EstimatorManagerBase::collectBlockAverages(), SkEstimator::registerCollectables(), TraceBuffer< TraceInt >::write_hdf(), and WalkerLogBuffer< WLog::Real >::writeHDF().

  {
    if (file_id != is_closed)
      H5Fflush(file_id, H5F_SCOPE_LOCAL);
  }

getFileID()

hid_t getFileID ( ) const

inline

return file_id. should be only be used for connecting to old codes when porting

Definition at line 126 of file hdf_archive.h.

References hdf_archive::file_id.

Referenced by PWParameterSet::checkVersion(), and SkEstimator::registerCollectables().

{ return file_id; }

getShape()

bool getShape ( const std::string &  aname, std::vector< int > &  sizes_out  )

inline

read the shape of multidimensional filespace from the group aname this function can be used to query dataset for preparing containers.

The dimensions contributed by T is excluded. See how exactly user dimensions are calculated in getDataShape function definition.

Returns

true if successful

Definition at line 231 of file hdf_archive.h.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::Mode, and hdf_archive::NOIO.

Referenced by EshdfFile::handleDensity(), EshdfFile::handleKpt(), SkParserHDF5::parse(), EshdfFile::readKptGvecs(), RotatedSPOs::readVariationalParameters(), and TEST_CASE().

  {
    if (Mode[NOIO])
      return true;
    hid_t p = group_id.empty() ? file_id : group_id.top();
    return getDataShape<T>(p, aname, sizes_out);
  }

group_path_as_string()

std::string group_path_as_string

(

)

const

Return a string representation of the current group stack.

Definition at line 246 of file hdf_archive.cpp.

References hdf_archive::group_names.

Referenced by hdf_archive::push(), and TEST_CASE().

{
  std::string group_path;
  for (auto it = group_names.begin(); it != group_names.end(); it++)
  {
    group_path += *it;
    if (it != group_names.end() - 1)
      group_path += "/";
  }

  return group_path;
}

is_dataset()

bool is_dataset ( const std::string &  aname )

inline

check if aname is a dataset

Parameters

aname

dataset's name

Returns

true, if aname exists and it is a dataset

Definition at line 165 of file hdf_archive.h.

References qmcplusplus::Units::charge::e, hdf_archive::file_id, hdf_archive::group_id, hdf_archive::Mode, and hdf_archive::NOIO.

Referenced by SlaterDetBuilder::readDetListH5(), and TEST_CASE().

  {
    if (Mode[NOIO])
      return true;
    hid_t p = group_id.empty() ? file_id : group_id.top();
    int dummy_data;
    h5data_proxy<int> e(dummy_data);
    return e.check_existence(p, aname);
  }

is_dataset_of_type()

bool is_dataset_of_type ( const std::string &  aname )

inline

check if aname is a dataset of type T

Parameters

aname

group's name

Returns

true, if aname is a dataset of type T

Definition at line 180 of file hdf_archive.h.

References qmcplusplus::Units::charge::e, hdf_archive::file_id, hdf_archive::group_id, hdf_archive::Mode, and hdf_archive::NOIO.

Referenced by SlaterDetBuilder::readDetListH5(), and TEST_CASE().

  {
    if (Mode[NOIO])
      return true;
    hid_t p = group_id.empty() ? file_id : group_id.top();
    T dummy_data;
    h5data_proxy<T> e(dummy_data);
    return e.check_type(p, aname);
  }

is_group()

bool is_group

(

const std::string &

aname

)

check if aname is a group

Parameters

aname

group's name

Returns

true, if aname exists and it is a group

Definition at line 165 of file hdf_archive.cpp.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::is_closed, hdf_archive::Mode, and hdf_archive::NOIO.

Referenced by HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), HDFWalkerInput_0_4::read_phdf5(), and RotatedSPOs::readVariationalParameters().

{
  if (Mode[NOIO])
    return true;
  if (file_id == is_closed)
    return false;
  hid_t p = group_id.empty() ? file_id : group_id.top();
  p       = (aname[0] == '/') ? file_id : p;

  if (H5Lexists(p, aname.c_str(), H5P_DEFAULT) > 0)
  {
#if H5_VERSION_GE(1, 12, 0)
    H5O_info2_t oinfo;
#else
    H5O_info_t oinfo;
#endif
    oinfo.type = H5O_TYPE_UNKNOWN;
#if H5_VERSION_GE(1, 12, 0)
    H5Oget_info_by_name3(p, aname.c_str(), &oinfo, H5O_INFO_BASIC, H5P_DEFAULT);
#else
    H5Oget_info_by_name(p, aname.c_str(), &oinfo, H5P_DEFAULT);
#endif

    if (oinfo.type != H5O_TYPE_GROUP)
      return false;
    return true;
  }
  else
  {
    return false;
  }
}

is_master()

bool is_master ( ) const

inline

return true if master in parallel i/o

Definition at line 123 of file hdf_archive.h.

References hdf_archive::IS_MASTER, and hdf_archive::Mode.

{ return Mode[IS_MASTER]; }

is_parallel()

bool is_parallel ( ) const

inline

return true if parallel i/o

Definition at line 120 of file hdf_archive.h.

References hdf_archive::IS_PARALLEL, and hdf_archive::Mode.

Referenced by RandomNumberControl::read(), RandomNumberControl::write(), and HDFWalkerOutput::write_configuration().

{ return Mode[IS_PARALLEL]; }

open()

bool open	(	const std::filesystem::path &	fname,
		unsigned	flags = H5F_ACC_RDWR
	)

open a file

Parameters

fname	name of hdf5 file
flags	i/o mode

Returns

file_id, if open is successful

Definition at line 155 of file hdf_archive.cpp.

References hdf_archive::access_id, hdf_archive::close(), hdf_archive::file_id, hdf_archive::is_closed, hdf_archive::Mode, hdf_archive::NOIO, and hdf_archive::possible_filename_.

Referenced by HybridRepSetReader< SA >::create_spline_set(), SplineSetReader< typename SA::SplineBase >::create_spline_set(), LCAOrbitalBuilder::createBasisSetH5(), QMCGaussianParserBase::createBasisSetWithHDF5(), QMCGaussianParserBase::createCenterH5(), QMCGaussianParserBase::createDeterminantSetWithHDF5(), QMCGaussianParserBase::createIonSet(), QMCGaussianParserBase::createMultiDeterminantSetCIHDF5(), QMCGaussianParserBase::createShellH5(), SplineSetReader< typename SA::SplineBase >::createSplineDataSpaceLookforDumpFile(), QMCGaussianParserBase::createSPOSetsH5(), LCAOrbitalBuilder::EvalPeriodicImagePhaseFactors(), RMGParser::getCell(), LCAOHDFParser::getCell(), LCAOHDFParser::getGeometry(), PWOrbitalSetBuilder::getH5(), LCAOHDFParser::getMO(), LCAOHDFParser::getSuperTwist(), EshdfFile::handleKpt(), LCAOrbitalBuilder::loadBasisSetFromH5(), LCAOSpinorBuilder::loadMO(), LCAOrbitalBuilder::loadMO(), main(), EshdfFile::openHdfFileForRead(), SkParserHDF5::parse(), RMGParser::parse(), LCAOHDFParser::parse(), GridExternalPotential::put(), LCAOSpinorBuilder::putFromH5(), LCAOrbitalBuilder::putFromH5(), LCAOrbitalBuilder::putPBCFromH5(), RandomNumberControl::read(), HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), HDFWalkerInput_0_4::read_phdf5(), SlaterDetBuilder::readDetListH5(), VariableSet::readFromHDF(), EinsplineSetBuilder::ReadOrbitalInfo(), TEST_CASE(), qmcplusplus::TEST_CASE(), and OneBodyDensityMatricesTests< T >::testRegisterAndWrite().

{
  possible_filename_ = fname;
  if (Mode[NOIO])
    return true;
  close();
  file_id = H5Fopen(fname.c_str(), flags, access_id);
  return file_id != is_closed;
}

open_groups()

bool open_groups ( )

inline

check if any groups are open group stack will have entries if so

Returns

true if any groups are open

Definition at line 198 of file hdf_archive.h.

References hdf_archive::group_id.

Referenced by TraceBuffer< TraceInt >::register_hdf_data(), and WalkerLogBuffer< WLog::Real >::registerHDFData().

{ return group_id.empty(); }

pop()

void pop ( )

inline

Definition at line 208 of file hdf_archive.h.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::group_names, and hdf_archive::is_closed.

Referenced by ObservableHelper::addProperty(), AOBasisBuilder< COT >::createAOSetH5(), LCAOrbitalBuilder::createBasisSetH5(), QMCGaussianParserBase::createIonSet(), QMCGaussianParserBase::createMultiDeterminantSetCIHDF5(), PWOrbitalSetBuilder::createPW(), QMCGaussianParserBase::createShellH5(), QMCGaussianParserBase::dump(), LCAOHDFParser::getGeometry(), LCAOHDFParser::getSuperTwist(), RMGParser::parse(), LCAOHDFParser::parse(), GaussianCombo< T >::putBasisGroupH5(), LCAOrbitalBuilder::putPBCFromH5(), RandomNumberControl::read_parallel(), RandomNumberControl::read_rank_0(), HybridRepCenterOrbitals< SPLINEBASE::DataType >::read_splines(), VariableSet::readFromHDF(), FakeOptimizableObject::readVariationalParameters(), RotatedSPOs::readVariationalParameters(), TraceSamples< std::complex< TraceReal > >::register_hdf_data(), TraceBuffer< TraceInt >::register_hdf_data(), WalkerLogBuffer< WLog::Real >::registerHDFData(), NEReferencePoints::write(), ObservableHelper::write(), NESpaceGrid< REAL >::write(), OperatorEstBase::write(), TraceBuffer< TraceInt >::write_hdf(), RandomNumberControl::write_parallel(), RandomNumberControl::write_rank_0(), HybridRepCenterOrbitals< SPLINEBASE::DataType >::write_splines(), WalkerLogBuffer< WLog::Real >::writeHDF(), VariableSet::writeToHDF(), FakeOptimizableObject::writeVariationalParameters(), and RotatedSPOs::writeVariationalParameters().

  {
    if (file_id == is_closed || group_id.empty())
      return;
    hid_t g = group_id.top();
    group_id.pop();
    group_names.pop_back();
    herr_t err = H5Gclose(g);
    if (err < 0)
      throw std::runtime_error("H5Gclose failed with error.");
  }

push() [1/2]

void push	(	const std::string &	gname,
		bool	createit = true
	)

push a group to the group stack

Parameters

gname	name of the group
createit	if true, group is create when missing

Definition at line 198 of file hdf_archive.cpp.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::group_names, hdf_archive::group_path_as_string(), hdf_archive::is_closed, hdf_archive::lcpl_id, hdf_archive::Mode, hdf_archive::NOIO, and hdf_archive::possible_filename_.

Referenced by ObservableHelper::addProperty(), AOBasisBuilder< COT >::createAOSetH5(), LCAOrbitalBuilder::createBasisSetH5(), QMCGaussianParserBase::createBasisSetWithHDF5(), QMCGaussianParserBase::createCenterH5(), QMCGaussianParserBase::createDeterminantSetWithHDF5(), QMCGaussianParserBase::createIonSet(), QMCGaussianParserBase::createMultiDeterminantSetCIHDF5(), PWOrbitalSetBuilder::createPW(), QMCGaussianParserBase::createShellH5(), QMCGaussianParserBase::createSPOSetsH5(), HDFWalkerOutput::dump(), QMCGaussianParserBase::dump(), LCAOrbitalBuilder::EvalPeriodicImagePhaseFactors(), RMGParser::getCell(), LCAOHDFParser::getCell(), LCAOHDFParser::getGeometry(), LCAOHDFParser::getSuperTwist(), LCAOrbitalBuilder::loadBasisSetFromH5(), LCAOSpinorBuilder::loadMO(), LCAOrbitalBuilder::loadMO(), RMGParser::parse(), LCAOHDFParser::parse(), hdf_archive::push(), GaussianCombo< T >::putBasisGroupH5(), LCAOrbitalBuilder::putPBCFromH5(), HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), RandomNumberControl::read_parallel(), HDFWalkerInput_0_4::read_phdf5(), RandomNumberControl::read_rank_0(), HybridRepCenterOrbitals< SPLINEBASE::DataType >::read_splines(), SlaterDetBuilder::readDetListH5(), VariableSet::readFromHDF(), FakeOptimizableObject::readVariationalParameters(), RotatedSPOs::readVariationalParameters(), TraceSamples< std::complex< TraceReal > >::register_hdf_data(), TraceBuffer< TraceInt >::register_hdf_data(), WalkerLogBuffer< WLog::Real >::registerHDFData(), QMCCostFunctionBase::reportParametersH5(), TEST_CASE(), qmcplusplus::TEST_CASE(), BranchIO< SFNB >::write(), NEReferencePoints::write(), ObservableHelper::write(), TraceBuffer< TraceInt >::write_hdf(), RandomNumberControl::write_parallel(), RandomNumberControl::write_rank_0(), HybridRepCenterOrbitals< SPLINEBASE::DataType >::write_splines(), WalkerLogBuffer< WLog::Real >::writeHDF(), VariableSet::writeToHDF(), FakeOptimizableObject::writeVariationalParameters(), and RotatedSPOs::writeVariationalParameters().

{
  hid_t g = is_closed;
  if (Mode[NOIO])
    return;

  if (file_id == is_closed)
    throw std::runtime_error("Failed to open group \"" + gname +
                             "\" because file is not open.  Expected file: " + possible_filename_);

  hid_t p = group_id.empty() ? file_id : group_id.top();

#if H5_VERSION_GE(1, 12, 0)
  H5O_info2_t oinfo;
#else
  H5O_info_t oinfo;
#endif
  oinfo.type = H5O_TYPE_UNKNOWN;
  if (H5Lexists(p, gname.c_str(), H5P_DEFAULT) > 0)
  {
#if H5_VERSION_GE(1, 12, 0)
    H5Oget_info_by_name3(p, gname.c_str(), &oinfo, H5O_INFO_BASIC, H5P_DEFAULT);
#else
    H5Oget_info_by_name(p, gname.c_str(), &oinfo, H5P_DEFAULT);
#endif
  }

  if ((oinfo.type != H5O_TYPE_GROUP) && createit)
  {
    g = H5Gcreate2(p, gname.c_str(), lcpl_id, H5P_DEFAULT, H5P_DEFAULT);
  }
  else
  {
    g = H5Gopen2(p, gname.c_str(), H5P_DEFAULT);
  }
  if (g != is_closed)
  {
    group_id.push(g);
    group_names.push_back(gname);
  }

  if (!createit && g < 0)
    throw std::runtime_error("Group \"" + gname + "\" not found in file " + possible_filename_ +
                             ". Group path: " + group_path_as_string());
}

push() [2/2]

void push	(	const hdf_path &	gname,
		bool	createit = true
	)

Definition at line 244 of file hdf_archive.cpp.

References hdf_archive::push(), and hdf_path::string().

{ push(gname.string(), createit); }

read()

void read ( T &  data, const std::string &  aname  )

inline

read the data from the group aname and check status runtime error is issued on I/O error

Definition at line 306 of file hdf_archive.h.

References hdf_archive::readEntry().

Referenced by RadialOrbitalSetBuilder< COT >::addGridH5(), RadialOrbitalSetBuilder< COT >::addRadialOrbitalH5(), PWParameterSet::checkVersion(), AOBasisBuilder< COT >::createAOSetH5(), LCAOrbitalBuilder::createBasisSetH5(), PWOrbitalSetBuilder::createPW(), PWOrbitalSetBuilder::createPWBasis(), LCAOrbitalBuilder::EvalPeriodicImagePhaseFactors(), RMGParser::getCell(), LCAOHDFParser::getCell(), LCAOHDFParser::getGeometry(), LCAOHDFParser::getMO(), LCAOHDFParser::getSuperTwist(), EshdfFile::handleDensity(), PWParameterSet::hasComplexData(), LCAOrbitalBuilder::LoadFullCoefsFromH5(), LCAOSpinorBuilder::loadMO(), LCAOrbitalBuilder::loadMO(), main(), EinsplineSetBuilder::OccupyBands(), EinsplineSetBuilder::OccupyBands_ESHDF(), RMGParser::parse(), LCAOHDFParser::parse(), GridExternalPotential::put(), GaussianCombo< T >::putBasisGroupH5(), LCAOrbitalBuilder::putFromH5(), AOBasisBuilder< COT >::putH5(), LCAOrbitalBuilder::putPBCFromH5(), HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), RandomNumberControl::read_parallel(), HDFWalkerInput_0_4::read_phdf5(), RandomNumberControl::read_rank_0(), PWBasis::readbasis(), SlaterDetBuilder::readCoeffs(), SlaterDetBuilder::readDetListH5(), VariableSet::readFromHDF(), EinsplineSetBuilder::ReadGvectors_ESHDF(), EinsplineSetBuilder::ReadOrbitalInfo(), EinsplineSetBuilder::ReadOrbitalInfo_ESHDF(), LCAOrbitalBuilder::readRealMatrixFromH5(), hdf_archive::readSlabReshaped(), hdf_archive::readSlabSelection(), FakeOptimizableObject::readVariationalParameters(), RotatedSPOs::readVariationalParameters(), and TEST_CASE().

  {
    if (!readEntry(data, aname))
    {
      throw std::runtime_error("HDF5 read failure in hdf_archive::read " + aname);
    }
  }

readEntry()

bool readEntry ( T &  data, const std::string &  aname  )

inline

read the data from the group aname and return status use read() for inbuilt error checking

Returns

true if successful

Definition at line 293 of file hdf_archive.h.

References qmcplusplus::Units::charge::e, hdf_archive::file_id, hdf_archive::group_id, hdf_archive::Mode, hdf_archive::NOIO, and hdf_archive::xfer_plist.

Referenced by AOBasisBuilder< COT >::createAOSetH5(), LCAOrbitalBuilder::createBasisSetH5(), SplineSetReader< typename SA::SplineBase >::createSplineDataSpaceLookforDumpFile(), LCAOrbitalBuilder::loadBasisSetFromH5(), LCAOHDFParser::parse(), LCAOrbitalBuilder::putFromH5(), hdf_archive::read(), HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), HDFWalkerInput_0_4::read_phdf5(), AtomicOrbitals< ST >::read_splines(), SplineR2R< ST >::read_splines(), SplineC2R< ST >::read_splines(), SplineC2C< ST >::read_splines(), SplineC2COMPTarget< ST >::read_splines(), SplineC2ROMPTarget< ST >::read_splines(), HybridRepCenterOrbitals< SPLINEBASE::DataType >::read_splines(), SlaterDetBuilder::readCoeffs(), SlaterDetBuilder::readDetListH5(), EinsplineSetBuilder::ReadGvectors_ESHDF(), SplineSetReader< typename SA::SplineBase >::readOneOrbitalCoefs(), EinsplineSetBuilder::ReadOrbitalInfo_ESHDF(), TEST_CASE(), and qmcplusplus::TEST_CASE().

  {
    if (Mode[NOIO])
      return true;
    hid_t p = group_id.empty() ? file_id : group_id.top();
    h5data_proxy<T> e(data);
    return e.read(data, p, aname, xfer_plist);
  }

readSlabReshaped()

void readSlabReshaped ( T &  data, const std::array< IT, RANK > &  shape, const std::string &  aname  )

inline

read file dataset with a specific shape into a container and check status

Parameters

data	container, linear storage required.
shape	shape on the hdf file
aname	dataset name in the file runtime error is issued on I/O error

Definition at line 321 of file hdf_archive.h.

References hdf_archive::read().

Referenced by EshdfFile::handleDensity(), EshdfFile::handleKpt(), SkParserHDF5::parse(), HDFWalkerInput_0_4::read_hdf5(), HDFWalkerInput_0_4::read_hdf5_scatter(), RandomNumberControl::read_rank_0(), EshdfFile::readKptGvecs(), TEST_CASE(), and OneBodyDensityMatricesTests< T >::testRegisterAndWrite().

  {
    std::array<hsize_t, RANK> globals, counts, offsets;
    for (int dim = 0; dim < RANK; dim++)
    {
      globals[dim] = static_cast<hsize_t>(shape[dim]);
      counts[dim]  = static_cast<hsize_t>(shape[dim]);
      offsets[dim] = 0;
    }

    hyperslab_proxy<T, RANK> pxy(data, globals, counts, offsets);
    read(pxy, aname);
  }

readSlabSelection()

void readSlabSelection ( T &  data, const std::array< IT, RANK > &  readSpec, const std::string &  aname  )

inline

read a portion of the data from the group aname and check status runtime error is issued on I/O error

note the readSpec array must have dimensionality corresponding to the dataset, values for a dimension must be [0,num_entries-1] for that dimension to specify which value to hold and a -1 to grab all elements from that dimension for example, if the dataset was [5,2,6] and the vector contained (2,1,-1), this would grab 6 elements corresponding to [2,1,:]

Definition at line 345 of file hdf_archive.h.

References hdf_archive::read().

Referenced by EshdfFile::handleKpt(), and TEST_CASE().

  {
    std::array<hsize_t, RANK> globals, counts, offsets;
    for (int dim = 0; dim < RANK; dim++)
    {
      globals[dim] = 0;
      if (readSpec[dim] < 0)
      {
        counts[dim]  = 0;
        offsets[dim] = 0;
      }
      else
      {
        counts[dim]  = 1;
        offsets[dim] = static_cast<hsize_t>(readSpec[dim]);
      }
    }

    hyperslab_proxy<T, RANK> pxy(data, globals, counts, offsets);
    read(pxy, aname);
  }

set_access_plist() [1/2]

void set_access_plist ( Communicate *  comm, bool  request_pio  )

private

set the access property

Definition at line 62 of file hdf_archive.cpp.

References hdf_archive::access_id, qmcplusplus::comm, Communicate::getMPI(), hdf_archive::IS_MASTER, hdf_archive::IS_PARALLEL, hdf_archive::lcpl_id, hdf_archive::Mode, hdf_archive::NOIO, Communicate::rank(), Communicate::size(), and hdf_archive::xfer_plist.

{
  access_id = H5P_DEFAULT;
  lcpl_id   = H5Pcreate(H5P_LINK_CREATE);
  H5Pset_create_intermediate_group(lcpl_id, true);
  if (comm && comm->size() > 1) //for parallel communicator
  {
    bool use_phdf5 = false;
#if defined(ENABLE_PHDF5)
    if (request_pio)
    {
      // enable parallel I/O
      MPI_Info info = MPI_INFO_NULL;
      access_id     = H5Pcreate(H5P_FILE_ACCESS);
      H5Pset_all_coll_metadata_ops(access_id, true);
      H5Pset_coll_metadata_write(access_id, true);
      H5Pset_fapl_mpio(access_id, comm->getMPI(), info);
      xfer_plist = H5Pcreate(H5P_DATASET_XFER);
      // enable parallel collective I/O
      H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
      use_phdf5 = true;
    }
#endif
    Mode.set(IS_PARALLEL, use_phdf5);
    Mode.set(IS_MASTER, !comm->rank());
    if (request_pio && !use_phdf5)
      Mode.set(NOIO, comm->rank()); // master only
    else
      Mode.set(NOIO, false); // pio or all.
  }
  else
  {
    Mode.set(IS_PARALLEL, false);
    Mode.set(IS_MASTER, true);
    Mode.set(NOIO, false);
  }
}

set_access_plist() [2/2]

void set_access_plist ( )

private

Definition at line 52 of file hdf_archive.cpp.

References hdf_archive::access_id, hdf_archive::IS_MASTER, hdf_archive::IS_PARALLEL, hdf_archive::lcpl_id, hdf_archive::Mode, and hdf_archive::NOIO.

Referenced by hdf_archive::hdf_archive().

{
  access_id = H5P_DEFAULT;
  lcpl_id   = H5Pcreate(H5P_LINK_CREATE);
  H5Pset_create_intermediate_group(lcpl_id, true);
  Mode.set(IS_PARALLEL, false);
  Mode.set(IS_MASTER, true);
  Mode.set(NOIO, false);
}

top()

hid_t top ( ) const

inline

return the top of the group stack

Definition at line 192 of file hdf_archive.h.

References hdf_archive::file_id, and hdf_archive::group_id.

Referenced by ObservableHelper::write(), TraceBuffer< TraceInt >::write_hdf(), and WalkerLogBuffer< WLog::Real >::writeHDF().

{ return group_id.empty() ? file_id : group_id.top(); }

unlink()

void unlink ( const std::string &  aname )

inline

Definition at line 367 of file hdf_archive.h.

References hdf_archive::file_id, hdf_archive::group_id, hdf_archive::Mode, and hdf_archive::NOIO.

  {
    if (Mode[NOIO])
      return;
    hid_t p       = group_id.empty() ? file_id : group_id.top();
    herr_t status = H5Ldelete(p, aname.c_str(), H5P_DEFAULT);
  }

write()

void write ( T &  data, const std::string &  aname  )

inline

write the data to the group aname and check status runtime error is issued on I/O error

Definition at line 259 of file hdf_archive.h.

References hdf_archive::writeEntry().

Referenced by ObservableHelper::addProperty(), HybridRepSetReader< SA >::create_spline_set(), SplineSetReader< typename SA::SplineBase >::create_spline_set(), QMCGaussianParserBase::createBasisSetWithHDF5(), QMCGaussianParserBase::createCenterH5(), QMCGaussianParserBase::createDeterminantSetWithHDF5(), QMCGaussianParserBase::createIonSet(), QMCGaussianParserBase::createMultiDeterminantSetCIHDF5(), QMCGaussianParserBase::createShellH5(), QMCGaussianParserBase::createSPOSetsH5(), HDFWalkerOutput::dump(), QMCGaussianParserBase::dump(), QMCFixedSampleLinearOptimizeBatched::one_shift_run(), TraceSamples< std::complex< TraceReal > >::register_hdf_data(), WalkerLogBuffer< WLog::Real >::registerHDFData(), QMCCostFunctionBase::reportParametersH5(), TEST_CASE(), BranchIO< SFNB >::write(), NEReferencePoints::write(), HDFWalkerOutput::write_configuration(), RandomNumberControl::write_parallel(), RandomNumberControl::write_rank_0(), hdf_archive::writeSlabReshaped(), VariableSet::writeToHDF(), FakeOptimizableObject::writeVariationalParameters(), and RotatedSPOs::writeVariationalParameters().

  {
    if (!writeEntry(data, aname))
    {
      throw std::runtime_error("HDF5 write failure in hdf_archive::write " + aname);
    }
  }

writeEntry()

bool writeEntry ( T &  data, const std::string &  aname  )

inline

write the data to the group aname and return status use write() for inbuilt error checking

Returns

true if successful

Definition at line 244 of file hdf_archive.h.

References qmcplusplus::Units::charge::e, hdf_archive::file_id, hdf_archive::group_id, hdf_archive::IS_MASTER, hdf_archive::IS_PARALLEL, hdf_archive::Mode, hdf_archive::NOIO, and hdf_archive::xfer_plist.

Referenced by TEST_CASE(), hdf_archive::write(), SplineR2R< ST >::write_splines(), SplineC2R< ST >::write_splines(), AtomicOrbitals< ST >::write_splines(), SplineC2C< ST >::write_splines(), SplineC2COMPTarget< ST >::write_splines(), SplineC2ROMPTarget< ST >::write_splines(), and HybridRepCenterOrbitals< SPLINEBASE::DataType >::write_splines().

  {
    if (Mode[NOIO])
      return true;
    if (!(Mode[IS_PARALLEL] || Mode[IS_MASTER]))
      throw std::runtime_error("Only write data in parallel or by master but not every rank!");
    hid_t p = group_id.empty() ? file_id : group_id.top();
    h5data_proxy<typename std::remove_const<T>::type> e(data);
    return e.write(data, p, aname, xfer_plist);
  }

writeSlabReshaped()

void writeSlabReshaped ( T &  data, const std::array< IT, RANK > &  shape, const std::string &  aname  )

inline

write the container data with a specific shape and check status

Parameters

data	container, linear storage required.
shape	shape on the hdf file
aname	dataset name in the file runtime error is issued on I/O error

Definition at line 274 of file hdf_archive.h.

References hdf_archive::write().

Referenced by TEST_CASE(), HDFWalkerOutput::write_configuration(), and RandomNumberControl::write_rank_0().

  {
    std::array<hsize_t, RANK> globals, counts, offsets;
    for (int dim = 0; dim < RANK; dim++)
    {
      globals[dim] = static_cast<hsize_t>(shape[dim]);
      counts[dim]  = static_cast<hsize_t>(shape[dim]);
      offsets[dim] = 0;
    }

    hyperslab_proxy<T, RANK> pxy(data, globals, counts, offsets);
    write(pxy, aname);
  }

Member Data Documentation

access_id

hid_t access_id

private

access id

Definition at line 70 of file hdf_archive.h.

Referenced by hdf_archive::create(), hdf_archive::open(), hdf_archive::set_access_plist(), and hdf_archive::~hdf_archive().

file_id

hid_t file_id

private

file id

Definition at line 68 of file hdf_archive.h.

Referenced by hdf_archive::close(), hdf_archive::closed(), hdf_archive::create(), hdf_archive::flush(), hdf_archive::getFileID(), hdf_archive::getShape(), hdf_archive::is_dataset(), hdf_archive::is_dataset_of_type(), hdf_archive::is_group(), hdf_archive::open(), hdf_archive::pop(), hdf_archive::push(), hdf_archive::readEntry(), hdf_archive::top(), hdf_archive::unlink(), and hdf_archive::writeEntry().

group_id

std::stack<hid_t> group_id

private

FILO to handle H5Group.

Definition at line 76 of file hdf_archive.h.

Referenced by hdf_archive::close(), hdf_archive::getShape(), hdf_archive::is_dataset(), hdf_archive::is_dataset_of_type(), hdf_archive::is_group(), hdf_archive::open_groups(), hdf_archive::pop(), hdf_archive::push(), hdf_archive::readEntry(), hdf_archive::top(), hdf_archive::unlink(), and hdf_archive::writeEntry().

group_names

std::vector<std::string> group_names

private

Track group names corresponding to group_id.

Definition at line 78 of file hdf_archive.h.

Referenced by hdf_archive::close(), hdf_archive::group_path_as_string(), hdf_archive::pop(), and hdf_archive::push().

is_closed

const hid_t is_closed = -1

staticprivate

Definition at line 60 of file hdf_archive.h.

Referenced by hdf_archive::close(), hdf_archive::closed(), hdf_archive::create(), hdf_archive::flush(), hdf_archive::is_group(), hdf_archive::open(), hdf_archive::pop(), and hdf_archive::push().

lcpl_id

hid_t lcpl_id

private

Link creation property list identifier.

Definition at line 74 of file hdf_archive.h.

Referenced by hdf_archive::push(), hdf_archive::set_access_plist(), and hdf_archive::~hdf_archive().

Mode

std::bitset<4> Mode

private

bitset of the io mode Mode[IS_PARALLEL] : true, if parallel Mode[IS_MASTER] : true, if the node is master Mode[NOIO] : true, if I/O is not performed

Definition at line 66 of file hdf_archive.h.

Referenced by hdf_archive::create(), hdf_archive::getShape(), hdf_archive::is_dataset(), hdf_archive::is_dataset_of_type(), hdf_archive::is_group(), hdf_archive::is_master(), hdf_archive::is_parallel(), hdf_archive::open(), hdf_archive::push(), hdf_archive::readEntry(), hdf_archive::set_access_plist(), hdf_archive::unlink(), and hdf_archive::writeEntry().

possible_filename_

std::string possible_filename_

private

Name of file that hdf_archive thinks is open.

This may not correspond to the actual file because the open call failed, or the file was closed. This information is useful for debugging.

Definition at line 84 of file hdf_archive.h.

Referenced by hdf_archive::create(), hdf_archive::open(), and hdf_archive::push().

xfer_plist

hid_t xfer_plist

private

transfer property

Definition at line 72 of file hdf_archive.h.

Referenced by hdf_archive::readEntry(), hdf_archive::set_access_plist(), hdf_archive::writeEntry(), and hdf_archive::~hdf_archive().

---

The documentation for this class was generated from the following files:

• /home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/io/hdf/hdf_archive.h
• /home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/io/hdf/hdf_archive.cpp