#include <data_reader_smiles.hpp>

Inheritance diagram for lbann::smiles_data_reader:

Collaboration diagram for lbann::smiles_data_reader:

Classes
struct	SampleData

Public Types
using	offset_t = std::pair< long long, unsigned short >

using	offset_map_t = std::unordered_map< size_t, offset_t >

Public Types inherited from lbann::data_reader_sample_list< sample_list_ifstream< long long > >
using	sample_name_type = typename sample_list_ifstream< long long > ::name_t

using	sample_file_id_type = typename sample_list_ifstream< long long > ::sample_file_id_t

using	sample_type = std::pair< sample_file_id_type, sample_name_type >

using	file_handle_type = typename sample_list_ifstream< long long > ::file_handle_t

Public Types inherited from lbann::generic_data_reader
using	unused_index_map_t = std::map< execution_mode, std::vector< int > >

Public Member Functions
	smiles_data_reader (const bool shuffle)

	smiles_data_reader (const smiles_data_reader &)

smiles_data_reader &	operator= (const smiles_data_reader &)

	~smiles_data_reader () override

smiles_data_reader *	copy () const override

std::string	get_type () const override

void	load () override

int	get_linearized_data_size () const override
	Get the linearized size (i.e. number of elements) in a sample. More...

int	get_linearized_label_size () const override
	Get the linearized size (i.e. number of elements) in a label. More...

int	get_linearized_response_size () const override
	Get the linearized size (i.e. number of elements) in a response. More...

const std::vector< El::Int >	get_data_dims () const override
	Get the dimensions of the data. More...

int	get_num_labels () const override
	Return the number of labels (classes) in this dataset. More...

void	set_sequence_length (int n)

int	get_sequence_length ()

void	use_unused_index_set (execution_mode m) override

void	get_sample_origin (const size_t index_in, std::string &filename_out, size_t &offset_out, unsigned short &length_out) const

std::set< int >	get_my_indices () const

bool	encode_smiles (const char *smiles, unsigned short size, std::vector< unsigned short > &data)

bool	encode_smiles (const std::string &smiles, std::vector< unsigned short > &data)

void	decode_smiles (const std::vector< unsigned short > &data, std::string &out)

void	load_vocab (std::string filename)

void	load_vocab (std::stringstream &s)

void	set_linearized_data_size (size_t s)

std::string	get_raw_sample (std::istream *istrm, size_t index, size_t buf_offset=0)

void	set_offset (size_t index, long long offset, unsigned short length)

void	load_list_of_samples (const std::string sample_list_file)

void	set_metadata_filename (std::string fn)
	Sets the name of the metadata file. More...

const std::string &	get_metadata_filename ()
	Returns the name of the metadata file. More...

Public Member Functions inherited from lbann::data_reader_sample_list< sample_list_ifstream< long long > >
	data_reader_sample_list (bool shuffle=true)

	data_reader_sample_list (const data_reader_sample_list &)

data_reader_sample_list &	operator= (const data_reader_sample_list &)

	~data_reader_sample_list () override

data_reader_sample_list *	copy () const override

void	copy_members (const data_reader_sample_list &rhs)

std::string	get_type () const override

std::pair< file_handle_type, sample_name_type >	open_file (size_t index)
	Open the file and get the sample name for the given index. More...

void	close_file (size_t index_in)

void	shuffle_indices (rng_gen &gen) override

void	load () override

sample_list_ifstream< long long > &	get_sample_list ()

sample_type	get_sample (size_t index)

Public Member Functions inherited from lbann::generic_data_reader
	generic_data_reader (bool shuffle=true)

	generic_data_reader (const generic_data_reader &)=default

generic_data_reader &	operator= (const generic_data_reader &)=default

virtual	~generic_data_reader ()

template<class Archive >
void	serialize (Archive &ar)

void	set_comm (lbann_comm *comm)
	set the comm object More...

lbann_comm *	get_comm () const
	returns a (possibly nullptr) to comm More...

virtual bool	has_conduit_output ()

void	set_file_dir (std::string s)

void	set_local_file_dir (std::string s)

void	set_max_files_to_load (size_t n)

std::string	get_file_dir () const

std::string	get_local_file_dir () const

void	set_data_sample_list (std::string s)

std::string	get_data_sample_list () const

void	keep_sample_order (bool same_order=false)

void	set_data_filename (std::string s)

std::string	get_data_filename () const

void	set_label_filename (std::string s)

std::string	get_label_filename () const

void	set_shuffle (bool b)

bool	is_shuffled () const

void	set_shuffled_indices (const std::vector< int > &indices)

const std::vector< int > &	get_shuffled_indices () const

void	set_first_n (int n)

void	set_absolute_sample_count (size_t s)

void	set_use_fraction (double s)

virtual void	set_execution_mode_split_fraction (execution_mode m, double s)

virtual void	set_role (std::string role)

std::string	get_role () const

virtual void	setup (int num_io_threads, observer_ptr< thread_pool > io_thread_pool)

int	fetch (std::map< data_field_type, CPUMat *> &input_buffers, El::Matrix< El::Int > &indices_fetched, size_t mb_size)
	Fetch a mini-batch worth of data, including samples, labels, responses (as appropriate) More...

int	fetch (std::vector< conduit::Node > &samples, El::Matrix< El::Int > &indices_fetched, size_t mb_size)

virtual bool	has_data_field (data_field_type data_field) const
	Check to see if the data reader supports this specific data field. More...

virtual bool	has_labels () const

virtual bool	has_responses () const

void	set_has_data_field (data_field_type const data_field, const bool b)
	Whether or not a data reader has a data field. More...

virtual void	set_has_labels (const bool b)
	Whether or not a data reader has labels. More...

virtual void	set_has_responses (const bool b)
	Whether or not a data reader has a response field. More...

void	start_data_store_mini_batch_exchange ()

void	finish_data_store_mini_batch_exchange ()

virtual bool	update (bool is_active_reader)

virtual int	get_num_responses () const
	Return the number of responses in this dataset. More...

virtual int	get_linearized_size (data_field_type const &data_field) const
	get the linearized size of what is identified by desc. More...

virtual std::vector< El::Int >	get_slice_points (const slice_points_mode var_category, bool &is_supported)

virtual bool	position_valid () const
	True if the data reader's current position is valid. More...

virtual bool	position_is_overrun () const

bool	at_new_epoch () const
	True if the data reader is at the start of an epoch. More...

void	set_mini_batch_size (const int s)
	Set the mini batch size. More...

int	get_mini_batch_size () const
	Get the mini batch size. More...

int	get_loaded_mini_batch_size () const
	Get the loaded mini-batch size. More...

int	get_current_mini_batch_size () const
	Get the current mini-batch size. More...

int	get_mini_batch_max () const
	Return the full mini_batch_size. More...

void	set_stride_to_next_mini_batch (const int s)
	Set the mini batch stride. More...

int	get_stride_to_next_mini_batch () const
	Return the mini batch stride. More...

void	set_sample_stride (const int s)
	Set the sample stride. More...

int	get_sample_stride () const
	Return the sample stride. More...

void	set_iteration_stride (const int s)
	Set the iteration stride. More...

int	get_iteration_stride () const
	Return the iteration stride. More...

virtual void	set_base_offset (const int s)
	Return the base offset. More...

int	get_base_offset () const
	Return the base offset. More...

void	set_last_mini_batch_size (const int s)
	Set the last mini batch size. More...

int	get_last_mini_batch_size () const
	Return the last mini batch size. More...

void	set_stride_to_last_mini_batch (const int s)
	Set the last mini batch stride. More...

int	get_stride_to_last_mini_batch () const
	Return the last mini batch stride. More...

void	set_num_parallel_readers (const int s)
	Set the number of parallel readers per model. More...

int	get_num_parallel_readers () const
	Return the number of parallel readers per model. More...

virtual void	set_reset_mini_batch_index (const int s)
	Set the starting mini-batch index for the epoch. More...

int	get_reset_mini_batch_index () const
	Return the starting mini-batch index for the epoch. More...

int	get_loaded_mini_batch_index () const
	Return the current mini-batch index for the epoch. More...

int	get_current_mini_batch_index () const
	Return the current mini-batch index for the epoch. More...

void	set_initial_position ()
	Set the current position based on the base and model offsets. More...

int	get_position () const
	Get the current position in the data reader. More...

int	get_next_position () const
	Get the next position in the data reader. More...

int *	get_indices ()
	Get a pointer to the start of the shuffled indices. More...

virtual int	get_num_data () const
	Get the number of samples in this dataset. More...

int	get_num_unused_data (execution_mode m) const
	Get the number of unused samples in this dataset. More...

int *	get_unused_data (execution_mode m)
	Get a pointer to the start of the unused sample indices. More...

const std::vector< int > &	get_unused_indices (execution_mode m)

void	set_num_iterations_per_epoch (int num_iterations_per_epoch)
	Set the number of iterations in each epoch. More...

int	get_num_iterations_per_epoch () const
	Get the number of iterations in each epoch. More...

int	get_current_step_in_epoch () const

void	resize_shuffled_indices ()

void	select_subset_of_data ()

virtual bool	has_list_per_model () const
	Does the data reader have a unique sample list per model. More...

virtual bool	has_list_per_trainer () const
	Does the data reader have a unique sample list per trainer. More...

bool	save_to_checkpoint_shared (persist &p, execution_mode mode)
	Given directory to store checkpoint files, write state to file and add to number of bytes written. More...

bool	load_from_checkpoint_shared (persist &p, execution_mode mode)
	Given directory to store checkpoint files, read state from file and add to number of bytes read. More...

bool	save_to_checkpoint_distributed (persist &p, execution_mode mode)

bool	load_from_checkpoint_distributed (persist &p, execution_mode mode)
	Given directory to store checkpoint files, read state from file and add to number of bytes read. More...

const data_store_conduit &	get_data_store () const
	returns a const ref to the data store More...

data_store_conduit &	get_data_store ()
	returns a non-const ref to the data store More...

data_store_conduit *	get_data_store_ptr () const

void	setup_data_store (int mini_batch_size)

void	instantiate_data_store ()

virtual void	preload_data_store ()

void	set_gan_labelling (bool has_gan_labelling)

void	set_gan_label_value (int gan_label_value)

void	set_data_store (data_store_conduit *g)
	support of data store functionality More...

virtual bool	data_store_active () const

virtual bool	priming_data_store () const

virtual void	post_update ()

void	set_transform_pipeline (transform::transform_pipeline &&tp)

void	print_get_methods (const std::string filename)
	Print the return values from various get_X methods to file. More...

size_t	get_num_indices_to_use () const

void	set_use_data_store (bool s)

Private Member Functions
void	copy_members (const smiles_data_reader &rhs)
	Contains common code for operator= and copy ctor. More...

void	do_preload_data_store () override

bool	fetch_datum (CPUMat &X, int data_id, int mb_idx) override

bool	fetch_label (CPUMat &Y, int data_id, int mb_idx) override

bool	fetch_response (CPUMat &Y, int data_id, int mb_idx) override

void	print_statistics () const

void	load_offsets_and_lengths ()

void	read_offset_data (std::vector< SampleData > &data)

void	construct_conduit_node (conduit::Node &node, std::istream *istream, size_t sample_id, size_t buf_offset=0)

void	load_sample (std::istream *istrm, size_t index, std::vector< unsigned short > &output, size_t buf_offset=0)

void	build_some_maps ()

void	read_metadata_file (std::vector< size_t > &samples_per_file, std::vector< std::string > &data_filenames, std::vector< std::string > &offsets_filenames)

bool	is_delimiter (const char c)

Private Attributes
int	m_sequence_length = 0

const size_t	OffsetBinarySize = sizeof(long long)

const size_t	LengthBinarySize = sizeof(unsigned short)

const std::streamsize	OffsetAndLengthBinarySize

int	m_linearized_data_size = 0

int	m_linearized_label_size = 0

int	m_linearized_response_size = 0

int	m_num_labels = 0

short	m_pad = 420

short	m_unk = 421

short	m_bos = 422

short	m_eos = 423

std::string	m_metadata_filename

std::unordered_map< char, short >	m_vocab

std::unordered_map< short, std::string >	m_vocab_inv

std::mutex	m_mutex

size_t	m_missing_char_in_vocab_count = 0

std::unordered_set< char >	m_missing_chars

offset_map_t	m_sample_offsets

std::unordered_map< size_t, size_t >	m_index_to_local_id

std::unordered_map< std::string, std::map< size_t, size_t > >	m_local_to_index

std::unordered_map< std::string, std::set< size_t > >	m_filename_to_local_id_set

std::unordered_map< size_t, std::string >	m_index_to_filename

Additional Inherited Members
Public Attributes inherited from lbann::generic_data_reader
int	m_mini_batch_size

int	m_current_pos

int	m_stride_to_next_mini_batch

int	m_base_offset

int	m_sample_stride

int	m_iteration_stride
	Stride used by parallel data readers within the model. More...

std::vector< int >	m_shuffled_indices

unused_index_map_t	m_unused_indices
	Record of the indicies that are not being used for training. More...

int	m_last_mini_batch_size

int	m_stride_to_last_mini_batch

int	m_reset_mini_batch_index
	The index at which this data reader starts its epoch. More...

int	m_loaded_mini_batch_idx
	The index of the current mini-batch that has been loaded. More...

int	m_current_mini_batch_idx

int	m_num_iterations_per_epoch

int	m_num_parallel_readers
	How many iterations all readers will execute. More...

size_t	m_max_files_to_load
	How many parallel readers are being used. More...

std::string	m_file_dir

std::string	m_local_file_dir

std::string	m_data_sample_list

std::string	m_data_fn

std::string	m_label_fn

bool	m_shuffle

size_t	m_absolute_sample_count

std::map< execution_mode, double >	m_execution_mode_split_fraction

double	m_use_fraction

int	m_first_n

std::string	m_role

Protected Member Functions inherited from lbann::data_reader_sample_list< sample_list_ifstream< long long > >
void	load_list_of_samples (const std::string sample_list_file)

void	load_list_of_samples_from_archive (const std::string &sample_list_archive)

Protected Member Functions inherited from lbann::generic_data_reader
size_t	get_absolute_sample_count () const

double	get_use_fraction () const

double	get_execution_mode_split_fraction (execution_mode m) const

virtual bool	fetch_data_block (std::map< data_field_type, CPUMat *> &input_buffers, El::Int block_offset, El::Int block_stride, El::Int mb_size, El::Matrix< El::Int > &indices_fetched)

bool	fetch_data_block_conduit (std::vector< conduit::Node > &samples, El::Int block_offset, El::Int block_stride, El::Int mb_size, El::Matrix< El::Int > &indices_fetched)

virtual bool	fetch_data_field (data_field_type data_field, CPUMat &Y, int data_id, int mb_idx)
	Called by fetch_data, fetch_label, fetch_response. More...

virtual bool	fetch_conduit_node (conduit::Node &sample, int data_id)

CPUMat	create_datum_view (CPUMat &X, const int mb_idx)

virtual void	preprocess_data_source (int tid)

virtual void	postprocess_data_source (int tid)

virtual void	shuffle_indices ()
	Shuffle indices (uses the data_seq_generator) More...

void	error_check_counts () const

Protected Attributes inherited from lbann::data_reader_sample_list< sample_list_ifstream< long long > >
sample_list_ifstream< long long >	m_sample_list

Protected Attributes inherited from lbann::generic_data_reader
bool	m_verbose = false

std::unordered_set< int >	m_using_random_node

data_store_conduit *	m_data_store

lbann_comm *	m_comm

bool	m_use_data_store = false

std::map< data_field_type, bool >	m_supported_input_types
	Holds a true value for each input data type that is supported. Use an ordered map so that checkpoints are stable. More...

bool	m_gan_labelling

int	m_gan_label_value

observer_ptr< thread_pool >	m_io_thread_pool

bool	m_keep_sample_order

transform::transform_pipeline	m_transform_pipeline

bool	m_issue_warning

Detailed Description

Data reader for SMILES (string) data. The string data is converted to a vector of shorts according to an arbitrary mapping.

Terminology and Notes: "local_id" (or similar name): refers to a line number in a file. "global_id" (aka, sample_id, etc) refers to an index from the m_shuffled_indices vector.

Definition at line 44 of file data_reader_smiles.hpp.

Member Typedef Documentation

◆ offset_map_t

using lbann::smiles_data_reader::offset_map_t = std::unordered_map<size_t, offset_t>

Definition at line 50 of file data_reader_smiles.hpp.

◆ offset_t

using lbann::smiles_data_reader::offset_t = std::pair<long long, unsigned short>

Definition at line 49 of file data_reader_smiles.hpp.

Constructor & Destructor Documentation

◆ smiles_data_reader() [1/2]

lbann::smiles_data_reader::smiles_data_reader ( const bool shuffle )

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◆ smiles_data_reader() [2/2]

lbann::smiles_data_reader::smiles_data_reader ( const smiles_data_reader & )

◆ ~smiles_data_reader()

lbann::smiles_data_reader::~smiles_data_reader ( )

override

Member Function Documentation

◆ build_some_maps()

void lbann::smiles_data_reader::build_some_maps ( )

private

◆ construct_conduit_node()

void lbann::smiles_data_reader::construct_conduit_node	(	conduit::Node &	node,
		std::istream *	istream,
		size_t	sample_id,
		size_t	buf_offset = `0`
	)

private

◆ copy()

smiles_data_reader* lbann::smiles_data_reader::copy ( ) const

inlineoverridevirtual

Implements lbann::generic_data_reader.

Definition at line 57 of file data_reader_smiles.hpp.

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◆ copy_members()

void lbann::smiles_data_reader::copy_members ( const smiles_data_reader & rhs )

private

Contains common code for operator= and copy ctor.

◆ decode_smiles()

void lbann::smiles_data_reader::decode_smiles	(	const std::vector< unsigned short > &	data,
		std::string &	out
	)

This method made public for use during testing. Decode SMILES string from a vector of shorts

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◆ do_preload_data_store()

void lbann::smiles_data_reader::do_preload_data_store ( )

overrideprivatevirtual

Reimplemented from lbann::generic_data_reader.

◆ encode_smiles() [1/2]

bool lbann::smiles_data_reader::encode_smiles	(	const char *	smiles,
		unsigned short	size,
		std::vector< unsigned short > &	data
	)

This method made public for use during testing. Convert SMILES string to a vector of shorts

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◆ encode_smiles() [2/2]

bool lbann::smiles_data_reader::encode_smiles	(	const std::string &	smiles,
		std::vector< unsigned short > &	data
	)

This method made public for use during testing. Convert SMILES string to a vector of shorts

◆ fetch_datum()

bool lbann::smiles_data_reader::fetch_datum	(	CPUMat &	X,
		int	data_id,
		int	mb_idx
	)

overrideprivatevirtual

Fetch a single sample into a matrix.

Parameters

X	The matrix to load data into.
data_id	The index of the datum to fetch.
mb_idx	The index within the mini-batch.

Reimplemented from lbann::generic_data_reader.

◆ fetch_label()

bool lbann::smiles_data_reader::fetch_label	(	CPUMat &	Y,
		int	data_id,
		int	mb_idx
	)

overrideprivatevirtual

Fetch a single label into a matrix.

Parameters

Y	The matrix to load data into.
data_id	The index of the datum to fetch.
mb_idx	The index within the mini-batch.

Reimplemented from lbann::generic_data_reader.

◆ fetch_response()

bool lbann::smiles_data_reader::fetch_response	(	CPUMat &	Y,
		int	data_id,
		int	mb_idx
	)

overrideprivatevirtual

Fetch a single response into a matrix.

Parameters

Y	The matrix to load data into.
data_id	The index of the datum to fetch.
mb_idx	The index within the mini-batch.

Reimplemented from lbann::generic_data_reader.

◆ get_data_dims()

const std::vector<El::Int> lbann::smiles_data_reader::get_data_dims ( ) const

inlineoverridevirtual

Get the dimensions of the data.

Reimplemented from lbann::generic_data_reader.

Definition at line 78 of file data_reader_smiles.hpp.

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◆ get_linearized_data_size()

int lbann::smiles_data_reader::get_linearized_data_size ( ) const

inlineoverridevirtual

Get the linearized size (i.e. number of elements) in a sample.

Reimplemented from lbann::generic_data_reader.

Definition at line 66 of file data_reader_smiles.hpp.

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◆ get_linearized_label_size()

int lbann::smiles_data_reader::get_linearized_label_size ( ) const

inlineoverridevirtual

Get the linearized size (i.e. number of elements) in a label.

Reimplemented from lbann::generic_data_reader.

Definition at line 70 of file data_reader_smiles.hpp.

◆ get_linearized_response_size()

int lbann::smiles_data_reader::get_linearized_response_size ( ) const

inlineoverridevirtual

Get the linearized size (i.e. number of elements) in a response.

Reimplemented from lbann::generic_data_reader.

Definition at line 74 of file data_reader_smiles.hpp.

◆ get_metadata_filename()

const std::string& lbann::smiles_data_reader::get_metadata_filename ( )

inline

Returns the name of the metadata file.

Definition at line 147 of file data_reader_smiles.hpp.

◆ get_my_indices()

std::set<int> lbann::smiles_data_reader::get_my_indices ( ) const

This method is for use during testing and development. Returns the set of indices whose samples are cached in the data_store

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◆ get_num_labels()

int lbann::smiles_data_reader::get_num_labels ( ) const

inlineoverridevirtual

Return the number of labels (classes) in this dataset.

This is called at the end of update; it permits data readers to perform actions that are specific to their data sets, for example, data_reader_jag_conduit_hdf5 has the 'primary' data reader bcast its shuffled indices to the other data readers. In general most data readers will probably not overide this method. It may also be called outside of update.

Reimplemented from lbann::generic_data_reader.

Definition at line 82 of file data_reader_smiles.hpp.

◆ get_raw_sample()

std::string lbann::smiles_data_reader::get_raw_sample	(	std::istream *	istrm,
		size_t	index,
		size_t	buf_offset = `0`
	)

This method made public for use during testing.

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◆ get_sample_origin()

void lbann::smiles_data_reader::get_sample_origin	(	const size_t	index_in,
		std::string &	filename_out,
		size_t &	offset_out,
		unsigned short &	length_out
	)		const

This method is for use during testing and development

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◆ get_sequence_length()

int lbann::smiles_data_reader::get_sequence_length ( )

inline

Definition at line 89 of file data_reader_smiles.hpp.

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◆ get_type()

std::string lbann::smiles_data_reader::get_type ( ) const

inlineoverridevirtual

Return this data_reader's type

Implements lbann::generic_data_reader.

Definition at line 62 of file data_reader_smiles.hpp.

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◆ is_delimiter()

bool lbann::smiles_data_reader::is_delimiter ( const char c )

inlineprivate

Definition at line 254 of file data_reader_smiles.hpp.

◆ load()

void lbann::smiles_data_reader::load ( )

overridevirtual

Load the dataset. Each data reader implementation should implement this to initialize its internal data structures, determine the number of samples and their dimensionality (if needed), and set up and shuffle samples.

Implements lbann::generic_data_reader.

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◆ load_list_of_samples()

void lbann::smiles_data_reader::load_list_of_samples ( const std::string sample_list_file )

This method made public for use during testing.

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◆ load_offsets_and_lengths()

void lbann::smiles_data_reader::load_offsets_and_lengths ( )

private

◆ load_sample()

void lbann::smiles_data_reader::load_sample	(	std::istream *	istrm,
		size_t	index,
		std::vector< unsigned short > &	output,
		size_t	buf_offset = `0`
	)

private

◆ load_vocab() [1/2]

void lbann::smiles_data_reader::load_vocab ( std::string filename )

This method made public for use during testing.

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◆ load_vocab() [2/2]

void lbann::smiles_data_reader::load_vocab ( std::stringstream & s )

This method made public for use during testing.

◆ operator=()

smiles_data_reader& lbann::smiles_data_reader::operator= ( const smiles_data_reader & )

◆ print_statistics()

void lbann::smiles_data_reader::print_statistics ( ) const

private

◆ read_metadata_file()

void lbann::smiles_data_reader::read_metadata_file	(	std::vector< size_t > &	samples_per_file,
		std::vector< std::string > &	data_filenames,
		std::vector< std::string > &	offsets_filenames
	)

private

◆ read_offset_data()

void lbann::smiles_data_reader::read_offset_data ( std::vector< SampleData > & data )

private

◆ set_linearized_data_size()

void lbann::smiles_data_reader::set_linearized_data_size ( size_t s )

inline

This method made public for use during testing.

Definition at line 126 of file data_reader_smiles.hpp.

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◆ set_metadata_filename()

void lbann::smiles_data_reader::set_metadata_filename ( std::string fn )

inline

Sets the name of the metadata file.

Definition at line 141 of file data_reader_smiles.hpp.

◆ set_offset()

void lbann::smiles_data_reader::set_offset	(	size_t	index,
		long long	offset,
		unsigned short	length
	)

This method made public only for use during testing. Insert an entry into a map: index -> (offset, length), where 'index' is an alias for an entry in the shuffled_indices

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◆ set_sequence_length()

void lbann::smiles_data_reader::set_sequence_length ( int n )

inline

Definition at line 84 of file data_reader_smiles.hpp.

◆ use_unused_index_set()

void lbann::smiles_data_reader::use_unused_index_set ( execution_mode m )

overridevirtual

Replaced the shuffled index set with the unused index set, empying the unused set.

Reimplemented from lbann::generic_data_reader.

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Member Data Documentation

◆ LengthBinarySize

const size_t lbann::smiles_data_reader::LengthBinarySize = sizeof(unsigned short)

private

Definition at line 155 of file data_reader_smiles.hpp.

◆ m_bos

short lbann::smiles_data_reader::m_bos = 422

private

Definition at line 178 of file data_reader_smiles.hpp.

◆ m_eos

short lbann::smiles_data_reader::m_eos = 423

private

Definition at line 179 of file data_reader_smiles.hpp.

◆ m_filename_to_local_id_set

std::unordered_map<std::string, std::set<size_t> > lbann::smiles_data_reader::m_filename_to_local_id_set

private

maps: filename -> {local_id}

Definition at line 207 of file data_reader_smiles.hpp.

◆ m_index_to_filename

std::unordered_map<size_t, std::string> lbann::smiles_data_reader::m_index_to_filename

private

maps: index -> filename

Definition at line 210 of file data_reader_smiles.hpp.

◆ m_index_to_local_id

std::unordered_map<size_t, size_t> lbann::smiles_data_reader::m_index_to_local_id

private

Here and elsewhere, 'index' refers to an entry in the shuffled indices; 'local_id' refers, loosely, to a line number in a file. Also, 'file' or 'filename' refers to a file containing SMILES strings.

maps: index -> local_id. Note: clearly the mapping is not unique, since a local_id requires a filename for full specification

Definition at line 201 of file data_reader_smiles.hpp.

◆ m_linearized_data_size

int lbann::smiles_data_reader::m_linearized_data_size = 0

private

Definition at line 170 of file data_reader_smiles.hpp.

◆ m_linearized_label_size

int lbann::smiles_data_reader::m_linearized_label_size = 0

private

Definition at line 171 of file data_reader_smiles.hpp.

◆ m_linearized_response_size

int lbann::smiles_data_reader::m_linearized_response_size = 0

private

Definition at line 172 of file data_reader_smiles.hpp.

◆ m_local_to_index

std::unordered_map<std::string, std::map<size_t, size_t> > lbann::smiles_data_reader::m_local_to_index

private

maps: filename -> { local_id -> index }

Definition at line 204 of file data_reader_smiles.hpp.

◆ m_metadata_filename

std::string lbann::smiles_data_reader::m_metadata_filename

private

Definition at line 181 of file data_reader_smiles.hpp.

◆ m_missing_char_in_vocab_count

size_t lbann::smiles_data_reader::m_missing_char_in_vocab_count = 0

private

Definition at line 188 of file data_reader_smiles.hpp.

◆ m_missing_chars

std::unordered_set<char> lbann::smiles_data_reader::m_missing_chars

private

Definition at line 189 of file data_reader_smiles.hpp.

◆ m_mutex

std::mutex lbann::smiles_data_reader::m_mutex

private

Definition at line 186 of file data_reader_smiles.hpp.

◆ m_num_labels

int lbann::smiles_data_reader::m_num_labels = 0

private

Definition at line 173 of file data_reader_smiles.hpp.

◆ m_pad

short lbann::smiles_data_reader::m_pad = 420

private

Definition at line 176 of file data_reader_smiles.hpp.

◆ m_sample_offsets

offset_map_t lbann::smiles_data_reader::m_sample_offsets

private

Definition at line 192 of file data_reader_smiles.hpp.

◆ m_sequence_length

int lbann::smiles_data_reader::m_sequence_length = 0

private

Definition at line 152 of file data_reader_smiles.hpp.

◆ m_unk

short lbann::smiles_data_reader::m_unk = 421

private

Definition at line 177 of file data_reader_smiles.hpp.

◆ m_vocab

std::unordered_map<char, short> lbann::smiles_data_reader::m_vocab

private

Definition at line 183 of file data_reader_smiles.hpp.

◆ m_vocab_inv

std::unordered_map<short, std::string> lbann::smiles_data_reader::m_vocab_inv

private

Definition at line 184 of file data_reader_smiles.hpp.

◆ OffsetAndLengthBinarySize

const std::streamsize lbann::smiles_data_reader::OffsetAndLengthBinarySize

private

Initial value:

=

OffsetBinarySize + LengthBinarySize

Definition at line 156 of file data_reader_smiles.hpp.

◆ OffsetBinarySize

const size_t lbann::smiles_data_reader::OffsetBinarySize = sizeof(long long)

private

Definition at line 154 of file data_reader_smiles.hpp.

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

data_reader_smiles.hpp

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ offset_map_t

◆ offset_t

Constructor & Destructor Documentation

◆ smiles_data_reader() [1/2]

◆ smiles_data_reader() [2/2]

◆ ~smiles_data_reader()

Member Function Documentation

◆ build_some_maps()

◆ construct_conduit_node()

◆ copy()

◆ copy_members()

◆ decode_smiles()

◆ do_preload_data_store()

◆ encode_smiles() [1/2]

◆ encode_smiles() [2/2]

◆ fetch_datum()

◆ fetch_label()

◆ fetch_response()

◆ get_data_dims()

◆ get_linearized_data_size()

◆ get_linearized_label_size()

◆ get_linearized_response_size()

◆ get_metadata_filename()

◆ get_my_indices()

◆ get_num_labels()

◆ get_raw_sample()

◆ get_sample_origin()

◆ get_sequence_length()

◆ get_type()

◆ is_delimiter()

◆ load()

◆ load_list_of_samples()

◆ load_offsets_and_lengths()

◆ load_sample()

◆ load_vocab() [1/2]

◆ load_vocab() [2/2]

◆ operator=()

◆ print_statistics()

◆ read_metadata_file()

◆ read_offset_data()

◆ set_linearized_data_size()

◆ set_metadata_filename()

◆ set_offset()

◆ set_sequence_length()

◆ use_unused_index_set()

Member Data Documentation

◆ LengthBinarySize

◆ m_bos

◆ m_eos

◆ m_filename_to_local_id_set

◆ m_index_to_filename

◆ m_index_to_local_id

◆ m_linearized_data_size

◆ m_linearized_label_size

◆ m_linearized_response_size

◆ m_local_to_index

◆ m_metadata_filename

◆ m_missing_char_in_vocab_count

◆ m_missing_chars

◆ m_mutex

◆ m_num_labels

◆ m_pad

◆ m_sample_offsets

◆ m_sequence_length

◆ m_unk

◆ m_vocab

◆ m_vocab_inv

◆ OffsetAndLengthBinarySize

◆ OffsetBinarySize