Package org.apache.sysds.runtime.data

Class SparseBlockCSR

java.lang.Object

org.apache.sysds.runtime.data.SparseBlock

org.apache.sysds.runtime.data.SparseBlockCSR

All Implemented Interfaces:

Serializable, Block

public class SparseBlockCSR
extends SparseBlock

SparseBlock implementation that realizes a traditional 'compressed sparse row' representation, where the entire sparse block is stored as three arrays: ptr of length rlen+1 to store offsets per row, and indexes/values of length nnz to store column indexes and values of non-zero entries. This format is very memory efficient for sparse (but not ultra-sparse) matrices and provides very good performance for common operations, partially due to lower memory bandwidth requirements. However, this format is slow on incremental construction (because it does not allow append/sort per row) without reshifting. Finally, the total nnz is limited to INTEGER_MAX, whereas for SparseBlockMCSR only the nnz per row are limited to INTEGER_MAX. TODO: extensions for faster incremental construction (e.g., max row) TODO more efficient fused setIndexRange impl to avoid repeated copies and updates

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	SparseBlockCSR.NonEmptyRowsIteratorCSR

Nested classes/interfaces inherited from class org.apache.sysds.runtime.data.SparseBlock

SparseBlock.Type

Constructor Summary

Constructors

Constructor	Description
SparseBlockCSR(int rlen)
SparseBlockCSR(int[] rowPtr, int[] colInd, double[] values, int nnz)
SparseBlockCSR(int rlen, int capacity)
SparseBlockCSR(int rows, int[] rowInd, int[] colInd, double[] values)	Copy constructor for COO representation
SparseBlockCSR(int rlen, int capacity, int size)
SparseBlockCSR(int rows, int nnz, int[] colInd)	Copy constructor for given array of column indexes, which identifies rows by position and implies values of 1.
SparseBlockCSR(SparseBlock sblock)	Copy constructor sparse block abstraction.
SparseBlockCSR(SparseRow[] rows, int nnz)	Copy constructor old sparse row representation.

Method Summary

Modifier and Type	Method	Description
boolean	add(int r, int c, double v)	Add a value to a matrix cell (r,c).
void	allocate(int r)	Allocate the underlying data structure holding non-zero values of row r if necessary.
void	allocate(int r, int nnz)	Allocate the underlying data structure holding non-zero values of row r if necessary, w/ given size.
void	allocate(int r, int ennz, int maxnnz)	Allocate the underlying data structure holding non-zero values of row r w/ the specified estimated nnz and max nnz.
void	append(int r, int c, double v)	Append a value to the end of the physical representation.
boolean	checkValidity(int rlen, int clen, long nnz, boolean strict)	Validate the correctness of the internal data structures of the different sparse block implementations.
void	compact()
void	compact(int r)	Re-allocate physical row if physical size exceeds logical size plus resize factor.
boolean	contains(double pattern, int rl, int ru)	Checks if the block contains at least one value of the given pattern.
void	deleteIndexRange(int r, int cl, int cu)	Deletes all non-zero values of the given column range [cl,cu) in row r.
static long	estimateSizeInMemory(long nrows, long ncols, double sparsity)	Get the estimated in-memory size of the sparse block in CSR with the given dimensions w/o accounting for overallocation.
SparseRow	get(int r)	Get values of row r in the format of a sparse row.
double	get(int r, int c)	Get value of matrix cell (r,c).
long	getExactSizeInMemory()	Computes the exact size in memory of the materialized block
Iterator<Integer>	getNonEmptyRowsIterator(int rl, int ru)
int[]	indexes()	Get raw access to underlying array of column indices For use in GPU code
int[]	indexes(int r)	Get the sorted array of column indexes of all non-zero entries in row r.
void	initSparse(int rlen, int nnz, DataInput in)	Initializes the CSR sparse block from an ordered input stream of sparse rows (rownnz, jv-pairs*).
void	initUltraSparse(int nnz, DataInput in)	Initializes the CSR sparse block from an ordered input stream of ultra-sparse ijv triples.
boolean	isAllocated(int r)	Indicates if the underlying data structure for a given row is already allocated.
boolean	isContiguous()	Indicates if the underlying data structures returned by values and indexes are contiguous arrays, which can be exploited for more efficient operations.
boolean	isEmpty(int r)	Get information if row r is empty, i.e., does not contain non-zero values.
boolean	isThreadSafe()	Indicates if the underlying implementation allows thread-safe row updates if concurrent threads update disjoint rows.
int	numRows()	Get the number of rows in the sparse block.
int	pos(int r)	Get the starting position of row r in the indexes/values arrays returned by indexes(r) and values(r).
int	posFIndexGT(int r, int c)	Get position of first column index greater than column c in row r.
int	posFIndexGTE(int r, int c)	Get position of first column index greater than or equal column c in row r.
int	posFIndexLTE(int r, int c)	Get position of first column index lower than or equal column c in row r.
void	reset()	Clears the sparse block by deleting non-zero values.
void	reset(int ennz, int maxnnz)	Clears the sparse block by deleting non-zero values.
void	reset(int r, int ennz, int maxnnz)	Clears row r of the sparse block by deleting non-zero values.
int[]	rowPointers()	Get raw access to underlying array of row pointers For use in GPU code
boolean	set(int r, int c, double v)	Set the value of a matrix cell (r,c).
void	set(int r, SparseRow row, boolean deep)	Set the values of row r to the given sparse row.
void	setIndexRange(int r, int cl, int cu, double[] v, int[] vix, int vpos, int vlen)	Sets a sparse array of non-zeros values and indexes into the column range [cl,cu) in row r.
void	setIndexRange(int r, int cl, int cu, double[] v, int vix, int vlen)	Sets a dense array of non-zeros values into the column range [cl,cu) in row r.
void	setIndexRange(int rl, int ru, int cl, int cu, double[] v, int vix, int vlen)	Inserts a sorted row-major array of non-zero values into the row and column range [rl,ru) and [cl,cu).
void	setIndexRange(int rl, int ru, int cl, int cu, SparseBlock sb)	Inserts a sparse block into the row and column range [rl,ru) and [cl,cu).
long	size()	Get the number of non-zero values in the sparse block.
int	size(int r)	Get the number of non-zero values in row r.
long	size(int rl, int ru)	Get the number of non-zeros values in the row range of [rl, ru).
long	size(int rl, int ru, int cl, int cu)	Get the number of non-zeros values in the row and column range of [rl/cl, ru/cu);
void	sort()	Sort all non-zero value/index pairs of the sparse block by row and column index.
void	sort(int r)	Sort all non-zero value/index pairs of row r column index.
String	toString()
double[]	values()	Get raw access to underlying array of values For use in GPU code
double[]	values(int r)	Get the array of all non-zero entries in row r, sorted by their column indexes.

Methods inherited from class org.apache.sysds.runtime.data.SparseBlock

contains, equals, equals, equals, equals, getIterator, getIterator, getIterator, getNonEmptyRows, getNonEmptyRows, isAligned, isAligned

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SparseBlockCSR

public SparseBlockCSR(int rlen)

SparseBlockCSR

public SparseBlockCSR(int rlen,
                      int capacity)

SparseBlockCSR

public SparseBlockCSR(int rlen,
                      int capacity,
                      int size)

SparseBlockCSR

public SparseBlockCSR(int[] rowPtr,
                      int[] colInd,
                      double[] values,
                      int nnz)

SparseBlockCSR

public SparseBlockCSR(SparseBlock sblock)

Copy constructor sparse block abstraction.

Parameters:

sblock - sparse block to copy

SparseBlockCSR

public SparseBlockCSR(SparseRow[] rows,
                      int nnz)

Copy constructor old sparse row representation.

Parameters:

rows - array of sparse rows

nnz - number of non-zeroes

SparseBlockCSR

public SparseBlockCSR(int rows,
                      int[] rowInd,
                      int[] colInd,
                      double[] values)

Copy constructor for COO representation

Parameters:

rows - number of rows

rowInd - row indices

colInd - column indices

values - non zero values

SparseBlockCSR

public SparseBlockCSR(int rows,
                      int nnz,
                      int[] colInd)

Copy constructor for given array of column indexes, which identifies rows by position and implies values of 1.

Parameters:

rows - number of rows

nnz - number of non-zeros

colInd - column indexes

Method Detail

initUltraSparse

public void initUltraSparse(int nnz,
                            DataInput in)
                     throws IOException

Initializes the CSR sparse block from an ordered input stream of ultra-sparse ijv triples.

Parameters:

nnz - number of non-zeros to read

in - data input stream of ijv triples, ordered by ij

Throws:

IOException - if deserialization error occurs

initSparse

public void initSparse(int rlen,
                       int nnz,
                       DataInput in)
                throws IOException

Initializes the CSR sparse block from an ordered input stream of sparse rows (rownnz, jv-pairs*).

Parameters:

rlen - number of rows

nnz - number of non-zeros to read

in - data input stream of sparse rows, ordered by i

Throws:

IOException - if deserialization error occurs

estimateSizeInMemory

public static long estimateSizeInMemory(long nrows,
                                        long ncols,
                                        double sparsity)

Get the estimated in-memory size of the sparse block in CSR with the given dimensions w/o accounting for overallocation.

Parameters:

nrows - number of rows

ncols - number of columns

sparsity - sparsity ratio

Returns:

memory estimate

getExactSizeInMemory

public long getExactSizeInMemory()

Description copied from class: SparseBlock

Computes the exact size in memory of the materialized block

Specified by:

getExactSizeInMemory in class SparseBlock

Returns:

the exact size in memory

rowPointers

public int[] rowPointers()

Get raw access to underlying array of row pointers For use in GPU code

Returns:

array of row pointers

indexes

public int[] indexes()

Get raw access to underlying array of column indices For use in GPU code

Returns:

array of column indexes

values

public double[] values()

Get raw access to underlying array of values For use in GPU code

Returns:

array of values

allocate

public void allocate(int r)

Description copied from class: SparseBlock

Allocate the underlying data structure holding non-zero values of row r if necessary.

Specified by:

allocate in class SparseBlock

Parameters:

r - row index

allocate

public void allocate(int r,
                     int nnz)

Description copied from class: SparseBlock

Allocate the underlying data structure holding non-zero values of row r if necessary, w/ given size.

Specified by:

allocate in class SparseBlock

Parameters:

r - row index

nnz - number of non-zeros

allocate

public void allocate(int r,
                     int ennz,
                     int maxnnz)

Description copied from class: SparseBlock

Allocate the underlying data structure holding non-zero values of row r w/ the specified estimated nnz and max nnz.

Specified by:

allocate in class SparseBlock

Parameters:

r - row index

ennz - estimated non-zeros

maxnnz - max non-zeros

compact

public void compact(int r)

Description copied from class: SparseBlock

Re-allocate physical row if physical size exceeds logical size plus resize factor.

Specified by:

compact in class SparseBlock

Parameters:

r - row index

compact

public void compact()

numRows

public int numRows()

Description copied from class: SparseBlock

Get the number of rows in the sparse block.

Specified by:

numRows in class SparseBlock

Returns:

number of rows

isThreadSafe

public boolean isThreadSafe()

Description copied from class: SparseBlock

Indicates if the underlying implementation allows thread-safe row updates if concurrent threads update disjoint rows.

Specified by:

isThreadSafe in class SparseBlock

Returns:

true if thread-safe row updates

isContiguous

public boolean isContiguous()

Description copied from class: SparseBlock

Indicates if the underlying data structures returned by values and indexes are contiguous arrays, which can be exploited for more efficient operations.

Specified by:

isContiguous in class SparseBlock

Returns:

true if underlying data structures are contiguous arrays

isAllocated

public boolean isAllocated(int r)

Description copied from class: SparseBlock

Indicates if the underlying data structure for a given row is already allocated.

Specified by:

isAllocated in class SparseBlock

Parameters:

r - row index

Returns:

true if already allocated

reset

public void reset()

Description copied from class: SparseBlock

Clears the sparse block by deleting non-zero values. After this call all size() calls are guaranteed to return 0.

Specified by:

reset in class SparseBlock

reset

public void reset(int ennz,
                  int maxnnz)

Description copied from class: SparseBlock

Clears the sparse block by deleting non-zero values. After this call all size() calls are guaranteed to return 0.

Specified by:

reset in class SparseBlock

Parameters:

ennz - estimated non-zeros

maxnnz - max non-zeros

reset

public void reset(int r,
                  int ennz,
                  int maxnnz)

Description copied from class: SparseBlock

Clears row r of the sparse block by deleting non-zero values. After this call size(r) is guaranteed to return 0.

Specified by:

reset in class SparseBlock

Parameters:

r - row index

ennz - estimated non-zeros

maxnnz - max non-zeros

size

public long size()

Description copied from class: SparseBlock

Get the number of non-zero values in the sparse block.

Specified by:

size in class SparseBlock

Returns:

number of non-zero values in sparse block

size

public int size(int r)

Description copied from class: SparseBlock

Get the number of non-zero values in row r.

Specified by:

size in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

number of non-zero values in row r

size

public long size(int rl,
                 int ru)

Description copied from class: SparseBlock

Get the number of non-zeros values in the row range of [rl, ru).

Specified by:

size in class SparseBlock

Parameters:

rl - row lower index

ru - row upper index

Returns:

number of non-zero values in the row range

size

public long size(int rl,
                 int ru,
                 int cl,
                 int cu)

Description copied from class: SparseBlock

Get the number of non-zeros values in the row and column range of [rl/cl, ru/cu);

Specified by:

size in class SparseBlock

Parameters:

rl - row lower index

ru - row upper index

cl - column lower index

cu - column upper index

Returns:

number of non-zero values in the row and column range

isEmpty

public boolean isEmpty(int r)

Description copied from class: SparseBlock

Get information if row r is empty, i.e., does not contain non-zero values. Equivalent to size(r)==0. Users should do this check if it is unknown if the underlying row data structure is allocated.

Specified by:

isEmpty in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

true if row does not contain non-zero values

indexes

public int[] indexes(int r)

Description copied from class: SparseBlock

Get the sorted array of column indexes of all non-zero entries in row r. Note that - for flexibility of the implementing format - the returned array may be larger, where the range for row r is given by [pos(r),pos(r)+size(r)).

Specified by:

indexes in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

sorted array of column indexes

values

public double[] values(int r)

Description copied from class: SparseBlock

Get the array of all non-zero entries in row r, sorted by their column indexes. Note that - for flexibility of the implementing format - the returned array may be larger, where the range for row r is given by [pos(r),pos(r)+size(r)).

Specified by:

values in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

array of all non-zero entries in row r sorted by column indexes

pos

public int pos(int r)

Description copied from class: SparseBlock

Get the starting position of row r in the indexes/values arrays returned by indexes(r) and values(r).

Specified by:

pos in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

starting position of row r

set

public boolean set(int r,
                   int c,
                   double v)

Description copied from class: SparseBlock

Set the value of a matrix cell (r,c). This might update an existing non-zero value, insert a new non-zero value, or delete a non-zero value.

Specified by:

set in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

v - zero or non-zero value

Returns:

true, if number of non-zeros changed

add

public boolean add(int r,
                   int c,
                   double v)

Description copied from class: SparseBlock

Add a value to a matrix cell (r,c). This might update an existing non-zero value, or insert a new non-zero value.

Specified by:

add in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

v - zero or non-zero value

Returns:

true, if number of non-zeros changed

set

public void set(int r,
                SparseRow row,
                boolean deep)

Description copied from class: SparseBlock

Set the values of row r to the given sparse row. This might update existing non-zero values, insert a new row, or delete a row. NOTE: This method exists for incremental runtime integration and might be deleted in the future.

Specified by:

set in class SparseBlock

Parameters:

r - row index starting at 0

row - sparse row

deep - indicator to create deep copy of sparse row

append

public void append(int r,
                   int c,
                   double v)

Description copied from class: SparseBlock

Append a value to the end of the physical representation. This should only be used for operations with sequential write pattern or if followed by a sort() operation. Note that this operation does not perform any matrix cell updates.

Specified by:

append in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

v - zero or non-zero value

setIndexRange

public void setIndexRange(int r,
                          int cl,
                          int cu,
                          double[] v,
                          int vix,
                          int vlen)

Description copied from class: SparseBlock

Sets a dense array of non-zeros values into the column range [cl,cu) in row r. The passed value array may be larger and the relevant range is given by [vix,vix+len).

Specified by:

setIndexRange in class SparseBlock

Parameters:

r - row index starting at 0

cl - lower column index starting at 0

cu - upper column index starting at 0

v - value array

vix - start index in value array

vlen - number of relevant values

setIndexRange

public void setIndexRange(int r,
                          int cl,
                          int cu,
                          double[] v,
                          int[] vix,
                          int vpos,
                          int vlen)

Description copied from class: SparseBlock

Sets a sparse array of non-zeros values and indexes into the column range [cl,cu) in row r. The passed value array may be larger.

Specified by:

setIndexRange in class SparseBlock

Parameters:

r - row index starting at 0

cl - lower column index starting at 0

cu - upper column index starting at 0

v - value array

vix - column index array

vpos - start index in value and index arrays

vlen - number of relevant values

setIndexRange

public void setIndexRange(int rl,
                          int ru,
                          int cl,
                          int cu,
                          double[] v,
                          int vix,
                          int vlen)

Inserts a sorted row-major array of non-zero values into the row and column range [rl,ru) and [cl,cu). Note: that this is a CSR-specific method to address performance issues due to repeated re-shifting on update-in-place.

Parameters:

rl - lower row index, starting at 0, inclusive

ru - upper row index, starting at 0, exclusive

cl - lower column index, starting at 0, inclusive

cu - upper column index, starting at 0, exclusive

v - right-hand-side dense block

vix - right-hand-side dense block index

vlen - right-hand-side dense block value length

setIndexRange

public void setIndexRange(int rl,
                          int ru,
                          int cl,
                          int cu,
                          SparseBlock sb)

Inserts a sparse block into the row and column range [rl,ru) and [cl,cu). Note: that this is a CSR-specific method to address performance issues due to repeated re-shifting on update-in-place.

Parameters:

rl - lower row index, starting at 0, inclusive

ru - upper row index, starting at 0, exclusive

cl - lower column index, starting at 0, inclusive

cu - upper column index, starting at 0, exclusive

sb - right-hand-side sparse block

deleteIndexRange

public void deleteIndexRange(int r,
                             int cl,
                             int cu)

Description copied from class: SparseBlock

Deletes all non-zero values of the given column range [cl,cu) in row r.

Specified by:

deleteIndexRange in class SparseBlock

Parameters:

r - row index starting at 0

cl - lower column index starting at 0

cu - upper column index starting at 0

sort

public void sort()

Description copied from class: SparseBlock

Sort all non-zero value/index pairs of the sparse block by row and column index.

Specified by:

sort in class SparseBlock

sort

public void sort(int r)

Description copied from class: SparseBlock

Sort all non-zero value/index pairs of row r column index.

Specified by:

sort in class SparseBlock

Parameters:

r - row index starting at 0

get

public double get(int r,
                  int c)

Description copied from class: SparseBlock

Get value of matrix cell (r,c). In case of non existing values this call returns 0.

Specified by:

get in interface Block

Specified by:

get in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

Returns:

value of cell at position (r,c)

get

public SparseRow get(int r)

Description copied from class: SparseBlock

Get values of row r in the format of a sparse row.

Specified by:

get in class SparseBlock

Parameters:

r - row index starting at 0

Returns:

values of row r as a sparse row

posFIndexLTE

public int posFIndexLTE(int r,
                        int c)

Description copied from class: SparseBlock

Get position of first column index lower than or equal column c in row r. The position is relative to the indexes/values arrays returned by indexes(r) and values(r). If no such value exists, this call returns -1.

Specified by:

posFIndexLTE in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

Returns:

position of the first column index lower than or equal to column c in row r

posFIndexGTE

public final int posFIndexGTE(int r,
                              int c)

Description copied from class: SparseBlock

Get position of first column index greater than or equal column c in row r. The position is relative to the indexes/values arrays returned by indexes(r) and values(r). If no such value exists, this call returns -1. Note if CSR the pos(r) is subtracted from the result.

Specified by:

posFIndexGTE in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

Returns:

position of the first column index greater than or equal to column c in row r

posFIndexGT

public int posFIndexGT(int r,
                       int c)

Description copied from class: SparseBlock

Get position of first column index greater than column c in row r. The position is relative to the indexes/values arrays returned by indexes(r) and values(r). If no such value exists, this call returns -1.

Specified by:

posFIndexGT in class SparseBlock

Parameters:

r - row index starting at 0

c - column index starting at 0

Returns:

position of the first column index greater than column c in row r

toString

public String toString()

Specified by:

toString in class SparseBlock

checkValidity

public boolean checkValidity(int rlen,
                             int clen,
                             long nnz,
                             boolean strict)

Description copied from class: SparseBlock

Validate the correctness of the internal data structures of the different sparse block implementations.

Specified by:

checkValidity in class SparseBlock

Parameters:

rlen - number of rows

clen - number of columns

nnz - number of non zeros

strict - enforce optional properties

Returns:

true if the sparse block is valid wrt the corresponding format such as COO, CSR, MCSR.

contains

public boolean contains(double pattern,
                        int rl,
                        int ru)

Description copied from class: SparseBlock

Checks if the block contains at least one value of the given pattern. Implementations need to handle NaN patterns as well (note that NaN==NaN yields false).

Overrides:

contains in class SparseBlock

Parameters:

pattern - checked pattern

rl - row lower bound (inclusive)

ru - row upper bound (exclusive)

Returns:

true if pattern appears at least once, otherwise false

getNonEmptyRowsIterator

public Iterator<Integer> getNonEmptyRowsIterator(int rl,
                                                 int ru)

Specified by:

getNonEmptyRowsIterator in class SparseBlock