Package org.apache.sysds.runtime.data

Class SparseBlockCOO

java.lang.Object

org.apache.sysds.runtime.data.SparseBlock

org.apache.sysds.runtime.data.SparseBlockCOO

All Implemented Interfaces:

Serializable

public class SparseBlockCOO
extends SparseBlock

SparseBlock implementation that realizes a traditional 'coordinate matrix' representation, where the entire sparse block is stored as triples in three arrays: row indexes, column indexes, and values, where row indexes and colunm indexes are sorted in order to allow binary search. This format is very memory efficient for ultra-sparse matrices, allows fast incremental construction but has performance drawbacks for row-major access through our sparse block abstraction since there is no constant-time random access to individual rows. Similar to CSR, the nnz is limited to Integer.MAX_VALUE. In contrast to COO matrix formats with three arrays, we use 1+#dims arrays to represent the values and indexes of all dimensions.

See Also:

Serialized Form

Nested Class Summary

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

SparseBlock.Type

Constructor Summary

Constructors

Constructor	Description
SparseBlockCOO(int rlen)
SparseBlockCOO(int rlen, int capacity)
SparseBlockCOO(SparseBlock sblock)	Copy constructor sparse block abstraction.
SparseBlockCOO(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(int r)	Re-allocate physical row if physical size exceeds logical size plus resize factor.
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 COO 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).
Iterator<IJV>	getIterator()	Get a non-zero iterator over the entire sparse block.
Iterator<IJV>	getIterator(int ru)	Get a non-zero iterator over the partial sparse block [0,ru).
Iterator<IJV>	getIterator(int rl, int ru)	Get a non-zero iterator over the subblock [rl, 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.
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[]	rowIndexes()	Get raw access to underlying array of row indices 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.
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

isAligned, isAligned

Methods inherited from class java.lang.Object

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

Constructor Detail

SparseBlockCOO

public SparseBlockCOO(int rlen)

SparseBlockCOO

public SparseBlockCOO(int rlen,
                      int capacity)

SparseBlockCOO

public SparseBlockCOO(SparseBlock sblock)

Copy constructor sparse block abstraction.

Parameters:

sblock - sparse block to copy

SparseBlockCOO

public SparseBlockCOO(SparseRow[] rows,
                      int nnz)

Copy constructor old sparse row representation.

Parameters:

rows - array of sparse rows

nnz - number of non-zeros

Method Detail

estimateSizeInMemory

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

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

Parameters:

nrows - number of rows

ncols - number of columns

sparsity - sparsity ratio

Returns:

memory estimate

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

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

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.

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

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

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

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

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 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. NOTE: This method exists for incremental runtime integration and might be deleted in the future.

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 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

getIterator

public Iterator<IJV> getIterator()

Description copied from class: SparseBlock

Get a non-zero iterator over the entire sparse block. Note that the returned IJV object is reused across next calls and should be directly consumed or deep copied.

Overrides:

getIterator in class SparseBlock

Returns:

IJV iterator

getIterator

public Iterator<IJV> getIterator(int ru)

Description copied from class: SparseBlock

Get a non-zero iterator over the partial sparse block [0,ru). Note that the returned IJV object is reused across next calls and should be directly consumed or deep copied.

Overrides:

getIterator in class SparseBlock

Parameters:

ru - exclusive upper row index starting at 0

Returns:

IJV iterator

getIterator

public Iterator<IJV> getIterator(int rl,
                                 int ru)

Description copied from class: SparseBlock

Get a non-zero iterator over the subblock [rl, ru). Note that the returned IJV object is reused across next calls and should be directly consumed or deep copied.

Overrides:

getIterator in class SparseBlock

Parameters:

rl - inclusive lower row index starting at 0

ru - exclusive upper row index starting at 0

Returns:

IJV iterator

toString

public String toString()

Specified by:

toString in class SparseBlock

rowIndexes

public int[] rowIndexes()

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

Returns:

array of row indices

indexes

public int[] indexes()

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

Returns:

array of column indices

values

public double[] values()

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

Returns:

array of values