SparseBlockCOO (SystemML 1.2.0 API)

java.lang.Object
- org.apache.sysml.runtime.matrix.data.SparseBlock
- - org.apache.sysml.runtime.matrix.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.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class org.apache.sysml.runtime.matrix.data.SparseBlock
  SparseBlock.Type

Field Summary
- Fields inherited from class org.apache.sysml.runtime.matrix.data.SparseBlock
  INIT_CAPACITY, RESIZE_FACTOR1, RESIZE_FACTOR2

Constructor Summary

Constructors
Constructor and 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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`	`estimateMemory(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.sysml.runtime.matrix.data.SparseBlock
isAligned, isAligned

Methods inherited from class java.lang.Object
clone, equals, finalize, 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
  - estimateMemory
```
public static long estimateMemory(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.
    
    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

Class SparseBlockCOO

Nested Class Summary

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

Field Summary

Fields inherited from class org.apache.sysml.runtime.matrix.data.SparseBlock

Constructor Summary

Method Summary

Methods inherited from class org.apache.sysml.runtime.matrix.data.SparseBlock

Methods inherited from class java.lang.Object

Constructor Detail

SparseBlockCOO

SparseBlockCOO

SparseBlockCOO

SparseBlockCOO

Method Detail

estimateMemory

allocate

allocate

allocate

compact

numRows

isThreadSafe

isContiguous

isAllocated

checkValidity

reset

reset

reset

size

size

size

size

isEmpty

indexes

values

pos

set

set

add

append

setIndexRange

setIndexRange

deleteIndexRange

sort

sort

get

get

posFIndexLTE

posFIndexGTE

posFIndexGT

getIterator

getIterator

getIterator

toString

rowIndexes

indexes

values