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, Block
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:

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    class 
    SparseBlockCOO.NonEmptyRowsIteratorCOO
     

    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()
    In-place compaction of non-zero-entries; removes zero entries and shifts non-zero entries to the left if necessary.
    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).
    long
    getExactSizeInMemory()
    Computes the exact size in memory of the materialized block
    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).
    Iterator<Integer>
    getNonEmptyRowsIterator(int rl, int ru)
     
    SparseBlock.Type
    getSparseBlockType()
    Get the type of the sparse block.
    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

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

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • 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 Details

    • 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

    • 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

    • 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()
      Description copied from class: SparseBlock
      In-place compaction of non-zero-entries; removes zero entries and shifts non-zero entries to the left if necessary.
      Specified by:
      compact in class SparseBlock

    • getSparseBlockType

      public SparseBlock.Type getSparseBlockType()
      Description copied from class: SparseBlock
      Get the type of the sparse block.
      Specified by:
      getSparseBlockType in class SparseBlock
      Returns:
      sparse block type

    • 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 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 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

    • getNonEmptyRowsIterator

      public Iterator<Integer> getNonEmptyRowsIterator(int rl, int ru)
      Specified by:
      getNonEmptyRowsIterator in class SparseBlock