Numpy Operations¶

Below is the list of the data-parallel Numpy operators that Bodo can optimize and parallelize.

Numpy element-wise array operations¶

Unary operators¶

+
-
~

Binary operators¶

+
-
*
/
/?
%
|
>>
^
<<
&
**
//

Comparison operators¶

==
!=
<
<=
>
>=

Data-parallel math operations¶

numpy.add
numpy.subtract
numpy.multiply
numpy.divide
numpy.logaddexp
numpy.logaddexp2
numpy.true_divide
numpy.floor_divide
numpy.negative
numpy.positive
numpy.power
numpy.remainder
numpy.mod
numpy.fmod
numpy.abs
numpy.absolute
numpy.fabs
numpy.rint
numpy.sign
numpy.conj
numpy.exp
numpy.exp2
numpy.log
numpy.log2
numpy.log10
numpy.expm1
numpy.log1p
numpy.sqrt
numpy.square
numpy.reciprocal
numpy.gcd
numpy.lcm
numpy.conjugate

Trigonometric functions¶

numpy.sin
numpy.cos
numpy.tan
numpy.arcsin
numpy.arccos
numpy.arctan
numpy.arctan2
numpy.hypot
numpy.sinh
numpy.cosh
numpy.tanh
numpy.arcsinh
numpy.arccosh
numpy.arctanh
numpy.deg2rad
numpy.rad2deg
numpy.degrees
numpy.radians

Bit manipulation functions¶

numpy.bitwise_and
numpy.bitwise_or
numpy.bitwise_xor
numpy.bitwise_not
numpy.invert
numpy.left_shift
numpy.right_shift

Comparison functions¶

numpy.logical_and
numpy.logical_or
numpy.logical_xor
numpy.logical_not

Floating functions¶

numpy.isfinite
numpy.isinf
numpy.signbit
numpy.ldexp
numpy.floor
numpy.ceil
numpy.trunc

Numpy reduction functions¶

numpy.sum
numpy.prod
numpy.min
numpy.max
numpy.argmin
numpy.argmax
numpy.all
numpy.any

Numpy array creation functions¶

numpy.empty
numpy.identity
numpy.zeros
numpy.ones
numpy.empty_like
numpy.zeros_like
numpy.ones_like
numpy.full_like
numpy.array
numpy.asarray
numpy.copy
numpy.arange
numpy.linspace
numpy.repeat only scalar num_repeats

Numpy array manipulation functions¶

numpy.shape
numpy.reshape

shape values cannot be -1.
numpy.sort
numpy.concatenate
numpy.append
numpy.unique The output is assumed to be "small" relative to input and is replicated. Use Series.drop_duplicates() if the output should remain distributed.
numpy.where (1 and 3 arguments)
numpy.select The default value for numeric/boolean types is 0/False. For all other types, the default is pd.NA. If any of the values in choicelist are nullable, or the default is pd.NA or None, the output will be a nullable pandas array instead of a numpy array.
numpy.nan_to_num converts infinity/NaN values to regular floats.
numpy.union1d
numpy.intersect1d no distributed support yet
numpy.setdiff1d no distributed support yet
numpy.hstack concatenates elements on each rank without maintaining order
numpy.tile Supported in 2 cases: the array is 2D and reps is in the form (1, x), or the array is 1D and reps is in the form (x, 1).
numpy.ndarray.T distributed array transpose is supported for 2D arrays.

Numpy mathematical and statistics functions¶

numpy.cumsum
numpy.diff
numpy.percentile
numpy.quantile
numpy.median
numpy.mean
numpy.std
numpy.interp no distributed support yet.
np.linalg.norm parallelized only for 2D inputs with axis=1.

Random number generator functions¶

numpy.random.rand
numpy.random.randn
numpy.random.ranf
numpy.random.random_sample
numpy.random.sample
numpy.random.random
numpy.random.standard_normal
numpy.random.multivariate_normal (must provide size)
numpy.random.chisquare
numpy.random.weibull
numpy.random.power
numpy.random.geometric
numpy.random.exponential
numpy.random.poisson
numpy.random.rayleigh
numpy.random.normal
numpy.random.uniform
numpy.random.beta
numpy.random.binomial
numpy.random.f
numpy.random.gamma
numpy.random.lognormal
numpy.random.laplace
numpy.random.randint
numpy.random.triangular

`numpy.dot` function¶

numpy.dot between a matrix and a vector or between two vectors.

Numpy I/O¶

numpy.ndarray.tofile
numpy.fromfile supports reading binary files. file, dtype, count, and offset arguments are supported (file and dtype are required). file should be a string. s3:// and hdfs:// file paths are also supported.

Our documentation on scalable I/O contains example usage and more system specific instructions.

Numpy matrix support¶

numpy.asmatrix parallelized only for array or matrix input.
* left-hand side argument can be distributed but right-hand side argument is replicated.

Miscellaneous¶

Numpy array comprehension : e.g. : A = np.array([i**2 for i in range(N)])

Note

Optional arguments are not supported unless if explicitly mentioned here. For operations on multi-dimensional arrays, automatic broadcast of dimensions of size 1 is not supported.

Numpy dot() Parallelization¶

The np.dot function has different distribution rules based on the number of dimensions and the distributions of its input arrays. The example below demonstrates two cases:

@bodo.jit
def example_dot(N, D):
    X = np.random.ranf((N, D))
    Y = np.random.ranf(N)
    w = np.dot(Y, X)
    z = np.dot(X, w)
    return z.sum()

example_dot(1024, 10)
example_dot.distributed_diagnostics()

Here is the output of distributed_diagnostics():

Data distributions:
  $X.130               1D_Block
  $Y.131               1D_Block
  $b.2.158             REP

Parfor distributions:
  0                    1D_Block
  1                    1D_Block
  3                    1D_Block

Distributed listing for function example_dot, ../tmp/dist_rep.py (4)
++++++++++++++++++++++++++++++++++| parfor_id/variable: distribution
@bodo.jit                         |
def example_dot(N, D):            |
    X = np.random.ranf((N, D))++++| #0: 1D_Block, $X.130: 1D_Block
    Y = np.random.ranf(N)+++++++++| #1: 1D_Block, $Y.131: 1D_Block
    w = np.dot(Y, X)++++++++++++++| $b.2.158: REP
    z = np.dot(X, w)++++++++++++++| #3: 1D_Block
    return z.sum()                |

The first dot has a 1D array with 1D_Block distribution as first input Y, while the second input X is a 2D array with 1D_Block distribution. Hence, dot is a sum reduction across distributed datasets and therefore, the output (w) is on the reduce side and is assigned REP distribution.

The second dot has a 2D array with 1D_Block distribution (X) as first input, while the second input is a REP array (w). Hence, the computation is data-parallel across rows of X, which implies a 1D_Block distribution for output (z).

Variable z does not exist in the distribution report since the compiler optimizations were able to eliminate it. Its values are generated and consumed on-the-fly, without memory load/store overheads.