sortingnumpynumexpr

Parallel in-place sort for numpy arrays

I often need to sort large numpy arrays (few billion elements), which became a bottleneck of my code. I am looking for a way to parallelize it.

Are there any parallel implementations for the ndarray.sort() function? Numexpr module provides parallel implementation for most math operations on numpy arrays, but lacks sorting capabilities.

Maybe, it is possible to make a simple wrapper around a C++ implementation of parallel sorting, and use it through Cython?

Solution

  • I ended up wrapping GCC parallel sort. Here is the code:

    parallelSort.pyx

    # cython: wraparound = False
# cython: boundscheck = False
import numpy as np
cimport numpy as np
import cython
cimport cython 

ctypedef fused real:
    cython.char
    cython.uchar
    cython.short
    cython.ushort
    cython.int
    cython.uint
    cython.long
    cython.ulong
    cython.longlong
    cython.ulonglong
    cython.float
    cython.double

cdef extern from "<parallel/algorithm>" namespace "__gnu_parallel":
    cdef void sort[T](T first, T last) nogil 

def numpyParallelSort(real[:] a):
    "In-place parallel sort for numpy types"
    sort(&a[0], &a[a.shape[0]])

    Extra compiler args: -fopenmp (compile) and -lgomp (linking)

    This makefile will do it: 

    all:
    cython --cplus parallelSort.pyx  
    g++  -g -march=native -Ofast -fpic -c    parallelSort.cpp -o parallelSort.o -fopenmp `python-config --includes`
    g++  -g -march=native -Ofast -shared  -o parallelSort.so parallelSort.o `python-config --libs` -lgomp 

clean:
    rm -f parallelSort.cpp *.o *.so

    And this shows that it works: 

    from parallelSort import numpyParallelSort
import numpy as np 
a = np.random.random(100000000)

numpyParallelSort(a) 
print a[:10]

    edit: fixed bug noticed in the comment below