Parallel in-place sort for numpy arrays

Question

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 i

Answer 1

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 "" 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