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pythonnumpyscipyfortranf2py

How do I use the avx flag when compiling Fortran code using f2py?


In doing some performance testing in Python, I compared the timing for different methods to calculate the Euclidean distance between an array of coordinates. I found my Fortran code compiled with F2PY to be roughly 4x slower than the C implementation used by SciPy. Comparing that C code, to my Fortran code I see no fundamental difference that would lead to the factor of 4 difference. Here is my code (with some comments explaining its use):

        subroutine distance(coor,dist,n)
        double precision coor(n,3),dist(n,n)
        integer n,i,j
        double precision xij,yij,zij

cf2py   intent(in):: coor,n
cf2py   intent(in,out):: dist
cf2py   intent(hide):: xij,yij,zij,

       do 200,i=1,n-1
           do 300,j=i+1,n
               xij=coor(i,1)-coor(j,1)
               yij=coor(i,2)-coor(j,2)
               zij=coor(i,3)-coor(j,3)

               dist(i,j)=dsqrt(xij*xij+yij*yij+zij*zij)

  300   continue
  200   continue

        end

c         1         2         3         4         5         6         7
c123456789012345678901234567890123456789012345678901234567890123456789012
c
c     to setup and incorporate into python (requires numpy):
c
c     # python setup_distance.py build
c     # cp build/lib*/distance.so ./
c
c     to call this from python add the following lines:
c
c     >>> import sys ; sys.path.append('./')
c     >>> from distance import distance
c
c     >>> dist = distance(coor, dist)

Looking at the compile command run by F2PY, I recognized there is no avx compile flag. I tried adding it in the Python setup file using extra_compile_args=['-mavx]` but this had no change to the compile command run by F2PY:

compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-I/home/user/anaconda/lib/python2.7/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-2.7 -I/home/user/anaconda/lib/python2.7/site-packages/numpy/core/include -I/home/user/anaconda/include/python2.7 -c'
gfortran:f77: ./distance.f
creating build/lib.linux-x86_64-2.7
/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/distancemodule.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/fortranobject.o build/temp.linux-x86_64-2.7/distance.o -L/home/user/anaconda/lib -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/distance.so

Solution

  • To answer how to add the avx flag into compiler options.
    In your case the f77 complier is being picked gfortran:f77: ./distance.f < That is the key line.
    You could try specifying --f77flags=-mavx