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
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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
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