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hi - i've only just started using python and
numpy... the program i wrote below runs much more
slowly than a fortran equivalent. ie. on a dataset
where the order of the matrix is (3325,3325),
python took this long:
362.25user 0.74system 6:09.78elapsed 98%CPU
and fortran took this long:
2.68user 1.12system 0:03.89elapsed 97%CPU
is this because the element by element
calculations involved are contained in python for
loops?
thanks
#!/usr/bin/python
from Numeric import *
def nrm(pedigree):
n_animals = len(pedigree) + 1
nrm = zeros((n_animals,n_animals),Float)
for i in xrange(1,n_animals):
isire = pedigree[i-1][1]
idam = pedigree[i-1][2]
nrm[i,i] = 1.0 + 0.5 * nrm[isire,idam]
for j in xrange(i+1,n_animals):
jsire = pedigree[j-1][1]
jdam = pedigree[j-1][2]
nrm[j,i] = 0.5 * (nrm[jsire,i] +
nrm[jdam,i])
nrm[i,j] = nrm[j,i]
return nrm
if __name__ == '__main__':
test_ped = [(1,0,0),(2,0,0),(3,1,0),(4,1,2),
(5,3,4),(6,1,4),(7,5,6)]
a = nrm(test_ped)
print a
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