Part of the problem (but certainly not all of it) is
https://trac.sagemath.org/ticket/26463
Sage was executing "from sage.rings.integer import Integer" 100 times.
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The method smith_form() for matrices over ZZ uses pari's matsnf() but is
vastly slower. Compare these:
sage: M=MatrixSpace(ZZ,1000,5).random_element()
sage: %timeit S=M.smith_form(transformation=True)
1 loop, best of 3: 2.57 s per loop
sage: pM=pari(M)
sage: %timeit S=pM.matsnf(1)
10 loops, best
