[Numpy-discussion] The mu.py script will keep running and never end.

[Andrea Gavana]

Hi,

On Sun, 11 Oct 2020 at 00.27, Hongyi Zhao <hongyi.zhao at gmail.com> wrote:

> On Sun, Oct 11, 2020 at 1:48 AM Robert Kern <robert.kern at gmail.com> wrote:
> >
> > You don't need to use vectorize() on fermi(). fermi() will work just
> fine on arrays and should be much faster.
>
> Yes, it really does the trick. See the following for the benchmark
> based on your suggestion:
>
> $ time python mu.py
> [-10.999 -10.999 -10.999 ...  20.     20.     20.   ] [4.973e-84
> 4.973e-84 4.973e-84 ... 4.973e-84 4.973e-84 4.973e-84]
>
> real    0m41.056s
> user    0m43.970s
> sys    0m3.813s
>
>
> But are there any ways to further improve/increase efficiency?



I believe it will get a bit better if you don’t column_stack an array 6000
times - maybe pre-allocate your output first?

Andrea.



>
> Regards,
> HY
>
> >
> > On Sat, Oct 10, 2020, 8:23 AM Hongyi Zhao <hongyi.zhao at gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> My environment is Ubuntu 20.04 and python 3.8.3 managed by pyenv. I
> >> try to run the script
> >> <
> https://notebook.rcc.uchicago.edu/files/acs.chemmater.9b05047/Data/bulk/dft/mu.py
> >,
> >> but it will keep running and never end. When I use 'Ctrl + c' to
> >> terminate it, it will give the following output:
> >>
> >> $ python mu.py
> >> [-10.999 -10.999 -10.999 ...  20.     20.     20.   ] [4.973e-84
> >> 4.973e-84 4.973e-84 ... 4.973e-84 4.973e-84 4.973e-84]
> >>
> >> I have to terminate it and obtained the following information:
> >>
> >> ^CTraceback (most recent call last):
> >>   File "mu.py", line 38, in <module>
> >>     integrand=DOS*fermi_array(energy,mu,kT)
> >>   File
> "/home/werner/.pyenv/versions/datasci/lib/python3.8/site-packages/numpy/lib/function_base.py",
> >> line 2108, in __call__
> >>     return self._vectorize_call(func=func, args=vargs)
> >>   File
> "/home/werner/.pyenv/versions/datasci/lib/python3.8/site-packages/numpy/lib/function_base.py",
> >> line 2192, in _vectorize_call
> >>     outputs = ufunc(*inputs)
> >>   File "mu.py", line 8, in fermi
> >>     return 1./(exp((E-mu)/kT)+1)
> >> KeyboardInterrupt
> >>
> >>
> >> Any helps and hints for this problem will be highly appreciated?
> >>
> >> Regards,
> >> --
> >> Hongyi Zhao <hongyi.zhao at gmail.com>
> >> _______________________________________________
> >> NumPy-Discussion mailing list
> >> NumPy-Discussion at python.org
> >> https://mail.python.org/mailman/listinfo/numpy-discussion
> >
> > _______________________________________________
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>
>
>
> --
> Hongyi Zhao <hongyi.zhao at gmail.com>
> _______________________________________________
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