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

[Andrea Gavana]

On Sun, 11 Oct 2020 at 07.52, Hongyi Zhao <hongyi.zhao at gmail.com> wrote:

> On Sun, Oct 11, 2020 at 1:33 PM Andrea Gavana <andrea.gavana at gmail.com>
> wrote:
> >
> >
> >
> > On Sun, 11 Oct 2020 at 07.14, Andrea Gavana <andrea.gavana at gmail.com>
> wrote:
> >>
> >> 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.
> >
> >
> >
> > I’m sorry, scratch that: I’ve seen a ghost white space in front of your
> column_stack call and made me think you were stacking your results very
> many times, which is not the case.
>
> Still not so clear on your solutions for this problem. Could you
> please post here the corresponding snippet of your enhancement?


I have no solution, I originally thought you were calling “column_stack”
6000 times in the loop, but that is not the case, I was mistaken. My
apologies for that.

The timings of your approach is highly dependent on the size of your
“energy” and “DOS” array - not to mention calling trapz 6000 times in a
loop. Maybe there’s a better way to do it with another approach, but at the
moment I can’t think of one...


>
> Regards,
> HY
> >
> >>
> >>
> >>>
> >>>
> >>> 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>
> >>> >> _______________________________________________
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> >>> >> NumPy-Discussion at python.org
> >>> >> https://mail.python.org/mailman/listinfo/numpy-discussion
> >>> >
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> >>>
> >>>
> >>>
> >>> --
> >>> 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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