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

[Hongyi Zhao]

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?

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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>>> >
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>>>
>>>
>>> --
>>> Hongyi Zhao <hongyi.zhao at gmail.com>
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>
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-- 
Hongyi Zhao <hongyi.zhao at gmail.com>