[AstroPy] Using quantities is slow

[Peter Teuben]

Hi all
    The AMUSE project uses the comma operator to append units to
numbers, would be interesting
to hear of its performance compared to the astropy one. The concept was
discussed at Python in Astronomy
in Arjen's talk on AMUSE.

peter


On 08/24/2015 06:13 PM, Andrew Hearin wrote:
> Hi Kevin,
>
> I’m really glad you asked this. I’m on the verge of implementing
> Quantities in my own work, and I will be very interested to hear what
> the workaround is.
>
> Cheers,
> Andrew
>
>
> On Aug 24, 2015, at 9:57 AM, Kevin Gullikson
> <kevin.gullikson at gmail.com <mailto:kevin.gullikson at gmail.com>> wrote:
>
>> Hi,
>>
>> I am writing an MCMC fitting code, and my current implementation uses
>> the (very useful) astropy quantities framework to take care of unit
>> conversions and such. However, the code is surprisingly slow so I
>> profiled it with %prun and it looks like the quantity utilities that
>> wrap numpy functions are taking a huge chunk of time. Is that just
>> the price of convenience?
>>
>> Here is an excerpt of the output from profiling my code.
>>
>>          1827310507 function calls (1823056217 primitive calls) in 3659.725 seconds
>>
>>    Ordered by: internal time
>>
>>    ncalls  tottime  percall  cumtime  percall filename:lineno(function)
>>  25719008  400.735    0.000 1944.942    0.000 quantity.py:263(__array_prepare__)
>> 159341911  157.611    0.000  182.754    0.000 {getattr}
>> 32101370/31134490  148.248    0.000  180.318    0.000 {method 'format' of 'unicode' objects}
>>  27459392  143.898    0.000  397.546    0.000 quantity.py:520(_new_view)
>>  25719008  141.664    0.000  566.152    0.000 quantity.py:421(__array_wrap__)
>>   6381408  137.927    0.000  733.341    0.000 core.py:2013(_expand_and_gather)
>>  63814347  136.370    0.000  373.226    0.000 {hasattr}
>> 188542970  135.470    0.000  300.222    0.000 {isinstance}
>>  30360032  112.239    0.000  136.142    0.000 core.py:695(__hash__)
>>  44089728   99.326    0.000  164.752    0.000 abc.py:128(__instancecheck__)
>>  42350301   97.285    0.000  191.681    0.000 {method 'view' of 'numpy.ndarray' objects}
>>  30553408   95.704    0.000  236.855    0.000 quantity.py:695(__getattr__)
>>   6961536   90.321    0.000  675.250    0.000 quantity.py:756(__mul__)
>>    386752   87.576    0.000  900.927    0.002 Orbit.py:133(get_true_anomaly)
>>    193376   78.895    0.000 1178.998    0.006 Orbit.py:15(__init__)
>>  13729696   65.363    0.000  353.957    0.000 core.py:891(_to)
>>  58012800   59.299    0.000  128.197    0.000 quantity.py:260(__array_finalize__)
>>    386752   59.201    0.000   79.588    0.000 interpolate.py:1581(_evaluate_linear)
>>  73869632   55.839    0.000   55.839    0.000 _weakrefset.py:70(__contains__)
>>  15083328   53.805    0.000  266.936    0.000 core.py:2014(add_unit)
>>   2900640   42.100    0.000  535.141    0.000 quantity.py:780(__div__)
>>
>> Kevin Gullikson
>> PhD Candidate
>> University of Texas Astronomy
>> RLM 15.310E
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