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Scipy code is faster in Pyodide v0.23.4 than in v0.24.0 and v0.25.0 #4486

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sebastianherreramonterrosa opened this issue Feb 6, 2024 · 7 comments
Closed

Scipy code is faster in Pyodide v0.23.4 than in v0.24.0 and v0.25.0 #4486

sebastianherreramonterrosa opened this issue Feb 6, 2024 · 7 comments
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bug Something isn't working

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@sebastianherreramonterrosa
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I currently use pyodide to code the kernel of https://phitter.io. The first version that I used of pyodide was v0.23.4 and all worked perfect. When I update my version to v0.24.0 or v0.25.0 the execution's time for simple operations increase and freeze the browser. An example of a simple operation is:

mode: function (arr: number[]): number {
    const pyodideStore = usePyodideStore();
    pyodideStore.pyodide.globals.set("arr", arr);
    pyodideStore.runPython(`
        def calc_shgo_mode(distribution, data):
            objective = lambda x: -distribution.pdf(x)[0]
            bnds = [[min(data), max(data)]]
            solution = scipy.optimize.shgo(objective, bounds=bnds, n=100 * len(data))
            return solution.x[0]
        data = arr.to_py()
        distribution = scipy.stats.gaussian_kde(data)
        mode = calc_shgo_mode(distribution, data)
    `);
    return pyodideStore.pyodide.globals.get("mode");
},

I don´t know if is an explanaition about this behaviour.
@sebastianherreramonterrosa sebastianherreramonterrosa added the bug Something isn't working label Feb 6, 2024
@hoodmane
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hoodmane commented Feb 6, 2024 •
edited

It would be nice if you could make benchmarks of how long the specific operations you are doing take on the different versions. You are using scipy which is it's own weird beast. Between 0.23.4 and 0.24.0 there were three PRs which might have an effect on this:
#3331
#3794
#3996

All three of which were generous contributions from @lesteve, maybe he has a guess. To get a better concept, it would be useful to break down how much time is spent in each of the scipy functions. One could also compare the same functions on native Python in scipy 1.9 vs 1.11, probably there there isn't much of a difference.

See this comment which has some benchmarks on the effects of these PRs. But it seems to show that Pyodide 0.24.0 should be a fair bit faster than 0.23.4 for most of the operations tested. Anyways it's hard to know without trying to measure what you are using specifically.

cc @rth

@hoodmane hoodmane changed the title Pyodide v0.23.4 is faster than v0.24.0 and v0.25.0 Scipy code is faster in Pyodide v0.23.4 than in v0.24.0 and v0.25.0 Feb 6, 2024
@lesteve
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lesteve commented Feb 7, 2024 •
edited

@sebastianherreramonterrosa what is the value of arr in your snippet?

Without a stand-alone snipet, we are pretty much reduced to random guessing ...

@sebastianherreramonterrosa
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@lesteve The value of arr is here: Dataset

// JS Representation
const arr = [782.1587476, 795.387086, 799.7345698, 806.9197855, 807.0463942, 807.3649597, 809.8982279, 812.8464141, 813.5454571, 814.0393853, 814.4982938, 814.7235583, 815.2237586, 815.3689112, 815.549188, 816.5616516, 816.6898013, 816.7170744, 816.9565214, 818.545773, 818.5851785, 818.6100861, 818.6707629, 818.8429549, 819.5863531, 820.7975631, 821.2037954, 821.2545802, 821.3866398, 822.7657442, 823.5462453, 823.6373205, 823.8577613, 824.4523423, 824.6145776, 826.8229941, 826.9143961, 827.4739583, 827.7353163, 828.1253071, 828.18333, 828.4066215, 828.4682931, 828.6164161, 828.7162096, 828.9112205, 829.0875069, 829.239806, 829.35716, 830.0010021, 830.1688936, 830.3358744, 831.4524552, 831.5245596, 831.7075856, 832.0860798, 832.2370759, 832.3447862, 833.2832111, 833.4840663, 833.5412179, 833.8488735, 833.939438, 834.0439737, 834.3184225, 834.4691618, 835.0099595, 835.3312188, 835.4768996, 835.6195047, 835.6228222, 835.6312219, 835.6332902, 835.7457027, 836.2510027, 836.2798312, 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In my browser, the duration of this operation with v0.23.4 is 0.21209999999403953 seconds. With v0.25.0 is 176.69040000000595 seconds. I hope it is possible to reproduce the scenario.

@lesteve
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lesteve commented Feb 8, 2024 •
edited by hoodmane

See Python reproducer below. In Python it goes from to less than 1s in scipy 1.10.1 to 40s in scipy 1.11.4. I would suggest to have a look at the scipy doc and github repo to see whether there are reasons for this performance change.

It could well be the case that much of the difference is unrelated to Pyodide and is due to a change in scipy, but that needs to be looked at in more details.

import numpy as np
import scipy.stats
import scipy.optimize


array = [782.1587476, 795.387086, 799.7345698, 806.9197855, 807.0463942, 807.3649597, 809.8982279, 812.8464141, 813.5454571, 814.0393853, 814.4982938, 814.7235583, 815.2237586, 815.3689112, 815.549188, 816.5616516, 816.6898013, 816.7170744, 816.9565214, 818.545773, 818.5851785, 818.6100861, 818.6707629, 818.8429549, 819.5863531, 820.7975631, 821.2037954, 821.2545802, 821.3866398, 822.7657442, 823.5462453, 823.6373205, 823.8577613, 824.4523423, 824.6145776, 826.8229941, 826.9143961, 827.4739583, 827.7353163, 828.1253071, 828.18333, 828.4066215, 828.4682931, 828.6164161, 828.7162096, 828.9112205, 829.0875069, 829.239806, 829.35716, 830.0010021, 830.1688936, 830.3358744, 831.4524552, 831.5245596, 831.7075856, 832.0860798, 832.2370759, 832.3447862, 833.2832111, 833.4840663, 833.5412179, 833.8488735, 833.939438, 834.0439737, 834.3184225, 834.4691618, 835.0099595, 835.3312188, 835.4768996, 835.6195047, 835.6228222, 835.6312219, 835.6332902, 835.7457027, 836.2510027, 836.2798312, 836.4761627, 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data = np.array(array)
def calc_shgo_mode(distribution, data):
    objective = lambda x: -distribution.pdf(x)[0]
    bnds = [[min(data), max(data)]]
    solution = scipy.optimize.shgo(objective, bounds=bnds, n=100 * len(data))
    return solution.x[0]

distribution = scipy.stats.gaussian_kde(data)
mode = calc_shgo_mode(distribution, data)

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hoodmane commented Feb 8, 2024

Thanks @lesteve!

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Okay let's close this since it's very likely a scipy regression not directly related to Pyodide.

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lesteve commented Feb 14, 2024

I was about to open an issue in scipy and realised @sebastianherreramonterrosa had already done it: scipy/scipy#20057

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