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Re: Perl PDL slower than python numpy (Updated2)

by vr (Curate)
on Sep 20, 2020 at 19:49 UTC ( [id://11121970]=note: print w/replies, xml ) Need Help??

in reply to Perl PDL slower than python numpy

Edit2. Here's PDL vs. numpy simple performance test in earnest, I hope Python code really does what I intended, and so no more blunders. I don't see any "numpy is better than PDL" as claimed, except PDL devs didn't bother to optimize "zeroes", as, it looks, it really fills every 8 bytes, cell by cell by cell... Too bad if initializing lots of arrays with zeroes is mission-critical. (That said, of course PDL isn't perfect.) Python3 and numpy are from 18.04LTS repositories.

import time import numpy as np d = (1000,500,500) t = time.time(); x = np.zeros(( d )); print( time.time() - t ) t = time.time(); y = np.ones(( d )); print( time.time() - t ) t = time.time(); z = x / y; print( time.time() - t ) 1.1920928955078125e-05 0.6920394897460938 1.205686330795288 use strict; use warnings; use feature 'say'; use Time::HiRes 'time'; use PDL; $PDL::BIGPDL = $PDL::BIGPDL = 1; my @d = (1000,500,500); my $t; $t = time; my $x = zeroes( @d ); say time - $t; $t = time; my $y = ones( @d ); say time - $t; $t = time; my $z = $x / $y; say time - $t; 0.727283954620361 0.730240821838379 0.971168994903564


Edit. I was wrong about 'float32' being default for numpy, sorry. My answer doesn't explain the observed speed comparison.


As quick googling shows, default data type for numpy is 32-bit "single precision" "float". PDL default is 64-bit "double precision" "double". Hence illusory 2x speed difference. Your example is just trivial allocation/arithmetic in underlying C, after all. In PDL, you can specify data type in constructor, as e.g. typing "?zeroes" in interactive shell will explain (and as shown below).

Complete cmd.exe window dump to show versions, etc.:

---------------------------------------------- Welcome to Strawberry Perl PDL Edition! * URL - + * to launch perl script run: perl c:\my\scripts\ * to start PDL console run: pdl2 * to update PDL run: cpanm PDL * to install extra module run: cpanm PDL::Any::Module or if previous fails: ppm PDL::Any::Module * or you can use dev tools like: gcc, g++, gfortran, gmake * see README.TXT for more info ---------------------------------------------- Perl executable: C:\berrybrew\strawberry-perl-\perl\ +bin\perl.exe Perl version : 5.30.1 / MSWin32-x64-multi-thread PDL version : 2.019 C:\berrybrew\strawberry-perl->pdl2 Unable to get Terminal Size. The Win32 GetConsoleScreenBufferInfo call + didn't work. The COLUMNS and LINES environment variables didn't work +. at C:/berrybrew/strawberry-perl- +Term/ReadLine/ line 410. load_rcfile: got $HOME = C:\berrybrew\strawberry-perl- +DL\data load_rcfile: loading PDL/default.pdl Perldl2 Shell v0.008 PDL comes with ABSOLUTELY NO WARRANTY. For details, see the file 'COPYING' in the PDL distribution. This is free software and you are welcome to redistribute it under certain conditions, see the same file for details. Loaded plugins: CleanErrors Commands Completion CompletionDriver::INC CompletionDriver::Keywords CompletionDriver::LexEnv CompletionDriver::Methods DDS FindVariable History LexEnv MultiLine::PPI NiceSlice PDLCommands Packages PrintControl ReadLineHistory Type 'help' for online help Type Ctrl-D or quit to exit Loaded PDL v2.019 pdl> pdl> $PDL::BIGPDL = 1 pdl> use Time::HiRes 'time'; *t = \&time pdl> @d=(500,500,500) # 8 GB RAM here, let's avoid swapping pdl> pdl> $t=t; $x=zeroes@d; $y=ones@d; $z=$x+$y; $z2=$x/$y; p t-$t 1.2526330947876 pdl> $t=t; $x=zeroes@d; $y=ones@d; $z=$x+$y; $z2=$x/$y; p t-$t 1.69825196266174 pdl> $t=t; $x=zeroes@d; $y=ones@d; $z=$x+$y; $z2=$x/$y; p t-$t 1.59618711471558 pdl> p $z2->info PDL: Double D [500,500,500] pdl> pdl> $t=t; $x=zeroes double,@d; $y=ones double,@d; $z=$x+$y; $z2=$x/$y +; p t-$t 1.64064288139343 pdl> $t=t; $x=zeroes double,@d; $y=ones double,@d; $z=$x+$y; $z2=$x/$y +; p t-$t 1.6656858921051 pdl> $t=t; $x=zeroes double,@d; $y=ones double,@d; $z=$x+$y; $z2=$x/$y +; p t-$t 1.68068408966064 pdl> pdl> $t=t; $x=zeroes float,@d; $y=ones float,@d; $z=$x+$y; $z2=$x/$y; +p t-$t 1.11372804641724 pdl> $t=t; $x=zeroes float,@d; $y=ones float,@d; $z=$x+$y; $z2=$x/$y; +p t-$t 0.841649055480957 pdl> $t=t; $x=zeroes float,@d; $y=ones float,@d; $z=$x+$y; $z2=$x/$y; +p t-$t 0.83014702796936 pdl> p $z2->info PDL: Float D [500,500,500] pdl>

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Re^2: Perl PDL slower than python numpy
by sgt (Deacon) on Sep 22, 2020 at 15:09 UTC
    As quick googling shows, default data type for numpy is 32-bit "single precision" "float"

    Are you really sure? I was surprised by your claim that numpy use a default C float. I am a longtime Perl and C hacker and no python expert. But I view the C float type as kind of archaic I use many math libs and the trend is to go past the C double. It would be surprising for a modern lib like numpy to use such a default. Also float() in python means floating point not C float.

    Note that I do not really care if tool X is faster that tool Y when the sun, jupiter and the moon are aligned. But I did a bit of web search and could not _quickly_ come up with a definite answer! so I decided to check. Seems that numpy default is a C double:

    % steph@kerangi (/tmp/cpanm_t.d) % % python3.8 -c 'import math as m; print(m.sin(float(1)))' 0.8414709848078965 % steph@kerangi (/tmp/cpanm_t.d) % % python3.7 Python 3.7.7 (default, Apr 10 2020, 07:59:19) [GCC 9.3.0] on cygwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy as np >>> np.float <class 'float'> >>> np.float64 <class 'numpy.float64'> >>> np.float32 <class 'numpy.float32'> >>> print(np.sin(float(1))) 0.8414709848078965 >>> print(np.sin(np.float64(1))) 0.8414709848078965 >>> print(np.sin(np.float32(1))) 0.84147096 >>>

    I think that PDL is really a fantastic piece of software and that it is pretty fast. One possible pitfall, common to all C extensions to Perl, is to go back and forth too many times between Perl and C as that can make a computation much slower. It is often possible to avoid it.

    hth cheers --sgt
      A single-precision float still has utility, including in machine-learning (where higher precision isn't useful, whereas speed is), and graphics (same consideration).
Re^2: Perl PDL slower than python numpy
by syphilis (Archbishop) on Sep 22, 2020 at 14:36 UTC
    My answer doesn't explain the observed speed comparison.

    Might it simply be that numpy is optimized to recognize that $X + $Y is $Y, and $X / $Y is $X ?
    (Whereas PDL goes to the trouble of doing the arithmetic.)

Re^2: Perl PDL slower than python numpy (Updated2)
by etj (Deacon) on Apr 19, 2022 at 22:55 UTC
    2022 updates to this excellent note:
    • with 2.058, zeroes was optimised so that the ndarray is initialised using memset (see for discussion and measurements).
    • with 2.077, the PDL shells have a with_time { code... } function to make this sort of measurement easier.
    Observation: the first command of the above snippet is slightly quicker than the rest; this may be because the following ones, in assigning to e.g. $y, will trigger the destruction of the previous contents of that variable, which is likely to take some time.
Re^2: Perl PDL slower than python numpy
by fanasy (Sexton) on Sep 22, 2020 at 11:49 UTC
    I have checked the document of numpy , the default type is float64
Re^2: Perl PDL slower than python numpy
by fanasy (Sexton) on Sep 22, 2020 at 11:50 UTC
    However, the thread should be close. I have compared as again, the numpy is better than PDL on large size of vectors. thanks! fan

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