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Perl PDL slower than python numpy

by fanasy (Sexton)
on Sep 20, 2020 at 12:44 UTC ( #11121959=perlquestion: print w/replies, xml ) Need Help??

fanasy has asked for the wisdom of the Perl Monks concerning the following question:

Hi all, I test on same machine with lastest version of perl and python

Perl version:v5.32.0
Python version:3.8.5
I have a little disappoint about the result:
Perl slower a lot than python.
weizhong@weizhong-VirtualBox:~/Git/compare-pdl_numpy$ ./compare.csh

Python test1.py:
0.5u 1.0s 0:01.84 88.0% 0+0k 0+0io 0pf+0w

Perl test1.pl:
1.2u 2.0s 0:05.83 55.5% 0+0k 19064+0io 907pf+0w

Python test1.py:
0.7u 0.7s 0:02.54 60.2% 0+0k 52008+0io 141pf+0w

Perl test1.pl:
1.3u 1.9s 0:05.28 61.3% 0+0k 30432+0io 1005pf+0w

Perl Code(test1.pl):
#!/home/weizhong/tools/perl-5.32.0/perl use PDL; $PDL::BIGPDL = 1; $X = zeroes(1000,500,500); $Y = ones(1000,500,500); $Z1 = $X + $Y; $Z2 = $X / $Y;
Python Code(test1.py):
#!/home/weizhong/tools/Python-3.8.5/python import numpy as np X = np.zeros((1000,500,500)) Y = np.ones((1000,500,500)) Z1 = X+Y Z2 = X/Y
compare.csh:

#!/bin/csh -f echo "Python test1.py:"; time ./test1.py echo "Perl test1.pl:"; time ./test1.pl echo "Python test1.py:"; time ./test1.py echo "Perl test1.pl:"; time ./test1.pl

Replies are listed 'Best First'.
Re: Perl PDL slower than python numpy (Updated2)
by vr (Curate) on Sep 20, 2020 at 19:49 UTC

    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 - http://strawberryperl.com + http://pdl.perl.org * to launch perl script run: perl c:\my\scripts\pdl-test.pl * 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-5.30.1.1-64bit-PDL\perl\ +bin\perl.exe Perl version : 5.30.1 / MSWin32-x64-multi-thread PDL version : 2.019 C:\berrybrew\strawberry-perl-5.30.1.1-64bit-PDL>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-5.30.1.1-64bit-PDL/perl/vendor/lib/ +Term/ReadLine/readline.pm line 410. load_rcfile: got $HOME = C:\berrybrew\strawberry-perl-5.30.1.1-64bit-P +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>
      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
      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.)

      Cheers,
      Rob
      I have checked the document of numpy , the default type is float64
      However, the thread should be close. I have compared as again, the numpy is better than PDL on large size of vectors. thanks! fan
Re: Perl PDL slower than python numpy
by swl (Priest) on Sep 22, 2020 at 22:19 UTC

    Three points.

    1.

    It would be interesting to see some profiling results showing where the time is spent. For perl you can use Devel::NYTProf. I'm not sure about python.

    I've profiled code with PDL in the past, and if there are many piddles being generated then the generation is a hotspot. Your profiling code regenerates the piddle each time.

    This might also be relevant here: https://sourceforge.net/p/pdl/mailman/message/35067272.

    2.

    Your code also includes the startup times, and PDL is a pretty heavy package that pulls in many dependencies. PDL::Lite is useful in such cases.

    That said, the cross-posted question on the pdl-general mailing list has updated numbers in the thread: https://sourceforge.net/p/pdl/mailman/message/37112311. numpy is faster than PDL, but not by double. (Cross-posting is OK, but it helps if it is noted in any posts).

    3.

    A last observation is that you appear to be running your code in a virtual machine. Does that have any effect on relative speed?

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