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Re^4: list of unique strings, also eliminating matching substrings

by lindsay_grey (Novice)
on May 29, 2011 at 22:43 UTC ( #907247=note: print w/replies, xml ) Need Help??


in reply to Re^3: list of unique strings, also eliminating matching substrings
in thread list of unique strings, also eliminating matching substrings

7 hours! for about 200,000 starting strings.

  • Comment on Re^4: list of unique strings, also eliminating matching substrings

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Re^5: list of unique strings, also eliminating matching substrings
by BrowserUk (Pope) on May 30, 2011 at 00:18 UTC

    Try this on that same dataset and let me know how you get on. On my generated test data it takes ~30 minutes for 200,000 strings, but how realistic that dataset is ...

    Use thisScript.pl inFile > outFile:

    #! perl -slw use strict; use Inline C => Config => BUILD_NOISY => 1; use Inline C => <<'END_C', NAME => '_906020', CLEAN_AFTER_BUILD => 0; #include <string.h> int longCmp( SV *needle, SV *haystack, SV *offset ) { STRLEN ln, lh, o = SvIV( offset ); char *n = SvPV( needle, ln ), *h = SvPV( haystack, lh ); char *nl = n + ln - 1; int diff = lh - ln; int flag = 0, i; h += o; lh -= o; diff -= o; if( diff <= 0 ) return 0; for( i = 0; i < diff; ++i ) { if( ! h[ i + ln - 1 ] ) { i += ln; continue; } if( h[ i ] != *n || h[ i+ ln-1 ] != *nl ) continue; if( strncmp( h+i, n, ln ) ) continue; return i; } return 0; } END_C use Time::HiRes qw[ time ]; sub uniq{ my %x; @x{@_} = (); keys %x } my $start = time; my @uniq = uniq <>; chomp @uniq; @uniq = sort{ length $a <=> length $b } @uniq; my $all = join chr(0), @uniq; my $p = 0; for my $x ( @uniq ) { $p += 1+ length $x; next if longCmp( $x, $all, $p ); print $x; } printf STDERR "Took %.3f\n", time() - $start; __END__

    Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
    "Science is about questioning the status quo. Questioning authority".
    In the absence of evidence, opinion is indistinguishable from prejudice.

      I seem to be having a problem with Inline. Maybe I just need to get one of the "apple-darwin" files it is looking for. I will keep trying. Thanks for posting your code.

      Starting "make" Stage i686-apple-darwin10-gcc-4.2.1: Module: No such file or directory i686-apple-darwin10-gcc-4.2.1: no input files i686-apple-darwin10-gcc-4.2.1: Module: No such file or directory i686-apple-darwin10-gcc-4.2.1: no input files powerpc-apple-darwin10-gcc-4.2.1: Module: No such file or directory powerpc-apple-darwin10-gcc-4.2.1: no input files lipo: can't figure out the architecture type of: /var/folders/Jx/Jx+cO +TNTFTSKERHsDjE+nU+++TI/-Tmp-//cch73GJV.out make: *** [_906020.o] Error 1 A problem was encountered while attempting to compile and install your + Inline C code. The command that failed was: make

        That looks like you do not have Inline::C installed correctly, but I can't help you with that. If it is the case...ie. if the Inline::C installation tests are failing, then you shoudl post a new thread about that to get help.

        In the interim, you can try this pure perl version which is only half as fast as the inline version, but that should still be 7 times faster than your current solution. Let me know how you get on.

        #! perl -slw use strict; use Time::HiRes qw[ time ]; $|++; sub uniq{ my %x; @x{@_} = (); keys %x } my $start = time; my @uniq = uniq <>; chomp @uniq; @uniq = sort{ length $a <=> length $b } @uniq; my $all = join chr(0), @uniq; my $p = 0; for my $x ( @uniq ) { $p += 1+ length $x; next if 1+ index $all, $x, $p; ## COrrected per LanX below. print $x; } printf STDERR "Took %.3f\n", time() - $start;

        Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
        "Science is about questioning the status quo. Questioning authority".
        In the absence of evidence, opinion is indistinguishable from prejudice.

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