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Re^4: Fast common substring matching

by marioroy (Vicar)
on Feb 17, 2016 at 06:39 UTC ( #1155429=note: print w/replies, xml ) Need Help??


in reply to Re^3: Fast common substring matching
in thread Fast common substring matching

Greetings Roy Johnson,

I learn more Perl from reading your code. It took me a while, but somehow overlooked the line sorting $strings before walking through the list.

Today, came to realization that Perl can do bitwise operations on strings.

my ($common) = map length, ($strings[$i1][0] ^ $strings[$i2][0]) =~ /^ +(\0*)/;

Thank you for this.

Replies are listed 'Best First'.
Re^5: Fast common substring matching
by marioroy (Vicar) on Feb 17, 2016 at 07:36 UTC

    Update: Added options chunk_size and bounds_only to MCE::Shared::Sequence in trunk, similar to MCE options. This allows MCE::Hobo workers to run as fast as MCE workers. Also, corrected the demonstration. Seeing this run faster than serial code made my day.

    I had to try something with the upcoming MCE 1.7 release. Parallelism may be beneficial for big sequences. MCE 1.7 will ship with MCE::Hobo, a threads-like module for processes. Thus, benefiting from Copy-on-Write feature of modern OS'es. In essence, the @strings array is not copied per each worker unless written to by the worker.

    Using Roy Johnson's demonstration, made the following changes to enable parallelism via MCE::Hobo workers. This requires MCE in trunk or a later dev 1.699_011 release.

    ... print "Sorted. Finding matches...\n"; # Now walk through the list. The best match for each string will be th +e # previous or next element in the list that is not from the original s +ubstring, # so for each entry, just look for the next one. See how many initial +letters # match and track the best matches # # my @matchdata = (0); # (length, index1-into-strings, index2-into-str +ings) # for my $i1 (0..($#strings - 1)) { # my $i2 = $i1 + 1; # ++$i2 while $i2 <= $#strings and $strings[$i2][1] eq $strings[$i1] +[1]; # next if $i2 > $#strings; # my ($common) = map length, ($strings[$i1][0] ^ $strings[$i2][0]) = +~ /^(\0*)/; # if ($common > $matchdata[0]) { # @matchdata = ($common, [$i1, $i2]); # } # elsif ($common == $matchdata[0]) { # push @matchdata, [$i1, $i2]; # } # } use MCE::Hobo; use MCE::Shared; my $sequence = MCE::Shared->sequence( { chunk_size => 500, bounds_only => 1 }, 0, $#strings - 1 ); sub walk_list { my @matchdata = (0); # (length, index1-into-strings, index2-into-str +ings) while ( my ( $beg, $end ) = $sequence->next ) { for my $i1 ( $beg .. $end ) { my $i2 = $i1 + 1; ++$i2 while $i2 <= $#strings and $strings[$i2][1] eq $strings[$i +1][1]; next if $i2 > $#strings; my ($common) = map length, ($strings[$i1][0] ^ $strings[$i2][0]) + =~ /^(\0*)/; if ($common > $matchdata[0]) { @matchdata = ($common, [$i1, $i2]); } elsif ($common == $matchdata[0]) { push @matchdata, [$i1, $i2]; } } } return @matchdata; }; MCE::Hobo->create( \&walk_list ) for 1 .. 8; my @matchdata = (0); # (length, index1-into-strings, index2-into-strin +gs) for my $hobo ( MCE::Hobo->list ) { my @ret = $hobo->join; if ( $ret[0] > $matchdata[0] ) { @matchdata = @ret; } elsif ( $ret[0] == $matchdata[0] ) { shift @ret; push @matchdata, @ret; } } print "Best match: $matchdata[0] chars\n"; ...

    MCE 1.7 is nearly completed in trunk. The MCE::Shared::Sequence module is helpful. I will try to finish MCE 1.7 by the end of the month.

    Regards, Mario

Re^5: Fast common substring matching
by marioroy (Vicar) on Feb 17, 2016 at 08:34 UTC

    Update: The update to MCE::Shared::Sequence in trunk allows MCE::Hobo workers to run as fast as MCE workers. Thank you for this. The MCE::Hobo demonstration made me realized the need to beef up MCE::Shared::Sequence with chunk_size and bounds_only options similar to MCE options.

    Using Roy Johnson's demonstration, made the following changes to enable parallelism via MCE::Loop.

    ... print "Sorted. Finding matches...\n"; use MCE::Loop; MCE::Loop::init( max_workers => 8, chunk_size => 500, bounds_only => 1, ); my @ret = mce_loop_s { my ( $mce, $seq, $chunk_id ) = @_; my @matchdata = (0); # (length, index1-into-strings, index2-into-str +ings) for my $i1 ( $seq->[0] .. $seq->[1] ) { my $i2 = $i1 + 1; ++$i2 while $i2 <= $#strings and $strings[$i2][1] eq $strings[$i1] +[1]; next if $i2 > $#strings; my ($common) = map length, ($strings[$i1][0] ^ $strings[$i2][0]) = +~ /^(\0*)/; if ($common > $matchdata[0]) { @matchdata = ($common, [$i1, $i2]); } elsif ($common == $matchdata[0]) { push @matchdata, [$i1, $i2]; } } MCE->gather( \@matchdata ); } 0, $#strings - 1; my @matchdata = (0); # (length, index1-into-strings, index2-into-strin +gs) for my $i ( 0 .. $#ret ) { if ( $ret[$i]->[0] > $matchdata[0] ) { @matchdata = @{ $ret[$i] }; } elsif ( $ret[$i]->[0] == $matchdata[0] ) { shift @{ $ret[$i] }; push @matchdata, @{ $ret[$i] }; } } print "Best match: $matchdata[0] chars\n"; ...

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