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Re: Suffix-prefix matching done right

by NERDVANA (Friar)
on Nov 05, 2021 at 11:18 UTC ( #11138458=note: print w/replies, xml ) Need Help??


in reply to Suffix-prefix matching done right

Find an algorithm you like for comparing edit-distance of two strings, and then just loop until it crosses a threshold or you run out of string.

use Text::WagnerFischer "distance"; use List::Util 'min'; my $a="abbaba"; my $b="ababbba"; my $limit= 3; my $n= 0; my $max= min(length $a, length $b); ++$n while $n < $max && distance(substr($a,-$n-1), substr($b,0,$n+1)) < $limit; if ($n) { printf "'%s' matches '%s' with edit distance %d", substr($a,-$n), substr($b,0,$n), distance(substr($a,-$n), substr($b,0,$n)) }

To parallelize for extremely long matches, you could have N threads step $n += N.

Edit: sorry, I skimmed the second half of your question. For batches of 10 million pairs of smallish strings, I think you want to use C or C++. If you have a need to integrate it with Perl code, you can use Inline::C, or just IPC::Run to run a pool of C++ workers which you could then pipe data into and collect the responses. Note that edit distances are a harder problem than your example code can solve, since sometimes having solved it for N characters, adding 1 character could have an optimal edit distance by a completely different set of changes to the string. But, Wagner-Fischer is O(N^2) each time you run it, so maybe you can look for a new variation that calculates "sideways" for each new character rather than starting from scratch each time.

Edit Again: as anonymous points out, a better edit distance might come after a worse edit distance, so actually you would need to iterate over the whole range of substrings.

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Re^2: Suffix-prefix matching done right
by vr (Curate) on Nov 05, 2021 at 12:18 UTC
    then just loop until it crosses a threshold

    then with A,B,X of OP's example, the correct result will be missed

      Ah, True. In a different example, "abcdef" and "abcdef" would iteratively have an edit distance of 1, 2, 3, 4, 2, and then suddenly 0. So you would need to check all lengths.
Re^2: Suffix-prefix matching done right
by karlgoethebier (Abbot) on Nov 05, 2021 at 18:16 UTC
    «…or just IPC::Run to run a pool of C++ workers…»

    I just wondered how this code would look. Or how you would do it - as you like. Regards, Karl

    «The Crux of the Biscuit is the Apostrophe»

      I was expecting IPC::Run to be the simplest way to orchestrate a pool of non-perl workers that stream text, but it might not actually be any less effort than than MCE; this bit of code took longer to write than I expected. It reads STDIN in large chunks, and hands off those chunks to the input queues of the worker with the least in its input queue. It also takes care to divide the input on line boundaries so that it isn't splitting a line between different workers. But, it should be much more efficient than the simpler design of reading STDIN one line at a time.

      I tested it with "wc" as a simple way to verify that all input lines were seen by a worker.

      $ time perl parallel.pl wc < LARGE_FILE (snip)... Waiting for workers to finish 955 5389459 56444912 252 6883234 68045448 284 3803959 62591850 422 6429932 63866545 real 0m1.438s user 0m3.864s sys 0m0.242s $ time wc < LARGE_FILE 1913 22506581 250948755 real 0m2.332s user 0m2.277s sys 0m0.052s

      parallel.pl

      use v5.20; use strict; use warnings; use IPC::Run 'start'; use List::Util qw/ all any reduce /; my $workers= 4; my $read_size= 512*1024; my $queue_full= 256*1024; my $command= [@ARGV]; # Start a pool of 10 workers my @jobs= map { { id => $_, in => '', out => '' } } 1..$workers; my @run_spec= map { ('&', $command, '<', \$_->{in}, '>', \$_->{out}) } + @jobs; shift @run_spec; my $harness= start(@run_spec); my $buf= ''; my $got= 1; while ($got) { # The reading of input could just use $buf .= <STDIN> but this is +much more efficient, # reading 1MB at a time. $got= read(STDIN, $buf, $read_size, length $buf); if ($got) { # look for the final newline within the buffer. This makes su +re we only pass whole # lines to the workers my $end= rindex $buf, '\n'; next unless $end >= 0; # append the lines to the input queue of the worker with the s +mallest input queue $jobs[0]{in} .= substr($buf, 0, $end+1, ''); say "Add ".($end+1)." bytes to job $jobs[0]{id}"; } elsif (!defined $got) { next if $!{EINTR} || $!{EAGAIN}; die "read: $!"; } # No more STDIN, so take any leftover string and add it to an inpu +t buffer elsif (length $buf) { $jobs[0]{in} .= $buf; say "Add ".length($buf)." bytes to job $jobs[0]{id}"; } # stay in this loop until there is room on one of the input buffer +s, # or after EOF, stay here until all input buffers are flushed while ($got? (all { length $_->{in} > $queue_full } @jobs) : (any { length $_->{in} > 0 } @jobs) ) { # say "I/O: ".join(' ', map sprintf("[%8d:%8d]", length $_->{ +in}, length $_->{out}), @jobs); # send input, receive output $harness->pump; # process all output from jobs so far process_results(); } # sort the worker with the smallest input queue to the front @jobs= sort { length $a->{in} <=> length $b->{in} } @jobs; } say "Waiting for workers to finish"; # Close the input pipes and wait for workers to exit $_->{in}= undef for @jobs; $harness->finish; # process all the rest process_results(); sub process_results { for (@jobs) { my $end= rindex $_->{out}, "\n"; print substr($_->{out}, 0, $end+1, '') if $end >= 0; } }
        I seriously doubt parallelization is the solution here.

        Reading the data from disk will take far more time than processing the data with a clever algorithm.

        Cheers Rolf
        (addicted to the Perl Programming Language :)
        Wikisyntax for the Monastery

        Dear friends of the monastery,

        Upon searching, there lives a MCE wc.pl example. Please note that timings for wc.pl include the time to load Perl itself plus modules and spawn/reap workers.

        Preparation:

        $ curl -O http://www.textfiles.com/etext/FICTION/lesms10.txt $ curl -O https://raw.githubusercontent.com/marioroy/mce-examples/mast +er/other/wc.pl $ chmod 755 wc.pl $ rm -f lesms10_big.txt $ for i in `seq 1 200`; do cat lesms10.txt >> lesms10_big.txt; done $ ls -lh lesms10* -rw-r--r-- 1 pmuser staff 3.1M Nov 13 19:27 lesms10.txt -rw-r--r-- 1 pmuser staff 623M Nov 13 19:39 lesms10_big.txt # Read once before testing to be fair for 1st and subsequent wc/wc.pl. # Sorry, I didn't want to go through the trouble clearing OS cache. $ cat lesms10_big.txt >/dev/null

        Results: wc

        $ time wc lesms10_big.txt 14152200 113528600 652751200 lesms10_big.txt real 0m2.132s user 0m2.076s sys 0m0.056s $ time wc < lesms10_big.txt 14152200 113528600 652751200 real 0m2.140s user 0m2.085s sys 0m0.055s

        Results: wc.pl

        $ time ./wc.pl lesms10_big.txt 14152200 113528600 652751200 lesms10_big.txt real 0m0.536s (3.98x) user 0m3.570s sys 0m0.591s $ time ./wc.pl < lesms10_big.txt 14152200 113528600 652751200 real 0m0.740s (2.89x) user 0m3.784s sys 0m1.166s

        Results: line count

        $ time wc -l lesms10_big.txt 14152200 lesms10_big.txt real 0m0.351s user 0m0.296s sys 0m0.055s $ time ./wc.pl -l lesms10_big.txt 14152200 lesms10_big.txt real 0m0.208s user 0m0.678s sys 0m0.835s

        Results: word count

        $ time wc -w lesms10_big.txt 113528600 lesms10_big.txt real 0m2.125s user 0m2.071s sys 0m0.054s $ time ./wc.pl -w lesms10_big.txt 113528600 lesms10_big.txt real 0m0.535s user 0m3.574s sys 0m0.599s

        Results: byte count

        $ time wc -c lesms10_big.txt 652751200 lesms10_big.txt real 0m0.003s user 0m0.001s sys 0m0.002s $ time ./wc.pl -c lesms10_big.txt 652751200 lesms10_big.txt real 0m0.054s user 0m0.042s sys 0m0.010s

        Clearing OS cache:

        The beliefs of yesterday may no longer be true today. These days, running on one core may be the bottleneck versus IO. Especially for hardware IO reaching gigabytes and beyond. Long ago, I removed old beliefs no longer matching with reality. This mind shift energized me to try, only to be surprised. So kudos to the OP for trying.

        Linux: sudo echo 1 >/proc/sys/vm/drop_caches macOS: sudo purge $ time wc lesms10_big.txt 14152200 113528600 652751200 lesms10_big.txt real 0m2.435s user 0m2.330s sys 0m0.098s Linux: sudo echo 1 >/proc/sys/vm/drop_caches macOS: sudo purge $ time ./wc.pl lesms10_big.txt 14152200 113528600 652751200 lesms10_big.txt real 0m0.662s (3.68x) user 0m3.598s sys 0m0.736s

        Bless to you all,

        Thank you very much and best regards, Karl

        «The Crux of the Biscuit is the Apostrophe»

      Searching through MCE repo, I found mce_grep which ships with MCE. It depends on the OS vender including it or a separate package. The script calls an external binary, grep in this case. One can rename the file, copy, or make a symbolic link to the script itself to have it called another external binary.

      It borrows bits from IPC::Run3 for capturing STDOUT/ERR on Unix platforms, but an attempt for lesser overhead it seems. See here. So this looks to be a full-fledged demonstration for doing just that; IPC::Run-like capability to run a pool of C/C++ workers. It exists :).

      See also: The pure-Perl grep-like implementation is found in the mce-examples repo named egrep.pl.

      Digging more, there lives another full-fledged demonstration calling Inline::C and an external C++ binary. This lives in the mce-sort repo. The Inline::C bits and corresponding user function partitions the data. Sorting the individual partitions in parallel (via an external C++ binary) is done here.

        «…It exists…»

        Big surprise? That’s the way it is 🤪😎. Best regards, Karl

        «The Crux of the Biscuit is the Apostrophe»

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