The Computer Language
Benchmarks Game

regex-redux Chapel #3 program

source code

/* The Computer Language Benchmarks Game
   https://salsa.debian.org/benchmarksgame-team/benchmarksgame/

   contributed by Engin Kayraklioglu
   derived from the converted regex-dna Chapel version by Ben Harshbarger
   which was derived from the GNU C++ RE2 version by Alexey Zolotov
*/

use IO, Regexp;

proc main(args: [] string) {
  var variants = [
    b"agggtaaa|tttaccct",
    b"[cgt]gggtaaa|tttaccc[acg]",
    b"a[act]ggtaaa|tttacc[agt]t",
    b"ag[act]gtaaa|tttac[agt]ct",
    b"agg[act]taaa|ttta[agt]cct",
    b"aggg[acg]aaa|ttt[cgt]ccct",
    b"agggt[cgt]aa|tt[acg]accct",
    b"agggta[cgt]a|t[acg]taccct",
    b"agggtaa[cgt]|[acg]ttaccct"
  ];

  var subst = [
    (b"tHa[Nt]", b"<4>"), (b"aND|caN|Ha[DS]|WaS", b"<3>"),
    (b"a[NSt]|BY", b"<2>"), (b"<[^>]*>", b"|"), (b"\\|[^|][^|]*\\|", b"-")
  ];

  var data: bytes;
  stdin.readbytes(data); // read in the entire file
  const initLen = data.size;

  // remove newlines
  data = compile(b">.*\n|\n").sub(b"", data);

  var copy = data; // make a copy so we can perform replacements in parallel

  var results: [variants.domain] int;

  sync {
    // fire off a task to perform replacements
    begin with (ref copy) {
      for (f, r) in subst do
        copy = compile(f).sub(r, copy);
    }

    // count patterns
    forall (pattern, result) in zip(variants, results) do
      for m in compile(pattern).matches(data) do
        result += 1;
  }

  // print results
  for (p,r) in zip(variants, results) do
    writeln(p, " ", r);
  writeln();

  writeln(initLen);
  writeln(data.size);
  writeln(copy.size);
}
    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
chpl version 1.23.0
Copyright 2020 Hewlett Packard Enterprise Development LP
Copyright (c) 2004-2019, Cray Inc.


Fri, 23 Oct 2020 23:08:54 GMT

MAKE:
mv regexredux.chapel-3.chapel regexredux.chapel-3.chpl
/opt/src/chapel-1.23.0/bin/linux64-x86_64/chpl --target-cpu=ivybridge --fast regexredux.chapel-3.chpl -o regexredux.chapel-3.chapel_run
rm regexredux.chapel-3.chpl

16.47s to complete and log all make actions

COMMAND LINE:
./regexredux.chapel-3.chapel_run --n=0 < regexredux-input5000000.txt

PROGRAM OUTPUT:
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
27388361