parallel/src/parsort

#!/usr/bin/perl

# SPDX-FileCopyrightText: 2021-2022 Ole Tange, http://ole.tange.dk and Free Software and Foundation, Inc.
# SPDX-License-Identifier: GPL-3.0-or-later

=pod

=head1 NAME

parsort - Sort (big files) in parallel


=head1 SYNOPSIS

B<parsort> I<options for sort>


=head1 DESCRIPTION

B<parsort> uses GNU B<sort> to sort in parallel. It works just like
B<sort> but faster on inputs with more than 1 M lines, if you have a
multicore machine.

Hopefully these ideas will make it into GNU B<sort> in the future.


=head1 EXAMPLE

Sort files:

  parsort *.txt > sorted.txt

Sort stdin (standard input) numerically:

  cat numbers | parsort -n > sorted.txt


=head1 PERFORMANCE

B<parsort> is faster on a file than on stdin (standard input), because
different parts of a file can be read in parallel.

On a 48 core machine you should see a speedup of 3x over B<sort>.


=head1 AUTHOR

Copyright (C) 2020-2022 Ole Tange,
http://ole.tange.dk and Free Software Foundation, Inc.


=head1 LICENSE

Copyright (C) 2012 Free Software Foundation, Inc.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
at your option any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.


=head1 DEPENDENCIES

B<parsort> uses B<sort>, B<bash>, and B<parallel>.


=head1 SEE ALSO

B<sort>


=cut

use strict;
use Getopt::Long;
use POSIX qw(mkfifo);

Getopt::Long::Configure("bundling","require_order");

my @ARGV_before = @ARGV;

GetOptions(
    "debug|D" => \$opt::D,
    "version" => \$opt::version,
    "verbose|v" => \$opt::verbose,
    "b|ignore-leading-blanks" => \$opt::ignore_leading_blanks,
    "d|dictionary-order" => \$opt::dictionary_order,
    "f|ignore-case" => \$opt::ignore_case,
    "g|general-numeric-sort" => \$opt::general_numeric_sort,
    "i|ignore-nonprinting" => \$opt::ignore_nonprinting,
    "M|month-sort" => \$opt::month_sort,
    "h|human-numeric-sort" => \$opt::human_numeric_sort,
    "n|numeric-sort" => \$opt::numeric_sort,
    "N|numascii" => \$opt::numascii,
    "r|reverse" => \$opt::reverse,
    "R|random-sort" => \$opt::random_sort,
    "sort=s" => \$opt::sort,
    "V|version-sort" => \$opt::version_sort,
    "k|key=s" => \@opt::key,
    "t|field-separator=s" => \$opt::field_separator,
    "z|zero-terminated" => \$opt::zero_terminated,
    "files0-from=s" => \$opt::files0_from,
    "random-source=s" => \$opt::dummy,
    "batch-size=s" => \$opt::dummy,
    "check=s" => \$opt::dummy,
    "c" => \$opt::dummy,
    "C" => \$opt::dummy,
    "compress-program=s" => \$opt::dummy,
    "T|temporary-directory=s" => \$opt::dummy,
    "parallel=s" => \$opt::dummy,
    "u|unique" => \$opt::dummy,
    "S|buffer-size=s" => \$opt::dummy,
    "s|stable" => \$opt::dummy,
    "help" => \$opt::dummy,
    ) || exit(255);
$Global::progname = ($0 =~ m:(^|/)([^/]+)$:)[1];
$Global::version = 20220722;
if($opt::version) { version(); exit 0; }
@Global::sortoptions = grep { ! /^-D$/ }
    shell_quote(@ARGV_before[0..($#ARGV_before-$#ARGV-1)]);

$ENV{'TMPDIR'} ||= "/tmp";

sub merge {
    # Input:
    #   @cmd = commands to 'cat' (part of) a file
    # 'cat a' 'cat b' 'cat c' =>
    # sort -m <(sort -m <(cat a) <(cat b)) <(sort -m <(cat c))
    my @cmd = @_;
    chomp(@cmd);
    while($#cmd > 0) {
	my @tmp;
	while($#cmd >= 0) {
	    my $a = shift @cmd;
	    my $b = shift @cmd;
	    $a &&= "<($a)";
	    $b &&= "<($b)";
	    # This looks like useless use of 'cat', but contrary to
	    # naive belief it increases performance dramatically.
	    push @tmp, "sort -m @Global::sortoptions $a $b | cat"
	}
	@cmd = @tmp;
    }
    return @cmd;
}

sub sort_files {
    # Input is files
    my @files = @_;
    # Let GNU Parallel generate the commands to read parts of files
    # The commands split at \n (or \0)
    # and there will be at least one for each CPU thread
    my @subopt = $opt::zero_terminated ? qw(--recend "\0") : ();
    open(my $par,"-|",qw(parallel), @subopt,
	 qw(--pipepart --block -1 --dryrun -vv sort),
	 @Global::sortoptions, '::::', @files) || die;
    my @cmd = merge(<$par>);
    close $par;
    debug(@cmd);
    # The command uses <(...) so it is incompatible with /bin/sh
    open(my $bash,"|-","bash") || die;
    print $bash @cmd;
    close $bash;
}

sub sort_stdin {
    # Input is stdin
    # Spread the input between n processes that each sort
    # n = number of CPU threads
    my $numthreads = `parallel --number-of-threads`;
    my @fifos = map { tmpfifo() } 1..$numthreads;
    map { mkfifo($_,0600) } @fifos;
    # This trick removes the fifo as soon as it is connected in the other end
    # (rm fifo; ...) < fifo 
    my @cmd = (map { "(rm $_; sort @Global::sortoptions) < $_" }
	       map { Q($_) } @fifos);
    @cmd = merge(@cmd);
    if(fork) {
    } else {
	my @subopt = $opt::zero_terminated ? qw(--recend "\0") : ();
	exec(qw(parallel -j), $numthreads, @subopt,
	     # 286k is the best mean value after testing 250..350
	     qw(--block 286k --pipe --roundrobin cat > {} :::),@fifos);
    }
    # The command uses <(...) so it is incompatible with /bin/sh
    open(my $bash,"|-","bash") || die;
    print $bash @cmd;
    close $bash;   
}

sub tmpname {
    # Select a name that does not exist
    # Do not create the file as it may be used for creating a socket (by tmux)
    # Remember the name in $Global::unlink to avoid hitting the same name twice
    my $name = shift;
    my($tmpname);
    if(not -w $ENV{'TMPDIR'}) {
	if(not -e $ENV{'TMPDIR'}) {
	    ::error("Tmpdir '$ENV{'TMPDIR'}' does not exist.","Try 'mkdir ".
		    Q($ENV{'TMPDIR'})."'");
	} else {
	    ::error("Tmpdir '$ENV{'TMPDIR'}' is not writable.","Try 'chmod +w ".
		    Q($ENV{'TMPDIR'})."'");
	}
	exit(255);
    }
    do {
	$tmpname = $ENV{'TMPDIR'}."/".$name.
	    join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
    } while(-e $tmpname);
    return $tmpname;
}

sub tmpfifo {
    # Find an unused name and mkfifo on it
    my $tmpfifo = tmpname("psort");
    mkfifo($tmpfifo,0600);
    return $tmpfifo;
}

sub debug {
    # Returns: N/A
    $opt::D or return;
    @_ = grep { defined $_ ? $_ : "" } @_;
    print STDERR @_[1..$#_];
}

sub version() {
    # Returns: N/A
    print join
	("\n",
	 "GNU $Global::progname $Global::version",
	 "Copyright (C) 2020-2022 Ole Tange, http://ole.tange.dk and Free Software",
	 "Foundation, Inc.",
	 "License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>",
	 "This is free software: you are free to change and redistribute it.",
	 "GNU $Global::progname comes with no warranty.",
	 "",
	 "Web site: https://www.gnu.org/software/parallel\n",
        );
}

sub shell_quote(@) {
    # Input:
    #   @strings = strings to be quoted
    # Returns:
    #   @shell_quoted_strings = string quoted as needed by the shell
    return wantarray ? (map { Q($_) } @_) : (join" ",map { Q($_) } @_);
}

sub shell_quote_scalar_rc($) {
    # Quote for the rc-shell
    my $a = $_[0];
    if(defined $a) {
	if(($a =~ s/'/''/g)
	   +
	   ($a =~ s/[\n\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]+/'$&'/go)) {
	    # A string was replaced
	    # No need to test for "" or \0
	} elsif($a eq "") {
	    $a = "''";
	} elsif($a eq "\0") {
	    $a = "";
	}
    }
    return $a;
}

sub shell_quote_scalar_csh($) {
    # Quote for (t)csh
    my $a = $_[0];
    if(defined $a) {
	# $a =~ s/([\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\>\<\~\|\; \"\!\$\&\'\202-\377])/\\$1/g;
	# This is 1% faster than the above
	if(($a =~ s/[\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]/\\$&/go)
	   +
	   # quote newline in csh as \\\n
	   ($a =~ s/[\n]/"\\\n"/go)) {
	    # A string was replaced
	    # No need to test for "" or \0
	} elsif($a eq "") {
	    $a = "''";
	} elsif($a eq "\0") {
	    $a = "";
	}
    }
    return $a;
}

sub shell_quote_scalar_default($) {
    # Quote for other shells (Bourne compatibles)
    # Inputs:
    #   $string = string to be quoted
    # Returns:
    #   $shell_quoted = string quoted as needed by the shell
    my $s = $_[0];
    if($s =~ /[^-_.+a-z0-9\/]/i) {
	$s =~ s/'/'"'"'/g; # "-quote single quotes
	$s = "'$s'";       # '-quote entire string
	$s =~ s/^''//;     # Remove unneeded '' at ends
	$s =~ s/''$//;     # (faster than s/^''|''$//g)
	return $s;
    } elsif ($s eq "") {
	return "''";
    } else {
	# No quoting needed
	return $s;
    }
}

sub shell_quote_scalar($) {
    # Quote the string so the shell will not expand any special chars
    # Inputs:
    #   $string = string to be quoted
    # Returns:
    #   $shell_quoted = string quoted as needed by the shell

    # Speed optimization: Choose the correct shell_quote_scalar_*
    # and call that directly from now on
    no warnings 'redefine';
    if($Global::cshell) {
	# (t)csh
	*shell_quote_scalar = \&shell_quote_scalar_csh;
    } elsif($Global::shell =~ m:(^|/)rc$:) {
	# rc-shell
	*shell_quote_scalar = \&shell_quote_scalar_rc;
    } else {
	# other shells
	*shell_quote_scalar = \&shell_quote_scalar_default;
    }
    # The sub is now redefined. Call it
    return shell_quote_scalar($_[0]);
}

sub Q($) {
    # Q alias for ::shell_quote_scalar
    my $ret = shell_quote_scalar($_[0]);
    no warnings 'redefine';
    *Q = \&::shell_quote_scalar;
    return $ret;
}


sub status(@) {
    my @w = @_;
    my $fh = $Global::status_fd || *STDERR;
    print $fh map { ($_, "\n") } @w;
    flush $fh;
}

sub status_no_nl(@) {
    my @w = @_;
    my $fh = $Global::status_fd || *STDERR;
    print $fh @w;
    flush $fh;
}

sub warning(@) {
    my @w = @_;
    my $prog = $Global::progname || "parsort";
    status_no_nl(map { ($prog, ": Warning: ", $_, "\n"); } @w);
}

{
    my %warnings;
    sub warning_once(@) {
	my @w = @_;
	my $prog = $Global::progname || "parsort";
	$warnings{@w}++ or
	    status_no_nl(map { ($prog, ": Warning: ", $_, "\n"); } @w);
    }
}

sub error(@) {
    my @w = @_;
    my $prog = $Global::progname || "parsort";
    status(map { ($prog.": Error: ". $_); } @w);
}

sub die_bug($) {
    my $bugid = shift;
    print STDERR
	("$Global::progname: This should not happen. You have found a bug. ",
	 "Please follow\n",
	 "https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS\n",
	 "\n",
	 "Include this in the report:\n",
	 "* The version number: $Global::version\n",
	 "* The bugid: $bugid\n",
	 "* The command line being run\n",
	 "* The files being read (put the files on a webserver if they are big)\n",
	 "\n",
	 "If you get the error on smaller/fewer files, please include those instead.\n");
    exit(255);
}

sub version() {
    # Returns: N/A
    print join
	("\n",
	 "GNU $Global::progname $Global::version",
	 "Copyright (C) 2007-2022 Ole Tange, http://ole.tange.dk and Free Software",
	 "Foundation, Inc.",
	 "License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>",
	 "This is free software: you are free to change and redistribute it.",
	 "GNU $Global::progname comes with no warranty.",
	 "",
	 "Web site: https://www.gnu.org/software/${Global::progname}\n",
	 "When using programs that use GNU Parallel to process data for publication",
	 "please cite as described in 'parallel --citation'.\n",
        );
}

if(@ARGV) {
    sort_files(@ARGV);
} elsif(length $opt::files0_from) {
    $/="\0";
    open(my $fh,"<",$opt::files0_from) || die;
    my @files = <$fh>;
    chomp(@files);
    sort_files(@files);
} else {
    sort_stdin();
}

# Test
# -z
# OK: cat bigfile | parsort
# OK: parsort -k4n files*.txt
# OK: parsort files*.txt
# OK: parsort "file with space"