mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-12-22 20:57:53 +00:00
436 lines
12 KiB
Perl
Executable file
436 lines
12 KiB
Perl
Executable file
#!/usr/bin/perl
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# SPDX-FileCopyrightText: 2021-2022 Ole Tange, http://ole.tange.dk and Free Software and Foundation, Inc.
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# SPDX-License-Identifier: GPL-3.0-or-later
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=pod
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=head1 NAME
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parsort - Sort (big files) in parallel
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=head1 SYNOPSIS
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B<parsort> I<options for sort>
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=head1 DESCRIPTION
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B<parsort> uses GNU B<sort> to sort in parallel. It works just like
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B<sort> but faster on inputs with more than 1 M lines, if you have a
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multicore machine.
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Hopefully these ideas will make it into GNU B<sort> in the future.
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=head1 EXAMPLE
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Sort files:
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parsort *.txt > sorted.txt
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Sort stdin (standard input) numerically:
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cat numbers | parsort -n > sorted.txt
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=head1 PERFORMANCE
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B<parsort> is faster on a file than on stdin (standard input), because
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different parts of a file can be read in parallel.
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On a 48 core machine you should see a speedup of 3x over B<sort>.
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=head1 AUTHOR
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Copyright (C) 2020-2022 Ole Tange,
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http://ole.tange.dk and Free Software Foundation, Inc.
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=head1 LICENSE
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Copyright (C) 2012 Free Software Foundation, Inc.
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 3 of the License, or
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at your option any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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=head1 DEPENDENCIES
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B<parsort> uses B<sort>, B<bash>, and B<parallel>.
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=head1 SEE ALSO
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B<sort>
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=cut
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use strict;
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use Getopt::Long;
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use POSIX qw(mkfifo);
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Getopt::Long::Configure("bundling","require_order");
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my @ARGV_before = @ARGV;
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GetOptions(
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"debug|D" => \$opt::D,
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"version" => \$opt::version,
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"verbose|v" => \$opt::verbose,
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"b|ignore-leading-blanks" => \$opt::ignore_leading_blanks,
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"d|dictionary-order" => \$opt::dictionary_order,
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"f|ignore-case" => \$opt::ignore_case,
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"g|general-numeric-sort" => \$opt::general_numeric_sort,
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"i|ignore-nonprinting" => \$opt::ignore_nonprinting,
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"M|month-sort" => \$opt::month_sort,
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"h|human-numeric-sort" => \$opt::human_numeric_sort,
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"n|numeric-sort" => \$opt::numeric_sort,
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"N|numascii" => \$opt::numascii,
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"r|reverse" => \$opt::reverse,
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"R|random-sort" => \$opt::random_sort,
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"sort=s" => \$opt::sort,
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"V|version-sort" => \$opt::version_sort,
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"k|key=s" => \@opt::key,
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"t|field-separator=s" => \$opt::field_separator,
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"z|zero-terminated" => \$opt::zero_terminated,
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"files0-from=s" => \$opt::files0_from,
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"random-source=s" => \$opt::dummy,
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"batch-size=s" => \$opt::dummy,
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"check=s" => \$opt::dummy,
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"c" => \$opt::dummy,
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"C" => \$opt::dummy,
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"compress-program=s" => \$opt::dummy,
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"T|temporary-directory=s" => \$opt::dummy,
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"parallel=s" => \$opt::dummy,
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"u|unique" => \$opt::dummy,
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"S|buffer-size=s" => \$opt::dummy,
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"s|stable" => \$opt::dummy,
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"help" => \$opt::dummy,
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) || exit(255);
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$Global::progname = ($0 =~ m:(^|/)([^/]+)$:)[1];
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$Global::version = 20211222;
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if($opt::version) { version(); exit 0; }
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@Global::sortoptions = grep { ! /^-D$/ }
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shell_quote(@ARGV_before[0..($#ARGV_before-$#ARGV-1)]);
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#if($opt::zero_terminated) { $/ = "\0"; }
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$ENV{'TMPDIR'} ||= "/tmp";
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sub merge {
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# Input:
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# @cmd = commands to 'cat' (part of) a file
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my @cmd = @_;
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chomp(@cmd);
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while($#cmd > 0) {
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my @tmp;
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while($#cmd >= 0) {
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my $a = shift @cmd;
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my $b = shift @cmd;
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$a &&= "<($a)";
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$b &&= "<($b)";
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# This looks like useless use of 'cat', but contrary to
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# naive belief it increases performance dramatically.
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push @tmp, "sort -m @Global::sortoptions $a $b | cat"
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}
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@cmd = @tmp;
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}
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return @cmd;
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}
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sub sort_files {
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# Input is files
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my @files = @_;
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# Let GNU Parallel generate the commands to read parts of files
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# The commands split at \n and there will be at least one for each CPU thread
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open(my $par,"-|",qw(parallel --pipepart --block -1 --dryrun -vv sort),
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@Global::sortoptions, '::::', @files) || die;
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my @cmd = merge(<$par>);
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close $par;
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debug(@cmd);
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# The command uses <(...) so it is incompatible with /bin/sh
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open(my $bash,"|-","bash") || die;
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print $bash @cmd;
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close $bash;
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}
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sub sort_stdin {
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# Input is stdin
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# Spread the input between n processes that each sort
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# n = number of CPU threads
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my $numthreads = `parallel --number-of-threads`;
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my @fifos = map { tmpfifo() } 1..$numthreads;
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map { mkfifo($_,0600) } @fifos;
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# This trick removes the fifo as soon as it is connected in the other end
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# (rm fifo; ...) < fifo
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my @cmd = (map { "(rm $_; sort @Global::sortoptions) < $_" }
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map { Q($_) } @fifos);
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@cmd = merge(@cmd);
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if(fork) {
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} else {
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exec(qw(parallel -j),$numthreads,
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# 286k is the best mean value after testing 250..350
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qw(--block 286k --pipe --roundrobin cat > {} :::),@fifos);
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}
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# The command uses <(...) so it is incompatible with /bin/sh
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open(my $bash,"|-","bash") || die;
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print $bash @cmd;
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close $bash;
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}
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sub tmpname {
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# Select a name that does not exist
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# Do not create the file as it may be used for creating a socket (by tmux)
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# Remember the name in $Global::unlink to avoid hitting the same name twice
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my $name = shift;
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my($tmpname);
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if(not -w $ENV{'TMPDIR'}) {
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if(not -e $ENV{'TMPDIR'}) {
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::error("Tmpdir '$ENV{'TMPDIR'}' does not exist.","Try 'mkdir ".
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Q($ENV{'TMPDIR'})."'");
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} else {
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::error("Tmpdir '$ENV{'TMPDIR'}' is not writable.","Try 'chmod +w ".
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Q($ENV{'TMPDIR'})."'");
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}
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exit(255);
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}
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do {
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$tmpname = $ENV{'TMPDIR'}."/".$name.
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join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
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} while(-e $tmpname);
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return $tmpname;
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}
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sub tmpfifo {
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# Find an unused name and mkfifo on it
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my $tmpfifo = tmpname("psort");
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mkfifo($tmpfifo,0600);
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return $tmpfifo;
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}
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sub debug {
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# Returns: N/A
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$opt::D or return;
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@_ = grep { defined $_ ? $_ : "" } @_;
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print STDERR @_[1..$#_];
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}
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sub version() {
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# Returns: N/A
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print join
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("\n",
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"GNU $Global::progname $Global::version",
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"Copyright (C) 2020-2022 Ole Tange, http://ole.tange.dk and Free Software",
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"Foundation, Inc.",
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"License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>",
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"This is free software: you are free to change and redistribute it.",
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"GNU $Global::progname comes with no warranty.",
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"",
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"Web site: https://www.gnu.org/software/parallel\n",
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);
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}
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sub shell_quote(@) {
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# Input:
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# @strings = strings to be quoted
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# Returns:
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# @shell_quoted_strings = string quoted as needed by the shell
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return wantarray ? (map { Q($_) } @_) : (join" ",map { Q($_) } @_);
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}
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sub shell_quote_scalar_rc($) {
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# Quote for the rc-shell
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my $a = $_[0];
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if(defined $a) {
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if(($a =~ s/'/''/g)
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+
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($a =~ s/[\n\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]+/'$&'/go)) {
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# A string was replaced
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# No need to test for "" or \0
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} elsif($a eq "") {
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$a = "''";
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} elsif($a eq "\0") {
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$a = "";
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}
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}
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return $a;
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}
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sub shell_quote_scalar_csh($) {
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# Quote for (t)csh
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my $a = $_[0];
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if(defined $a) {
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# $a =~ s/([\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\>\<\~\|\; \"\!\$\&\'\202-\377])/\\$1/g;
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# This is 1% faster than the above
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if(($a =~ s/[\002-\011\013-\032\\\#\?\`\(\)\{\}\[\]\^\*\<\=\>\~\|\; \"\!\$\&\'\202-\377]/\\$&/go)
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+
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# quote newline in csh as \\\n
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($a =~ s/[\n]/"\\\n"/go)) {
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# A string was replaced
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# No need to test for "" or \0
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} elsif($a eq "") {
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$a = "''";
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} elsif($a eq "\0") {
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$a = "";
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}
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}
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return $a;
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}
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sub shell_quote_scalar_default($) {
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# Quote for other shells (Bourne compatibles)
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# Inputs:
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# $string = string to be quoted
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# Returns:
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# $shell_quoted = string quoted as needed by the shell
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my $s = $_[0];
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if($s =~ /[^-_.+a-z0-9\/]/i) {
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$s =~ s/'/'"'"'/g; # "-quote single quotes
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$s = "'$s'"; # '-quote entire string
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$s =~ s/^''//; # Remove unneeded '' at ends
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$s =~ s/''$//; # (faster than s/^''|''$//g)
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return $s;
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} elsif ($s eq "") {
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return "''";
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} else {
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# No quoting needed
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return $s;
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}
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}
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sub shell_quote_scalar($) {
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# Quote the string so the shell will not expand any special chars
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# Inputs:
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# $string = string to be quoted
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# Returns:
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# $shell_quoted = string quoted as needed by the shell
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# Speed optimization: Choose the correct shell_quote_scalar_*
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# and call that directly from now on
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no warnings 'redefine';
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if($Global::cshell) {
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# (t)csh
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*shell_quote_scalar = \&shell_quote_scalar_csh;
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} elsif($Global::shell =~ m:(^|/)rc$:) {
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# rc-shell
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*shell_quote_scalar = \&shell_quote_scalar_rc;
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} else {
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# other shells
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*shell_quote_scalar = \&shell_quote_scalar_default;
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}
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# The sub is now redefined. Call it
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return shell_quote_scalar($_[0]);
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}
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sub Q($) {
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# Q alias for ::shell_quote_scalar
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my $ret = shell_quote_scalar($_[0]);
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no warnings 'redefine';
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*Q = \&::shell_quote_scalar;
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return $ret;
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}
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sub status(@) {
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my @w = @_;
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my $fh = $Global::status_fd || *STDERR;
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print $fh map { ($_, "\n") } @w;
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flush $fh;
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}
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sub status_no_nl(@) {
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my @w = @_;
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my $fh = $Global::status_fd || *STDERR;
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print $fh @w;
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flush $fh;
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}
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sub warning(@) {
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my @w = @_;
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my $prog = $Global::progname || "parsort";
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status_no_nl(map { ($prog, ": Warning: ", $_, "\n"); } @w);
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}
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{
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my %warnings;
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sub warning_once(@) {
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my @w = @_;
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my $prog = $Global::progname || "parsort";
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$warnings{@w}++ or
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status_no_nl(map { ($prog, ": Warning: ", $_, "\n"); } @w);
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}
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}
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sub error(@) {
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my @w = @_;
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my $prog = $Global::progname || "parsort";
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status(map { ($prog.": Error: ". $_); } @w);
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}
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sub die_bug($) {
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my $bugid = shift;
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print STDERR
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("$Global::progname: This should not happen. You have found a bug. ",
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"Please follow\n",
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"https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS\n",
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"\n",
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"Include this in the report:\n",
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"* The version number: $Global::version\n",
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"* The bugid: $bugid\n",
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"* The command line being run\n",
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"* The files being read (put the files on a webserver if they are big)\n",
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"\n",
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"If you get the error on smaller/fewer files, please include those instead.\n");
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exit(255);
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}
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sub version() {
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# Returns: N/A
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print join
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("\n",
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"GNU $Global::progname $Global::version",
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"Copyright (C) 2007-2022 Ole Tange, http://ole.tange.dk and Free Software",
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"Foundation, Inc.",
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"License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>",
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"This is free software: you are free to change and redistribute it.",
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"GNU $Global::progname comes with no warranty.",
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"",
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"Web site: https://www.gnu.org/software/${Global::progname}\n",
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"When using programs that use GNU Parallel to process data for publication",
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"please cite as described in 'parallel --citation'.\n",
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);
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}
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if(@ARGV) {
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sort_files(@ARGV);
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} elsif(length $opt::files0_from) {
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$/="\0";
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open(my $fh,"<",$opt::files0_from) || die;
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my @files = <$fh>;
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chomp(@files);
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sort_files(@files);
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} else {
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sort_stdin();
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}
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# Test
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# -z
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# OK: cat bigfile | parsort
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# OK: parsort -k4n files*.txt
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# OK: parsort files*.txt
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# OK: parsort "file with space"
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