plotpipe: Added README.
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Ole Tange
parent
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4
README
4
README
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@ -30,10 +30,14 @@ mirrorpdf - mirror PDF-file horizontally.
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neno - no error no output. Only print STDERR and STDOUT if the command fails.
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neno - no error no output. Only print STDERR and STDOUT if the command fails.
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not - flip exit value of command.
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off - turn off monitor.
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off - turn off monitor.
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pdfman - convert man page to pdf and display it using evince.
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pdfman - convert man page to pdf and display it using evince.
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plotpipe - plot CSV data from a pipe.
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puniq - print unique lines the first time they are seen.
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puniq - print unique lines the first time they are seen.
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ramusage - display the ram usage of a program using `time -v`.
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ramusage - display the ram usage of a program using `time -v`.
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@ -48,3 +48,5 @@ your initramfs, you need to add them by adding to
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When all is done, update the initramfs:
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When all is done, update the initramfs:
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update-initramfs -u
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update-initramfs -u
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(C) 2014 Ole Tange, GPLv2 or later
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214
parsort/parsort
214
parsort/parsort
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@ -1,214 +0,0 @@
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#!/usr/bin/perl
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=pod
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=head1 NAME
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parsort - Sort 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 B<sort> to sort in parallel. It works just like
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B<sort> but faster, if you have a multicore machine.
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Hopefully these ideas will make it into GNU 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 files, because these 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 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>, B<parallel>, and B<mbuffer>.
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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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) || exit(255);
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$Global::progname = ($0 =~ m:(^|/)([^/]+)$:)[1];
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$Global::version = 20200411;
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if($opt::version) { version(); exit 0; }
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if($opt::zero_terminated) { $/ = "\0"; }
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@Global::sortoptions = @ARGV_before[0..($#ARGV_before-$#ARGV-1)];
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$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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# Ignore errors from mbuffer - it gives errors when a pipe is closed
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push @tmp, "sort -m @Global::sortoptions $a $b | mbuffer -v0 -q -m 30M;";
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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 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 $ENV{'TMPDIR'}'");
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} else {
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::error("Tmpdir '$ENV{'TMPDIR'}' is not writable.","Try 'chmod +w $ENV{'TMPDIR'}'");
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}
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::wait_and_exit(255);
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}
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do {
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$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 or $Global::unlink{$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 sort_files {
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my @files = @ARGV;
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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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# 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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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) < $_" } @fifos;
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@cmd = merge(@cmd);
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if(fork) {
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} else {
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exec(qw(parallel -j),$numthreads,
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# 1M 30M = 43s
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# 3M 30M = 59s
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# 300k 30M = 40-45s
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# 100k 30M = 47s
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# 500k 30M = 44s
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# 300k 10M = 41-45s
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# 256k 10M = 44s
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# 300k 3M = 42-45s
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# 300k - = 47s
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qw(--block 256k --pipe --roundrobin mbuffer -v0 -q -m 10M > {} :::),@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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if(@ARGV) {
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sort_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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39
plotpipe/README
Normal file
39
plotpipe/README
Normal file
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@ -0,0 +1,39 @@
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PLOTPIPE
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- plot data from a pipe -
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URL: https://gitlab.com/ole.tange/tangetools/-/tree/master/plotpipe
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We have all been there: You have a bunch of data from a pipe that you
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would like to get a better understanding of.
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You know you can plot them by saving the data to a file, opening the
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file in a spreadsheet, and making a graph; but it is just too much
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bother because you do not need a fancy graph: You just need a quick
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graph based on the data, and spending 5 minutes on generating that
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graph is just too much hassle.
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Plotpipe is designed for this situation.
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Plotpipe reads data from a pipe (or a file) and plots it. If the input
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is a CSV-file it tries to autodetect the separator and whether there
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is a column header. It assumes the first column is the x-axis and that
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all other columns are data series. If there is only a single
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column, the line number is treated as the x-axis.
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Examples:
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seq 1 100 | plotpipe
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seq 1 100 | shuf | plotpipe
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paste <(seq 1 100) <(seq 1 100) <(seq 1 100 | shuf) | plotpipe
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(echo "#Title"; echo "#Subtitle";
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echo "Column1 Column2 Column3";
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paste <(seq 1 100) <(seq 1 100) <(seq 1 100 | shuf) ) | plotpipe
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Copyright (C) 2020 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 <http://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 plotpipe comes with no warranty.
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@ -59,20 +59,21 @@ usage will be 10 times I<blocksize> per CPU core. Default is 100M.
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# Generate 100000x100000 matrix
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# Generate 100000x100000 matrix
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100kx100k() {
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100kx100k() {
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100000x() {
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XbyY() {
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while seq 123456 | shuf; do true; done |
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while seq 123456 | shuf; do true; done |
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paste $(perl -e 'print map {"- "} 1..100000') |
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paste $(perl -e 'print map {"- "} 1..'$1) |
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head -n $1
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head -n $2
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}
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}
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export -f 100000x
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export -f XbyY
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seq 1000 | parallel --nice 18 --delay 0.05 --files 100000x 100 |
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seq 1000 |
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parallel --nice 18 --delay 0.05 --files XbyY 100000 100 |
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parallel -uj1 'cat {}; nice rm {} &'
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parallel -uj1 'cat {}; nice rm {} &'
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}
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}
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100kx100k > 100kx100k
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100kx100k > 100kx100k
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# Transpose it
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# Transpose it
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transpose 100kx100k > 100kx100k.t
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transpose 100kx100k > 100kx100k.t
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This takes around 700 MB/core and 20 minutes to run on 64C64T.
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This takes around 1 GB/core and 18 minutes to run on 64C64T.
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=head1 LIMITATIONS
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=head1 LIMITATIONS
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@ -107,7 +108,7 @@ cleaned up, if B<transpose> is stopped abnormally (e.g. killed).
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=head1 REPORTING BUGS
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=head1 REPORTING BUGS
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Report bugs to <tange@gnu.org>.
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Report bugs: https://gitlab.com/ole.tange/tangetools/-/issues
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=head1 AUTHOR
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=head1 AUTHOR
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@ -502,7 +503,7 @@ main() {
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block_size=100M
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block_size=100M
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while getopts ":b:d:V" o; do
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while getopts ":b:d:V" o; do
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case "$o" in
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case "$o" in
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d)
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(d)
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# Convert \t to TAB using printf
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# Convert \t to TAB using printf
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d=$(printf "$OPTARG")
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d=$(printf "$OPTARG")
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if [ "'" = "$d" ] ; then
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if [ "'" = "$d" ] ; then
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@ -511,14 +512,14 @@ main() {
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exit 0
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exit 0
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fi
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fi
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;;
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;;
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b)
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(b)
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block_size="$OPTARG"
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block_size="$OPTARG"
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;;
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;;
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V)
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(V)
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version
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version
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exit 0
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exit 0
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;;
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;;
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*)
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(*)
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usage
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usage
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;;
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;;
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esac
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esac
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@ -19,7 +19,6 @@ searchlen = int(sys.argv[1])
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def readparts():
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def readparts():
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# Read file
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# Read file
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part = []
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part = []
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partno = 0
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# Block of text ending in \n that is followed by a \t in next section
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# Block of text ending in \n that is followed by a \t in next section
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section = ""
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section = ""
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for i in sys.stdin:
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for i in sys.stdin:
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@ -61,7 +60,7 @@ def recur(pre,n):
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bits = searchlen*4
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bits = searchlen*4
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part = readparts();
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part = readparts();
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tabs = math.ceil(bits/3.0)
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tabs = int(math.ceil(bits/3.0))
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if tabs > len(part)-1:
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if tabs > len(part)-1:
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print("Too few tabs: %s hex values is %s bits which needs %d tabs and there are only %s"
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print("Too few tabs: %s hex values is %s bits which needs %d tabs and there are only %s"
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% (searchlen,bits,tabs,len(part)))
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% (searchlen,bits,tabs,len(part)))
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