plotpipe: Added README.

This commit is contained in:
Ole Tange 2020-12-04 18:33:50 +01:00
parent 6d141ac74e
commit 8be6d39649
6 changed files with 59 additions and 228 deletions

4
README
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@ -30,10 +30,14 @@ mirrorpdf - mirror PDF-file horizontally.
neno - no error no output. Only print STDERR and STDOUT if the command fails.
not - flip exit value of command.
off - turn off monitor.
pdfman - convert man page to pdf and display it using evince.
plotpipe - plot CSV data from a pipe.
puniq - print unique lines the first time they are seen.
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
When all is done, update the initramfs:
update-initramfs -u
(C) 2014 Ole Tange, GPLv2 or later

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@ -1,214 +0,0 @@
#!/usr/bin/perl
=pod
=head1 NAME
parsort - Sort in parallel
=head1 SYNOPSIS
B<parsort> I<options for sort>
=head1 DESCRIPTION
B<parsort> uses B<sort> to sort in parallel. It works just like
B<sort> but faster, if you have a multicore machine.
Hopefully these ideas will make it into GNU 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 files, because these 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 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>, B<parallel>, and B<mbuffer>.
=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,
) || exit(255);
$Global::progname = ($0 =~ m:(^|/)([^/]+)$:)[1];
$Global::version = 20200411;
if($opt::version) { version(); exit 0; }
if($opt::zero_terminated) { $/ = "\0"; }
@Global::sortoptions = @ARGV_before[0..($#ARGV_before-$#ARGV-1)];
$ENV{'TMPDIR'} ||= "/tmp";
sub merge {
# Input:
# @cmd = commands to 'cat' (part of) a file
my @cmd = @_;
chomp(@cmd);
while($#cmd > 0) {
my @tmp;
while($#cmd >= 0) {
my $a = shift @cmd;
my $b = shift @cmd;
$a &&= "<($a)";
$b &&= "<($b)";
# Ignore errors from mbuffer - it gives errors when a pipe is closed
push @tmp, "sort -m @Global::sortoptions $a $b | mbuffer -v0 -q -m 30M;";
}
@cmd = @tmp;
}
return @cmd;
}
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 $ENV{'TMPDIR'}'");
} else {
::error("Tmpdir '$ENV{'TMPDIR'}' is not writable.","Try 'chmod +w $ENV{'TMPDIR'}'");
}
::wait_and_exit(255);
}
do {
$tmpname = $ENV{'TMPDIR'}."/".$name.
join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
} while(-e $tmpname or $Global::unlink{$tmpname}++);
return $tmpname;
}
sub tmpfifo {
# Find an unused name and mkfifo on it
my $tmpfifo = tmpname("psort");
mkfifo($tmpfifo,0600);
return $tmpfifo;
}
sub sort_files {
my @files = @ARGV;
# Let GNU Parallel generate the commands to read parts of files
# The commands split at \n and there will be at least one for each CPU thread
open(my $par,"-|",qw(parallel --pipepart --block -1 --dryrun -vv sort),
@Global::sortoptions, '::::', @files) || die;
my @cmd = merge(<$par>);
close $par;
# The command uses <(...) so it is incompatible with /bin/sh
open(my $bash,"|-","bash") || die;
print $bash @cmd;
close $bash;
}
sub sort_stdin {
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) < $_" } @fifos;
@cmd = merge(@cmd);
if(fork) {
} else {
exec(qw(parallel -j),$numthreads,
# 1M 30M = 43s
# 3M 30M = 59s
# 300k 30M = 40-45s
# 100k 30M = 47s
# 500k 30M = 44s
# 300k 10M = 41-45s
# 256k 10M = 44s
# 300k 3M = 42-45s
# 300k - = 47s
qw(--block 256k --pipe --roundrobin mbuffer -v0 -q -m 10M > {} :::),@fifos);
}
# The command uses <(...) so it is incompatible with /bin/sh
open(my $bash,"|-","bash") || die;
print $bash @cmd;
close $bash;
}
if(@ARGV) {
sort_files();
} else {
sort_stdin();
}
# Test
# -z
# OK: cat bigfile | parsort
# OK: parsort -k4n files*.txt
# OK: parsort files*.txt
# OK: parsort "file with space"

39
plotpipe/README Normal file
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@ -0,0 +1,39 @@
PLOTPIPE
- plot data from a pipe -
URL: https://gitlab.com/ole.tange/tangetools/-/tree/master/plotpipe
We have all been there: You have a bunch of data from a pipe that you
would like to get a better understanding of.
You know you can plot them by saving the data to a file, opening the
file in a spreadsheet, and making a graph; but it is just too much
bother because you do not need a fancy graph: You just need a quick
graph based on the data, and spending 5 minutes on generating that
graph is just too much hassle.
Plotpipe is designed for this situation.
Plotpipe reads data from a pipe (or a file) and plots it. If the input
is a CSV-file it tries to autodetect the separator and whether there
is a column header. It assumes the first column is the x-axis and that
all other columns are data series. If there is only a single
column, the line number is treated as the x-axis.
Examples:
seq 1 100 | plotpipe
seq 1 100 | shuf | plotpipe
paste <(seq 1 100) <(seq 1 100) <(seq 1 100 | shuf) | plotpipe
(echo "#Title"; echo "#Subtitle";
echo "Column1 Column2 Column3";
paste <(seq 1 100) <(seq 1 100) <(seq 1 100 | shuf) ) | plotpipe
Copyright (C) 2020 Ole Tange, http://ole.tange.dk and Free Software
Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
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.
# Generate 100000x100000 matrix
100kx100k() {
100000x() {
XbyY() {
while seq 123456 | shuf; do true; done |
paste $(perl -e 'print map {"- "} 1..100000') |
head -n $1
paste $(perl -e 'print map {"- "} 1..'$1) |
head -n $2
}
export -f 100000x
seq 1000 | parallel --nice 18 --delay 0.05 --files 100000x 100 |
parallel -uj1 'cat {}; nice rm {} &'
export -f XbyY
seq 1000 |
parallel --nice 18 --delay 0.05 --files XbyY 100000 100 |
parallel -uj1 'cat {}; nice rm {} &'
}
100kx100k > 100kx100k
# Transpose it
transpose 100kx100k > 100kx100k.t
This takes around 700 MB/core and 20 minutes to run on 64C64T.
This takes around 1 GB/core and 18 minutes to run on 64C64T.
=head1 LIMITATIONS
@ -107,7 +108,7 @@ cleaned up, if B<transpose> is stopped abnormally (e.g. killed).
=head1 REPORTING BUGS
Report bugs to <tange@gnu.org>.
Report bugs: https://gitlab.com/ole.tange/tangetools/-/issues
=head1 AUTHOR
@ -502,7 +503,7 @@ main() {
block_size=100M
while getopts ":b:d:V" o; do
case "$o" in
d)
(d)
# Convert \t to TAB using printf
d=$(printf "$OPTARG")
if [ "'" = "$d" ] ; then
@ -511,14 +512,14 @@ main() {
exit 0
fi
;;
b)
(b)
block_size="$OPTARG"
;;
V)
(V)
version
exit 0
;;
*)
(*)
usage
;;
esac

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@ -19,7 +19,6 @@ searchlen = int(sys.argv[1])
def readparts():
# Read file
part = []
partno = 0
# Block of text ending in \n that is followed by a \t in next section
section = ""
for i in sys.stdin:
@ -61,7 +60,7 @@ def recur(pre,n):
bits = searchlen*4
part = readparts();
tabs = math.ceil(bits/3.0)
tabs = int(math.ceil(bits/3.0))
if tabs > len(part)-1:
print("Too few tabs: %s hex values is %s bits which needs %d tabs and there are only %s"
% (searchlen,bits,tabs,len(part)))