transpose: parallelized.
w4it-for-port-open: -q (quiet) implemented.
This commit is contained in:
Ole Tange
parent
0a9b2b3503
commit
f6a34e1200
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@ -1,125 +1,160 @@
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#!/usr/bin/perl -w
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#!/bin/bash
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use English;
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# transpose [-d delimiter] [-b blocksize] table.csv > transposed.csv
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use FileCache;
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# cat table.csv | transpose [-d delimiter] [-b blocksize] > transposed.csv
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use File::Temp;
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my $delimiter = shift;
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transpose_inner() {
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my $buffer = shift;
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# simple in-memory transpose
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# -d sep
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# Input:
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# data to be transposed
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# Output:
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# transposed data
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perl <(cat <<'cut-here-UbsAqi0j6GoOuk5W5yWA'
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use Text::CSV;
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use Getopt::Long;
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$delimiter ||= ",";
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Getopt::Long::Configure("bundling","require_order");
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# Use at most 1000M before flushing
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my $retval = GetOptions("debug|D=s" => \$opt::debug,
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$buffer ||= "1000M";
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"delimiter|d=s" => \$opt::delimiter,
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$buffer = multiply_binary_prefix($buffer);
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"verbose|v" => \@opt::verbose,
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# Perl makes the buffer baloon to 10 times the requested value
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"simple|s" => \$opt::simple,
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$buffer /= 10;
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);
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# max_col_size will be lowered after first line read.
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$max_col_size = $buffer;
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if(defined $opt::delimiter) {
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my $delimiter_regexp = $delimiter;
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simple();
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$delimiter_regexp =~ s/(\W)/\\$1/g;
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} else {
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my @current;
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die("-d must be set");
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my $col_no_last_line = 0;
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}
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my $lineno = 0;
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my %col;
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sub simple {
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while(<>) {
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my (@table);
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chomp;
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my $col = 0;
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my $col_no = 0;
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my $csv_setting = { binary => 1, sep_char => $opt::delimiter };
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my @to_be_flushed = ();
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my $sep = $csv_setting->{sep_char};
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map {
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my $csv = Text::CSV->new($csv_setting)
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push(@{$col{$col_no}},$_);
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or die "Cannot use CSV: ".Text::CSV->error_diag ();
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$col_size{$col_no} += length $_;
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if($col_size{$col_no} > $max_col_size) {
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while(my $l = <>) {
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push @to_be_flushed, $col_no;
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if(not $csv->parse($l)) {
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$col_size{$col_no} = 0;
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die "CSV has unexpected format";
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}
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}
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$col_no++;
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# append to each row
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} split /$delimiter_regexp/o, $_; # This should do de-csv'ing
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my $row = 0;
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if(@to_be_flushed) {
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for($csv->fields()) {
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flush(\%col,@to_be_flushed);
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$table[$row][$col] = defined($_) ? $_ : '';
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}
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$row++;
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if($col_no != $col_no_last_line) {
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if(0 == $col_no_last_line) {
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# This is first time around
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$col_no_last_line = $col_no;
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$max_col_size = $buffer/$col_no_last_line;
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} else {
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warning("Number of columns in line $NR: $col_no != $col_no_last_line\n");
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}
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}
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$col++;
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}
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}
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print map { join($sep,@$_),"\n" } @table;
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}
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}
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flush(\%col);
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cut-here-UbsAqi0j6GoOuk5W5yWA
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merge();
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) "$@"
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}
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export -f transpose_inner
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sub flush {
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stdin_to_paste_files() {
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my $col_ref = shift;
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# Run transpose_inner on blocks from stdin
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my @cols_to_flush = @_;
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# output each block as file name
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if(not @cols_to_flush) {
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local block_size
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@cols_to_flush = keys %$col_ref;
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local sep
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}
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block_size="$1"
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for my $c (@cols_to_flush) {
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sep="$2"
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$Global::tempfile{$c} ||= tmpnam();
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PARALLEL="-k --files --block $block_size" \
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my $fh = cacheout $Global::tempfile{$c};
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parallel --pipe transpose_inner -d "'$sep'"
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# This will print one delimiter too much, which we will deal with later
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print $fh map { $_,$delimiter } @{$col_ref->{$c}};
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delete $col_ref->{$c};
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}
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}
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}
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sub merge {
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file_to_paste_files() {
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for my $c (sort keys %Global::tempfile) {
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# Run transpose_inner on blocks from $file
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my $fh = cacheout $Global::tempfile{$c};
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# output each block as file name
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# truncate by length of delimiter to get rid of the last $delimiter
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local block_size
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seek $fh,-length($delimiter),SEEK_END;
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local sep
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truncate $fh, tell $fh;
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block_size="$1"
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# Make sure the file is closed of writing
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sep="$2"
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close $fh;
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file="$3"
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open($fh, "<", $Global::tempfile{$c}) || die;
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PARALLEL="-k --files --block $block_size" \
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my $buf;
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parallel --pipe-part -a "$file" transpose_inner -d "'$sep'"
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while(sysread($fh,$buf,1000_000)) {
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print $buf;
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}
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print "\n";
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unlink $Global::tempfile{$c};
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}
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}
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}
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sub warning {
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super_paste() {
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my @w = @_;
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# Like 'paste' up to 1000000 files
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print STDERR "transpose: Warning: ", @w;
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# The files are read from stdin
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local sep
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local paste_files
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local fifo
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sep="$1"
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paste_files=`tempfile`
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# basename
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fifo=`tempfile`
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rm $fifo
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cat > $paste_files
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# Define replacement string {0#} to 0-pad job number
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PARALLEL="--rpl "\''{0#} $f=1+int("".(log(total_jobs())/log(10)));
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$_=sprintf("%0${f}d",seq())'\'
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# Make fifos that can be read from
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cat $paste_files | parallel -n1000 "rm -f $fifo{0#}; mkfifo $fifo{0#}"
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# Start a paste process for every 1000 files
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cat $paste_files | parallel -n1000 -j0 "paste -d '$sep' {} > $fifo{0#}" &
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# Paste all the fifos
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eval paste -d "'$sep'" $fifo*
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# Cleanup
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cat $paste_files | parallel -n1000 "rm -f {} $fifo{0#}"
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rm $paste_files
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}
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}
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sub error {
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stdin_detect_sep() {
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my @w = @_;
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# Read the first 3 lines and detect the separator
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print STDERR "transpose: Error: ", @w;
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# Save the read input to file
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local file
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file="$1"
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# TODO
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echo "$d"
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}
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}
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sub multiply_binary_prefix {
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usage() {
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# Evalualte numbers with binary prefix
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echo "Usage: $0 [-d delimiter] [-b blocksize]" 1>&2; exit 1;
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# k=10^3, m=10^6, g=10^9, t=10^12, p=10^15, e=10^18, z=10^21, y=10^24
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# K=2^10, M=2^20, G=2^30, T=2^40, P=2^50, E=2^70, Z=2^80, Y=2^80
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# Ki=2^10, Mi=2^20, Gi=2^30, Ti=2^40, Pi=2^50, Ei=2^70, Zi=2^80, Yi=2^80
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# ki=2^10, mi=2^20, gi=2^30, ti=2^40, pi=2^50, ei=2^70, zi=2^80, yi=2^80
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# 13G = 13*1024*1024*1024 = 13958643712
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my $s = shift;
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$s =~ s/k/*1000/g;
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$s =~ s/M/*1000*1000/g;
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$s =~ s/G/*1000*1000*1000/g;
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$s =~ s/T/*1000*1000*1000*1000/g;
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$s =~ s/P/*1000*1000*1000*1000*1000/g;
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$s =~ s/E/*1000*1000*1000*1000*1000*1000/g;
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$s =~ s/Z/*1000*1000*1000*1000*1000*1000*1000/g;
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$s =~ s/Y/*1000*1000*1000*1000*1000*1000*1000*1000/g;
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$s =~ s/X/*1000*1000*1000*1000*1000*1000*1000*1000*1000/g;
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$s =~ s/Ki?/*1024/gi;
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$s =~ s/Mi?/*1024*1024/gi;
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$s =~ s/Gi?/*1024*1024*1024/gi;
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$s =~ s/Ti?/*1024*1024*1024*1024/gi;
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$s =~ s/Pi?/*1024*1024*1024*1024*1024/gi;
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$s =~ s/Ei?/*1024*1024*1024*1024*1024*1024/gi;
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$s =~ s/Zi?/*1024*1024*1024*1024*1024*1024*1024/gi;
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$s =~ s/Yi?/*1024*1024*1024*1024*1024*1024*1024*1024/gi;
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$s =~ s/Xi?/*1024*1024*1024*1024*1024*1024*1024*1024*1024/gi;
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$s = eval $s;
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return $s;
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}
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}
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block_size=10M
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while getopts ":b:d:" o; do
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case "${o}" in
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d)
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d="$(printf "${OPTARG}")"
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if [ "'" = "${d}" ] ; then
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echo "Delimiter cannot be '"
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usage
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exit
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fi
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;;
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b)
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block_size="${OPTARG}"
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;;
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*)
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usage
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;;
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esac
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done
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shift $((OPTIND-1))
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if [ -z "${d}" ] ; then
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d="$(printf "\t")"
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fi
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# Sep cannot be '
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file="$@"
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first_lines=`tempfile`
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if [ -z "$file" ]; then
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sep="$(stdin_detect_sep $first_lines)"
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(cat $first_lines; rm $first_lines; cat) |
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stdin_to_paste_files $block_size "$sep" | super_paste "$sep"
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else
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sep="$(stdin_detect_sep < "$file" $first_lines)"
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rm $first_lines
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file_to_paste_files $block_size "$sep" "$file" | super_paste "$sep"
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fi
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12
treeoflife/treeoflife
Executable file
12
treeoflife/treeoflife
Executable file
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@ -0,0 +1,12 @@
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#!/bin/bash
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# Download tree-of-life.jpg
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# from http://www.open.edu/openlearn/nature-environment/natural-history/tree-life
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base=www2.open.ac.uk/openlearn/treeoflife/treeOfLifePoster/TileGroup
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parallel -j30 wget -c $base{3}/6-{1}-{2}.jpg ::: {0..28} ::: {4..42} ::: {1..7}
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parallel eval convert +append 6-{0..28}-{}.jpg line{}.jpg ::: {4..42}
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convert -append line{4..42}.jpg tree-of-life.jpg
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echo Cleanup with
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echo rm line*.jpg 6-*-*.jpg
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@ -1,5 +1,19 @@
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#!/bin/bash
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#!/bin/bash
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QUIET=false
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while getopts ":q" opt; do
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case $opt in
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q)
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QUIET=true
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shift
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;;
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\?)
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echo "Invalid option: -$OPTARG" >&2
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;;
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esac
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done
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HOST=$1
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HOST=$1
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PORT=$2
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PORT=$2
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@ -13,7 +27,11 @@ usage () {
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}
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}
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print_not_reachable () {
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print_not_reachable () {
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echo -n .
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if $QUIET; then
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true skip
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else
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echo -n .
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fi
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}
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}
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is_port_open () {
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is_port_open () {
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@ -70,7 +70,7 @@ if tty -s ; then
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# timeout 12 forever dmesg | puniq
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# timeout 12 forever dmesg | puniq
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fi
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fi
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sudo bash -c 'cat >> /etc/resolv.conf' < /etc/resolvconf/resolv.conf.d/head
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#sudo bash -c 'cat >> /etc/resolv.conf' < /etc/resolvconf/resolv.conf.d/head
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sudo iwconfig wls1 essid Turris
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#sudo iwconfig wls1 essid Turris
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sudo dhclient wls1 &
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#sudo dhclient wls1 &
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sudo wpa_supplicant -Dwext -c/etc/wpa_supplicant.conf -iwls1 -d &
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#sudo wpa_supplicant -Dwext -c/etc/wpa_supplicant.conf -iwls1 -d &
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