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--pipepart --group-by implemented (except column names).
This commit is contained in:
Ole Tange
parent
324a9f3a07
commit
aa62104eb5
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@ -206,7 +206,7 @@ from:tange@gnu.org
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to:parallel@gnu.org, bug-parallel@gnu.org
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stable-bcc: Jesse Alama <jessealama@fastmail.fm>
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Subject: GNU Parallel 20190522 ('') released <<[stable]>>
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Subject: GNU Parallel 20190522 ('Akihito') released <<[stable]>>
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GNU Parallel 20190522 ('') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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@ -223,6 +223,12 @@ Quote of the month:
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New in this release:
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* --group-by groups lines depending on value of a column. The value can be computed.
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* How to compress (bzip / gzip) a very large text quickly? https://medium.com/@gchandra/how-to-compress-bzip-gzip-a-very-large-text-quickly-27c11f4c6681
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* Simple tutorial to install & use GNU Parallel https://medium.com/@gchandra/simple-tutorial-to-install-use-gnu-parallel-79251120d618
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* Introducing Parallel into Shell https://petelawson.com/post/parallel-in-shell/
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* Bug fixes and man page updates.
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138
src/parallel
138
src/parallel
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@ -462,7 +462,7 @@ sub pipe_part_files(@) {
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}
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my $header = find_header(\$buf,open_or_exit($file));
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# find positions
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my @pos = find_split_positions($file,$Global::blocksize,length $header);
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my @pos = find_split_positions($file,$Global::blocksize,$header);
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# Make @cat_prepends
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my @cat_prepends = ();
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for(my $i=0; $i<$#pos; $i++) {
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@ -507,19 +507,23 @@ sub find_split_positions($$$) {
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# Input:
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# $file = the file to read
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# $block = (minimal) --block-size of each chunk
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# $headerlen = length of header to be skipped
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# $header = header to be skipped
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# Uses:
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# $opt::recstart
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# $opt::recend
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# Returns:
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# @positions of block start/end
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my($file, $block, $headerlen) = @_;
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my($file, $block, $header) = @_;
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my $headerlen = length $header;
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my $size = -s $file;
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if(-b $file) {
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# $file is a blockdevice
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$size = size_of_block_dev($file);
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}
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$block = int $block;
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if($opt::groupby) {
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return split_positions_for_group_by($file,$size,$block,$header);
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}
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# The optimal dd blocksize for mint, redhat, solaris, openbsd = 2^17..2^20
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# The optimal dd blocksize for freebsd = 2^15..2^17
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my $dd_block_size = 131072; # 2^17
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@ -563,12 +567,126 @@ sub find_split_positions($$$) {
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}
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if($pos[$#pos] != $size) {
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# Last splitpoint was not at end of the file: add it
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push(@pos,$size);
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push @pos, $size;
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}
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close $fh;
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return @pos;
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}
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sub split_positions_for_group_by($$$$) {
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my($fh);
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sub value_at($) {
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my $pos = shift;
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if($pos != 0) {
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seek($fh, $pos-1, 0) || die;
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# Read half line
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<$fh>;
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}
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# Read full line
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my $linepos = tell($fh);
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$_ = <$fh>;
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if(defined $_) {
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# Not end of file
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my @F;
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if(defined $Global::group_by_column) {
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$opt::colsep ||= "\t";
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@F = split /$opt::colsep/, $_;
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$_ = $F[$Global::group_by_column];
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}
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eval $Global::group_by_perlexpr;
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}
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return ($_,$linepos);
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}
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sub binary_search_end($$$) {
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my ($s,$spos,$epos) = @_;
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# value_at($spos) == $s
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# value_at($epos) != $s
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my $posdif = $epos - $spos;
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my ($v,$vpos);
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while($posdif) {
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($v,$vpos) = value_at($spos+$posdif);
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if($v eq $s) {
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$spos = $vpos;
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$posdif = $epos - $spos;
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} else {
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$epos = $vpos;
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}
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$posdif = int($posdif/2);
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}
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return($v,$vpos);
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}
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sub binary_search_start($$$) {
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my ($s,$spos,$epos) = @_;
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# value_at($spos) != $s
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# value_at($epos) == $s
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my $posdif = $epos - $spos;
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my ($v,$vpos);
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while($posdif) {
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($v,$vpos) = value_at($spos+$posdif);
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if($v eq $s) {
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$epos = $vpos;
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} else {
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$spos = $vpos;
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$posdif = $epos - $spos;
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}
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$posdif = int($posdif/2);
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}
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return($v,$vpos);
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}
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my ($file,$size,$block,$header) = @_;
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my ($a,$b,$c,$apos,$bpos,$cpos);
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my @pos;
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$fh = open_or_exit($file);
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# Set $Global::group_by_column $Global::group_by_perlexpr
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group_by_loop($opt::recsep);
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# $xpos = linestart, $x = value at $xpos, $apos < $bpos < $cpos
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$apos = length $header;
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for(($a,$apos) = value_at($apos); $apos < $size;) {
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push @pos, $apos;
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$bpos = $apos + $block;
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($b,$bpos) = value_at($bpos);
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if(eof($fh)) {
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push @pos, $size; last;
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}
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$cpos = $bpos + $block;
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($c,$cpos) = value_at($cpos);
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if($a eq $b) {
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while($b eq $c) {
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# Move bpos, cpos a block forward until $a == $b != $c
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$bpos = $cpos;
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$cpos += $block;
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($c,$cpos) = value_at($cpos);
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if($cpos >= $size) {
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$cpos = $size;
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last;
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}
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}
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# $a == $b != $c
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# Binary search for $b ending between ($bpos,$cpos)
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($b,$bpos) = binary_search_end($b,$bpos,$cpos);
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} else {
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if($b eq $c) {
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# $a != $b == $c
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# Binary search for $b starting between ($apos,$bpos)
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($b,$bpos) = binary_search_start($b,$apos,$bpos);
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} else {
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# $a != $b != $c
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# Binary search for $b ending between ($bpos,$cpos)
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($b,$bpos) = binary_search_end($b,$bpos,$cpos);
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}
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}
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($a,$apos) = ($b,$bpos);
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}
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if($pos[$#pos] != $size) {
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# Last splitpoint was not at end of the file: add it
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push @pos, $size;
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}
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return @pos;
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}
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sub cat_partial($@) {
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# Efficient command to copy from byte X to byte Y
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# Input:
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@ -637,6 +755,8 @@ sub group_by_loop($) {
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}
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# What is left of $groupby is $perlexpr
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$perlexpr = $groupby;
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$Global::group_by_perlexpr = $perlexpr;
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$Global::group_by_column = $col;
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my $loop = ::spacefree(0,'{
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local $_=COLVALUE;
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@ -1792,7 +1912,7 @@ sub check_invalid_option_combinations() {
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::wait_and_exit(255);
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}
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if($opt::groupby) {
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if(not $opt::pipe) {
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if(not $opt::pipe and not $opt::pipepart) {
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$opt::pipe = 1;
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}
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if($opt::remove_rec_sep) {
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@ -1807,12 +1927,6 @@ sub check_invalid_option_combinations() {
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::error("--recend is not compatible with --groupby");
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::wait_and_exit(255);
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}
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if($opt::pipepart) {
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# TODO This may be possible to do later
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# Finding split points might be a bitch though
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::error("--pipepart is not compatible with --groupby");
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::wait_and_exit(255);
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}
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}
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}
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@ -12558,7 +12672,7 @@ sub main() {
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pipe_shard_setup();
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}
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if($opt::groupby) {
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if(not $opt::pipepart and $opt::groupby) {
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group_by_stdin_filter();
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}
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if($opt::eta or $opt::bar or $opt::shuf or $Global::halt_pct) {
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@ -797,8 +797,8 @@ See also: B<--line-buffer> B<--ungroup>
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=item B<--group-by> I<val> (alpha testing)
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Group input by value. Combined with B<--pipe> B<--group-by> groups
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lines with the same value into a record.
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Group input by value. Combined with B<--pipe>/B<--pipepart>
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B<--group-by> groups lines with the same value into a record.
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The value can be computed from the full line or from a single column.
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@ -815,6 +815,8 @@ Use the value in the column numbered.
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Treat the first line as a header and use the value in the column
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named.
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(Not supported with B<--pipepart>).
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=item Z<> perl expression
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Run the perl expression and use $_ as the value.
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@ -827,17 +829,19 @@ Put the value of the column put in $_, run the perl expression, and use $_ as th
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Put the value of the column put in $_, run the perl expression, and use $_ as the value.
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(Not supported with B<--pipepart>).
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=back
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Example:
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UserID, Consumption
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123, 1
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123, 2
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12-3, 1
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221, 3
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221, 1
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2/21, 5
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123, 1
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123, 2
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12-3, 1
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221, 3
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221, 1
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2/21, 5
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If you want to group 123, 12-3, 221, and 2/21 into 4 records and pass
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one record at a time to B<wc>:
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@ -861,7 +865,7 @@ UserID when grouping:
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cat table.csv | parallel --pipe --colsep , --header : \
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--group-by 'UserID s/\D//g' -kN1 wc
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See also B<--shard>.
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See also B<--shard>, B<--roundrobin>.
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=item B<--help>
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@ -1975,6 +1979,8 @@ impossible to track which input block corresponds to which output.
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B<--roundrobin> implies B<--pipe>, except if B<--pipepart> is given.
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See also B<--group-by>, B<--shard>.
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=item B<--rpl> 'I<tag> I<perl expression>'
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@ -2164,6 +2170,8 @@ I<shardkey> is small (<10), slower if it is big (>100).
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B<--shard> requires B<--pipe> and a fixed numeric value for B<--jobs>.
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See also B<--group-by>, B<--roundrobin>.
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=item B<--shebang>
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@ -4462,6 +4470,46 @@ files:
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$ tracefile -un ./configure | tail | parallel -j0 apt-file search
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=head1 SPREADING BLOCKS OF DATA
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B<--round-robin>, B<--pipe-part>, B<--shard>, and B<--group-by> are
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all specialized versions of B<--pipe>.
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In the following I<n> is the number of jobslots given by B<--jobs>. A
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record starts with B<--recstart> and ends with B<--recend>. It is
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typically a full line. A chunk is a number of full records that is
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approximately the size of a block. A block can contain half records, a
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chunk cannot.
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B<--pipe> starts one job per chunk. It reads blocks from stdin
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(standard input). It finds a record end near a block border and passes
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a chunk to the program.
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B<--pipe-part> starts one job per chunk - just like normal
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B<--pipe>. It first finds record endings near all block borders in the
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file and then starts the jobs. By using B<--block -1> it will set the
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block size to 1/I<n> * size-of-file. Used this way it will start I<n>
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jobs in total.
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B<--round-robin> starts I<n> jobs in total. It reads a block and
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passes a chunk to whichever job is ready to read. It does not parse
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the content except for identifying where a record ends to make sure it
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only passes full records.
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B<--shard> starts I<n> jobs in total. It parses each line to read the
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value in the given column. Based on this value the line is passed to
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one of the I<n> jobs. All lines having this value will be given to the
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same jobslot.
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B<--group-by> starts one job per chunk. Record borders are not given
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by B<--recend>/B<--recstart>. Instead a record is defined by a number
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of lines having the same value in a given column. So the value of a
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given column changes at a chunk border. With B<--pipe> every line is
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parsed, with B<--pipe-part> only a few lines are parsed to find the
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chunk border.
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B<--group-by> can be combined with B<--round-robin> or B<--pipe-part>.
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=head1 QUOTING
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GNU B<parallel> is very liberal in quoting. You only need to quote
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@ -189,5 +189,13 @@ par_test_build_and_install() {
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sudo parallel mv {} {.}
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}
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#par_crashing() {
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# echo '### bug #56322: sem crashed when running with input from seq'
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# echo "### This should not fail"
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# doit() { seq 100000000 |xargs -P 80 -n 1 sem true; }
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# export -f doit
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# parallel -j1 --timeout 100 --nice 11 doit ::: 1
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#}
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export -f $(compgen -A function | grep par_)
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compgen -A function | grep par_ | sort | parallel -vj0 -k --tag --joblog /tmp/jl-`basename $0` '{} 2>&1'
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