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parallel: Include parcat code in sharding to avoid depending on parcat.
This commit is contained in:
Ole Tange
parent
904cda6e19
commit
79666b4906
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@ -1,5 +1,14 @@
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Quote of the month:
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With GNU Parallel you sure can!
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I like getting things done
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--Kyle Lady @kylelady@twitter
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Y'all need some GNU parallel in your lives
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-- ChaKu @ChaiLovesChai@twitter
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286
src/parallel
286
src/parallel
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@ -196,9 +196,215 @@ sub pipe_tee_setup() {
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@Global::cat_appends = map { ") < $_" } @fifos;
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}
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sub pipe_demultiplex_setup() {
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sub parcat_script() {
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my $script = q'{
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use Symbol qw(gensym);
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use IPC::Open3;
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use POSIX qw(:errno_h);
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use IO::Select;
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use strict;
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use threads;
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use threads::shared;
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use Thread::Queue;
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use Fcntl qw(:DEFAULT :flock);
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my $opened :shared;
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my $q = Thread::Queue->new();
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my $okq = Thread::Queue->new();
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my @producers;
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if(not @ARGV) {
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if(-t *STDIN) {
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print "Usage:\n";
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print " parcat file(s)\n";
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print " cat argfile | parcat\n";
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} else {
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# Read arguments from stdin
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chomp(@ARGV = <STDIN>);
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}
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}
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my $files_to_open = 0;
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# Default: fd = stdout
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my $fd = 1;
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for (@ARGV) {
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# --rm = remove file when opened
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/^--rm$/ and do { $opt::rm = 1; next; };
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# -1 = output to fd 1, -2 = output to fd 2
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/^-(\d+)$/ and do { $fd = $1; next; };
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push @producers, threads->create("producer", $_, $fd);
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$files_to_open++;
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}
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sub producer {
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# Open a file/fifo, set non blocking, enqueue fileno of the file handle
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my $file = shift;
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my $output_fd = shift;
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open(my $fh, "<", $file) || do {
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print STDERR "parcat: Cannot open $file\n";
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exit(1);
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};
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# Remove file when it has been opened
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if($opt::rm) {
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unlink $file;
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}
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set_fh_non_blocking($fh);
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$opened++;
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# Pass the fileno to parent
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$q->enqueue(fileno($fh),$output_fd);
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# Get an OK that the $fh is opened and we can release the $fh
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while(1) {
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my $ok = $okq->dequeue();
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if($ok == fileno($fh)) { last; }
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# Not ours - very unlikely to happen
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$okq->enqueue($ok);
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}
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return;
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}
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my $s = IO::Select->new();
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my %buffer;
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sub add_file {
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my $infd = shift;
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my $outfd = shift;
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open(my $infh, "<&=", $infd) || die;
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open(my $outfh, ">&=", $outfd) || die;
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$s->add($infh);
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# Tell the producer now opened here and can be released
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$okq->enqueue($infd);
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# Initialize the buffer
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@{$buffer{$infh}{$outfd}} = ();
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$Global::fh{$outfd} = $outfh;
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}
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sub add_files {
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# Non-blocking dequeue
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my ($infd,$outfd);
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do {
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($infd,$outfd) = $q->dequeue_nb(2);
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if(defined($outfd)) {
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add_file($infd,$outfd);
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}
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} while(defined($outfd));
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}
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sub add_files_block {
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# Blocking dequeue
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my ($infd,$outfd) = $q->dequeue(2);
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add_file($infd,$outfd);
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}
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my $fd;
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my (@ready,$infh,$rv,$buf);
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do {
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# Wait until at least one file is opened
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add_files_block();
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while($q->pending or keys %buffer) {
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add_files();
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while(keys %buffer) {
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@ready = $s->can_read(0.01);
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if(not @ready) {
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add_files();
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}
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for $infh (@ready) {
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# There is only one key, namely the output file descriptor
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for my $outfd (keys %{$buffer{$infh}}) {
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$rv = sysread($infh, $buf, 65536);
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if (!$rv) {
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if($! == EAGAIN) {
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# Would block: Nothing read
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next;
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} else {
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# Nothing read, but would not block:
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# This file is done
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$s->remove($infh);
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for(@{$buffer{$infh}{$outfd}}) {
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syswrite($Global::fh{$outfd},$_);
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}
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delete $buffer{$infh};
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# Closing the $infh causes it to block
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# close $infh;
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add_files();
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next;
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}
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}
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# Something read.
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# Find \n or \r for full line
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my $i = (rindex($buf,"\n")+1);
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if($i) {
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# Print full line
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for(@{$buffer{$infh}{$outfd}}, substr($buf,0,$i)) {
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syswrite($Global::fh{$outfd},$_);
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}
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# @buffer = remaining half line
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$buffer{$infh}{$outfd} = [substr($buf,$i,$rv-$i)];
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} else {
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# Something read, but not a full line
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push @{$buffer{$infh}{$outfd}}, $buf;
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}
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redo;
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}
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}
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}
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}
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} while($opened < $files_to_open);
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for (@producers) {
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$_->join();
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}
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sub set_fh_non_blocking {
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# Set filehandle as non-blocking
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# Inputs:
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# $fh = filehandle to be blocking
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# Returns:
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# N/A
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my $fh = shift;
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my $flags;
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fcntl($fh, &F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
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$flags |= &O_NONBLOCK; # Add non-blocking to the flags
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fcntl($fh, &F_SETFL, $flags) || die $!; # Set the flags on the filehandle
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}
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}';
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return ::spacefree(1, $script);
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}
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sub sharder_script() {
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my $script = q{
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use B;
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# Column separator
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my $sep = shift;
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# Which columns to shard on (count from 1)
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my $col = shift;
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# Which columns to shard on (count from 0)
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my $col0 = $col - 1;
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my $bins = @ARGV;
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# Open fifos for writing, fh{0..$bins}
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my $t = 0;
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my %fh;
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for(@ARGV) {
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open $fh{$t++}, ">", $_;
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# open blocks until it is opened by reader
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# so unlink only happens when it is ready
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unlink $_;
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}
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while(<STDIN>) {
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# Split into $col columns (no need to split into more)
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@F = split $sep, $_, $col+1;
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$fh = $fh{ hex(B::hash($F[$col0]))%$bins };
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print $fh $_;
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}
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# Close all open fifos
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close values %fh;
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};
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return ::spacefree(1, $script);
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}
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sub pipe_shard_setup() {
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# Create temporary fifos
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# Run 'demux.pl sep col fifo1 fifo2 fifo3 ... fifoN' in the background
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# Run 'shard.pl sep col fifo1 fifo2 fifo3 ... fifoN' in the background
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# This will spread the input to fifos
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# Generate commands that reads from fifo1..N:
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# cat fifo | user_command
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@ -206,51 +412,37 @@ sub pipe_demultiplex_setup() {
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# @Global::cat_prepends
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my @fifos;
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# TODO $opt::jobs should be evaluated (100%)
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for(1..$opt::jobs) {
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push @fifos, tmpfifo();
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for(0..$opt::jobs-1) {
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# push @fifos, tmpfifo();
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push @{$fifos[$_]}, tmpfifo();
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}
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my $script = ::spacefree(1,q{
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BEGIN {
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use B;
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# Which columns to demultiplex on (count from 1)
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$col = (shift) - 1;
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$bins = @ARGV;
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# Open fifos for writing, fh{0..$bins}
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my $t = 0;
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for(@ARGV) {
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open $fh{$t++}, ">", $_;
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# open blocks until it is opened by reader
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# so unlink only happens when it is ready
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unlink $_;
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}
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# the -n wrapper should read from STDIN - not files
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@ARGV = ();
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};
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# Wrapped in while(<>) due to -n
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$fh = $fh{ hex(B::hash($F[$col]))%$bins };
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print $fh $_;
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END {
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# Close all open fifos
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close values %fh;
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}
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});
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# cat foo | demuxer sep col fifo1 fifo2 fifo3 ... fifoN
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::debug("demux",'perl', '-F', $opt::colsep,
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'-ane', $script, $opt::demultiplex, @fifos);
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my $script = sharder_script();
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# cat foo | sharder sep col fifo1 fifo2 fifo3 ... fifoN
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my @fif = map { $_->[0] } @fifos;
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# ::debug("shard",'perl', '-e', $script, ($opt::colsep || ","), $opt::shard, @fif);
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if(not fork()){
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# Let the demuxer inherit our stdin
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# Let the sharder inherit our stdin
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# and redirect stdout to null
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open STDOUT, ">","/dev/null";
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exec 'perl', "-F".($opt::colsep || ","),
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'-ane', $script, $opt::demultiplex, @fifos;
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# exec 'perl', '-e', $script, ($opt::colsep || ","), $opt::shard, @fifos;
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@fif = map { $_->[0] } @fifos;
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exec 'perl', '-e', $script, ($opt::colsep || ","), $opt::shard, @fif;
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}
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# parallel --round-robin $script $opt ::: @fifos[0] ::: @fifos[1]
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# For each fifo
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# (rm fifo1; grep 1) < fifo1
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# (rm fifo2; grep 2) < fifo2
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# (rm fifo3; grep 3) < fifo3
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# Remove the tmpfifo as soon as it is open
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@Global::cat_prepends = map { "(true $_;" } @fifos;
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@Global::cat_appends = map { ") < $_" } @fifos;
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my $parcat = Q(parcat_script());
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if(not $parcat) {
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::error("'parcat' must be in path.");
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::wait_and_exit(255);
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}
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# @Global::cat_prepends = map { "perl -e $parcat $_ | " } @fifos;
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@Global::cat_prepends = map { "perl -e $parcat @$_ | " } @fifos;
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# warn map { "$_\n" } @Global::cat_prepends;
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}
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sub pipe_part_files(@) {
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@ -343,7 +535,7 @@ sub find_split_positions($$$) {
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while(read($fh,substr($buf,length $buf,0),$dd_block_size)) {
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if($opt::regexp) {
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# If match /$recend$recstart/ => Record position
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if($buf =~ /^(.*$recend)$recstart/os) {
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if($buf =~ m:^(.*$recend)$recstart:os) {
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# Start looking for next record _after_ this match
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$pos += length($1);
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push(@pos,$pos);
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@ -1065,7 +1257,7 @@ sub options_hash() {
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"fifo" => \$opt::fifo,
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"pipepart|pipe-part" => \$opt::pipepart,
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"tee" => \$opt::tee,
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"demultiplex|demux=s" => \$opt::demultiplex,
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"shard=s" => \$opt::shard,
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"hgrp|hostgrp|hostgroup|hostgroups" => \$opt::hostgroups,
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"embed" => \$opt::embed,
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);
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@ -4892,7 +5084,7 @@ sub which(@) {
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push(@which, grep { not -d $_ and -x $_ } $prg);
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}
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}
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return @which;
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return wantarray ? @which : $which[0];
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}
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{
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@ -8023,7 +8215,7 @@ sub wrapped($) {
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# --pipe --tee: wrap:
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# (rm fifo; ... ) < fifo
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#
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# --pipe --demux X:
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# --pipe --shard X:
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# (rm fifo; ... ) < fifo
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$command = (shift @Global::cat_prepends). "($command)".
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(shift @Global::cat_appends);
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@ -8796,7 +8988,7 @@ sub start($) {
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::set_fh_non_blocking($stdin_fh);
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}
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$job->set_fh(0,"w",$stdin_fh);
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if($opt::tee or $opt::demultiplex) { $job->set_virgin(0); }
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if($opt::tee or $opt::shard) { $job->set_virgin(0); }
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} elsif ($opt::tty and -c "/dev/tty" and
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open(my $devtty_fh, "<", "/dev/tty")) {
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# Give /dev/tty to the command if no one else is using it
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@ -12205,8 +12397,8 @@ sub main() {
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pipepart_setup();
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} elsif($opt::pipe and $opt::tee) {
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pipe_tee_setup();
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} elsif($opt::pipe and $opt::demultiplex) {
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pipe_demultiplex_setup();
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} elsif($opt::pipe and $opt::shard) {
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pipe_shard_setup();
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}
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if($opt::eta or $opt::bar or $opt::shuf or $Global::halt_pct) {
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@ -12226,8 +12418,8 @@ sub main() {
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}
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$SIG{TERM} = \&start_no_new_jobs;
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if($opt::tee or $opt::demultiplex) {
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# All jobs must be running in parallel for --tee
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if($opt::tee or $opt::shard) {
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# All jobs must be running in parallel for --tee/--shard
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while(start_more_jobs()) {}
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$Global::start_no_new_jobs = 1;
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if(not $Global::JobQueue->empty()) {
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|
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@ -61,15 +61,16 @@ or download it at: https://doi.org/10.5281/zenodo.1146014
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Otherwise start by watching the intro videos for a quick introduction:
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http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
|
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|
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Then look at the B<EXAMPLE>s after the list of B<OPTIONS> (Use
|
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B<LESS=+/EXAMPLE: man parallel>). That will give you an idea of what
|
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GNU B<parallel> is capable of.
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Then browse through the B<EXAMPLE>s after the list of B<OPTIONS> in
|
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B<man parallel> (Use B<LESS=+/EXAMPLE: man parallel>). That will give
|
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you an idea of what GNU B<parallel> is capable of.
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Then spend an hour walking through the tutorial (B<man
|
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parallel_tutorial>). Your command line will love you for it.
|
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If you want to dive even deeper: spend a couple of hours walking
|
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through the tutorial (B<man parallel_tutorial>). Your command line
|
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will love you for it.
|
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|
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Finally you may want to look at the rest of this manual if you have
|
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special needs not already covered.
|
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Finally you may want to look at the rest of the manual (B<man
|
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parallel>) if you have special needs not already covered.
|
||||
|
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If you want to know the design decisions behind GNU B<parallel>, try:
|
||||
B<man parallel_design>. This is also a good intro if you intend to
|
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|
|
@ -634,21 +635,6 @@ escape codes are understood as for the printf command. Multibyte
|
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characters are not supported.
|
||||
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=item B<--demux> I<col> (alpha testing)
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=item B<--demultiplex> I<col> (alpha testing)
|
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Demultiplex input on column number I<col>. Input is split using
|
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B<--colsep>. The value in the column is hashed so that all lines of a
|
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given value is given to the same job slot.
|
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|
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This is a bit similar to B<--roundrobin> in that all data is given to
|
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a limited number of jobs, but opposite B<--roundrobin> data is given
|
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to a specific job slot based on the value in a column.
|
||||
|
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The performance is in the order of 1M rows per second.
|
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|
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|
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=item B<--dirnamereplace> I<replace-str>
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=item B<--dnr> I<replace-str>
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|
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@ -2086,6 +2072,20 @@ Only supported in B<Ash, Bash, Dash, Ksh, Sh, and Zsh>.
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See also B<--env>, B<--record-env>.
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=item B<--shard> I<shardkey> (alpha testing)
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Use column I<shardkey> as shard key and shard input to the jobs.
|
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Each input line is split using B<--colsep>. The value in the
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I<shardkey> column is hashed so that all lines of a given value is
|
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given to the same job slot.
|
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|
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This is similar to sharding in databases.
|
||||
|
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The performance is in the order of 100K rows per second. Faster if the
|
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I<shardkey> is small (<10), slower if it is big (>100).
|
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|
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|
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=item B<--shebang>
|
||||
|
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=item B<--hashbang>
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|
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|
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|
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@ -9,15 +9,28 @@ real world.
|
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|
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=head2 Reader's guide
|
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|
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Start by watching the intro videos for a quick introduction:
|
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If you prefer reading a book buy B<GNU Parallel 2018> at
|
||||
http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
|
||||
or download it at: https://doi.org/10.5281/zenodo.1146014
|
||||
|
||||
Otherwise start by watching the intro videos for a quick introduction:
|
||||
http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
|
||||
|
||||
Then look at the B<EXAMPLE>s after the list of B<OPTIONS> in B<man
|
||||
parallel> (Use B<LESS=+/EXAMPLE: man parallel>). That will give you
|
||||
an idea of what GNU B<parallel> is capable of.
|
||||
Then browse through the B<EXAMPLE>s after the list of B<OPTIONS> in
|
||||
B<man parallel> (Use B<LESS=+/EXAMPLE: man parallel>). That will give
|
||||
you an idea of what GNU B<parallel> is capable of.
|
||||
|
||||
If you want to dive even deeper: spend a couple of hours walking
|
||||
through the tutorial (B<man parallel_tutorial>). Your command line
|
||||
will love you for it.
|
||||
|
||||
Finally you may want to look at the rest of the manual (B<man
|
||||
parallel>) if you have special needs not already covered.
|
||||
|
||||
If you want to know the design decisions behind GNU B<parallel>, try:
|
||||
B<man parallel_design>. This is also a good intro if you intend to
|
||||
change GNU B<parallel>.
|
||||
|
||||
Then spend a couple of hours walking through this tutorial (B<man
|
||||
parallel_tutorial>). Your command line will love you for it.
|
||||
|
||||
|
||||
=head1 Prerequisites
|
||||
|
|
|
|||
|
|
@ -901,9 +901,28 @@ par_wd_dotdotdot() {
|
|||
parallel --wd ... 'echo $OLDPWD' ::: foo
|
||||
}
|
||||
|
||||
par_demux() {
|
||||
echo '### --demux'
|
||||
seq 100000 | parallel --pipe --demux 1 -j5 'echo {#}; cat' | wc
|
||||
par_shard() {
|
||||
echo '### --shard'
|
||||
# Each of the 5 lines should match:
|
||||
# ##### ##### ######
|
||||
seq 100000 | parallel --pipe --shard 1 -j5 wc |
|
||||
perl -pe 's/(.*\d{5,}){3}/OK/'
|
||||
# Data should be sharded to all processes
|
||||
shard_on_col() {
|
||||
col=$1
|
||||
seq 10 99 | shuf | perl -pe 's/(.)/$1\t/g' |
|
||||
parallel --pipe --shard $col -j2 --colsep "\t" sort -k$col |
|
||||
field $col | uniq -c | sort
|
||||
}
|
||||
shard_on_col 1
|
||||
shard_on_col 2
|
||||
echo '*** broken'
|
||||
# Shorthand for --pipe -j+0
|
||||
seq 100000 | parallel --shard 1 wc |
|
||||
perl -pe 's/(.*\d{5,}){3}/OK/'
|
||||
# Combine with arguments
|
||||
seq 100000 | parallel --shard 1 echo {}\;wc ::: {1..5} ::: a b |
|
||||
perl -pe 's/(.*\d{5,}){3}/OK/'
|
||||
}
|
||||
|
||||
export -f $(compgen -A function | grep par_)
|
||||
|
|
|
|||
|
|
@ -1299,8 +1299,6 @@ par_csv_pipe 11000"
|
|||
par_csv_pipe More records in single block
|
||||
par_csv_pipe 9000"
|
||||
par_csv_pipe 11000"
|
||||
par_demux ### --demux
|
||||
par_demux 100005 100005 588905
|
||||
par_dryrun_append_joblog --dry-run should not append to joblog
|
||||
par_dryrun_append_joblog 1
|
||||
par_dryrun_append_joblog 2
|
||||
|
|
@ -1519,6 +1517,33 @@ par_retries_replacement_string 33
|
|||
par_sem_quote ### sem --quote should not add empty argument
|
||||
par_sem_quote echo
|
||||
par_sem_quote
|
||||
par_shard ### --shard
|
||||
par_shard OK
|
||||
par_shard OK
|
||||
par_shard OK
|
||||
par_shard OK
|
||||
par_shard OK
|
||||
par_shard 10 1
|
||||
par_shard 10 2
|
||||
par_shard 10 3
|
||||
par_shard 10 4
|
||||
par_shard 10 5
|
||||
par_shard 10 6
|
||||
par_shard 10 7
|
||||
par_shard 10 8
|
||||
par_shard 10 9
|
||||
par_shard 9 0
|
||||
par_shard 9 1
|
||||
par_shard 9 2
|
||||
par_shard 9 3
|
||||
par_shard 9 4
|
||||
par_shard 9 5
|
||||
par_shard 9 6
|
||||
par_shard 9 7
|
||||
par_shard 9 8
|
||||
par_shard 9 9
|
||||
par_shard parallel: Error: --tee requres --jobs to be higher. Try --jobs 0.
|
||||
par_shard parallel: Error: --tee requres --jobs to be higher. Try --jobs 0.
|
||||
par_slow_pipe_regexp ### bug #53718: --pipe --regexp -N blocks
|
||||
par_slow_pipe_regexp This should take a few ms, but took more than 2 hours
|
||||
par_slow_pipe_regexp 980 981 5881
|
||||
|
|
|
|||
Loading…
Reference in a new issue