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parallel: Fixed bug #56275: --shard with named column and perl expr.
This commit is contained in:
Ole Tange
parent
17a5fd702d
commit
5d81c7c053
12
doc/haikus
12
doc/haikus
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@ -1,5 +1,17 @@
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Quote of the month:
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I love so much @GnuParallel to parallelize my SQL requests on @PostgreSQL
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-- @rmaziere_85 Romain
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I want to make a shout-out for @GnuParallel, it's a work of beauty and power
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-- Cristian Consonni @CristianCantoro
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Parallel is the BEST command.
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-- Nick @NickInfoSec
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It is SUPER easy to speed up jobs from the command line w/ GNU parallel.
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-- B3n @B3njaminHimes@twitter
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GNU parallel really changed how I do a lot of data processing stuff
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-- Brendan Dolan-Gavitt @moyix@twitter
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17
doc/promo
17
doc/promo
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@ -38,11 +38,20 @@ newest version.
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Before GNU Parallel was a GNU tool, it started as a wrapper around
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`make -j`. But GNU Parallel grew, and was no longer just a small
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hack. To make the code easier to maintain it was rewritten to object
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orientation.
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hack.
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This would not have been possible if the test suite had not been so
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thorough: It made it much easier to see if
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The design goals included not requiring a compiler, compatibility with
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old operating systems, and single file program. This limited the
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languages tremendously.
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Perl and Python were in practice the only possibilities. Python was at
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the time quite slow, ressource hungry, and not as widely installed as
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Perl. So Perl was the choice.
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To make the code easier to maintain it was rewritten to object
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orientation. This would not have been possible if the test suite had
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not been so thorough: It made it much easier to see if a code change
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cause change in behaviour.
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=head2 --tollef
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@ -206,9 +206,9 @@ 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 ('Akihito') released <<[stable]>>
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Subject: GNU Parallel 20190622 ('Frederiksen/Saybie/HongKong') 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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GNU Parallel 20190622 ('') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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@ -218,19 +218,16 @@ See https://www.gnu.org/software/parallel/10-years-anniversary.html
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Quote of the month:
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Amazingly useful script!
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-- unxusr@reddit.com
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<<>>
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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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https://livefreeordichotomize.com/2019/06/04/using_awk_and_r_to_parse_25tb/
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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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https://zh.wikipedia.org/wiki/GNU_parallel
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chck NEWS http://parallelandvisualtestingwithbehat.blogspot.com/p/blog-page.html
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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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* GNU Parallel Akihito released https://linuxreviews.org/GNU_Parallel_Akihito_released
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* Bug fixes and man page updates.
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42
src/parallel
42
src/parallel
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@ -378,6 +378,8 @@ sub sharder_script() {
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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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# Perl expression
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my $perlexpr = shift;
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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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@ -388,11 +390,25 @@ sub sharder_script() {
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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 $_;
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if($perlexpr) {
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my $subref = eval("sub { no strict; no warnings; $perlexpr }");
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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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{
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local $_ = $F[$col0];
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&$subref();
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$fh = $fh{ hex(B::hash($_))%$bins };
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}
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print $fh $_;
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}
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} else {
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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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}
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# Close all open fifos
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close values %fh;
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@ -423,6 +439,20 @@ sub pipe_shard_setup() {
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my $script = sharder_script();
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# cat foo | sharder sep col fifo1 fifo2 fifo3 ... fifoN
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if($opt::shard =~ /^[a-z_][a-z_0-9]*(\s|$)/i) {
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# Group by column name
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# (Yes, this will also wrongly match a perlexpr like: chop)
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my($read,$char,@line);
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# A full line, but nothing more (the rest must be read by the child)
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# $Global::header used to prepend block to each job
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do {
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$read = sysread(STDIN,$char,1);
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push @line, $char;
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} while($read and $char ne "\n");
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$Global::header = join "", @line;
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}
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my ($col, $perlexpr, $subref) =
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column_perlexpr($opt::shard, $Global::header, $opt::colsep);
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if(not fork()) {
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# Let the sharder inherit our stdin
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# and redirect stdout to null
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@ -432,7 +462,7 @@ sub pipe_shard_setup() {
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$ENV{'PERL_HASH_SEED'} = $$;
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exec qw(parallel --block 100k -q --pipe -j), $njobs,
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qw(--roundrobin -u perl -e), $script, ($opt::colsep || ","),
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$opt::shard, '{}', (map { (':::+', @{$_}) } @parcatfifos);
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$col, $perlexpr, '{}', (map { (':::+', @{$_}) } @parcatfifos);
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}
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# For each fifo
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# (rm fifo1; grep 1) < fifo1
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@ -2155,13 +2155,17 @@ 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<shardcol> (beta testing)
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=item B<--shard> I<shardexpr> (alpha testing)
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Use column I<shardcol> as shard key and shard input to the jobs.
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Use I<shardexpr> 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<shardcol> 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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I<shardexpr> is [column number|column name] [perlexpression] e.g. 3,
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Address, 3 $_%=100, Address s/\d//g.
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Each input line is split using B<--colsep>. The value of the column is
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put into $_, the perl expression is executed, the resulting value is
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hashed so that all lines of a given value is given to the same job
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slot.
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This is similar to sharding in databases.
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@ -68,8 +68,12 @@ The commands to run can be an array:
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echo "${data[1]}"
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echo "${data[2]}"
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B<parset> can not be part of a pipe. In particular this means it
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cannot read anything from standard input (stdin) or write to a pipe:
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B<parset> can read from stdin (standard input) if it is a file:
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parset res echo < parallel_input_file
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but B<parset> can not be part of a pipe. In particular this means it
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cannot read from a pipe or write to a pipe:
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seq 10 | parset res echo Does not work
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@ -124,8 +128,12 @@ Put output into vars B<$seq, $pwd, $ls>:
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parset "seq pwd ls" ::: "seq 10" pwd ls
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echo "$ls"
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B<parset> can not be part of a pipe. In particular this means it
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cannot read anything from standard input (stdin) or write to a pipe:
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B<parset> can read from stdin (standard input) if it is a file:
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parset res1,res2,res3 echo < parallel_input_file
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but B<parset> can not be part of a pipe. In particular this means it
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cannot read from a pipe or write to a pipe:
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seq 3 | parset res1,res2,res3 echo Does not work
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@ -4,6 +4,18 @@
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# Each should be taking 10-30s and be possible to run in parallel
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# I.e.: No race conditions, no logins
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par_kill_hup() {
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echo '### Are children killed if GNU Parallel receives HUP? There should be no sleep at the end'
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parallel -j 2 -q bash -c 'sleep {} & pid=$!; wait $pid' ::: 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 &
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T=$!
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sleep 9.9
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pstree $$
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kill -HUP $T
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sleep 2
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pstree $$
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}
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par_parset() {
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echo '### test parset'
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. `which env_parallel.bash`
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@ -61,6 +61,37 @@ par_shard() {
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}
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shard_on_col 1
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shard_on_col 2
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shard_on_col_name() {
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colname=$1
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col=$2
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(echo AB; seq 10 99 | shuf) | perl -pe 's/(.)/$1\t/g' |
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parallel --header : --pipe --shard $colname -j2 --colsep "\t" sort -k$col |
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field $col | uniq -c | sort
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}
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shard_on_col_name A 1
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shard_on_col_name B 2
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shard_on_col_expr() {
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colexpr="$1"
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col=$2
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(seq 10 99 | shuf) | perl -pe 's/(.)/$1\t/g' |
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parallel --pipe --shard "$colexpr" -j2 --colsep "\t" "sort -k$col; echo c1 c2" |
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field $col | uniq -c | sort
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}
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shard_on_col_expr '1 $_%=3' 1
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shard_on_col_expr '2 $_%=3' 2
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shard_on_col_name_expr() {
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colexpr="$1"
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col=$2
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(echo AB; seq 10 99 | shuf) | perl -pe 's/(.)/$1\t/g' |
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parallel --header : --pipe --shard "$colexpr" -j2 --colsep "\t" "sort -k$col; echo c1 c2" |
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field $col | uniq -c | sort
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}
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shard_on_col_name_expr 'A $_%=3' 1
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shard_on_col_name_expr 'B $_%=3' 2
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echo '*** broken'
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# Shorthand for --pipe -j+0
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seq 100000 | parallel --shard 1 wc |
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@ -148,18 +179,6 @@ par_kill_term() {
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pstree $$
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}
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par_kill_hup() {
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echo '### Are children killed if GNU Parallel receives HUP? There should be no sleep at the end'
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parallel -j 2 -q bash -c 'sleep {} & pid=$!; wait $pid' ::: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 &
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T=$!
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sleep 2.9
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pstree $$
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kill -HUP $T
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sleep 2
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pstree $$
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}
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par_kill_int_twice() {
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echo '### Are children killed if GNU Parallel receives INT twice? There should be no sleep at the end'
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@ -258,6 +258,15 @@ par_kill_children_timeout parallel: Warning: This job was killed because it time
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par_kill_children_timeout parallel: Warning: doit 1000000001
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par_kill_children_timeout 2
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par_kill_children_timeout 0 0 0
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par_kill_hup ### Are children killed if GNU Parallel receives HUP? There should be no sleep at the end
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par_kill_hup bash-+-perl
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par_kill_hup `-pstree
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par_kill_hup parallel: SIGHUP received. No new jobs will be started.
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par_kill_hup parallel: Waiting for these 2 jobs to finish. Send SIGTERM to stop now.
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par_kill_hup parallel: bash -c 'sleep 3 & pid=$!; wait $pid'
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par_kill_hup parallel: bash -c 'sleep 3 & pid=$!; wait $pid'
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par_kill_hup bash-+-perl---2*[bash---sleep]
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par_kill_hup `-pstree
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par_line_buffer ### --line-buffer
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par_line_buffer 55 55 120
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par_line_buffer These must diff: 1
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@ -1122,14 +1122,6 @@ par_jobslot_repl 2
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par_jobslot_repl 1
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par_jobslot_repl 2
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par_jobslot_repl 1
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par_kill_hup ### Are children killed if GNU Parallel receives HUP? There should be no sleep at the end
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par_kill_hup bash-+-perl---2*[bash---sleep]
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par_kill_hup `-pstree
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par_kill_hup parallel: SIGHUP received. No new jobs will be started.
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par_kill_hup parallel: Waiting for these 2 jobs to finish. Send SIGTERM to stop now.
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par_kill_hup parallel: bash -c 'sleep 1 & pid=$!; wait $pid'
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par_kill_hup parallel: bash -c 'sleep 1 & pid=$!; wait $pid'
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par_kill_hup bash---pstree
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par_kill_int_twice ### Are children killed if GNU Parallel receives INT twice? There should be no sleep at the end
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par_kill_int_twice bash-+-perl---bash---sleep
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par_kill_int_twice `-pstree
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@ -1288,6 +1280,71 @@ par_shard 9 6
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par_shard 9 7
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par_shard 9 8
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par_shard 9 9
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par_shard 10 1
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par_shard 10 2
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par_shard 10 3
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par_shard 10 4
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par_shard 10 5
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par_shard 10 6
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par_shard 10 7
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par_shard 10 8
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par_shard 10 9
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par_shard 9 0
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par_shard 9 1
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par_shard 9 2
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par_shard 9 3
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par_shard 9 4
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par_shard 9 5
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par_shard 9 6
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par_shard 9 7
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par_shard 9 8
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par_shard 9 9
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par_shard 10 1
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par_shard 10 2
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par_shard 10 3
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par_shard 10 4
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par_shard 10 5
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par_shard 10 6
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par_shard 10 7
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par_shard 10 8
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par_shard 10 9
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par_shard 1 c1
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par_shard 1 c1
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par_shard 1 c2
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par_shard 1 c2
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par_shard 9 0
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par_shard 9 1
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par_shard 9 2
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par_shard 9 3
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par_shard 9 4
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par_shard 9 5
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par_shard 9 6
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par_shard 9 7
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par_shard 9 8
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par_shard 9 9
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par_shard 10 1
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par_shard 10 2
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par_shard 10 3
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par_shard 10 4
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par_shard 10 5
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par_shard 10 6
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par_shard 10 7
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par_shard 10 8
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par_shard 10 9
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par_shard 1 c1
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par_shard 1 c1
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par_shard 1 c2
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par_shard 1 c2
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par_shard 9 0
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par_shard 9 1
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par_shard 9 2
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par_shard 9 3
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par_shard 9 4
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par_shard 9 5
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par_shard 9 6
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par_shard 9 7
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par_shard 9 8
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par_shard 9 9
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par_shard *** broken
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par_shard parallel: Error: --tee requres --jobs to be higher. Try --jobs 0.
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par_shard parallel: Error: --tee requres --jobs to be higher. Try --jobs 0.
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