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Fixed bug #52740: Bash redirection with process substitution blocks.
This commit is contained in:
Ole Tange
parent
d9bac1136f
commit
d1aa26c1c9
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@ -210,20 +210,6 @@ Haiku of the month:
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New in this release:
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* env_parset for ash, dash, ksh, sh, zsh
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* Automatically create hostgroups if argument ends in @sshlogin
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* Tips for running jobs on your VM https://support.ehelp.edu.au/support/solutions/articles/6000089713-tips-for-running-jobs-on-your-vm#parallel
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* Node-local scheduling https://mogonwiki.zdv.uni-mainz.de/dokuwiki/node_local_scheduling
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* GNU Parallel https://docs.computecanada.ca/wiki/GNU_Parallel
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* GNU Parallel のエラー処理 https://qiita.com/inouet/items/bfc208668c86caf8ff74
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* Using GNU Parallel https://wiki.ncsa.illinois.edu/display/ROGER/Using+GNU+Parallel
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<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20171222;
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$Global::version = 20171224;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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27
src/parallel
27
src/parallel
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@ -1100,8 +1100,13 @@ sub get_options_from_array {
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sub parse_options {
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# Returns: N/A
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init_globals();
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my @argv_before = @ARGV;
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@ARGV = read_options();
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if(defined $opt::citation) {
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citation(\@argv_before,\@ARGV);
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wait_and_exit(0);
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}
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# no-* overrides *
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if($opt::nokeeporder) { $opt::keeporder = undef; }
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@ -1162,7 +1167,6 @@ sub parse_options {
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print Limits::Command::real_max_length(),"\n"; wait_and_exit(0);
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}
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if(defined $opt::version) { version(); wait_and_exit(0); }
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if(defined $opt::citation) { citation(); wait_and_exit(0); }
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if(defined $opt::record_env) { record_env(); wait_and_exit(0); }
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if(defined $opt::show_limits) { show_limits(); }
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if(@opt::sshlogin) { @Global::sshlogin = @opt::sshlogin; }
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@ -1387,7 +1391,7 @@ sub check_invalid_option_combinations {
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sub init_globals {
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# Defaults:
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$Global::version = 20171222;
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$Global::version = 20171224;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -2750,8 +2754,8 @@ sub drain_job_queue {
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if($Global::start_sqlworker) {
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# Start an SQL worker as we are now sure there is work to do
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$Global::start_sqlworker = 0;
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if(fork()) {
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# skip
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if(my $pid = fork()) {
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$Global::unkilled_sqlworker = $pid;
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} else {
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# Replace --sql/--sqlandworker with --sqlworker
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my @ARGV = map { s/^--sql(andworker)?$/--sqlworker/; $_ } @Global::options_in_argv;
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@ -4010,11 +4014,13 @@ sub wait_and_exit {
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}
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for (keys %Global::unkilled_children) {
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# Kill any (non-jobs) children
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kill 9, $_;
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kill 9, $_;
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waitpid($_,0);
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delete $Global::unkilled_children{$_};
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}
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wait();
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if($Global::unkilled_sqlworker) {
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waitpid($Global::unkilled_sqlworker,0);
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}
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exit($error);
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}
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@ -4160,6 +4166,15 @@ sub version {
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sub citation {
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# Returns: N/A
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my ($all_argv_ref,$argv_options_removed_ref) = @_;
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my $all_argv = "@$all_argv_ref";
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my $no_opts = "@$argv_options_removed_ref";
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$all_argv=~s/--citation//;
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if($all_argv ne $no_opts) {
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::warning("--citation ignores all other options and arguments.");
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::status("");
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}
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::status(
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"Academic tradition requires you to cite works you base your article on.",
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"If you use programs that use GNU Parallel to process data for an article in a",
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@ -470,8 +470,8 @@ Implies B<--semaphore>.
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=item B<--citation>
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Print the BibTeX entry for GNU B<parallel> and silence citation
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notice.
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Print the BibTeX entry for GNU B<parallel>, silence citation
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notice and exit. It will not run any commands.
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If it is impossible for you to run B<--bibtex> you can use
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B<--will-cite>.
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@ -1327,6 +1327,47 @@ It can be emulated with GNU B<parallel> using this Bash function:
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This works execpt for the B<--exclude> option.
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=head2 DIFFERENCES BETWEEN pyargs AND GNU Parallel
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B<pyargs> deals badly with input containing spaces. It buffers stdout,
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but not stderr. It buffers in RAM. {} does not work as replacement
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string. It does not support running functions.
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B<pyargs> does not support composed commands if run with B<--lines>,
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and fails on B<pyargs traceroute pi.dk fi.dk>.
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=head3 Examples
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seq 5 | pyargs -P50 -L seq
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seq 5 | parallel -P50 --lb seq
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seq 5 | pyargs -P50 --mark -L seq
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seq 5 | parallel -P50 --lb \
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--tagstring OUTPUT'[{= $_=$job->replaced()=}]' seq
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# Similar, but not precisely the same
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seq 5 | parallel -P50 --lb --tag seq
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seq 5 | pyargs -P50 --mark command
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# Somewhat longer with GNU Parallel due to the special
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# --mark formatting
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cmd="$(echo "command" | parallel --shellquote)"
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wrap_cmd() {
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echo "MARK $cmd $@================================" >&3
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echo "OUTPUT START[$cmd $@]:"
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eval $cmd "$@"
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echo "OUTPUT END[$cmd $@]"
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}
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(seq 5 | env_parallel -P2 wrap_cmd) 3>&1
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# Similar, but not exactly the same
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seq 5 | parallel -t --tag command
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(echo '1 2 3';echo 4 5 6) | pyargs --stream seq
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(echo '1 2 3';echo 4 5 6) | perl -pe 's/\n/ /' |
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parallel -r -d' ' seq
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# Similar, but not exactly the same
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parallel seq ::: 1 2 3 4 5 6
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=head2 Todo
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machma. Requires Go >= 1.7.
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@ -1344,6 +1385,8 @@ https://github.com/Julian/Verge
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https://github.com/amattn/paral
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pyargs
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=head1 TESTING OTHER TOOLS
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@ -1363,18 +1406,22 @@ will most likely mix.
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cat <<-EOF > mycommand
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#!/bin/bash
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# If 'a', 'b' and 'c' mix: Very bad
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perl -e 'print "a"x3000_000," "'
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perl -e 'print "b"x3000_000," "'
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perl -e 'print "c"x3000_000," "'
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# If a, b, c, d, e, and f mix: Very bad
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perl -e 'print STDOUT "a"x3000_000," "'
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perl -e 'print STDERR "b"x3000_000," "'
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perl -e 'print STDOUT "c"x3000_000," "'
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perl -e 'print STDERR "d"x3000_000," "'
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perl -e 'print STDOUT "e"x3000_000," "'
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perl -e 'print STDERR "f"x3000_000," "'
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echo
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echo >&2
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EOF
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chmod +x mycommand
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# Run 30 jobs in parallel
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seq 30 | $paralleltool -j0 ./mycommand | tr -s abc
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seq 30 | $paralleltool -j0 ./mycommand > >(tr -s abcdef) 2> >(tr -s abcdef >&2)
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# 'a b c' should always stay together
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# 'a c e' and 'b d f' should always stay together
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# and there should only be a single line per job
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=head2 B: Output limited by RAM
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2
src/sql
2
src/sql
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@ -576,7 +576,7 @@ $Global::Initfile && unlink $Global::Initfile;
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exit ($err);
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sub parse_options {
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$Global::version = 20171222;
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$Global::version = 20171224;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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@ -94,7 +94,7 @@ portable:
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time bash Portable.sh
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timings: tests-to-run/* ../src/parallel
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ls tests-to-run/*.sh | parallel echo /usr/bin/time -f %e bash >/tmp/timing.script
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ls tests-to-run/*.sh | parallel echo /usr/bin/time -f "'%e\ %P'" bash >/tmp/timing.script
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stdout bash -x /tmp/timing.script | tee /tmp/timing.out
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echo + .usr.bin.time_END >>/tmp/timing.out
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perl -ne '/\+ .usr.bin.time/ and do { print $$last.$$h; $$h=$$_ }; chomp; s/.*\0//;$$last = $$_' /tmp/timing.out |sort -n >timings
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@ -804,6 +804,17 @@ par_halt_one_job() {
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parallel -j1 --halt soon,fail=1 'echo {#};exit {}' ::: 1 0 1
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}
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par_blocking_redir() {
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(
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echo 'bug #52740: Bash redirection with process substitution blocks'
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echo Test stdout
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echo 3 | parallel seq > >(echo stdout;wc) 2> >(echo stderr >&2; wc >&2)
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echo Test stderr
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echo nOfilE | parallel ls > >(echo stdout;wc) 2> >(echo stderr >&2; wc >&2)
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) 2>&1 | sort
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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 |
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parallel -j6 --tag -k --joblog +/tmp/jl-`basename $0` '{} 2>&1'
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@ -1344,6 +1344,17 @@ par_basic_halt true
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par_basic_halt parallel: Error: --halt must have 'never', 'soon', or 'now'.
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par_basic_halt parallel: Error: --halt soon must be followed by ,success or ,fail.
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par_basic_halt parallel: Error: --halt now must be followed by ,success or ,fail.
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par_blocking_redir 0 0 0
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par_blocking_redir 0 0 0
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par_blocking_redir 1 9 54
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par_blocking_redir 3 3 6
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par_blocking_redir Test stderr
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par_blocking_redir Test stdout
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par_blocking_redir bug #52740: Bash redirection with process substitution blocks
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par_blocking_redir stderr
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par_blocking_redir stderr
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par_blocking_redir stdout
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par_blocking_redir stdout
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par_colsep_0 bug --colsep 0
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par_colsep_0 OK
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par_colsep_0 OK
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