mirror of
https://git.savannah.gnu.org/git/parallel.git
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parallel: Fixed bug #44995: parallel echo {#} ::: 1 2 ::: 1 2.
Passes testsuite.
This commit is contained in:
Ole Tange
parent
8110572719
commit
fc0c6cee08
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@ -226,13 +226,14 @@ New in this release:
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* <<afventer opdatering>> CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf
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* <<afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345
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taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
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* << afventer svar fra Rachel >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
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* GNU Parallel was cited in: Toward Enhanced Metadata Quality of Large-Scale Digital Libraries: Estimating Volume Time Range https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
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* GNU Parallel was cited in: Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv333.full.pdf
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* GNU Parallel was cited in: Genome assemblyusing Nanopore-guided long and error-free DNA reads http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
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@ -247,6 +248,10 @@ taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
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* Functions and GNU parallel for effective cluster load management http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
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* Use parallel processing to save time importing databases http://drupalsun.com/node/41854
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* Run multiple ssh commands in parallel with GNU Parallel http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html
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* Bug fixes and man page updates.
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GNU Parallel - For people who live life in the parallel lane.
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58
src/parallel
58
src/parallel
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@ -1053,7 +1053,7 @@ sub parse_options {
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sub init_globals {
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# Defaults:
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$Global::version = 20150424;
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$Global::version = 20150426;
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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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@ -3032,8 +3032,11 @@ sub reaper {
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next;
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}
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my $job = $Global::running{$stiff};
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# '-a <(seq 10)' will give us a pid not in %Global::running
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$job or next;
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delete $Global::running{$stiff};
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$Global::total_running--;
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$job->set_exitstatus($? >> 8);
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$job->set_exitsignal($? & 127);
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debug("run", "seq ",$job->seq()," died (", $job->exitstatus(), ")");
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@ -3042,7 +3045,9 @@ sub reaper {
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# The process that died had the tty => release it
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$Global::tty_taken = 0;
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}
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my $sshlogin = $job->sshlogin();
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$sshlogin->dec_jobs_running();
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$sshlogin->inc_jobs_completed();
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if(not $job->should_be_retried()) {
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# The job is done
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# Free the jobslot
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@ -3058,14 +3063,9 @@ sub reaper {
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}
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if($job->should_we_halt() eq "now") {
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::killall();
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::wait_and_exit($Global::exitstatus);
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::wait_and_exit($Global::halt_exitstatus);
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}
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}
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my $sshlogin = $job->sshlogin();
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$sshlogin->dec_jobs_running();
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$sshlogin->inc_jobs_completed();
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$Global::total_running--;
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delete $Global::running{$stiff};
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start_more_jobs();
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if($opt::progress) {
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my %progress = progress();
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@ -7490,9 +7490,16 @@ sub set_exitsignal {
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$Global::halt_pct <=
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$Global::total_failed / $Global::total_started
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and $Global::total_failed > 3)) {
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# More than N jobs or more than N% failed
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# At least N jobs had failed
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# or at least N% had failed and more than 3
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if($Global::halt_count and $Global::halt_count == 1) {
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$Global::halt_exitstatus = $job->exitstatus();
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if($Global::halt_when eq "soon") {
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} else {
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$Global::halt_exitstatus = $Global::total_failed;
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}
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::debug("halt","Pct: ",$Global::halt_pct,"<=",$Global::total_failed / $Global::total_started," count: ",$Global::halt_count,"\n");
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if($Global::halt_when eq "soon"
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and scalar(keys %Global::running) > 0) {
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::status
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("$Global::progname: Starting no more jobs. ",
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"Waiting for ", scalar(keys %Global::running),
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@ -7504,19 +7511,23 @@ sub set_exitsignal {
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}
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} else {
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if($Global::halt_success) {
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$Global::halt_exitstatus = $Global::total_failed;
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::status("$Global::progname: This job succeeded:\n",
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$job->replaced(),"\n");
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if(($Global::halt_count and
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$Global::halt_count <=
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1+$Global::total_completed-$Global::total_failed)
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$Global::total_completed-$Global::total_failed)
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or
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($Global::halt_pct and
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$Global::halt_pct <=
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(1+$Global::total_completed-$Global::total_failed)
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($Global::total_completed-$Global::total_failed)
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/ $Global::total_completed
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and ($Global::total_completed-$Global::total_failed) > 3)) {
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$Global::halt_exitstatus = $job->exitstatus();
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if($Global::halt_when eq "soon") {
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# At least N jobs had success
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# or at least N% had success and more than 3
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$Global::halt_exitstatus = 0;
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if($Global::halt_when eq "soon"
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and scalar(keys %Global::running) > 0) {
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::status
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("$Global::progname: Starting no more jobs. ",
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"Waiting for ", scalar(keys %Global::running),
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@ -8845,6 +8856,9 @@ sub new {
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}, ref($class) || $class;
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}
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{
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my %perleval;
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sub replace {
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# Calculates the corresponding value for a given perl expression
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# Returns:
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@ -8855,8 +8869,7 @@ sub replace {
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# This is actually a CommandLine-object,
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# but it looks nice to be able to say {= $job->slot() =}
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my $job = shift;
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$perlexpr =~ s/^-?\d+ //; # Positional replace treated as normal replace
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if(not defined $self->{"rpl",0,$perlexpr}) {
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$perlexpr =~ s/^-?\d+ +//; # Positional replace treated as normal replace
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local $_;
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if($Global::trim eq "n") {
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$_ = $self->{'orig'};
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@ -8864,10 +8877,10 @@ sub replace {
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$_ = trim_of($self->{'orig'});
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}
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::debug("replace", "eval ", $perlexpr, " ", $_, "\n");
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if(not $Global::perleval{$perlexpr}) {
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if(not $perleval{$perlexpr}) {
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# Make an anonymous function of the $perlexpr
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# And more importantly: Compile it only once
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if($Global::perleval{$perlexpr} =
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if($perleval{$perlexpr} =
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eval('sub { no strict; no warnings; my $job = shift; '.
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$perlexpr.' }')) {
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# All is good
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@ -8878,14 +8891,9 @@ sub replace {
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}
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}
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# Execute the function
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$Global::perleval{$perlexpr}->($job);
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$self->{"rpl",0,$perlexpr} = $_;
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$perleval{$perlexpr}->($job);
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return $quote ? ::shell_quote_scalar($_) : $_;
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}
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if(not defined $self->{"rpl",$quote,$perlexpr}) {
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$self->{"rpl",1,$perlexpr} =
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::shell_quote_scalar($self->{"rpl",0,$perlexpr});
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}
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return $self->{"rpl",$quote,$perlexpr};
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}
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sub orig {
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13
src/sem.pod
13
src/sem.pod
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@ -161,10 +161,17 @@ available.
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pod2html creates two files: pod2htmd.tmp and pod2htmi.tmp which it
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does not clean up. It uses these two files for a short time. But if
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you run multiple pod2html in parallel (e.g. in a Makefile with make
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-j) you need to protect pod2html from running twice at the same
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time. B<sem> running as a mutex will do just that:
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-j) there is a risk that two different instances of pod2html will
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write to the files at the same time:
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sem --fg --id pod2html pod2html foo.pod > foo.html
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# This may fail due to shared pod2htmd.tmp/pod2htmi.tmp files
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pod2html foo.pod --outfile foo.html & pod2html bar.pod --outfile bar.html
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You need to protect pod2html from running twice at the same time.
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B<sem> running as a mutex will make sure only one runs:
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sem --id pod2html pod2html foo.pod --outfile foo.html
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sem --id pod2html pod2html bar.pod --outfile bar.html
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sem --fg --id pod2html rm -f pod2htmd.tmp pod2htmi.tmp
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@ -14,6 +14,7 @@ echo '**'
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echo '### Test --halt-on-error 0';
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 0;
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echo $?;
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true";echo "sleep 4; non_exist") | parallel -j10 --halt 0;
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echo $?
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@ -22,6 +23,7 @@ echo '**'
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echo '### Test --halt-on-error 1';
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 1;
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echo $?;
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true";echo "sleep 4; non_exist") | parallel -j10 --halt 1;
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echo $?
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@ -30,6 +32,7 @@ echo '**'
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echo '### Test --halt-on-error 2';
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 2;
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echo $?;
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(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true";echo "sleep 4; non_exist") | parallel -j10 --halt 2;
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echo $?
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@ -38,6 +41,7 @@ echo '**'
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echo '### Test --halt -1';
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(echo "sleep 1;false"; echo "sleep 2;true";echo "sleep 3;false") | parallel -j10 --halt-on-error -1;
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echo $?;
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(echo "sleep 1;false"; echo "sleep 2;true";echo "sleep 3;false";echo "sleep 4; non_exist") | parallel -j10 --halt -1;
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echo $?
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@ -46,6 +50,7 @@ echo '**'
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echo '### Test --halt -2';
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(echo "sleep 1;false"; echo "sleep 2;true";echo "sleep 3;false") | parallel -j10 --halt-on-error -2;
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echo $?;
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(echo "sleep 1;false"; echo "sleep 2;true";echo "sleep 3;false";echo "sleep 4; non_exist") | parallel -j10 --halt -2;
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echo $?
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@ -19,12 +19,13 @@ echo '### Test --halt-on-error 1'; (echo "sleep 1;true"; echo "sleep 2;false";
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127
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parallel: This job failed:
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sleep 2;false
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parallel: Starting no more jobs. Waiting for 3 jobs to finish. This job failed:
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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parallel: This job failed:
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sleep 2;false
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
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/bin/bash: non_exist: command not found
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parallel: This job failed:
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sleep 4; non_exist
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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echo '**'
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**
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echo '### Test --halt-on-error 2'; (echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 2; echo $?; (echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true";echo "sleep 4; non_exist") | parallel -j10 --halt 2; echo $?
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@ -43,9 +44,10 @@ echo '### Test --halt -1'; (echo "sleep 1;false"; echo "sleep 2;true";echo "sl
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0
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parallel: This job succeeded:
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sleep 2;true
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parallel: Starting no more jobs. Waiting for 3 jobs to finish. This job succeeded:
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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parallel: This job succeeded:
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sleep 2;true
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parallel: Starting no more jobs. Waiting for 3 jobs to finish.
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
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/bin/bash: non_exist: command not found
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echo '**'
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**
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@ -66,40 +68,39 @@ exit code 9
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1
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 1
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parallel: Starting no more jobs. Waiting for 9 jobs to finish.
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parallel: Starting no more jobs. Waiting for 8 jobs to finish.
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2
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 2
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parallel: Starting no more jobs. Waiting for 8 jobs to finish.
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parallel: Starting no more jobs. Waiting for 7 jobs to finish.
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3
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 3
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parallel: Starting no more jobs. Waiting for 7 jobs to finish.
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parallel: Starting no more jobs. Waiting for 6 jobs to finish.
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4
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 4
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parallel: Starting no more jobs. Waiting for 6 jobs to finish.
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parallel: Starting no more jobs. Waiting for 5 jobs to finish.
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5
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 5
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parallel: Starting no more jobs. Waiting for 5 jobs to finish.
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parallel: Starting no more jobs. Waiting for 4 jobs to finish.
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6
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 6
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parallel: Starting no more jobs. Waiting for 4 jobs to finish.
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parallel: Starting no more jobs. Waiting for 3 jobs to finish.
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7
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 7
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parallel: Starting no more jobs. Waiting for 3 jobs to finish.
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
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8
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0
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 8
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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9
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parallel: This job failed:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ shift 9
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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echo '### Test last dying print --halt-on-error 2'; (seq 0 8;echo 0; echo 9) | parallel -j10 -kq --halt 2 perl -e 'sleep $ARGV[0];print STDERR @ARGV,"\n"; exit shift'; echo exit code $?
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### Test last dying print --halt-on-error 2
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exit code 1
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@ -114,40 +115,39 @@ exit code 0
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1
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 1
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parallel: Starting no more jobs. Waiting for 9 jobs to finish.
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parallel: Starting no more jobs. Waiting for 8 jobs to finish.
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2
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 2
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parallel: Starting no more jobs. Waiting for 8 jobs to finish.
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parallel: Starting no more jobs. Waiting for 7 jobs to finish.
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3
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 3
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parallel: Starting no more jobs. Waiting for 7 jobs to finish.
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parallel: Starting no more jobs. Waiting for 6 jobs to finish.
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4
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 4
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parallel: Starting no more jobs. Waiting for 6 jobs to finish.
|
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parallel: Starting no more jobs. Waiting for 5 jobs to finish.
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5
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 5
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parallel: Starting no more jobs. Waiting for 5 jobs to finish.
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parallel: Starting no more jobs. Waiting for 4 jobs to finish.
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6
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 6
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parallel: Starting no more jobs. Waiting for 4 jobs to finish.
|
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parallel: Starting no more jobs. Waiting for 3 jobs to finish.
|
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7
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 7
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parallel: Starting no more jobs. Waiting for 3 jobs to finish.
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
|
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8
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0
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parallel: This job succeeded:
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 8
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parallel: Starting no more jobs. Waiting for 2 jobs to finish.
|
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
|
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9
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parallel: This job succeeded:
|
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perl -e sleep\ \$ARGV\[0\]\;print\ STDERR\ @ARGV,\"\\n\"\;\ exit\ not\ shift 9
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parallel: Starting no more jobs. Waiting for 1 jobs to finish.
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echo '### Test last dying print --halt-on-error -2'; (seq 0 8;echo 0; echo 9) | parallel -j10 -kq --halt -2 perl -e 'sleep $ARGV[0];print STDERR @ARGV,"\n"; exit not shift'; echo exit code $?
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### Test last dying print --halt-on-error -2
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exit code 0
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|
|
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@ -478,9 +478,10 @@ Seq Host Starttime JobRuntime Send Receive Exitval Signal Command
|
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0
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1
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2
|
||||
parallel: Starting no more jobs. Waiting for 2 jobs to finish. This job failed:
|
||||
parallel: This job failed:
|
||||
echo 1; exit 1
|
||||
parallel: Starting no more jobs. Waiting for 1 jobs to finish. This job failed:
|
||||
parallel: Starting no more jobs. Waiting for 1 jobs to finish.
|
||||
parallel: This job failed:
|
||||
echo 2; exit 2
|
||||
parallel -j2 --halt 2 echo {}\; exit {} ::: 0 0 1 2 3
|
||||
0
|
||||
|
|
@ -496,9 +497,16 @@ echo 1; exit 1
|
|||
3
|
||||
4
|
||||
5
|
||||
parallel: Starting no more jobs. Waiting for 2 jobs to finish. This job failed:
|
||||
parallel: This job failed:
|
||||
echo 1; exit 1
|
||||
parallel: This job failed:
|
||||
echo 2; exit 2
|
||||
parallel: This job failed:
|
||||
echo 3; exit 3
|
||||
parallel: This job failed:
|
||||
echo 4; exit 4
|
||||
parallel: Starting no more jobs. Waiting for 1 jobs to finish. This job failed:
|
||||
parallel: Starting no more jobs. Waiting for 1 jobs to finish.
|
||||
parallel: This job failed:
|
||||
echo 5; exit 5
|
||||
parallel -k --retries 3 'echo tried {} >>/tmp/runs; echo completed {}; exit {}' ::: 1 2 0
|
||||
cat /tmp/runs
|
||||
|
|
@ -931,7 +939,7 @@ This helps funding further development; and it won't cost you a cent.
|
|||
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
||||
|
||||
parallel --version
|
||||
GNU parallel 20150422
|
||||
GNU parallel 20150426
|
||||
Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange
|
||||
and Free Software Foundation, Inc.
|
||||
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
|
||||
|
|
@ -943,7 +951,7 @@ Web site: http://www.gnu.org/software/parallel
|
|||
When using programs that use GNU Parallel to process data for publication
|
||||
please cite as described in 'parallel --bibtex'.
|
||||
parallel --minversion 20130722 && echo Your version is at least 20130722.
|
||||
20150422
|
||||
20150426
|
||||
Your version is at least 20130722.
|
||||
parallel --bibtex
|
||||
Academic tradition requires you to cite works you base your article on.
|
||||
|
|
@ -989,4 +997,4 @@ C
|
|||
\nice -n17 /bin/bash -c echo\ A
|
||||
\nice -n17 /bin/bash -c echo\ B
|
||||
\nice -n17 /bin/bash -c echo\ C
|
||||
7
|
||||
6
|
||||
|
|
|
|||
Loading…
Reference in a new issue