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src/parallel: --trc works for minimal examples.
This commit is contained in:
Ole Tange
parent
fc7fba878b
commit
26868cdc4f
138
src/parallel
138
src/parallel
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@ -911,7 +911,7 @@ the currently running jobs are finished before exiting.
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=head1 DIFFERENCES BETWEEN xargs/find -exec AND parallel
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B<xargs> and B<find -exec> offer some of the same possibilites as
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GNU B<parallel>.
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GNU B<parallel>.
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B<find -exec> only works on files. So processing other input (such as
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hosts or URLs) will require creating these inputs as files. B<find
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@ -924,7 +924,7 @@ B<xargs> deals badly with special characters (such as space, ' and
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touch 'not important_file'
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ls not* | xargs rm
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mkdir -p '12" records'
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ls | xargs rmdir
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ls | xargs rmdir
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You can specify B<-0> or B<-d "\n">, but many input generators are not
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optimized for using B<NUL> as separator but are optimized for
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@ -948,7 +948,7 @@ B<xargs> has no support for keeping the order of the output, therefore
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if running jobs in parallel using B<xargs> the output of the second
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job cannot be postponed till the first job is done.
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B<xargs> has no support for context replace, so you will have to create the
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B<xargs> has no support for context replace, so you will have to create the
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arguments.
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If you use a replace string in B<xargs> (B<-I>) you can not force
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@ -957,17 +957,17 @@ B<xargs> to use more than one argument.
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Quoting in B<xargs> works like B<-q> in GNU B<parallel>. This means
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composed commands and redirection requires using B<bash -c>.
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B<ls | parallel "wc {} >> B<{}.wc">
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B<ls | parallel "wc {} >> B<{}.wc">
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becomes
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becomes
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B<ls | xargs -d "\n" -P10 -I {} bash -c "wc {} >>B< {}.wc">
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and
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and
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B<ls | parallel "echo {}; ls {}|wc">
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B<ls | parallel "echo {}; ls {}|wc">
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becomes
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becomes
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B<ls | xargs -d "\n" -P10 -I {} bash -c "echo {}; ls {}|wc">
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@ -1161,7 +1161,7 @@ sub parse_options {
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$Global::argfile = *STDIN;
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$Global::interactive = 0;
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$Global::stderr_verbose = 0;
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Getopt::Long::Configure ("bundling","require_order");
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GetOptions("debug|D" => \$::opt_D,
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"xargs|m" => \$::opt_m,
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@ -1181,8 +1181,12 @@ sub parse_options {
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"max-line-length-allowed" => \$::opt_max_line_length_allowed,
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"number-of-cpus" => \$::opt_number_of_cpus,
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"number-of-cores" => \$::opt_number_of_cores,
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"sshlogin|S=s" => \@Global::sshlogin,
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"sshlogin|S=s" => \@::opt_sshlogin,
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"sshloginfile=s" => \$::opt_sshloginfile,
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"return=s" => \@::opt_return,
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"trc=s" => \@::opt_trc,
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"transfer" => \$::opt_transfer,
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"cleanup" => \$::opt_cleanup,
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# xargs-compatibility - implemented, man, unittest
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"max-procs|P=s" => \$::opt_P,
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"delimiter|d=s" => \$::opt_d,
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@ -1200,7 +1204,6 @@ sub parse_options {
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## xargs-compatibility - implemented, man - unittest missing
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"interactive|p" => \$::opt_p,
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## How to unittest? tty skal emuleres
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# xargs-compatibility - unimplemented
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"L=i" => \$::opt_L,
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"max-lines|l:i" => \$::opt_l,
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@ -1236,7 +1239,14 @@ sub parse_options {
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if(defined $::opt_max_line_length_allowed) { print real_max_length(),"\n"; exit(0); }
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if(defined $::opt_version) { version(); exit(0); }
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if(defined $::opt_show_limits) { show_limits(); }
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if(defined @::opt_sshlogin) { @Global::sshlogin = @::opt_sshlogin; }
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if(defined $::opt_sshloginfile) { read_sshloginfile($::opt_sshloginfile); }
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if(defined @::opt_return) { push @Global::ret_files, @::opt_return; }
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if(defined @::opt_trc) {
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push @Global::ret_files, @::opt_trc;
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$::opt_transfer = 1;
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$::opt_cleanup = 1;
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}
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if(defined $::opt_a) {
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if(not open(ARGFILE,"<".$::opt_a)) {
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@ -1246,11 +1256,11 @@ sub parse_options {
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$Global::argfile = *ARGFILE;
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}
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if(@ARGV) {
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if(@ARGV) {
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if($Global::quoting) {
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$Global::command = join(" ", shell_quote(@ARGV));
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$Global::command = shell_quote(@ARGV);
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} else {
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$Global::command = join(" ", @ARGV);
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$Global::command = join(" ", @ARGV);
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}
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}
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@ -1258,7 +1268,7 @@ sub parse_options {
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# Needs to be done after setting $Global::command and $Global::command_line_max_len
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# as '-m' influences the number of commands that needs to be run
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if(defined $::opt_P) {
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if(defined $::opt_P) {
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for my $sshlogin (keys %Global::host) {
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$Global::host{$sshlogin}{'max_no_of_running'} =
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compute_number_of_processes($::opt_P,$sshlogin);
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@ -1276,6 +1286,12 @@ sub parse_options {
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# Generating the command line
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#
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sub no_extension {
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my $no_ext = shift;
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$no_ext =~ s/\.[^\.]*$//; # Remove .ext from argument
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return $no_ext;
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}
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sub generate_command_line {
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my $command = shift;
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my ($job_line,$last_good);
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@ -1290,8 +1306,7 @@ sub generate_command_line {
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# max number of lines (-L) =
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# number_of_read_lines = 0
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while (defined($next_arg = get_next_arg())) {
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my $next_arg_no_ext = $next_arg;
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$next_arg_no_ext =~ s/\.[^\.]*$//; # Remove .ext from argument
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my $next_arg_no_ext = no_extension($next_arg);
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# if defined max_number_of_lines
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# number_of_read_lines++
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# if $next_arg =~ /\w$/ then number_of_read_lines--
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@ -1349,7 +1364,7 @@ sub generate_command_line {
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}
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debug("Return jobline: $job_line\n");
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}
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return $job_line;
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return ($job_line,\@quoted_args);
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}
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@ -1364,7 +1379,7 @@ sub xargs_computations {
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# Count number of {.}'s on the command line
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my $no_of_no_ext = ($command =~ s/\Q$Global::replace_no_ext\E/$Global::replace_no_ext/go);
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my $number_of_substitution_no_ext = $no_of_no_ext || 0;
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# Count
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# Count
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my $c = $command;
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if($Global::xargs) {
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# remove all {}s
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@ -1376,7 +1391,6 @@ sub xargs_computations {
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if($Global::Xargs) {
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$c =~ s/\S*\Q$Global::replacestring\E\S*//go;
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$c =~ s/\S*\Q$Global::replace_no_ext\E\S*//go;
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$length_of_command_no_args = length($c) - 1;
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$length_of_context = length($command) - $length_of_command_no_args
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- $no_of_replace * length($Global::replacestring)
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@ -1384,7 +1398,7 @@ sub xargs_computations {
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$spaces = 0;
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}
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@Calculated::xargs_computations =
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@Calculated::xargs_computations =
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($number_of_substitution, $number_of_substitution_no_ext,
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$spaces,$length_of_command_no_args,$length_of_context);
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}
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@ -1395,7 +1409,7 @@ sub xargs_computations {
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sub shell_quote {
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# Quote the string so shell will not expand any special chars
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my (@strings) = (@_);
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my $arg;
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my $arg;
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for $arg (@strings) {
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$arg =~ s/\\/\\\\/g;
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@ -1403,8 +1417,7 @@ sub shell_quote {
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$arg =~ s/([\002-\011\013-\032])/\\$1/g;
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$arg =~ s/([\n])/'\n'/g; # filenames with '\n' is quoted using \'
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}
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#return wantarray ? @strings : "@strings";
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return @strings;
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return wantarray ? @strings : "@strings";
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}
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# Replace foo{}bar or foo{.}bar
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@ -1508,7 +1521,7 @@ sub processes_available_by_system_limit {
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my $sshlogin = shift;
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my $system_limit=0;
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my @command_lines=();
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my $next_command_line;
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my ($next_command_line, $args_ref);
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my $more_filehandles;
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my $max_system_proc_reached=0;
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my $spawning_too_slow=0;
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@ -1528,13 +1541,13 @@ sub processes_available_by_system_limit {
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# If there are no more command lines, then we have a process
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# per command line, so no need to go further
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$next_command_line = next_command_line();
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if(defined $next_command_line) {
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push(@command_lines, $next_command_line);
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($next_command_line, $args_ref) = next_command_line();
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if(defined $next_command_line) {
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push(@command_lines, $next_command_line, $args_ref);
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}
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# Every simultaneous process uses 2 filehandles when grouping
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$more_filehandles = open($fh{$system_limit*2},"</dev/null")
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$more_filehandles = open($fh{$system_limit*2},"</dev/null")
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&& open($fh{$system_limit*2+1},"</dev/null");
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# System process limit
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@ -1559,7 +1572,7 @@ sub processes_available_by_system_limit {
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$system_limit = int ($system_limit * 0.9)+1;
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$spawning_too_slow = 1;
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}
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} while($system_limit < $wanted_processes
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} while($system_limit < $wanted_processes
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and defined $next_command_line
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and $more_filehandles
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and not $max_system_proc_reached
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@ -1585,7 +1598,7 @@ sub processes_available_by_system_limit {
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waitpid($pid,0);
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}
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wait();
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# Cleanup: Unget the command_lines
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# Cleanup: Unget the command_lines (and args_refs)
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unget_command_line(@command_lines);
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return $system_limit;
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}
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@ -1727,26 +1740,49 @@ sub init_run_jobs {
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$SIG{TERM} = \&StartNoNewJobs;
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}
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sub login_and_host {
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my $sshlogin = shift;
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$sshlogin =~ /(\S+$)/ or die;
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return $1;
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}
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sub next_command_line_with_sshlogin {
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my $sshlogin = shift;
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my $next_command_line = next_command_line();
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my ($next_command_line, $args_ref) = next_command_line();
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my ($pre,$post)=("","");
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if($next_command_line and $sshlogin ne ":") {
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return "ssh $sshlogin ".join("",shell_quote($next_command_line));
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my $remote = login_and_host($sshlogin);
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for my $file (@$args_ref) {
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$file =~ s:^([^/]):./$1:; # If relative path: prepend ./ (to avoid problems with ':')
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if($::opt_transfer) {
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$pre = "rsync -az $file $remote:".shell_quote($file)." ;";
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}
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for my $ret_file (@Global::ret_files) {
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my $remove = $::opt_cleanup ? "--remove-source-files" : "";
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my $replaced = context_replace($ret_file,[$file],[no_extension($file)]);
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$post .= "rsync -az $remove $remote:".shell_quote($replaced)." $replaced ;";
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}
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if($::opt_cleanup) {
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$post .= "ssh $sshlogin rm ".shell_quote($file).";";
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}
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}
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return "$pre ssh $sshlogin ".shell_quote($next_command_line)."; $post";
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} else {
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return $next_command_line;
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}
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}
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sub next_command_line {
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my $cmd_line;
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my ($cmd_line,$args_ref);
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if(@Global::unget_next_command_line) {
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$cmd_line = shift @Global::unget_next_command_line;
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$args_ref = shift @Global::unget_next_command_line;
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} else {
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do {
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$cmd_line = generate_command_line($Global::command);
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($cmd_line,$args_ref) = generate_command_line($Global::command);
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} while (defined $cmd_line and $cmd_line =~ /^\s*$/); # Skip empty lines
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}
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return $cmd_line;
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return ($cmd_line,$args_ref);
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}
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sub unget_command_line {
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@ -1774,10 +1810,10 @@ sub get_next_arg {
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}
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}
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if($Global::input_is_filename) {
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($arg) = shell_quote($arg);
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$arg = shell_quote($arg);
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}
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}
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debug("Next arg: ".$arg."\n");
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debug("Next arg: ".$arg."\n");
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return $arg;
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}
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@ -1797,7 +1833,7 @@ sub start_more_jobs {
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if(not $Global::StartNoNewJobs) {
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for my $sshlogin (keys %Global::host) {
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debug("Running jobs on $sshlogin: $Global::host{$sshlogin}{'no_of_running'}\n");
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while ($Global::host{$sshlogin}{'no_of_running'} <
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while ($Global::host{$sshlogin}{'no_of_running'} <
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$Global::host{$sshlogin}{'max_no_of_running'}) {
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if(start_another_job($sshlogin) == 0) {
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# No more jobs to start
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@ -1813,7 +1849,7 @@ sub start_more_jobs {
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}
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sub start_another_job {
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# Grab a job from @Global::command, start it
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# Grab a job from @Global::command, start it
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# and remember the pid, the STDOUT and the STDERR handles
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# Return 1.
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# If no more jobs: do nothing and return 0
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@ -1887,12 +1923,12 @@ sub start_job {
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if($::opt_a and $Global::job_start_sequence == 1) {
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# Give STDIN to the first job if using -a
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$pid = open3("<&STDIN", ">&STDOUT", ">&STDERR", $command) ||
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$pid = open3("<&STDIN", ">&STDOUT", ">&STDERR", $command) ||
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die("open3 failed. Report a bug to <bug-parallel\@gnu.org>\n");
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# Re-open to avoid complaining
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open STDIN, "<&", $Global::original_stdin or die "Can't dup \$Global::original_stdin: $!";
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} else {
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$pid = open3(gensym, ">&STDOUT", ">&STDERR", $command) ||
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$pid = open3(gensym, ">&STDOUT", ">&STDERR", $command) ||
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die("open3 failed. Report a bug to <bug-parallel\@gnu.org>\n");
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}
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debug("started: $command\n");
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@ -1908,7 +1944,7 @@ sub start_job {
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"command" => $command);
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} else {
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return ("seq" => $Global::job_start_sequence,
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"pid" => $pid,
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"pid" => $pid,
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"sshlogin" => $sshlogin,
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"command" => $command);
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}
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@ -1978,7 +2014,7 @@ sub parse_sshlogin {
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if($sshlogin =~ s:^(\d+)/::) {
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# Override default autodetected ncpus
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$Global::host{$sshlogin}{'ncpus'} = $1;
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}
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}
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$Global::host{$sshlogin}{'no_of_running'} = 0;
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$Global::host{$sshlogin}{'maxlength'} = max_length_of_command_line();
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}
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@ -1998,7 +2034,7 @@ sub ListRunningJobs {
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sub StartNoNewJobs {
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print STDERR ("$Global::progname: SIGTERM received. No new jobs will be started.\n",
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"$Global::progname: Waiting for these ", scalar(keys %Global::running),
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"$Global::progname: Waiting for these ", scalar(keys %Global::running),
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" jobs to finish. Send SIGTERM again to stop now.\n");
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ListRunningJobs();
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$Global::StartNoNewJobs++;
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@ -2022,7 +2058,7 @@ sub ReapIfNeeded {
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$Global::SigChildCaught = 0;
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Reaper();
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}
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$SIG{CHLD} = \&Reaper;
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$SIG{CHLD} = \&Reaper;
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}
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sub Reaper {
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@ -2172,10 +2208,10 @@ $main::opt_E = $main::opt_r = $Global::xargs = $Global::keeporder = 0;
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# Per host variables:
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# Can depend on OS
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#$Global::command_line_max_len =
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#$Global::command_line_max_len =
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# Can depend on processes_available_by_system_limit
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#$Global::processes_to_run =
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#
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#
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# $sshlogin, $ncpus
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# $Global::running_jobs = 0;
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# $Global::running{$pid}{'seq'} = printsequence
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@ -2193,3 +2229,9 @@ $main::opt_E = $main::opt_r = $Global::xargs = $Global::keeporder = 0;
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# blokkene samlet med den mest egnede algoritme.
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# Moved parse options to parse_options
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# TODO max_line_length on remote
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# TODO compute how many can be transferred within max_line_length
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# TODO Unittest with filename that is long and requires a lot of quoting. Will there be to many
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# TODO Unittest --trc without -S should warn
|
||||
# TODO Unittest --transfer file called ' : & ) *.jpg'
|
||||
|
|
|
|||
|
|
@ -1,53 +1,53 @@
|
|||
1
|
||||
2
|
||||
3
|
||||
sleep 1; echo 1
|
||||
1
|
||||
sleep 1; echo 2
|
||||
2
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 3
|
||||
sleep 1; echo 1
|
||||
1
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 3;
|
||||
3
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ \\\>/tmp/fire
|
||||
sleep 1; echo \>/tmp/fire
|
||||
>/tmp/fire
|
||||
sleep 1; echo 5
|
||||
5
|
||||
sleep 1; echo 6
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 6;
|
||||
6
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 7
|
||||
sleep 1; echo 7
|
||||
7
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 8
|
||||
sleep 1; echo 8
|
||||
8
|
||||
sleep 1; echo 9
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 9;
|
||||
9
|
||||
sleep 1; echo 10
|
||||
10
|
||||
sleep 1; hostname; echo 1
|
||||
alpha
|
||||
1
|
||||
sleep 1; hostname; echo 2
|
||||
alpha
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 2;
|
||||
nlv.pi.dk
|
||||
2
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 3
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 3;
|
||||
nlv.pi.dk
|
||||
3
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ \\\>/tmp/fire
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ \\\>/tmp/fire;
|
||||
nlv.pi.dk
|
||||
>/tmp/fire
|
||||
sleep 1; hostname; echo 5
|
||||
alpha
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 5;
|
||||
nlv.pi.dk
|
||||
5
|
||||
sleep 1; hostname; echo 6
|
||||
alpha
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 6;
|
||||
nlv.pi.dk
|
||||
6
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 7
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 7;
|
||||
nlv.pi.dk
|
||||
7
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 8
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 8;
|
||||
nlv.pi.dk
|
||||
8
|
||||
sleep 1; hostname; echo 9
|
||||
alpha
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 9;
|
||||
nlv.pi.dk
|
||||
9
|
||||
sleep 1; hostname; echo 10
|
||||
alpha
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 10;
|
||||
nlv.pi.dk
|
||||
10
|
||||
|
|
|
|||
53
unittest/wanted-results/test17
Normal file
53
unittest/wanted-results/test17
Normal file
|
|
@ -0,0 +1,53 @@
|
|||
1
|
||||
2
|
||||
3
|
||||
sleep 1; echo 2
|
||||
2
|
||||
sleep 1; echo 1
|
||||
1
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 3;
|
||||
3
|
||||
sleep 1; echo \>/tmp/fire
|
||||
>/tmp/fire
|
||||
sleep 1; echo 5
|
||||
5
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 6;
|
||||
6
|
||||
sleep 1; echo 7
|
||||
7
|
||||
sleep 1; echo 8
|
||||
8
|
||||
ssh nlv.pi.dk sleep\ 1\;\ echo\ 9;
|
||||
9
|
||||
sleep 1; echo 10
|
||||
10
|
||||
sleep 1; hostname; echo 1
|
||||
alpha
|
||||
1
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 2;
|
||||
nlv.pi.dk
|
||||
2
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 3;
|
||||
nlv.pi.dk
|
||||
3
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ \\\>/tmp/fire;
|
||||
nlv.pi.dk
|
||||
>/tmp/fire
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 5;
|
||||
nlv.pi.dk
|
||||
5
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 6;
|
||||
nlv.pi.dk
|
||||
6
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 7;
|
||||
nlv.pi.dk
|
||||
7
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 8;
|
||||
nlv.pi.dk
|
||||
8
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 9;
|
||||
nlv.pi.dk
|
||||
9
|
||||
ssh nlv.pi.dk sleep\ 1\;\ hostname\;\ echo\ 10;
|
||||
nlv.pi.dk
|
||||
10
|
||||
Loading…
Reference in a new issue