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https://git.savannah.gnu.org/git/parallel.git
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Fixed: parallel -a not_existing --pipepart wc
This commit is contained in:
Ole Tange
parent
0a7b38c257
commit
df5e2231d0
109
src/parallel
109
src/parallel
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@ -184,8 +184,7 @@ sub pipe_part_files {
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# @commands to run to pipe the blocks of the file to the command given
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my ($file) = @_;
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my $buf = "";
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open(my $fh, "<", $file) || die;
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my $header = find_header(\$buf,$fh);
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my $header = find_header(\$buf,open_or_exit($file));
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# find positions
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my @pos = find_split_positions($file,$opt::blocksize,length $header);
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# unshift job with cat_partial
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@ -693,6 +692,10 @@ sub get_options_from_array {
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# false if parsing failed
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# @array is changed
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my ($array_ref, @keep_only) = @_;
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if(not @$array_ref) {
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# Empty array: No need to look more at that
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return 1;
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}
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# A bit of shuffling of @ARGV needed as GetOptionsFromArray is not
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# supported everywhere
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my @save_argv;
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@ -818,7 +821,7 @@ sub parse_options {
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# E.g: "{..} s:\.[^.]+$:;s:\.[^.]+$:;"
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my ($shorthand,$long) = split/ /,$_,2;
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$Global::rpl{$shorthand} = $long;
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}
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}
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if(defined $opt::E) { $Global::end_of_file_string = $opt::E; }
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if(defined $opt::max_args) { $Global::max_number_of_args = $opt::max_args; }
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if(defined $opt::timeout) { $Global::timeoutq = TimeoutQueue->new($opt::timeout); }
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@ -1110,7 +1113,7 @@ sub open_joblog {
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} else {
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# Just match the job number
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$joblog_regexp='^(\d+)';
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}
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}
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while(<$joblog_fh>) {
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if(/$joblog_regexp/o) {
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# This is 30% faster than set_job_already_run($1);
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@ -3194,7 +3197,7 @@ sub swap_activity {
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# 5 0 51208 1701096 198012 18857888 0 0 37 153 28 19 56 11 33 1
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# 3 0 51208 1701288 198012 18857972 0 0 0 0 3638 10412 15 3 82 0
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'linux' => ['vmstat 1 2 | tail -n1', '$7*$8'],
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# solaris: $6*$7
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# $ vmstat -S 1 2
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# kthr memory page disk faults cpu
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@ -3202,7 +3205,7 @@ sub swap_activity {
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# 0 0 0 4628952 3208408 0 0 3 1 1 0 0 -0 2 0 0 263 613 246 1 2 97
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# 0 0 0 4552504 3166360 0 0 0 0 0 0 0 0 0 0 0 246 213 240 1 1 98
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'solaris' => ['vmstat -S 1 2 | tail -1', '$6*$7'],
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# darwin (macosx): $21*$22
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# $ vm_stat -c 2 1
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# Mach Virtual Memory Statistics: (page size of 4096 bytes)
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@ -3210,7 +3213,7 @@ sub swap_activity {
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# 346306 829050 74871 606027 0 240231 90367 544858K 62343596 270837K 14178 415070 570102 939846 356 370 116 922 4019813 4 0 0
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# 345740 830383 74875 606031 0 239234 90369 2696 359 553 0 0 570110 941179 356 370 0 0 0 0 0 0
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'darwin' => ['vm_stat -c 2 1 | tail -n1', '$21*$22'],
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# ultrix: $12*$13
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# $ vmstat -S 1 2
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# procs faults cpu memory page disk
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@ -3218,7 +3221,7 @@ sub swap_activity {
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# 1 0 0 4 23 2 3 0 97 7743 217k 0 0 0 0 0 0 0 0
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# 1 0 0 6 40 8 0 1 99 7743 217k 0 0 3 0 0 0 0 0
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'ultrix' => ['vmstat -S 1 2 | tail -1', '$12*$13'],
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# aix: $6*$7
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# $ vmstat 1 2
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# System configuration: lcpu=1 mem=2048MB
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@ -3229,7 +3232,7 @@ sub swap_activity {
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# 0 0 333933 241803 0 0 0 0 0 0 10 143 90 0 0 99 0
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# 0 0 334125 241569 0 0 0 0 0 0 37 5368 184 0 9 86 5
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'aix' => ['vmstat 1 2 | tail -n1', '$6*$7'],
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# freebsd: $8*$9
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# $ vmstat -H 1 2
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# procs memory page disks faults cpu
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@ -3237,7 +3240,7 @@ sub swap_activity {
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# 1 0 0 596716 19560 32 0 0 0 33 8 0 0 11 220 277 0 0 99
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# 0 0 0 596716 19560 2 0 0 0 0 0 0 0 11 144 263 0 1 99
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'freebsd' => ['vmstat -H 1 2 | tail -n1', '$8*$9'],
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# mirbsd: $8*$9
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# $ vmstat 1 2
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# procs memory page disks traps cpu
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@ -3245,7 +3248,7 @@ sub swap_activity {
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# 0 0 0 25776 164968 34 0 0 0 0 0 0 0 230 259 38 4 0 96
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# 0 0 0 25776 164968 24 0 0 0 0 0 0 0 237 275 37 0 0 100
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'mirbsd' => ['vmstat 1 2 | tail -n1', '$8*$9'],
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# netbsd: $7*$8
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# $ vmstat 1 2
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# procs memory page disks faults cpu
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@ -3253,7 +3256,7 @@ sub swap_activity {
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# 0 0 138452 6012 54 0 0 0 1 2 3 0 4 100 23 0 0 100
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# 0 0 138456 6008 1 0 0 0 0 0 0 0 7 26 19 0 0 100
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'netbsd' => ['vmstat 1 2 | tail -n1', '$7*$8'],
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# openbsd: $8*$9
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# $ vmstat 1 2
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# procs memory page disks traps cpu
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@ -3261,7 +3264,7 @@ sub swap_activity {
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# 0 0 0 76596 109944 73 0 0 0 0 0 0 1 5 259 22 0 1 99
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# 0 0 0 76604 109936 24 0 0 0 0 0 0 0 7 114 20 0 1 99
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'openbsd' => ['vmstat 1 2 | tail -n1', '$8*$9'],
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# hpux: $8*$9
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# $ vmstat 1 2
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# procs memory page faults cpu
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@ -3269,7 +3272,7 @@ sub swap_activity {
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# 1 0 0 247211 216476 4 1 0 0 0 0 0 102 73005 54 6 11 83
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# 1 0 0 247211 216421 43 9 0 0 0 0 0 144 1675 96 25269512791222387000 25269512791222387000 105
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'hpux' => ['vmstat 1 2 | tail -n1', '$8*$9'],
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# dec_osf (tru64): $11*$12
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# $ vmstat 1 2
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# Virtual Memory Statistics: (pagesize = 8192)
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@ -3278,7 +3281,7 @@ sub swap_activity {
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# 3 181 36 51K 1895 8696 348M 59M 122M 259 79M 0 5 218 302 4 1 94
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# 3 181 36 51K 1893 8696 3 15 21 0 28 0 4 81 321 1 1 98
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'dec_osf' => ['vmstat 1 2 | tail -n1', '$11*$12'],
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# gnu (hurd): $7*$8
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# $ vmstat -k 1 2
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# (pagesize: 4, size: 512288, swap size: 894972)
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@ -3286,7 +3289,7 @@ sub swap_activity {
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# 371940 30844 89228 20276 298348 0 48192 19016 756105 99808 98% 876 20628 894972
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# 371940 30844 89228 20276 +0 +0 +0 +0 +42 +2 98% 876 20628 894972
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'gnu' => ['vmstat -k 1 2 | tail -n1', '$7*$8'],
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# -nto (qnx has no swap)
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#-irix
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#-svr5 (scosysv)
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@ -3742,7 +3745,8 @@ sub user_requested_processes {
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my $j = $1;
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$processes =
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$self->ncpus() - $j;
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} elsif ($opt_P =~ /^(\d+)\%$/) {
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} elsif ($opt_P =~ /^(\d+(\.\d+)?)\%$/) {
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# E.g. -P 10.5%
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my $j = $1;
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$processes =
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$self->ncpus() * $j / 100;
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@ -4543,22 +4547,22 @@ sub slot {
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# cat followed by tail.
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# If $writerpid dead: finish after this round
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use Fcntl;
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$|=1;
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my ($cmd, $writerpid, $read_file, $unlink_file) = @ARGV;
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if($read_file) {
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open(IN,"<",$read_file) || die("cattail: Cannot open $read_file");
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} else {
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*IN = *STDIN;
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}
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my $flags;
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fcntl(IN, F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
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$flags |= O_NONBLOCK; # Add non-blocking to the flags
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fcntl(IN, F_SETFL, $flags) || die $!; # Set the flags on the filehandle
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open(OUT,"|-",$cmd) || die("cattail: Cannot run $cmd");
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while(1) {
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# clear EOF
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seek(IN,0,1);
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@ -4587,7 +4591,7 @@ sub slot {
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usleep($sleep);
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}
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}
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sub usleep {
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# Sleep this many milliseconds.
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my $secs = shift;
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@ -4917,10 +4921,10 @@ sub kill {
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{
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my %pid_parentpid_cmd;
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sub family_pids {
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# Find the pids with this->pid as (grand)*parent
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my $self = shift;
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my $pid = $self->pid();
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sub pid_table {
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# return two tables:
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# pid -> children of pid
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# pid -> commandname
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%pid_parentpid_cmd or %pid_parentpid_cmd =
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(
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@ -4932,7 +4936,7 @@ sub kill {
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'freebsd' => q( ps -o pid,ppid -ax ),
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'gnu' => q( ps -ef | awk '{print $2" "$3}' ),
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'hpux' => q( ps -ef | awk '{print $2" "$3}' ),
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'linux' => q( ps -ef | awk '{print $2" "$3}' ),
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'linux' => q( ps -ef | grep tange | awk '{print $2" "$3" "$8}' ),
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'mirbsd' => q( ps -o pid,ppid -ax ),
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'netbsd' => q( ps -o pid,ppid -ax ),
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'nto' => q( ps -ef | awk '{print $2" "$3}' ),
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@ -4942,31 +4946,42 @@ sub kill {
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);
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$pid_parentpid_cmd{$^O} or ::die_bug("pid_parentpid_cmd for $^O missing");
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my (@pidtable,%children_of,@pids);
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# Table with pid parentpid
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my (@pidtable,%children_of,%name_of);
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# Table with pid -> children of pid
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@pidtable = `$pid_parentpid_cmd{$^O}`;
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for (@pidtable) {
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/(\S+)\s+(\S+)/ or ::die_bug("pidtable format");
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/(\S+)\s+(\S+)\s+(\S+)/ or ::die_bug("pidtable format: $_");
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push @{$children_of{$2}}, $1;
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$name_of{$2} = $3;
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}
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my @more = ($pid);
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# While more (grand)*children
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while(@more) {
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my @m;
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push @pids, @more;
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for my $parent (@more) {
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if($children_of{$parent}) {
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# add the children of this parent
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push @m, @{$children_of{$parent}};
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}
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}
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@more = @m;
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}
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return (@pids);
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return(\%children_of, \%name_of);
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}
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}
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sub family_pids {
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# Find the pids with this->pid as (grand)*parent
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my $self = shift;
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my $pid = $self->pid();
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my @pids;
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my ($children_of_ref,$name_of_ref) = pid_table();
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my @more = ($pid);
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# While more (grand)*children
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while(@more) {
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my @m;
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push @pids, @more;
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for my $parent (@more) {
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if($children_of_ref->{$parent}) {
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# add the children of this parent
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push @m, @{$children_of_ref->{$parent}};
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}
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}
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@more = @m;
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}
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return (@pids);
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}
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sub failed {
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# return number of times failed for this $sshlogin
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my $self = shift;
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@ -5574,7 +5589,7 @@ sub print {
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# Check for disk full
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exit_if_disk_full();
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my $command = $self->sshlogin_wrap();
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if(($opt::dryrun or $Global::verbose) and $Global::grouped
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and
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not $self->{'verbose_printed'}) {
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@ -6313,7 +6328,7 @@ sub replace_placeholders {
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: "")
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.$4 }egx;# Context (post)
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::debug("replace", "Positional replaced $word with: $w\n");
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if($w !~ /\257/) {
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# No more replacement strings in $w: No need to do more
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CORE::push(@{$replace{$word}}, $w);
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@ -3198,6 +3198,7 @@ There are a lot programs with some of the functionality of GNU
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B<parallel>. GNU B<parallel> strives to include the best of the
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functionality without sacrificing ease of use.
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=head2 SUMMARY TABLE
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The following features are in some of the comparable tools:
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@ -3325,6 +3326,9 @@ supports (See REPORTING BUGS).
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paexec: TODO - Please file a bug-report if you know what features paexec
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supports (See REPORTING BUGS).
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ladon: TODO - Please file a bug-report if you know what features ladon
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supports (See REPORTING BUGS).
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ClusterSSH: TODO - Please file a bug-report if you know what features ClusterSSH
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supports (See REPORTING BUGS).
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@ -3504,6 +3508,8 @@ B<9> killall -SIGUSR2 parallel
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B<pexec> is also a tool for running jobs in parallel.
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=head3 EXAMPLES FROM pexec MANUAL
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Here are the examples from B<pexec>'s info page with the equivalent
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using GNU B<parallel>:
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@ -3557,6 +3563,7 @@ faster as only one process will be either reading or writing:
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B<8> ls *jpg | parallel -j8 'sem --id diskio cat {} | jpegtopnm |' \
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'pnmscale 0.5 | pnmtojpeg | sem --id diskio cat > th_{}'
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=head2 DIFFERENCES BETWEEN xjobs AND GNU Parallel
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B<xjobs> is also a tool for running jobs in parallel. It only supports
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@ -3644,6 +3651,7 @@ B<cat files | parallel cmd>
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B<find dir -execdir sem cmd {} \;>
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=head2 DIFFERENCES BETWEEN xapply AND GNU Parallel
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B<xapply> can run jobs in parallel on the local computer.
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@ -3745,6 +3753,7 @@ using GNU B<parallel>:
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=back
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=head2 DIFFERENCES BETWEEN map AND GNU Parallel
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B<map> sees it as a feature to have less features and in doing so it
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@ -3825,7 +3834,7 @@ processing, and dynamically timeouts.
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=head2 DIFFERENCES BETWEEN ladon AND GNU Parallel
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B<ladon> https://www.npmjs.org/package/ladon can run multiple jobs on files in parallel.
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B<ladon> can run multiple jobs on files in parallel.
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B<ladon> only works on files and the only way to specify files is
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using a quoted glob string (such as \*.jpg). It is not possible to
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@ -3836,10 +3845,10 @@ As replacement strings it uses FULLPATH DIRNAME BASENAME EXT RELDIR RELPATH
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These can be simulated using GNU B<parallel> by putting this in B<~/.parallel/config>:
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--rpl 'FULLPATH $_=::shell_quote($_);chomp($_=qx{readlink -f $_});'
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--rpl 'DIRNAME $_=::dirname($_); $_=::shell_quote($_);chomp($_=qx{readlink -f $_});'
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--rpl 'BASENAME s:.*/::; s:\.[^/.]+$::;'
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--rpl 'DIRNAME $_=::shell_quote(::dirname($_));chomp($_=qx{readlink -f $_});'
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--rpl 'BASENAME s:.*/::;s:\.[^/.]+$::;'
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--rpl 'EXT s:.*\.::'
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--rpl 'RELDIR $_=::shell_quote($_);chomp(($_,$c)=qx{readlink -f $_;pwd});s:\Q$c/\E::;$_ = ::dirname($_);'
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--rpl 'RELDIR $_=::shell_quote($_);chomp(($_,$c)=qx{readlink -f $_;pwd});s:\Q$c/\E::;$_=::dirname($_);'
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--rpl 'RELPATH $_=::shell_quote($_);chomp(($_,$c)=qx{readlink -f $_;pwd});s:\Q$c/\E::;'
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B<ladon> deals badly with filenames containing " and newline, and it fails for output larger than 200k:
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@ -3867,6 +3876,7 @@ B<4> ladon "~/Music/*.wav" -- lame -V 2 FULLPATH DIRNAME/BASENAME.mp3
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B<4> parallel lame -V 2 FULLPATH DIRNAME/BASENAME.mp3 ::: ~/Music/*.wav
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=head2 DIFFERENCES BETWEEN ClusterSSH AND GNU Parallel
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ClusterSSH solves a different problem than GNU B<parallel>.
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