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Preparations for option -x

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Ole Tange 2009-02-17 04:58:13 +01:00
parent 937e204b1e
commit d5e29c73a2
13 changed files with 206 additions and 111 deletions
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180
parallel
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@ -93,6 +93,10 @@ output from different commands to be mixed. Can be reversed with B<-g>.
Verbose. Print the job to be run. Can be reversed with B<-s>.
=item B<-x>
xargs. Insert as many arguments as the command line length permits.
=back
=head1 EXAMPLE 1: Working as cat | sh. Ressource inexpensive jobs and evaluation
@ -185,6 +189,10 @@ files in each directory:
B<ls | parallel 'echo -n {}" "; ls {}|wc -l'>
To put the output in a file called <name>.dir:
B<ls | parallel '(echo -n {}" "; ls {}|wc -l) >>B< {}.dir'>
=head1 QUOTING
For more advanced use quoting may be an issue. The following will
@ -208,6 +216,12 @@ B<ls | parallel -q "diff {} foo >>B<{}.diff">
because > needs to be interpreted by the shell.
If you get errors like:
B<sh: -c: line 0: syntax error near unexpected token>
then you might try using B<-q>.
B<Conclusion>: To avoid dealing with the quoting problems it may be
easier just to write a small script and have B<parallel> call that
script.
@ -240,19 +254,24 @@ cat | tr '\n' '\0' | xargs -0 -n1 I<command>
B<xargs> can run a given number of jobs in parallel, but has no
support for running no_of_cpus jobs in parallel.
B<xargs> has no support for grouping the output, so output may run
together, so the first half of a line is from one process and the last
half of the line is from another process.
B<xargs> has no support for grouping the output, therefore output may
run together, e.g. the first half of a line is from one process and
the last half of the line is from another process.
If no command is given to B<xargs> it defaults to /bin/echo. So the
B<cat | sh> functionality is missing.
Quoting in B<xargs> works like B<-q> in B<parallel>. Doing B<ls |
parallel "wc {} >> B<{}.wc"> using B<xargs> seems to be impossible.
=head1 BUGS
Filenames beginning with '-' can cause some commands to give
unexpected results, as it will often be interpreted as an option.
If you have a lot of filehandles, then computing the max no
takes a long time.
=head1 REPORTING BUGS
@ -261,7 +280,8 @@ Report bugs to <bug-parallel@tange.dk>.
=head1 AUTHOR
Copyright (C) 2007 Ole Tange, http://ole.tange.dk
Copyright (C) 2007-10-18 Ole Tange, http://ole.tange.dk
Copyright (C) 2008-2009 Ole Tange, http://ole.tange.dk
=head1 LICENSE
@ -294,6 +314,7 @@ B<find>(1), B<xargs>(1)
=cut
use IPC::Open3;
use Symbol qw(gensym);
use IO::File;
@ -316,6 +337,7 @@ $/="\n";
$Global::debug = (defined $::opt_d);
if(defined $::opt_j) { $processes = compute_number_of_processes($::opt_j); }
if(defined $::opt_x) { $Global::xargs = 1; }
if(defined $::opt_v) { $Global::verbose = 1; }
if(defined $::opt_s) { $Global::verbose = 0; }
if(defined $::opt_g) { $Global::grouped = 1; }
@ -326,17 +348,20 @@ if(defined $::opt_0) { $/ = "\0"; }
if(defined $::opt_q) { $Global::quoting = 1; }
if(@ARGV) {
if($Global::quoting) {
$command = join(" ", shell_quote(@ARGV));
$Global::command = join(" ", shell_quote(@ARGV));
} else {
$command = join(" ", @ARGV);
$Global::command = join(" ", @ARGV);
}
}
init_run_jobs();
while($args = <STDIN>) {
my $cmd_line = generate_command_line($command, $args);
queue_job($processes, $cmd_line);
DoNotReap();
while($Global::running_jobs < $processes
and
start_another_job()) {
# skip
}
ReapIfNeeded();
drain_job_queue();
#
@ -345,12 +370,15 @@ drain_job_queue();
sub generate_command_line {
my $command = shift;
my $line = shift;
chomp($line);
my ($job_line,$arg);
my @args = @_;
chomp(@args);
if($Global::input_is_filename) {
($line) = (shell_quote($line));
for my $arg (@args) {
($arg) = (shell_quote($arg));
}
}
my $line = join(" ",@args);
my ($job_line,$arg);
if($command) {
$job_line = $command;
$arg = $line;
@ -385,9 +413,13 @@ sub shell_quote {
}
#
# Number of processes
# Number of processes, filehandles, max length of command line
#
sub max_length_of_command_line {
}
sub compute_number_of_processes {
my $opt_j = shift;
my $processes = 0;
@ -416,13 +448,16 @@ sub compute_number_of_processes {
$processes = 1;
}
}
my $free_handles = compute_no_of_free_filehandles();
if($processes > $free_handles / 2) {
# Every simultaneous process uses 2 filehandles when grouping
# perl uses 7 for something?
$processes = int (($free_handles -7) / 2);
# Every simultaneous process uses 2 filehandles when grouping
# perl uses 7 for something?
# parallel uses 1 for memory_usage
my $file_handles_needed = $processes*2+7+1;
my $free_handles = compute_no_of_free_filehandles($file_handles_needed);
if($file_handles_needed > $free_handles) {
$processes = int (($free_handles -7 -1) / 2);
print STDERR ("Warning: Only enough filehandles to run ",
$processes, " jobs in parallel\n");
$processes, " jobs in parallel. ",
"Raising ulimit -n may help\n");
}
debug("Computed processes: ".(int $processes)."\n");
@ -430,11 +465,12 @@ sub compute_number_of_processes {
}
sub compute_no_of_free_filehandles {
my $needed = shift;
my $i=1;
my %fh;
while(open($fh{$i},"</dev/null")) { $i++ }
while(open($fh{$i},"</dev/null")) { $i++; $i > $needed and last }
for (keys %fh) { close $fh{$_} }
debug("Number of free handles: ".."\n");
debug("Number of free handles: ".$i."\n");
return $i;
}
@ -491,42 +527,21 @@ sub init_run_jobs {
$Global::running_jobs=0;
}
sub queue_job {
my $processes = shift;
my $command = shift;
if($command =~ /\S/) {
# Only run commands - not empty lines
push @Global::command, $command;
}
if($Global::running_jobs < $processes) {
debug("queing $command\n");
start_another_job();
debug("queued $command\n");
}
sub next_command_line {
my $cmd_line;
do {
if(eof STDIN) {
return undef;
}
my $args = <STDIN>;
$cmd_line = generate_command_line($Global::command, $args);
} while ($cmd_line =~ /^\s*$/); # Skip empty lines
return $cmd_line;
}
sub drain_job_queue {
while(1) {
if($Global::running_jobs == 0) { last }
debug("jobs running: $Global::running_jobs\n");
sleep 1;
}
}
sub run_jobs {
# Run the jobs in @Global::command with $processes simultaneously
my $processes = shift;
for my $i (1..$processes) {
# Start $processes jobs.
# When a job dies, the handler will take care of starting another
start_another_job();
}
while(1) {
if($Global::running_jobs == 0) { last }
debug("jobs running: $Global::running_jobs\n");
while($Global::running_jobs > 0) {
debug("jobs running: $Global::running_jobs Memory usage:".my_memory_usage()."\n");
sleep 1;
}
}
@ -535,12 +550,13 @@ sub start_another_job {
# Grab a job from @Global::command, start it
# and remember the pid, the STDOUT and the STDERR handles
# If no more jobs: do nothing
my $command = shift @Global::command;
my $command = next_command_line();
if(defined $command) {
DoNotReap();
my %jobinfo = start_job($command);
$Global::running{$jobinfo{"pid"}} = \%jobinfo;
ReapIfNeeded();
return 1;
} else {
return 0;
}
}
@ -567,9 +583,9 @@ sub start_job {
print STDOUT $command,"\n";
}
$Global::running_jobs++;
debug("starting: $command\n");
debug("$Global::running_jobs processes. Starting: $command\n");
$pid = open3(gensym, ">&STDOUT", ">&STDERR", $command) ||
die("open3 failed. Report a bug\n");
die("open3 failed. Report a bug to <parallel\@tange.dk>\n");
debug("started: $command\n");
open STDOUT, ">&", $Global::original_stdout or die "Can't dup \$oldout: $!";
open STDERR, ">&", $Global::original_stderr or die "Can't dup \$oldout: $!";
@ -593,7 +609,7 @@ sub print_job {
my $err = $fhs->{err};
my $command = $fhs->{command};
debug(">>job\n");
debug(">>joboutput $command\n");
if($Global::verbose and $Global::grouped) {
print STDOUT $command,"\n";
# If STDOUT and STDERR is merged, we want the command to be printed first
@ -605,10 +621,10 @@ sub print_job {
while( <$err> ) { print STDERR "ERR: $_" }
while( <$out> ) { print STDOUT "OUT: $_" }
} else {
while( <$err> ) { print STDERR }
while( <$out> ) { print STDOUT }
print STDERR <$err>;
print STDOUT <$out>;
}
debug("<<job\n");
debug("<<joboutput $command\n");
close $out;
close $err;
}
@ -642,8 +658,9 @@ sub Reaper {
# Print the output.
# Start another job
DoNotReap();
$Global::reaperlevel++;
my $stiff;
debug("Reaper called\n");
debug("Reaper called $Global::reaperlevel\n");
while (($stiff = waitpid(-1, &WNOHANG)) > 0) {
print_job($Global::running{$stiff});
delete $Global::running{$stiff};
@ -651,6 +668,8 @@ sub Reaper {
start_another_job();
}
ReapIfNeeded();
debug("Reaper exit $Global::reaperlevel\n");
$Global::reaperlevel--;
}
#
@ -680,6 +699,33 @@ sub debug {
}
}
sub my_memory_usage {
use strict;
use FileHandle;
my $pid = $$;
my $fh = FileHandle->new("</proc/$pid/stat");
my $data = <$fh>;
chomp $data;
$fh->close;
my @procinfo = split(/\s+/,$data);
return $procinfo[22];
}
sub my_size {
my @size_this = (@_);
eval "use Devel::Size qw(size total_size)";
if ($@) {
return -1;
} else {
return total_size(@_);
}
}
sub my_dump {
my @dump_this = (@_);
eval "use Data::Dump qw(dump);";
@ -703,7 +749,7 @@ sub my_dump {
# Keep perl -w happy
$main::opt_u = $main::opt_c = $main::opt_f = $main::opt_q =
$main::opt_0 = $main::opt_s = $main::opt_v = $main::opt_g =
$main::opt_j = $main::opt_d=1;
$main::opt_j = $main::opt_d = $main::opt_x =1;
$Global::xargs = 1;

87
parallel.1
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@ -1,15 +1,7 @@
.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.32
.\" Automatically generated by Pod::Man 2.18 (Pod::Simple 3.05)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sh \" Subsection heading
.br
.if t .Sp
.ne 5
.PP
\fB\\$1\fR
.PP
..
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
@ -48,22 +40,25 @@
. ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD. Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.if \nF \{\
.ie \nF \{\
. de IX
. tm Index:\\$1\t\\n%\t"\\$2"
..
. nr % 0
. rr F
.\}
.\"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.hy 0
.if n .na
.el \{\
. de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear. Run. Save yourself. No user-serviceable parts.
@ -129,7 +124,11 @@
.\" ========================================================================
.\"
.IX Title "PARALLEL 1"
.TH PARALLEL 1 "2007-09-14" "perl v5.8.8" "User Contributed Perl Documentation"
.TH PARALLEL 1 "2009-02-17" "perl v5.10.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
parallel \- build and execute command lines from standard input in parallel
.SH "SYNOPSIS"
@ -204,9 +203,12 @@ output from different commands to be mixed. Can be reversed with \fB\-g\fR.
.IP "\fB\-v\fR" 9
.IX Item "-v"
Verbose. Print the job to be run. Can be reversed with \fB\-s\fR.
.IP "\fB\-x\fR" 9
.IX Item "-x"
xargs. Insert as many arguments as the command line length permits.
.SH "EXAMPLE 1: Working as cat | sh. Ressource inexpensive jobs and evaluation"
.IX Header "EXAMPLE 1: Working as cat | sh. Ressource inexpensive jobs and evaluation"
\&\fBparallel\fR can work similar to \fBcat | sh\fR.
\&\fBparallel\fR can work similar to \fBcat | sh\fR.
.PP
A ressource inexpensive job is a job that takes very little \s-1CPU\s0, disk
I/O and network I/O. Ping is an example of a ressource inexpensive
@ -232,7 +234,7 @@ As there is not a \fBcommand\fR the option \fB\-c\fR is default because the
jobs needs to be evaluated by the shell.
.SH "EXAMPLE 2: Working as xargs \-n1. Argument appending"
.IX Header "EXAMPLE 2: Working as xargs -n1. Argument appending"
\&\fBparallel\fR can work similar to \fBxargs \-n1\fR.
\&\fBparallel\fR can work similar to \fBxargs \-n1\fR.
.PP
To output all html files run:
.PP
@ -264,8 +266,8 @@ thumb_./foo/bar.jpg\fR would clearly be wrong). It will result in files
like ./foo/bar.jpg_thumb.jpg. If that is not wanted this can fix it:
.PP
.Vb 3
\& find . \-name '*.jpg' | \e
\& perl \-pe 'chomp; $a=$_; s:/([^/]+)$:/thumb_$1:; $_="convert \-geometry 120 $a $_\en"' | \e
\& find . \-name \*(Aq*.jpg\*(Aq | \e
\& perl \-pe \*(Aqchomp; $a=$_; s:/([^/]+)$:/thumb_$1:; $_="convert \-geometry 120 $a $_\en"\*(Aq | \e
\& parallel \-c \-j +0
.Ve
.PP
@ -274,8 +276,8 @@ characters (such as space or quotes). If you have \fBren\fR installed this
is a better solution:
.PP
.Vb 2
\& find . \-name '*.jpg' | parallel \-j +0 convert \-geometry 120 {} {}_thumb.jpg
\& find . \-name '*_thumb.jpg' | ren 's:/([^/]+)_thumb.jpg$:/thumb_$1:'
\& find . \-name \*(Aq*.jpg\*(Aq | parallel \-j +0 convert \-geometry 120 {} {}_thumb.jpg
\& find . \-name \*(Aq*_thumb.jpg\*(Aq | ren \*(Aqs:/([^/]+)_thumb.jpg$:/thumb_$1:\*(Aq
.Ve
.SH "EXAMPLE 4: Substitution and redirection"
.IX Header "EXAMPLE 4: Substitution and redirection"
@ -294,6 +296,10 @@ A job can consist of several commands. This will print the number of
files in each directory:
.PP
\&\fBls | parallel 'echo \-n {}\*(L" \*(R"; ls {}|wc \-l'\fR
.PP
To put the output in a file called <name>.dir:
.PP
\&\fBls | parallel '(echo \-n {}\*(L" \*(R"; ls {}|wc \-l) \fR>\fB {}.dir'\fR
.SH "QUOTING"
.IX Header "QUOTING"
For more advanced use quoting may be an issue. The following will
@ -313,17 +319,23 @@ the quoting by using option \fB\-q\fR:
However, this means you cannot make the shell interpret special
characters. For example this \fBwill not work\fR:
.PP
\&\fBls | parallel \-q "diff {} foo \fR>\fB{}.diff"\fR
\&\fBls | parallel \-q "diff {} foo \fR>\fB{}.diff"\fR
.PP
because > needs to be interpreted by the shell.
.PP
If you get errors like:
.PP
\&\fBsh: \-c: line 0: syntax error near unexpected token\fR
.PP
then you might try using \fB\-q\fR.
.PP
\&\fBConclusion\fR: To avoid dealing with the quoting problems it may be
easier just to write a small script and have \fBparallel\fR call that
script.
.SH "DIFFERENCES BETWEEN xargs/find \-exec AND parallel"
.IX Header "DIFFERENCES BETWEEN xargs/find -exec AND parallel"
\&\fBxargs\fR and \fBfind \-exec\fR offer some of the same possibilites as
\&\fBparallel\fR.
\&\fBparallel\fR.
.PP
\&\fBfind \-exec\fR only works on files. So processing other input (such as
hosts or URLs) will require creating these inputs as files. \fBfind
@ -336,7 +348,7 @@ hosts or URLs) will require creating these inputs as files. \fBfind
(\-0 and \e0 instead of \en), \fBlocate\fR (requires using \-0), \fBfind\fR
(requires using \-print0), \fBgrep\fR (requires user to use \-z or \-Z).
.PP
The input \fIcan\fR be fixed for \fBxargs\fR with:
The input \fIcan\fR be fixed for \fBxargs\fR with:
.PP
tr '\en' '\e0'
.PP
@ -347,22 +359,37 @@ cat | tr '\en' '\e0' | xargs \-0 \-n1 \fIcommand\fR
\&\fBxargs\fR can run a given number of jobs in parallel, but has no
support for running no_of_cpus jobs in parallel.
.PP
\&\fBxargs\fR has no support for grouping the output, so output may run
together, so the first half of a line is from one process and the last
half of the line is from another process.
\&\fBxargs\fR has no support for grouping the output, therefore output may
run together, e.g. the first half of a line is from one process and
the last half of the line is from another process.
.PP
If no command is given to \fBxargs\fR it defaults to /bin/echo. So the
\&\fBcat | sh\fR functionality is missing.
.PP
Quoting in \fBxargs\fR works like \fB\-q\fR in \fBparallel\fR. Doing \fBls |
parallel "wc {} \fR> \fB{}.wc"\fR using \fBxargs\fR seems to be impossible.
.SH "BUGS"
.IX Header "BUGS"
Filenames beginning with '\-' can cause some commands to give
unexpected results, as it will often be interpreted as an option.
.PP
This takes up all memory:
.PP
.Vb 1
\& seq 1 1000000000 | parallel very_loong_command
.Ve
.PP
Should be fixed by only generating a new command when needed
(i.e. when a command has finished).
.PP
If you have a lot of filehandles, then computing the max no
takes a long time.
.SH "REPORTING BUGS"
.IX Header "REPORTING BUGS"
Report bugs to <bug\-parallel@tange.dk>.
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (C) 2007 Ole Tange, http://ole.tange.dk
Copyright (C) 2007\-10\-18 Ole Tange, http://ole.tange.dk
.SH "LICENSE"
.IX Header "LICENSE"
Copyright (C) 2007 Free Software Foundation, Inc.

12
unittest/actual-results/test02
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@ -1,13 +1,13 @@
.
./中国 (Zhōngguó)
./中国 (Zhōngguó)/thumb_China's (中国) road.jpg
./中国 (Zhōngguó)/China's (中国) road.jpg
./a
./a/foo2
./a/foo
./a/bar
./2-col.txt
./a/foo
./b
./b/foo
./b/bar
./b/foo
./2-col.txt
./中国 (Zhōngguó)
./中国 (Zhōngguó)/China's (中国) road.jpg
./中国 (Zhōngguó)/thumb_China's (中国) road.jpg
./1-col.txt

2
unittest/actual-results/test05
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@ -4,5 +4,5 @@ Removing files
4e2ffc66811f839854f2f0071c1e0541 -
There are 6246 dirs with files
Removing dirs
14e628fb222c872cf383280269b2397f -
1c91bf0327094531133e6ad95d2e23f5 -
There are 1 dirs with files

2
unittest/actual-results/test08 Normal file
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@ -0,0 +1,2 @@
b
d

3
unittest/input-files/test08/a Normal file
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@ -0,0 +1,3 @@
flyp
_PRE 8
hatchname> 8

3
unittest/input-files/test08/b Normal file
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@ -0,0 +1,3 @@
flyp
_PRE 9
hatchname> 8

3
unittest/input-files/test08/c Normal file
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@ -0,0 +1,3 @@
flyp
_PRE 19
hatchname> 19

4
unittest/input-files/test08/d Normal file
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@ -0,0 +1,4 @@
flyp
_PRE 19
hatchname> 9

5
unittest/tests-to-run/test08.sh Normal file
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@ -0,0 +1,5 @@
#!/bin/bash
cd input-files/test08
ls | parallel -q perl -ne '/_PRE (\d+)/ and $p=$1; /hatchname> (\d+)/ and $1!=$p and print $ARGV,"\n"'

12
unittest/wanted-results/test02
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@ -1,13 +1,13 @@
.
./中国 (Zhōngguó)
./中国 (Zhōngguó)/thumb_China's (中国) road.jpg
./中国 (Zhōngguó)/China's (中国) road.jpg
./a
./a/foo2
./a/foo
./a/bar
./2-col.txt
./a/foo
./b
./b/foo
./b/bar
./b/foo
./2-col.txt
./中国 (Zhōngguó)
./中国 (Zhōngguó)/China's (中国) road.jpg
./中国 (Zhōngguó)/thumb_China's (中国) road.jpg
./1-col.txt

2
unittest/wanted-results/test05
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@ -4,5 +4,5 @@ Removing files
4e2ffc66811f839854f2f0071c1e0541 -
There are 6246 dirs with files
Removing dirs
14e628fb222c872cf383280269b2397f -
1c91bf0327094531133e6ad95d2e23f5 -
There are 1 dirs with files

2
unittest/wanted-results/test08 Normal file
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@ -0,0 +1,2 @@
b
d