Released as 20151022 ('LiquidWater')

NEWS

@@ -1,3 +1,40 @@
+20151022
+
+* --plus makes it possible to use {##} as a short had for {=
+  $_=$Global::JobQueue->total_jobs() =} which gives the the number of
+  jobs to run.
+
+* {= $_=$Global::JobQueue->total_jobs() =} is incompatible with -X,
+  -m, and --xargs.
+
+* GNU Parallel is now mostly compatible with lsh
+  (http://www.lysator.liu.se/~nisse/lsh/) and somewhat compatible with
+  autossh (http://www.harding.motd.ca/autossh/).
+
+* --workdir ... now also works when run locally.
+
+* GNU Parallel was cited in: There is no (75, 32, 10, 16) strongly
+  regular graph http://arxiv.org/pdf/1509.05933.pdf
+
+* GNU Parallel was cited in: Roary: rapid large-scale prokaryote pan
+  genome analysis
+  http://bioinformatics.oxfordjournals.org/content/early/2015/08/05/bioinformatics.btv421.full.pdf+html
+
+* GNU Parallel is used in TraitAR:
+  https://testpypi.python.org/pypi/traitar/0.1.4
+
+* GNU Parallel is used in youtube-dl-parallel:
+  https://github.com/dlh/youtube-dl-parallel
+
+* A parallel and fast way to download multiple files
+  http://onetipperday.blogspot.com/2015/10/a-parallel-and-fast-way-to-download.html
+
+* Usar GNU Parallel para aumentar el rendimiento de tus scripts
+  http://adrianarroyocalle.github.io/blog/2015/10/20/usar-gnu-parallel/
+
+* Bug fixes and man page updates.
+
+
 20150922
 
 * GNU Parallel was cited in: Flexible Modeling of Epidemics with an Empirical Bayes Framework http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004382

README

@@ -40,9 +40,9 @@ document.
 
 Full installation of GNU Parallel is as simple as:
 
-    wget http://ftpmirror.gnu.org/parallel/parallel-20150922.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20151022.tar.bz2
-    bzip2 -dc parallel-20150922.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20151022.tar.bz2 | tar xvf -
-    cd parallel-20150922
+    cd parallel-20151022
     ./configure && make && sudo make install
 
 
@@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
 If you are not root you can add ~/bin to your path and install in
 ~/bin and ~/share:
 
-    wget http://ftpmirror.gnu.org/parallel/parallel-20150922.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20151022.tar.bz2
-    bzip2 -dc parallel-20150922.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20151022.tar.bz2 | tar xvf -
-    cd parallel-20150922
+    cd parallel-20151022
     ./configure --prefix=$HOME && make && make install
 
 Or if your system lacks 'make' you can simply copy src/parallel

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for parallel 20150922.
+# Generated by GNU Autoconf 2.69 for parallel 20151022.
 #
 # Report bugs to <bug-parallel@gnu.org>.
 #
@@ -579,8 +579,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='parallel'
 PACKAGE_TARNAME='parallel'
-PACKAGE_VERSION='20150922'
+PACKAGE_VERSION='20151022'
-PACKAGE_STRING='parallel 20150922'
+PACKAGE_STRING='parallel 20151022'
 PACKAGE_BUGREPORT='bug-parallel@gnu.org'
 PACKAGE_URL=''
 
@@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures parallel 20150922 to adapt to many kinds of systems.
+\`configure' configures parallel 20151022 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1269,7 +1269,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of parallel 20150922:";;
+     short | recursive ) echo "Configuration of parallel 20151022:";;
    esac
   cat <<\_ACEOF
 
@@ -1345,7 +1345,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-parallel configure 20150922
+parallel configure 20151022
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by parallel $as_me 20150922, which was
+It was created by parallel $as_me 20151022, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2225,7 +2225,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='parallel'
- VERSION='20150922'
+ VERSION='20151022'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by parallel $as_me 20150922, which was
+This file was extended by parallel $as_me 20151022, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2929,7 +2929,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-parallel config.status 20150922
+parallel config.status 20151022
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20150922], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20151022], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

doc/release_new_version

@@ -220,7 +220,9 @@ GNU Parallel 20151022 ('Liquid Water') <<[stable]>> has been released. It is ava
 
 Haiku of the month:
 
-  <<>>
+  In parallel land
+  everything is quick and fast
+  Use GNU Parallel.
     -- Ole Tange
 
 New in this release:
@@ -234,6 +236,14 @@ New in this release:
 * <<kontaktet 2015-06-22 Afventer svar fra journal>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
 http://www.researchgate.net/profile/Christoph_Junghans/publication/276178326_TADSim_Discrete_Event-Based_Performance_Prediction_for_Temperature-Accelerated_Dynamics/links/55562b6708ae980ca60c8369.pdf
 
+* --plus makes it possible to use {##} as a short had for {= $_=$Global::JobQueue->total_jobs() =} which gives the the number of jobs to run.
+
+* {= $_=$Global::JobQueue->total_jobs() =} is incompatible with -X, -m, and --xargs.
+
+* GNU Parallel is now mostly compatible with lsh (http://www.lysator.liu.se/~nisse/lsh/) and somewhat compatible with autossh (http://www.harding.motd.ca/autossh/).
+
+* --workdir ... now also works when run locally.
+
 * GNU Parallel was cited in: There is no (75, 32, 10, 16) strongly regular graph http://arxiv.org/pdf/1509.05933.pdf
 
 * GNU Parallel was cited in: Roary: rapid large-scale prokaryote pan genome analysis http://bioinformatics.oxfordjournals.org/content/early/2015/08/05/bioinformatics.btv421.full.pdf+html
@@ -244,6 +254,8 @@ http://www.researchgate.net/profile/Christoph_Junghans/publication/276178326_TAD
 
 * A parallel and fast way to download multiple files http://onetipperday.blogspot.com/2015/10/a-parallel-and-fast-way-to-download.html
 
+* Usar GNU Parallel para aumentar el rendimiento de tus scripts http://adrianarroyocalle.github.io/blog/2015/10/20/usar-gnu-parallel/
+
 * Bug fixes and man page updates.
 
 GNU Parallel - For people who live life in the parallel lane.

packager/obs/home:tange/parallel/parallel.spec

@@ -1,6 +1,6 @@
 Summary:	Shell tool for executing jobs in parallel
 Name: 		parallel
-Version: 	20150922
+Version: 	20151022
 Release: 	1
 License: 	GPL
 Group: 		Productivity/File utilities

src/niceload

@@ -24,7 +24,7 @@
 use strict;
 use Getopt::Long;
 $Global::progname="niceload";
-$Global::version = 20150922;
+$Global::version = 20151022;
 Getopt::Long::Configure("bundling","require_order");
 get_options_from_array(\@ARGV) || die_usage();
 if($opt::version) {

src/parallel

@@ -1100,7 +1100,7 @@ sub parse_options {
 
 sub init_globals {
     # Defaults:
-    $Global::version = 20151001;
+    $Global::version = 20151022;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;

src/parallel.pod

@@ -426,7 +426,7 @@ string that is not in the command line.
 See also: B<:::>.
 
 
-=item B<--bar>
+=item B<--bar> (alpha testing)
 
 Show progress as a progress bar. In the bar is shown: % of jobs
 completed, estimated seconds left, and number of jobs started.
@@ -513,7 +513,7 @@ I<size> defaults to 1M.
 See B<--pipe> and B<--pipepart> for use of this.
 
 
-=item B<--cat>
+=item B<--cat> (alpha testing)
 
 Create a temporary file with content. Normally B<--pipe>/B<--pipepart>
 will give data to the program on stdin (standard input). With B<--cat>
@@ -613,7 +613,7 @@ I<secs> seconds after starting each job. I<secs> can be less than 1
 second.
 
 
-=item B<--dry-run>
+=item B<--dry-run> (alpha testing)
 
 Print the job to run on stdout (standard output), but do not run the
 job. Use B<-v -v> to include the wrapping that GNU Parallel generates
@@ -672,7 +672,7 @@ and functions) use env_parallel as described under the option I<command>.
 See also: B<--record-env>.
 
 
-=item B<--eta>
+=item B<--eta> (alpha testing)
 
 Show the estimated number of seconds before finishing. This forces GNU
 B<parallel> to read all jobs before starting to find the number of
@@ -693,7 +693,7 @@ Implies B<--semaphore>.
 See also B<--bg>, B<man sem>.
 
 
-=item B<--fifo>
+=item B<--fifo> (alpha testing)
 
 Create a temporary fifo with content. Normally B<--pipe> and
 B<--pipepart> will give data to the program on stdin (standard
@@ -725,7 +725,7 @@ over B<--tollef>. The B<--tollef> option is now retired, and therefore
 may not be used. B<--gnu> is kept for compatibility.
 
 
-=item B<--group>
+=item B<--group> (alpha testing)
 
 Group output. Output from each jobs is grouped together and is only
 printed when the command is finished. stderr (standard error) first
@@ -747,9 +747,9 @@ See also: B<--line-buffer> B<--ungroup>
 Print a summary of the options to GNU B<parallel> and exit.
 
 
-=item B<--halt-on-error> I<val>
+=item B<--halt-on-error> I<val> (alpha testing)
 
-=item B<--halt> I<val>
+=item B<--halt> I<val> (alpha testing)
 
 When should GNU B<parallel> terminate? In some situations it makes no
 sense to run all jobs. GNU B<parallel> should simply give up as soon
@@ -1172,7 +1172,7 @@ performance is important use B<--pipepart>.
 See also: B<--recstart>, B<--recend>, B<--fifo>, B<--cat>, B<--pipepart>.
 
 
-=item B<--pipepart>
+=item B<--pipepart> (alpha testing)
 
 Pipe parts of a physical file. B<--pipepart> works similar to
 B<--pipe>, but is much faster. It has a few limitations:
@@ -1288,7 +1288,7 @@ Overrides an earlier B<--keep-order> (e.g. if set in
 B<~/.parallel/config>).
 
 
-=item B<--nice> I<niceness>
+=item B<--nice> I<niceness> (alpha testing)
 
 Run the command at this niceness. For simple commands you can just add
 B<nice> in front of the command. But if the command consists of more
@@ -1737,7 +1737,7 @@ Does not run the command but quotes it. Useful for making quoted
 composed commands for GNU B<parallel>.
 
 
-=item B<--shuf>
+=item B<--shuf> (alpha testing)
 
 Shuffle jobs. When having multiple input sources it is hard to
 randomize jobs. --shuf will generate all jobs, and shuffle them before
@@ -1765,13 +1765,13 @@ I<secs> seconds after starting each ssh. I<secs> can be less than 1
 seconds.
 
 
-=item B<-S> I<[@hostgroups/][ncpu/]sshlogin[,[@hostgroups/][ncpu/]sshlogin[,...]]>
+=item B<-S> I<[@hostgroups/][ncpu/]sshlogin[,[@hostgroups/][ncpu/]sshlogin[,...]]> (alpha testing)
 
-=item B<-S> I<@hostgroup>
+=item B<-S> I<@hostgroup> (alpha testing)
 
-=item B<--sshlogin> I<[@hostgroups/][ncpu/]sshlogin[,[@hostgroups/][ncpu/]sshlogin[,...]]>
+=item B<--sshlogin> I<[@hostgroups/][ncpu/]sshlogin[,[@hostgroups/][ncpu/]sshlogin[,...]]> (alpha testing)
 
-=item B<--sshlogin> I<@hostgroup>
+=item B<--sshlogin> I<@hostgroup> (alpha testing)
 
 Distribute jobs to remote computers. The jobs will be run on a list of
 remote computers.
@@ -2088,9 +2088,9 @@ Use B<-v> B<-v> to print the wrapping ssh command when running remotely.
 Print the version GNU B<parallel> and exit.
 
 
-=item B<--workdir> I<mydir>
+=item B<--workdir> I<mydir> (alpha testing)
 
-=item B<--wd> I<mydir>
+=item B<--wd> I<mydir> (alpha testing)
 
 Files transferred using B<--transfer> and B<--return> will be relative
 to I<mydir> on remote computers, and the command will be executed in

src/parallel_design.pod

@@ -129,11 +129,9 @@ echo I<shell double quoted input>
 
 =item --nice I<pri>
 
-\nice -n I<pri> I<shell> -c I<shell quoted input>
+Remote: See B<The remote system wrapper>.
 
-The \ is needed to avoid using the builtin nice command, which does not
+Local: B<setpriority(0,0,$nice)>
-support -n in B<tcsh>. B<I<shell> -c> is needed to nice composed commands
-command.
 
 =item --cat
 
@@ -374,7 +372,12 @@ the %%-version, and the function definition works on both pre- and
 post-shellshock versions of B<bash>.
 
 
-=head2 Remote Ctrl-C and standard error (stderr)
+=head2 The remote system wrapper
+
+The remote system wrapper does some initialization before starting the
+command on the remote system.
+
+=head3 Ctrl-C and standard error (stderr)
 
 If the user presses Ctrl-C the user expects jobs to stop. This works
 out of the box if the jobs are run locally. Unfortunately it is not so
@@ -394,28 +397,51 @@ propagate the hang-up signal from B<sshd>. But when B<sshd> dies, the
 parent of the login shell becomes B<init> (process id 1). So by
 exec'ing a Perl wrapper to monitor the parent pid and kill the child
 if the parent pid becomes 1, then Ctrl-C works and stderr is kept on
-stderr. The wrapper looks like this:
+stderr.
 
+=head3 --nice
+
+B<nice>ing the remote process is done by B<setpriority(0,0,$nice)>. A
+few old systems do not implement this and is thus unsupported.
+
+=head3 Setting $PARALLEL_TMP
+
+B<$PARALLEL_TMP> is used by B<--fifo> and B<--cat> and must point to a
+non-exitent file in B<$TMPDIR>. This file name is computed on the
+remote system.
+
+=head3 The wrapper
+
+The wrapper looks like this:
+
+    $shell = $PARALLEL_SHELL || $SHELL;
+    $tmpdir = $TMPDIR;
+    $nice = $opt::nice;
+    # Set $PARALLEL_TMP to a non-existent file name in $TMPDIR
+    do {
+	$ENV{PARALLEL_TMP} = $tmpdir."/par".
+	    join"", map { (0..9,"a".."z","A".."Z")[rand(62)] } (1..5);
+    } while(-e $ENV{PARALLEL_TMP});
     $SIG{CHLD} = sub { $done = 1; };
     $pid = fork;
     unless($pid) {
-        # Make own process group to be able to kill HUP it later
+	# Make own process group to be able to kill HUP it later
-        setpgrp;
+	setpgrp;
-        exec $ENV{SHELL}, "-c", ($bashfunc."@ARGV");
+	eval { setpriority(0,0,$nice) };
-        die "exec: $!\n";
+	exec $shell, "-c", ($bashfunc."@ARGV");
+	die "exec: $!\n";
     }
     do {
-        # Parent is not init (ppid=1), so sshd is alive
+	# Parent is not init (ppid=1), so sshd is alive
-        # Exponential sleep up to 1 sec
+	# Exponential sleep up to 1 sec
-        $s = $s < 1 ? 0.001 + $s * 1.03 : $s;
+	$s = $s < 1 ? 0.001 + $s * 1.03 : $s;
-        select(undef, undef, undef, $s);
+	select(undef, undef, undef, $s);
     } until ($done || getppid == 1);
     # Kill HUP the process group if job not done
     kill(SIGHUP, -${pid}) unless $done;
     wait;
     exit ($?&127 ? 128+($?&127) : 1+$?>>8)
 
-
 =head2 Transferring of variables and functions
 
 Transferring of variables and functions given by B<--env> is done by

src/sql

@@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20150922;
+    $Global::version = 20151022;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself