Released as 20120622 ('Chiang Mai')

NEWS

@@ -1,3 +1,42 @@
+20120622
+
+* '-L n --pipe' will use records of n lines. This is useful when
+  processing data that have fixed records with a fixed number of
+  lines (e.g. fastq).
+
+* --filter-hosts will remove down hosts. For each remote host: check
+  that login through ssh works. If not: do not use this host.
+  Currently you can not put --filter-hosts in a profile, $PARALLEL,
+  /etc/parallel/config or similar. This is because GNU Parallel uses
+  GNU Parallel to compute this, so you will get an infinite loop. This
+  will likely be fixed in a later release.
+
+* --pipe now uses fork() instead of busy wait. The performance should
+  be better on computers with >10 cores while remaining the same on
+  computers with few cores.
+
+* GNU Parallel will be represented at Chiang Mai Bar Camp
+  http://barcampchiangmai.org/
+
+* Indexing Big Data on Amazon AWS: The Screencast
+  (Check out his T-shirt at 18:40-21:00)
+  http://www.opensourceconnections.com/2012/06/06/indexing-big-data-on-amazon-aws-screencast/
+
+* biotoolbox uses GNU Parallel.
+  https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper
+
+* Spiceweasel uses GNU Parallel.
+  https://github.com/mattray/spiceweasel
+
+* GNU Parallel part of The Administrators Challenge
+  http://challenge.twistedrack.com/questions/qs3.php
+
+* Finding Oldest Firefox Code using GNU Parallel
+  http://gregoryszorc.com/blog/2012/06/18/finding-oldest-firefox-code/
+
+* Bug fixes (quite a few for remote job running) and man page updates.
+
+
 20120522
 
 * Timings in --joblog now with milliseconds.

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for parallel 20120524.
+# Generated by GNU Autoconf 2.68 for parallel 20120622.
 #
 # Report bugs to <bug-parallel@gnu.org>.
 #
@@ -559,8 +559,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='parallel'
 PACKAGE_TARNAME='parallel'
-PACKAGE_VERSION='20120524'
+PACKAGE_VERSION='20120622'
-PACKAGE_STRING='parallel 20120524'
+PACKAGE_STRING='parallel 20120622'
 PACKAGE_BUGREPORT='bug-parallel@gnu.org'
 PACKAGE_URL=''
 
@@ -1176,7 +1176,7 @@ 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 20120524 to adapt to many kinds of systems.
+\`configure' configures parallel 20120622 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1242,7 +1242,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of parallel 20120524:";;
+     short | recursive ) echo "Configuration of parallel 20120622:";;
    esac
   cat <<\_ACEOF
 
@@ -1309,7 +1309,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-parallel configure 20120524
+parallel configure 20120622
 generated by GNU Autoconf 2.68
 
 Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1326,7 +1326,7 @@ 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 20120524, which was
+It was created by parallel $as_me 20120622, which was
 generated by GNU Autoconf 2.68.  Invocation command line was
 
   $ $0 $@
@@ -2141,7 +2141,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='parallel'
- VERSION='20120524'
+ VERSION='20120622'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2704,7 +2704,7 @@ 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 20120524, which was
+This file was extended by parallel $as_me 20120622, which was
 generated by GNU Autoconf 2.68.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2766,7 +2766,7 @@ _ACEOF
 cat >>$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 20120524
+parallel config.status 20120622
 configured by $0, generated by GNU Autoconf 2.68,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20120524], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20120622], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

doc/release_new_version

@@ -171,21 +171,48 @@ cc:Sandro Cazzaniga <kharec@mandriva.org>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20120622 ('Thailand') released
+Subject: GNU Parallel 20120622 ('Chiang Mai') released
 
-GNU Parallel 20120622 ('Thailand') has been released. It is
+GNU Parallel 20120622 ('Chiang Mai') has been released. It is
 available for download at: http://ftp.gnu.org/gnu/parallel/
 
 New in this release:
 
-* biotoolbox uses GNU Parallel.
+* '-L n --pipe' will use records of n lines. This is useful when
-  https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper
+  processing data that have fixed records with a fixed number of
+  lines (e.g. fastq).
+
+* --filter-hosts will remove down hosts. For each remote host: check
+  that login through ssh works. If not: do not use this host.
+  Currently you can not put --filter-hosts in a profile, $PARALLEL,
+  /etc/parallel/config or similar. This is because GNU Parallel uses
+  GNU Parallel to compute this, so you will get an infinite loop. This
+  will likely be fixed in a later release.
+
+* --pipe now uses fork() instead of busy wait. The performance should
+  be better on computers with >10 cores while remaining the same on
+  computers with few cores.
+
+* GNU Parallel will be represented at Chiang Mai Bar Camp
+  http://barcampchiangmai.org/
 
 * Indexing Big Data on Amazon AWS: The Screencast
   (Check out his T-shirt at 18:40-21:00)
   http://www.opensourceconnections.com/2012/06/06/indexing-big-data-on-amazon-aws-screencast/
 
-* Bug fixes and man page updates.
+* biotoolbox uses GNU Parallel.
+  https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper
+
+* Spiceweasel uses GNU Parallel.
+  https://github.com/mattray/spiceweasel
+
+* GNU Parallel part of The Administrators Challenge
+  http://challenge.twistedrack.com/questions/qs3.php
+
+* Finding Oldest Firefox Code using GNU Parallel
+  http://gregoryszorc.com/blog/2012/06/18/finding-oldest-firefox-code/
+
+* Bug fixes (quite a few for remote job running) and man page updates.
 
 
 = About GNU Parallel =

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

@@ -1,6 +1,6 @@
 Summary:	Shell tool for executing jobs in parallel
 Name: 		parallel
-Version: 	20120522
+Version: 	20120622
 Release: 	1
 License: 	GPL
 Group: 		Productivity/File utilities
@@ -12,21 +12,27 @@ BuildRoot: 	%{_tmppath}/%{name}-%{version}-buildroot
 
 %description
 GNU Parallel is a shell tool for executing jobs in parallel using one
-or more computers. A job is typically a single command or a small
+or more computers. A job can be a single command or a small script
-script that has to be run for each of the lines in the input. The
+that has to be run for each of the lines in the input. The typical
-typical input is a list of files, a list of hosts, a list of users, or
+input is a list of files, a list of hosts, a list of users, a list of
-a list of tables.
+URLs, or a list of tables. A job can also be a command that reads from
+a pipe. GNU Parallel can then split the input and pipe it into
+commands in parallel.
 
-If you use xargs today you will find GNU Parallel very easy to use. If
+If you use xargs and tee today you will find GNU Parallel very easy to
+use as GNU Parallel is written to have the same options as xargs. If
 you write loops in shell, you will find GNU Parallel may be able to
-replace most of the loops and make them run faster by running jobs in
+replace most of the loops and make them run faster by running several
-parallel. If you use ppss or pexec you will find GNU Parallel will
+jobs in parallel.
-often make the command easier to read.
 
-GNU Parallel also makes sure output from the commands is the same
+GNU Parallel makes sure output from the commands is the same output as
-output as you would get had you run the commands sequentially. This
+you would get had you run the commands sequentially. This makes it
-makes it possible to use output from GNU Parallel as input for other
+possible to use output from GNU Parallel as input for other programs.
-programs.
+
+For each line of input GNU Parallel will execute command with the line
+as arguments. If no command is given, the line of input is
+executed. Several lines will be run in parallel. GNU Parallel can
+often be used as a substitute for xargs or cat | bash.
 
 %prep
 if [ "${RPM_BUILD_ROOT}x" == "x" ]; then

src/niceload

@@ -24,7 +24,7 @@
 use strict;
 use Getopt::Long;
 $Global::progname="niceload";
-$Global::version = 20120524;
+$Global::version = 20120622;
 Getopt::Long::Configure("bundling","require_order");
 get_options_from_array(\@ARGV) || die_usage();
 if($::opt_version) {

src/parallel

@@ -485,7 +485,7 @@ sub options_hash {
 	 "tagstring=s" => \$::opt_tagstring,
 	 "onall" => \$::opt_onall,
 	 "nonall" => \$::opt_nonall,
-	 "filter-hosts" => \$::opt_filter_hosts,
+	 "filter-hosts|filterhosts|filter-host" => \$::opt_filter_hosts,
 	 "sshlogin|S=s" => \@::opt_sshlogin,
 	 "sshloginfile|slf=s" => \@::opt_sshloginfile,
 	 "controlmaster|M" => \$::opt_controlmaster,
@@ -584,7 +584,7 @@ sub get_options_from_array {
 sub parse_options {
     # Returns: N/A
     # Defaults:
-    $Global::version = 20120614;
+    $Global::version = 20120622;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;

src/parallel.pod

@@ -462,6 +462,17 @@ See also: B<--bg>, B<man sem>
 Implies B<--semaphore>.
 
 
+=item B<--filter-hosts> (alpha testing)
+
+Remove down hosts. For each remote host: check that login through ssh
+works. If not: do not use this host.
+
+Currently you can <i>not</i> put B<--filter-hosts> in a profile,
+$PARALLEL, /etc/parallel/config or similar. This is because GNU
+B<parallel> uses GNU B<parallel> to compute this, so you will get an
+infinite loop. This will likely be fixed in a later release.
+
+
 =item B<--gnu>
 
 Behave like GNU B<parallel>. If B<--tollef> and B<--gnu> are both set,
@@ -634,7 +645,7 @@ to see the difference:
   parallel -j4 sleep {}\; echo {} ::: 2 1 4 3
   parallel -j4 -k sleep {}\; echo {} ::: 2 1 4 3
 
-=item B<-L> I<max-lines>
+=item B<-L> I<max-lines> (alpha testing)
 
 When used with B<--pipe>: Read records of I<max-lines>.
 
@@ -1221,14 +1232,14 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
 setting $TMPDIR.
 
 
-=item B<--timeout> I<sec>
+=item B<--timeout> I<sec> (alpha testing)
 
 Time out for command. If the command runs for longer than I<sec>
 seconds it will get killed with SIGTERM, followed by SIGTERM 200 ms
 later, followed by SIGKILL 200 ms later.
 
 
-=item B<--tollef>
+=item B<--tollef> (alpha testing)
 
 Make GNU B<parallel> behave more like Tollef's parallel command. It
 activates B<-u>, B<-q>, and B<--arg-sep -->. It also causes B<-l> to
@@ -1434,9 +1445,9 @@ Compare these two:
 See also B<--header>.
 
 
-=item B<--shebang>
+=item B<--shebang> (alpha testing)
 
-=item B<--hashbang>
+=item B<--hashbang> (alpha testing)
 
 GNU B<Parallel> can be called as a shebang (#!) command as the first line of a script. Like this:
 

src/parallel.texi

@@ -489,6 +489,17 @@ See also: @strong{--bg}, @strong{man sem}
 
 Implies @strong{--semaphore}.
 
+@item @strong{--filter-hosts} (alpha testing)
+@anchor{@strong{--filter-hosts} (alpha testing)}
+
+Remove down hosts. For each remote host: check that login through ssh
+works. If not: do not use this host.
+
+Currently you can <i>not</i> put @strong{--filter-hosts} in a profile,
+$PARALLEL, /etc/parallel/config or similar. This is because GNU
+@strong{parallel} uses GNU @strong{parallel} to compute this, so you will get an
+infinite loop. This will likely be fixed in a later release.
+
 @item @strong{--gnu}
 @anchor{@strong{--gnu}}
 
@@ -685,8 +696,8 @@ to see the difference:
   parallel -j4 -k sleep {}\; echo {} ::: 2 1 4 3
 @end verbatim
 
-@item @strong{-L} @emph{max-lines}
+@item @strong{-L} @emph{max-lines} (alpha testing)
-@anchor{@strong{-L} @emph{max-lines}}
+@anchor{@strong{-L} @emph{max-lines} (alpha testing)}
 
 When used with @strong{--pipe}: Read records of @emph{max-lines}.
 
@@ -1300,15 +1311,15 @@ into temporary files in /tmp. By setting @strong{--tmpdir} you can use a
 different dir for the files. Setting @strong{--tmpdir} is equivalent to
 setting $TMPDIR.
 
-@item @strong{--timeout} @emph{sec}
+@item @strong{--timeout} @emph{sec} (alpha testing)
-@anchor{@strong{--timeout} @emph{sec}}
+@anchor{@strong{--timeout} @emph{sec} (alpha testing)}
 
 Time out for command. If the command runs for longer than @emph{sec}
 seconds it will get killed with SIGTERM, followed by SIGTERM 200 ms
 later, followed by SIGKILL 200 ms later.
 
-@item @strong{--tollef}
+@item @strong{--tollef} (alpha testing)
-@anchor{@strong{--tollef}}
+@anchor{@strong{--tollef} (alpha testing)}
 
 Make GNU @strong{parallel} behave more like Tollef's parallel command. It
 activates @strong{-u}, @strong{-q}, and @strong{--arg-sep --}. It also causes @strong{-l} to
@@ -1529,11 +1540,11 @@ Compare these two:
 
 See also @strong{--header}.
 
-@item @strong{--shebang}
+@item @strong{--shebang} (alpha testing)
-@anchor{@strong{--shebang}}
+@anchor{@strong{--shebang} (alpha testing)}
 
-@item @strong{--hashbang}
+@item @strong{--hashbang} (alpha testing)
-@anchor{@strong{--hashbang}}
+@anchor{@strong{--hashbang} (alpha testing)}
 
 GNU @strong{Parallel} can be called as a shebang (#!) command as the first line of a script. Like this:
 

src/sql

@@ -556,7 +556,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20120524;
+    $Global::version = 20120622;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself

testsuite/tests-to-run/test30.sh

@@ -18,7 +18,7 @@ echo '### bug #34422: parallel -X --eta crashes with div by zero'
 seq 2 | stdout parallel -X --eta echo
 
 echo '### --timeout on remote machines'
-parallel -j0 --timeout 4 --onall -S localhost,parallel@parallel-server1 'sleep {}; echo slept {}' ::: 1 8 9 ; echo jobs failed: $?
+parallel -j0 --timeout 6 --onall -S localhost,parallel@parallel-server1 'sleep {}; echo slept {}' ::: 1 8 9 ; echo jobs failed: $?
 
 echo '### --pipe without command'
 seq -w 10 | stdout parallel --pipe