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Released as 20150922 ('AylanKurdi')

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Ole Tange 2015-09-21 20:03:52 +02:00
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32
NEWS
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@ -1,3 +1,35 @@
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
* GNU Parallel was cited in: BL1: 2D Potts Model with a Twist https://sucs.swan.ac.uk/~rjames93/Dissertation.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations http://www.mdpi.com/1420-3049/20/6/9977/pdf
* GNU Parallel was cited in: A Scalable Parallel Implementation of Evolutionary Algorithms for
Multi-Objective Optimization on GPUs http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7257074
* GNU Parallel was cited in: Tools and techniques for computational reproducibility http://biorxiv.org/content/biorxiv/early/2015/07/17/022707.full.pdf
* GNU Parallel was cited in: How Can We Measure the Similarity Between Résumés of Selected Candidates for a Job? http://crawl.prod.proquest.com.s3.amazonaws.com/fpcache/c79b355e6e441a51de3c7fcd52866184.pdf?AWSAccessKeyId=AKIAJF7V7KNV2KKY2NUQ&Expires=1442658364&Signature=soRDi6Xqw1zHhSmBrqJ5KiD%2B8Sw%3D
* GNU Parallel was cited in: Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing http://www.researchgate.net/profile/Raphael_Etournay/publication/279061859_Interplay_of_cell_dynamics_and_epithelial_tension_during_morphogenesis_of_the_Drosophila_pupal_wing/links/558a95ad08aeae8413bcceea.pdf
* Third-party selling GNU Parallel T-shirts http://www.aliexpress.com/item/2015F-BSO-GNU-LOGO-GNU-PARALLEL-men-s-shirt-sleeve-visual-illusion-error/32464827966.html
* Joys of gnu parallel http://scottolesen.com/index.php/2015/08/26/joys-of-gnu-parallel/
* Crop and resize images with bash and ImageMagick https://www.simonholywell.com/post/2015/08/image-resize-crop-bash-imagemagick/
* Three Ways to Script Processes in Parallel http://www.codeword.xyz/2015/09/02/three-ways-to-script-processes-in-parallel/
* What It Looks Like to Process 3.5 Million Books http://blog.gdeltproject.org/what-it-looks-like-to-process-3-5-million-books/
* L’Exploration De Données Twitter http://blog.inovia-conseil.fr/?p=233
* Bug fixes and man page updates.
20150822 20150822
* If $job->skip() is called in {= =} the job will not be run. * If $job->skip() is called in {= =} the job will not be run.

12
README
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@ -40,9 +40,9 @@ document.
Full installation of GNU Parallel is as simple as: Full installation of GNU Parallel is as simple as:
wget http://ftpmirror.gnu.org/parallel/parallel-20150822.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20150922.tar.bz2
bzip2 -dc parallel-20150822.tar.bz2 | tar xvf - bzip2 -dc parallel-20150922.tar.bz2 | tar xvf -
cd parallel-20150822 cd parallel-20150922
./configure && make && sudo make install ./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 If you are not root you can add ~/bin to your path and install in
~/bin and ~/share: ~/bin and ~/share:
wget http://ftpmirror.gnu.org/parallel/parallel-20150822.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20150922.tar.bz2
bzip2 -dc parallel-20150822.tar.bz2 | tar xvf - bzip2 -dc parallel-20150922.tar.bz2 | tar xvf -
cd parallel-20150822 cd parallel-20150922
./configure --prefix=$HOME && make && make install ./configure --prefix=$HOME && make && make install
Or if your system lacks 'make' you can simply copy src/parallel Or if your system lacks 'make' you can simply copy src/parallel

20
configure vendored
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@ -1,6 +1,6 @@
#! /bin/sh #! /bin/sh
# Guess values for system-dependent variables and create Makefiles. # Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for parallel 20150822. # Generated by GNU Autoconf 2.69 for parallel 20150922.
# #
# Report bugs to <bug-parallel@gnu.org>. # Report bugs to <bug-parallel@gnu.org>.
# #
@ -579,8 +579,8 @@ MAKEFLAGS=
# Identity of this package. # Identity of this package.
PACKAGE_NAME='parallel' PACKAGE_NAME='parallel'
PACKAGE_TARNAME='parallel' PACKAGE_TARNAME='parallel'
PACKAGE_VERSION='20150822' PACKAGE_VERSION='20150922'
PACKAGE_STRING='parallel 20150822' PACKAGE_STRING='parallel 20150922'
PACKAGE_BUGREPORT='bug-parallel@gnu.org' PACKAGE_BUGREPORT='bug-parallel@gnu.org'
PACKAGE_URL='' 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. # 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. # This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF cat <<_ACEOF
\`configure' configures parallel 20150822 to adapt to many kinds of systems. \`configure' configures parallel 20150922 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]... Usage: $0 [OPTION]... [VAR=VALUE]...
@ -1269,7 +1269,7 @@ fi
if test -n "$ac_init_help"; then if test -n "$ac_init_help"; then
case $ac_init_help in case $ac_init_help in
short | recursive ) echo "Configuration of parallel 20150822:";; short | recursive ) echo "Configuration of parallel 20150922:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1345,7 +1345,7 @@ fi
test -n "$ac_init_help" && exit $ac_status test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then if $ac_init_version; then
cat <<\_ACEOF cat <<\_ACEOF
parallel configure 20150822 parallel configure 20150922
generated by GNU Autoconf 2.69 generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc. Copyright (C) 2012 Free Software Foundation, Inc.
@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake. running configure, to aid debugging if configure makes a mistake.
It was created by parallel $as_me 20150822, which was It was created by parallel $as_me 20150922, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2225,7 +2225,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20150822' VERSION='20150922'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their # report actual input values of CONFIG_FILES etc. instead of their
# values after options handling. # values after options handling.
ac_log=" ac_log="
This file was extended by parallel $as_me 20150822, which was This file was extended by parallel $as_me 20150922, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES CONFIG_FILES = $CONFIG_FILES
@ -2929,7 +2929,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\ ac_cs_version="\\
parallel config.status 20150822 parallel config.status 20150922
configured by $0, generated by GNU Autoconf 2.69, configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\" with options \\"\$ac_cs_config\\"

2
configure.ac
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@ -1,4 +1,4 @@
AC_INIT([parallel], [20150822], [bug-parallel@gnu.org]) AC_INIT([parallel], [20150922], [bug-parallel@gnu.org])
AM_INIT_AUTOMAKE([-Wall -Werror foreign]) AM_INIT_AUTOMAKE([-Wall -Werror foreign])
AC_CONFIG_HEADERS([config.h]) AC_CONFIG_HEADERS([config.h])
AC_CONFIG_FILES([ AC_CONFIG_FILES([

11
doc/release_new_version
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@ -229,6 +229,17 @@ New in this release:
* GNU Parallel was cited in: BL1: 2D Potts Model with a Twist https://sucs.swan.ac.uk/~rjames93/Dissertation.pdf * GNU Parallel was cited in: BL1: 2D Potts Model with a Twist https://sucs.swan.ac.uk/~rjames93/Dissertation.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations http://www.mdpi.com/1420-3049/20/6/9977/pdf
* GNU Parallel was cited in: A Scalable Parallel Implementation of Evolutionary Algorithms for
Multi-Objective Optimization on GPUs http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7257074
* GNU Parallel was cited in: Tools and techniques for computational reproducibility http://biorxiv.org/content/biorxiv/early/2015/07/17/022707.full.pdf
* GNU Parallel was cited in: How Can We Measure the Similarity Between Résumés of Selected Candidates for a Job? http://crawl.prod.proquest.com.s3.amazonaws.com/fpcache/c79b355e6e441a51de3c7fcd52866184.pdf?AWSAccessKeyId=AKIAJF7V7KNV2KKY2NUQ&Expires=1442658364&Signature=soRDi6Xqw1zHhSmBrqJ5KiD%2B8Sw%3D
* GNU Parallel was cited in: Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing http://www.researchgate.net/profile/Raphael_Etournay/publication/279061859_Interplay_of_cell_dynamics_and_epithelial_tension_during_morphogenesis_of_the_Drosophila_pupal_wing/links/558a95ad08aeae8413bcceea.pdf
* << kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>> * << kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>>
* <<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345 * <<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345

2
packager/obs/home:tange/parallel/parallel.spec
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@ -1,6 +1,6 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20150822 Version: 20150922
Release: 1 Release: 1
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities

2
src/niceload
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@ -24,7 +24,7 @@
use strict; use strict;
use Getopt::Long; use Getopt::Long;
$Global::progname="niceload"; $Global::progname="niceload";
$Global::version = 20150822; $Global::version = 20150922;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

9
src/parallel
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@ -1097,7 +1097,7 @@ sub parse_options {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20150909; $Global::version = 20150922;
$Global::progname = 'parallel'; $Global::progname = 'parallel';
$Global::infinity = 2**31; $Global::infinity = 2**31;
$Global::debug = 0; $Global::debug = 0;
@ -6006,10 +6006,10 @@ sub empty_input_wrapper {
# Returns: # Returns:
# $wrapped_command = the wrapped command # $wrapped_command = the wrapped command
my $command = shift; my $command = shift;
my $script = '$c="'.::perl_quote_scalar($Global::shell." -c ".::shell_quote_scalar($command)).'";'. my $script =
::spacefree(0,q{ ::spacefree(0,q{
if(sysread(STDIN, $buf, 1)) { if(sysread(STDIN, $buf, 1)) {
open($fh, "|-", $c) || die; open($fh, "|-", "@ARGV") || die;
syswrite($fh, $buf); syswrite($fh, $buf);
while($read = sysread(STDIN, $buf, 32768)) { while($read = sysread(STDIN, $buf, 32768)) {
syswrite($fh, $buf); syswrite($fh, $buf);
@ -6019,7 +6019,8 @@ sub empty_input_wrapper {
} }
}); });
::debug("run",'Empty wrap: perl -e '.::shell_quote_scalar($script)."\n"); ::debug("run",'Empty wrap: perl -e '.::shell_quote_scalar($script)."\n");
return 'perl -e '.::shell_quote_scalar($script); return 'perl -e '.::shell_quote_scalar($script)." ".
::shell_quote_scalar($Global::shell." -c ".::shell_quote_scalar($command));
} }
sub filter_through_compress { sub filter_through_compress {

5
src/parallel.pod
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@ -4497,7 +4497,10 @@ version.
=item * =item *
A complete example that others can run that shows the problem A minimal, complete, and verifiable example (See description on
http://stackoverflow.com/help/mcve).
It should be a complete example that others can run that shows the problem
including all files needed to run the example. This should preferably including all files needed to run the example. This should preferably
be small and simple, so try to remove as many options as possible. A be small and simple, so try to remove as many options as possible. A
combination of B<yes>, B<seq>, B<cat>, B<echo>, and B<sleep> can combination of B<yes>, B<seq>, B<cat>, B<echo>, and B<sleep> can

2
src/sql
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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err); exit ($err);
sub parse_options { sub parse_options {
$Global::version = 20150822; $Global::version = 20150922;
$Global::progname = 'sql'; $Global::progname = 'sql';
# This must be done first as this may exec myself # This must be done first as this may exec myself