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Released as 20160122 ('Bowie')

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This commit is contained in:
Ole Tange 2016-01-23 10:46:58 +01:00
parent a4ead8224d
commit 7fd33c205a
12 changed files with 84 additions and 52 deletions
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50
NEWS
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@ -1,3 +1,53 @@
20160122
* --sql DBURL uses DBURL as storage for jobs and output. It does not
run any jobs so it requires at least one --sqlworker. DBURL must
point to a table.
* --sqlworker DBURL gets jobs from DBURL and stores the result back to
DBURL.
* --sqlandworker is a shorthand for --sql and --sqlworker.
* --sqlworker requires the output of a single job to fit in memory.
* --results now also saves a file called 'seq' containing the sequence
number.
* If $PARALLEL_ENV is a file, then that file will be read into
$PARALLEL_ENV.
* man parallel_tutorial has been given an overhaul.
* --workdir now accepts replacementstrings.
* GNU Parallel was cited in: Possum - A Framework for
Three-Dimensional Reconstruction of Brain Images rfom Serial
Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
* GNU Parallel was cited in: A Genetic Algorithm for the selection of
structural MRI features for classification of Mild Cognitive
Impairment and Alzheimer's Disease
http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7359909&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7359909
* GNU Parallel was cited in: The Effect of Domain Modeling on
Performance of Planning Algorithms
http://isaim2016.cs.virginia.edu/papers/ISAIM2016_Bartak_Vodrazka.pdf
* Plotting time tables for jobs run by GNU Parallel
https://github.com/ziotom78/plot_joblog
* GNU Parallel was used in: Mission Impossible: you have 1 minute to
analyze the Ebola Genome https://www.biostars.org/p/119397
* GNU Parallel is used in LAST: http://last.cbrc.jp/
* Distributed Log Search Using GNU Parallel
http://codehate.com/blog/2015/12/01/distributed-log-search-using-gnu-parallel/
* Bug fixes and man page updates.
20151222 20151222
* --transfer is now an alias for --transferfile {}. * --transfer is now an alias for --transferfile {}.

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-20160101.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20160122.tar.bz2
bzip2 -dc parallel-20160101.tar.bz2 | tar xvf - bzip2 -dc parallel-20160122.tar.bz2 | tar xvf -
cd parallel-20160101 cd parallel-20160122
./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-20160101.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20160122.tar.bz2
bzip2 -dc parallel-20160101.tar.bz2 | tar xvf - bzip2 -dc parallel-20160122.tar.bz2 | tar xvf -
cd parallel-20160101 cd parallel-20160122
./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 20160101. # Generated by GNU Autoconf 2.69 for parallel 20160122.
# #
# 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='20160101' PACKAGE_VERSION='20160122'
PACKAGE_STRING='parallel 20160101' PACKAGE_STRING='parallel 20160122'
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 20160101 to adapt to many kinds of systems. \`configure' configures parallel 20160122 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 $ac_init_help in
short | recursive ) echo "Configuration of parallel 20160101:";; short | recursive ) echo "Configuration of parallel 20160122:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1345,7 +1345,7 @@ fi
test -n "$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 20160101 parallel configure 20160122
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 20160101, which was It was created by parallel $as_me 20160122, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2225,7 +2225,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20160101' VERSION='20160122'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2867,7 +2867,7 @@ cat >>$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 20160101, which was This file was extended by parallel $as_me 20160122, 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 20160101 parallel config.status 20160122
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], [20160101], [bug-parallel@gnu.org]) AC_INIT([parallel], [20160122], [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([

32
doc/release_new_version
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@ -4,7 +4,7 @@
Check that documentation is updated (compare to web): Check that documentation is updated (compare to web):
Fixet for 20151122 Fixet for 20160122
git diff last-release-commit git diff last-release-commit
Unmodified beta since last version => production Unmodified beta since last version => production
Unmodified alpha since last version => beta Unmodified alpha since last version => beta
@ -212,18 +212,16 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>, Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
Jesse Alama <jesse.alama@gmail.com> Jesse Alama <jesse.alama@gmail.com>
Subject: GNU Parallel 20160122 ('') released <<[stable]>> Subject: GNU Parallel 20160122 ('Bowie') released
GNU Parallel 20160122 ('') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/ GNU Parallel 20160122 ('Bowie') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
<<No new functionality was introduced so this is a good candidate for a stable release.>>
Haiku of the month: Haiku of the month:
||||| Dash dash pipe too slow?
||||||| Dash dash pipepart is your friend.
Use GNU Parallel Use GNU Parallel
-- Malcolm Cook -- Ole Tange
New in this release: New in this release:
@ -243,22 +241,6 @@ New in this release:
* --workdir now accepts replacementstrings. * --workdir now accepts replacementstrings.
* << 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
* <<Afventer updateret publisering>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487
* <<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
* << Update forventet juni Rachel har lige svaret >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
* <<Citation needed: A Cache- and Memory-Aware Mapping Algorithm
for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7323015>>
* <<Citation needed: Introspecting for RSA Key Material to Assist Intrusion Detection http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7331177&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7331177>>
* GNU Parallel was cited in: Possum - A Framework for Three-Dimensional Reconstruction of Brain Images rfom Serial Sections http://link.springer.com/article/10.1007/s12021-015-9286-1 * GNU Parallel was cited in: Possum - A Framework for Three-Dimensional Reconstruction of Brain Images rfom Serial Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
* GNU Parallel was cited in: A Genetic Algorithm for the selection of structural MRI features for classification of Mild Cognitive Impairment and Alzheimer's Disease http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7359909&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7359909 * GNU Parallel was cited in: A Genetic Algorithm for the selection of structural MRI features for classification of Mild Cognitive Impairment and Alzheimer's Disease http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7359909&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7359909
@ -271,7 +253,7 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
* GNU Parallel is used in LAST: http://last.cbrc.jp/ * GNU Parallel is used in LAST: http://last.cbrc.jp/
* Distributed Log Search Using GNU Parallel http://blog.codehate.com/post/134320079974/distributed-log-search-using-gnu-parallel * Distributed Log Search Using GNU Parallel http://codehate.com/blog/2015/12/01/distributed-log-search-using-gnu-parallel/
* Bug fixes and man page updates. * Bug fixes and man page updates.

4
packager/obs/home:tange/parallel/parallel.spec
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@ -1,7 +1,7 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20151222 Version: 20160122
Release: 1 Release: 1.1
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities
URL: ftp://ftp.gnu.org/gnu/parallel URL: ftp://ftp.gnu.org/gnu/parallel

2
src/Makefile.in
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@ -78,7 +78,7 @@ NORMAL_UNINSTALL = :
PRE_UNINSTALL = : PRE_UNINSTALL = :
POST_UNINSTALL = : POST_UNINSTALL = :
subdir = src subdir = src
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am README
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \

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 = 20160101; $Global::version = 20160122;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

4
src/niceload.pod
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@ -32,9 +32,9 @@ run 1 second, suspend (3.00-1.00) seconds, run 1 second, suspend
=over 9 =over 9
=item B<-B> (beta testing) =item B<-B>
=item B<--battery> (beta testing) =item B<--battery>
Suspend if the system is running on battery. Short hand for: -l -1 --sensor 'cat /sys/class/power_supply/BAT0/status /proc/acpi/battery/BAT0/state 2>/dev/null |grep -i -q discharging; echo $?' Suspend if the system is running on battery. Short hand for: -l -1 --sensor 'cat /sys/class/power_supply/BAT0/status /proc/acpi/battery/BAT0/state 2>/dev/null |grep -i -q discharging; echo $?'

2
src/parallel
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@ -1176,7 +1176,7 @@ sub check_invalid_option_combinations {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20160102; $Global::version = 20160122;
$Global::progname = 'parallel'; $Global::progname = 'parallel';
$Global::infinity = 2**31; $Global::infinity = 2**31;
$Global::debug = 0; $Global::debug = 0;

4
src/sem.pod
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@ -138,9 +138,9 @@ takes a person to the toilet, waits for the person to finish, and
exits. exits.
=item B<--semaphoretimeout> I<secs> (beta testing) =item B<--semaphoretimeout> I<secs>
=item B<--st> I<secs> (beta testing) =item B<--st> I<secs>
If I<secs> > 0: If the semaphore is not released within I<secs> If I<secs> > 0: If the semaphore is not released within I<secs>
seconds, take it anyway. seconds, take it anyway.

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 = 20160101; $Global::version = 20160122;
$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