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https://git.savannah.gnu.org/git/parallel.git
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parallel: {choose_k} added to --plus.
This commit is contained in:
Ole Tange
parent
68114b93e7
commit
f09e0384ff
12
README
12
README
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@ -44,9 +44,9 @@ document.
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Full installation of GNU Parallel is as simple as:
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wget http://ftpmirror.gnu.org/parallel/parallel-20170822.tar.bz2
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bzip2 -dc parallel-20170822.tar.bz2 | tar xvf -
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cd parallel-20170822
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wget http://ftpmirror.gnu.org/parallel/parallel-20170922.tar.bz2
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bzip2 -dc parallel-20170922.tar.bz2 | tar xvf -
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cd parallel-20170922
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./configure && make && sudo make install
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@ -55,9 +55,9 @@ Full installation of GNU Parallel is as simple as:
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If you are not root you can add ~/bin to your path and install in
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~/bin and ~/share:
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wget http://ftpmirror.gnu.org/parallel/parallel-20170822.tar.bz2
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bzip2 -dc parallel-20170822.tar.bz2 | tar xvf -
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cd parallel-20170822
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wget http://ftpmirror.gnu.org/parallel/parallel-20170922.tar.bz2
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bzip2 -dc parallel-20170922.tar.bz2 | tar xvf -
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cd parallel-20170922
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./configure --prefix=$HOME && make && make install
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Or if your system lacks 'make' you can simply copy src/parallel
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20
configure
vendored
20
configure
vendored
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@ -1,6 +1,6 @@
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#! /bin/sh
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# Guess values for system-dependent variables and create Makefiles.
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# Generated by GNU Autoconf 2.69 for parallel 20170822.
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# Generated by GNU Autoconf 2.69 for parallel 20170922.
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#
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# Report bugs to <bug-parallel@gnu.org>.
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#
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@ -579,8 +579,8 @@ MAKEFLAGS=
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# Identity of this package.
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PACKAGE_NAME='parallel'
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PACKAGE_TARNAME='parallel'
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PACKAGE_VERSION='20170822'
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PACKAGE_STRING='parallel 20170822'
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PACKAGE_VERSION='20170922'
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PACKAGE_STRING='parallel 20170922'
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PACKAGE_BUGREPORT='bug-parallel@gnu.org'
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PACKAGE_URL=''
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@ -1214,7 +1214,7 @@ if test "$ac_init_help" = "long"; then
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# Omit some internal or obsolete options to make the list less imposing.
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# This message is too long to be a string in the A/UX 3.1 sh.
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cat <<_ACEOF
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\`configure' configures parallel 20170822 to adapt to many kinds of systems.
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\`configure' configures parallel 20170922 to adapt to many kinds of systems.
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Usage: $0 [OPTION]... [VAR=VALUE]...
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@ -1281,7 +1281,7 @@ fi
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if test -n "$ac_init_help"; then
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case $ac_init_help in
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short | recursive ) echo "Configuration of parallel 20170822:";;
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short | recursive ) echo "Configuration of parallel 20170922:";;
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esac
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cat <<\_ACEOF
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@ -1357,7 +1357,7 @@ fi
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test -n "$ac_init_help" && exit $ac_status
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if $ac_init_version; then
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cat <<\_ACEOF
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parallel configure 20170822
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parallel configure 20170922
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generated by GNU Autoconf 2.69
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Copyright (C) 2012 Free Software Foundation, Inc.
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@ -1374,7 +1374,7 @@ cat >config.log <<_ACEOF
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This file contains any messages produced by compilers while
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running configure, to aid debugging if configure makes a mistake.
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It was created by parallel $as_me 20170822, which was
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It was created by parallel $as_me 20170922, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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$ $0 $@
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@ -2237,7 +2237,7 @@ fi
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# Define the identity of the package.
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PACKAGE='parallel'
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VERSION='20170822'
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VERSION='20170922'
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cat >>confdefs.h <<_ACEOF
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@ -2880,7 +2880,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
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# report actual input values of CONFIG_FILES etc. instead of their
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# values after options handling.
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ac_log="
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This file was extended by parallel $as_me 20170822, which was
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This file was extended by parallel $as_me 20170922, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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CONFIG_FILES = $CONFIG_FILES
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@ -2942,7 +2942,7 @@ _ACEOF
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cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
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ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
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ac_cs_version="\\
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parallel config.status 20170822
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parallel config.status 20170922
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configured by $0, generated by GNU Autoconf 2.69,
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with options \\"\$ac_cs_config\\"
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@ -1,4 +1,4 @@
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AC_INIT([parallel], [20170822], [bug-parallel@gnu.org])
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AC_INIT([parallel], [20170922], [bug-parallel@gnu.org])
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AM_INIT_AUTOMAKE([-Wall -Werror foreign])
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AC_CONFIG_HEADERS([config.h])
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AC_CONFIG_FILES([
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@ -198,20 +198,26 @@ to:parallel@gnu.org, bug-parallel@gnu.org
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stable-bcc: Jesse Alama <jessealama@fastmail.fm>
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Subject: GNU Parallel 20170922 ('Harvey/Peter Madsen') released <<[stable]>>
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Subject: GNU Parallel 20170922 ('Mexico City') released <<[stable]>>
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GNU Parallel 20170922 ('') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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GNU Parallel 20170922 ('Mexico City') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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Haiku of the month:
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<<>>
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-- Ole Tange
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--limit can
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limit jobs dynamic'ly
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given a command
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--ole-tange
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New in this release:
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https://til.hashrocket.com/posts/ggt1jaes4y-download-all-of-humble-bundle-books-in-parallel
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* Use '--limit myprog' to make a dynamic job limit. Just return 0 to spawn another job, 1 to not spawn another job, and 2 to kill the youngest job.
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* PARALLEL_RSYNC_OPTS and --rsync-opts sets the options for rsync (Default: -rlDzR).
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* Download all of humble bundle books in parallel https://til.hashrocket.com/posts/ggt1jaes4y-download-all-of-humble-bundle-books-in-parallel
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<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20170822;
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$Global::version = 20170922;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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10
src/parallel
10
src/parallel
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@ -1381,7 +1381,7 @@ sub check_invalid_option_combinations {
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sub init_globals {
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# Defaults:
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$Global::version = 20170822;
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$Global::version = 20170922;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -1415,6 +1415,7 @@ sub init_globals {
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'{...}' => 's:\.[^/.]+$::; s:\.[^/.]+$::; s:\.[^/.]+$::',
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'{/..}' => 's:.*/::; s:\.[^/.]+$::; s:\.[^/.]+$::',
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'{/...}' => 's:.*/::; s:\.[^/.]+$::; s:\.[^/.]+$::; s:\.[^/.]+$::',
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'{choose_k}' => 'for $t (2..$#arg){ if($arg[$t-1] ge $arg[$t]) { skip() } }',
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# {##} = number of jobs
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'{##}' => '$_=total_jobs()',
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# Bash ${a:-myval}
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@ -2925,7 +2926,7 @@ sub progress {
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# $pctcomplete = percent of jobs completed
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# $avgtime = averaged time
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# $eta = smoothed eta
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$total ||= $Global::JobQueue->total_jobs();
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$total = $Global::JobQueue->total_jobs();
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my $completed = $Global::total_completed;
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my $left = $total - $completed;
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if(not $completed) {
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@ -5156,7 +5157,7 @@ sub limit {
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my ($cmd,@args) = split /\s+/,$opt::limit;
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if($limitscripts{$cmd}) {
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my $tmpfile = ::tmpname("parlmt");
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$Global::unlink{$tmpfile};
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++$Global::unlink{$tmpfile};
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$self->{'limitscript'} =
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::spacefree(1, sprintf($limitscripts{$cmd},
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::multiply_binary_prefix(@args),$tmpfile));
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@ -9832,7 +9833,8 @@ sub new {
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if($posrpl =~ s/^\{//) {
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# Only do this if the shorthand start with {
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$prefix=~s/^\{//;
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while(s{( (?: ^|\257> ) (?: (?! \257[<>]). )*? ) # Don't replace after \257 unless \257>
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# Don't replace after \257 unless \257>
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while(s{( (?: ^|\257> ) (?: (?! \257[<>]). )*? )
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\{(-?\d+) \s* \Q$prefix\E $grp_regexp \Q$postfix\E}
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{
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# The start remains the same
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@ -1328,6 +1328,11 @@ Activate additional replacement strings: {+/} {+.} {+..} {+...} {..}
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B<{##}> is the number of jobs to be run. It is incompatible with
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B<-X>/B<-m>/B<--xargs>.
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B<{choose_k}> is inspired by n choose k: Given a list of n elements,
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choose k. k is the number of input sources and n is the number of
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arguments in an input source. The content of the input sources must
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be the same and the arguments must be unique.
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The following dynamic replacement strings are also activated. They are
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inspired by bash's parameter expansion:
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@ -3098,6 +3103,24 @@ This also works if the input file is a file with columns:
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parallel --colsep '\t' --header : echo {Name} {E-mail address}
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=head1 EXAMPLE: All combinations in a list
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GNU B<parallel> makes all combinations when given two lists.
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To make all combinations in a single list with unique values, you
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repeat the list and use replacement string with a Perl expression that
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skips the job if the value from input source 1 is greater than or
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equal to the value from input source 2:
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parallel echo {= 'if($arg[1] ge $arg[2]) { skip() }' =} ::: A B C D ::: A B C D
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Or more generally:
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parallel echo \
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'{= for $t (2..$#arg){ if($arg[$t-1] ge $arg[$t]) { skip() } } =}' \
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::: A B C D ::: A B C D ::: A B C D
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=head1 EXAMPLE: From a to b and b to c
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Assume you have input like:
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@ -1269,20 +1269,6 @@ The failed commands can be resumed with:
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=back
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=head2 DIFFERENCES BETWEEN k-bx/par AND GNU Parallel
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kbx requires Haskell to work. This limits the number of platforms this
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can work on.
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Todo https://github.com/k-bx/par
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=head2 DIFFERENCES BETWEEN machma AND GNU Parallel
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Todo. Requires Go >= 1.7.
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=head2 DIFFERENCES BETWEEN ClusterSSH AND GNU Parallel
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ClusterSSH solves a different problem than GNU B<parallel>.
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@ -1303,6 +1289,24 @@ GNU B<parallel> can be used as a poor-man's version of ClusterSSH:
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B<parallel --nonall -S server-a,server-b do_stuff foo bar>
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=head2 Todo
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machma. Requires Go >= 1.7.
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https://github.com/k-bx/par requires Haskell to work. This limits the
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number of platforms this can work on.
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https://github.com/otonvm/Parallel
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https://github.com/flesler/parallel
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https://github.com/kou1okada/lesser-parallel
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https://github.com/Julian/Verge
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https://github.com/amattn/paral
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=head1 TESTING OTHER TOOLS
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There are certain issues that are very common on parallelizing
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2
src/sql
2
src/sql
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@ -576,7 +576,7 @@ $Global::Initfile && unlink $Global::Initfile;
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exit ($err);
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sub parse_options {
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$Global::version = 20170822;
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$Global::version = 20170922;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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@ -124,8 +124,15 @@ par_remote_symlink_dir() {
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ssh parallel@lo 'mkdir -p tmp; rm -rf wd; ln -s tmp wd'
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mkdir -p wd
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touch wd/testfile
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parallel --nonall --rsync-opts '--keep-dirlinks -rlDzR' -S parallel@lo --basefile wd/testfile
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ssh parallel@lo rm wd && echo OK: wd is still a symlink with --rsync-opts
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ssh parallel@lo 'mkdir -p tmp; rm -rf wd; ln -s tmp wd'
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mkdir -p wd
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touch wd/testfile
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export PARALLEL_RSYNC_OPTS='--keep-dirlinks -rlDzR'
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parallel --nonall -S parallel@lo --basefile wd/testfile
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ssh parallel@lo rm wd && echo OK: wd is still a symlink
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ssh parallel@lo rm wd && echo OK: wd is still a symlink with PARALLEL_RSYNC_OPTS
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}
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export -f $(compgen -A function | grep par_)
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@ -24,7 +24,8 @@ par_read_sshloginfile_from_stdin foo
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par_read_sshloginfile_from_stdin /home/parallel
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par_read_sshloginfile_from_stdin foo
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par_remote_symlink_dir bug #51293: parallel does not preserve symlinked directory structure on remote
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par_remote_symlink_dir OK: wd is still a symlink
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par_remote_symlink_dir OK: wd is still a symlink with --rsync-opts
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par_remote_symlink_dir OK: wd is still a symlink with PARALLEL_RSYNC_OPTS
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par_test_nonall ### Test --nonall
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par_test_nonall /home/csh
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par_test_nonall /home/parallel
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