mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-11-25 15:37:56 +00:00
parallel: $XDG_*
This commit is contained in:
Ole Tange
parent
4548ebd756
commit
c63881c4cc
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@ -131,6 +131,7 @@ git diff
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YYYYMMDD=`yyyymmdd`
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TAG=MyTag
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echo "Released as $YYYYMMDD ('$TAG')." | grep MyTag && (STOP;STOP;STOP)
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echo "$TAG" | grep ' ' && (STOP;STOP;STOP)
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git commit -a -m "Released as $YYYYMMDD ('$TAG')"
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git tag -s -u 88888888 -m "Released as $YYYYMMDD ('$TAG')" $TAG
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@ -198,26 +199,27 @@ 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 ('Mexico City') released <<[stable]>>
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Subject: GNU Parallel 20171022 ('Peter Madsen/Catalonia/Las Vegas') released <<[stable]>>
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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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GNU Parallel 20171022 ('Peter Madsen') <<[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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--limit can
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limit jobs dynamic'ly
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given a command
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<<>>
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--ole-tange
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New in this release:
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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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*
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https://www.turing.ac.uk/events/masterclass-cluster-computing/
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* PARALLEL_RSYNC_OPTS and --rsync-opts sets the options for rsync (Default: -rlDzR).
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https://openwetware.org/wiki/Butlin:Unix_for_Bioinformatics_-_advanced_tutorial
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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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https://veer66.wordpress.com/2017/09/02/use-multi-core/
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https://gist.github.com/drmalex07/de8ff1379a560f6d84a0d863e60ae378
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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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@ -168,6 +168,7 @@ function env_parallel
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s/\n/\001/g'
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end;
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)
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# If --record-env: exit
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perl -e 'exit grep { /^--record-env$/ } @ARGV' -- $argv; and parallel $argv;
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set _parallel_exit_CODE $status
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set -e PARALLEL_ENV
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20170922;
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$Global::version = 20170923;
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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($opt::version) {
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68
src/parallel
68
src/parallel
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@ -1381,7 +1381,7 @@ sub check_invalid_option_combinations {
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sub init_globals {
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# Defaults:
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$Global::version = 20170922;
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$Global::version = 20170923;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -1458,7 +1458,30 @@ sub init_globals {
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::warning("\$HOME not set. Using /tmp.");
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$ENV{HOME} = "/tmp";
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}
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$ENV{'PARALLEL_HOME'} ||= $ENV{'HOME'} . "/.parallel";
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# no warnings to allow for undefined $XDG_*
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no warnings 'uninitialized';
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# $xdg_config_home is needed to make env_parallel.fish stop complaining
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my $xdg_config_home = $ENV{'XDG_CONFIG_HOME'};
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# config_dirs = $PARALLEL_HOME, $XDG_CONFIG_HOME/parallel,
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# $(each XDG_CONFIG_DIRS)/parallel, $HOME/.parallel
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# Keep only dirs that exist
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@Global::config_dirs =
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(grep { -d $_ }
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$ENV{'PARALLEL_HOME'},
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(map { "$_/parallel" }
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$xdg_config_home,
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split /:/, $ENV{'XDG_CONFIG_DIRS'}),
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$ENV{'HOME'} . "/.parallel");
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# Use first dir as config dir
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$Global::config_dir = $Global::config_dirs[0] ||
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$ENV{'HOME'} . "/.parallel";
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# cache_dirs = $PARALLEL_HOME, $XDG_CACHE_HOME/parallel,
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# Keep only dirs that exist
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@Global::cache_dirs =
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(grep { -d $_ }
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$ENV{'PARALLEL_HOME'}, $ENV{'XDG_CACHE_HOME'}."/parallel");
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$Global::cache_dir = $Global::cache_dirs[0] ||
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$ENV{'HOME'} . "/.parallel";
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}
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sub parse_halt {
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@ -1633,7 +1656,7 @@ sub parse_semaphore {
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sub record_env {
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# Record current %ENV-keys in $PARALLEL_HOME/ignored_vars
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# Returns: N/A
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my $ignore_filename = $ENV{'PARALLEL_HOME'} . "/ignored_vars";
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my $ignore_filename = $Global::config_dir . "/ignored_vars";
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if(open(my $vars_fh, ">", $ignore_filename)) {
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print $vars_fh map { $_,"\n" } keys %ENV;
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} else {
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@ -1905,18 +1928,16 @@ sub read_options {
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# Add options from $PARALLEL_HOME/config and other profiles
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my @config_profiles = (
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"/etc/parallel/config",
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$ENV{'PARALLEL_HOME'}."/config",
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(map { "$_/config" } @Global::config_dirs),
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$ENV{'HOME'}."/.parallelrc");
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my @profiles = @config_profiles;
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if(@opt::profile) {
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# --profile overrides default profiles
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@profiles = ();
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for my $profile (@opt::profile) {
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if(-r $profile) {
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push @profiles, $profile;
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} else {
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push @profiles, $ENV{'PARALLEL_HOME'}."/".$profile;
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}
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# Look for the $profile in . and @Global::config_dirs
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push @profiles, grep { -r $_ }
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map { "$_/$profile" } ".", @Global::config_dirs;
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}
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}
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for my $profile (@profiles) {
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@ -3116,16 +3137,19 @@ sub expand_slf_shorthand {
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if($file eq "-") {
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# skip: It is stdin
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} elsif($file eq "..") {
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$file = $ENV{'PARALLEL_HOME'}."/sshloginfile";
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$file = $Global::config_dir."/sshloginfile";
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} elsif($file eq ".") {
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$file = "/etc/parallel/sshloginfile";
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} elsif(not -r $file) {
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if(not -r $ENV{'PARALLEL_HOME'}."/".$file) {
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for(@Global::config_dirs) {
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if(not -r $_."/".$file) {
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# Try prepending $PARALLEL_HOME
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::error("Cannot open $file.");
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::wait_and_exit(255);
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} else {
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$file = $ENV{'PARALLEL_HOME'}."/".$file;
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} else {
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$file = $_."/".$file;
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last;
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}
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}
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}
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return $file;
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@ -4049,7 +4073,7 @@ sub citation_notice {
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or
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not -t $Global::original_stderr
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or
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-e $ENV{'PARALLEL_HOME'}."/will-cite") {
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grep { -e "$_/will-cite" } @Global::config_dirs) {
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# skip
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} else {
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::status
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@ -4158,15 +4182,15 @@ sub citation {
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"mentioned in the release notes of next version of GNU Parallel.",
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""
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);
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while(not -e $ENV{'PARALLEL_HOME'}."/will-cite") {
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while(not grep { -e "$_/will-cite" } @Global::config_dirs) {
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print "\nType: 'will cite' and press enter.\n> ";
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my $input = <STDIN>;
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if(not defined $input) {
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exit(255);
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}
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if($input =~ /will cite/i) {
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mkdir $ENV{'PARALLEL_HOME'};
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if(open (my $fh, ">", $ENV{'PARALLEL_HOME'}."/will-cite")) {
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mkdir $Global::config_dir;
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if(open (my $fh, ">", $Global::config_dir."/will-cite")) {
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close $fh;
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::status(
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"",
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@ -4917,11 +4941,11 @@ sub new {
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'control_path' => undef,
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'time_to_login' => undef,
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'last_login_at' => undef,
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'loadavg_file' => $ENV{'PARALLEL_HOME'} . "/tmp/sshlogin/" .
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'loadavg_file' => $Global::cache_dir . "/tmp/sshlogin/" .
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$no_slash_string . "/loadavg",
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'loadavg' => undef,
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'last_loadavg_update' => 0,
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'swap_activity_file' => $ENV{'PARALLEL_HOME'} . "/tmp/sshlogin/" .
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'swap_activity_file' => $Global::cache_dir . "/tmp/sshlogin/" .
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$no_slash_string . "/swap_activity",
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'swap_activity' => undef,
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}, ref($class) || $class;
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@ -7762,7 +7786,7 @@ sub sshlogin_wrap {
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local $/ = "\n";
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# --env _
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# Include all vars that are not in a clean environment
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if(open(my $vars_fh, "<", $ENV{'PARALLEL_HOME'} . "/ignored_vars")) {
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if(open(my $vars_fh, "<", $Global::config_dir . "/ignored_vars")) {
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my @ignore = <$vars_fh>;
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chomp @ignore;
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my %ignore;
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@ -10113,7 +10137,7 @@ sub max_length {
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# number of chars on the longest command line allowed
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if(not $Limits::Command::line_max_len) {
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# Disk cache of max command line length
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my $len_cache = $ENV{'PARALLEL_HOME'} . "/tmp/sshlogin/" . ::hostname() .
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my $len_cache = $Global::cache_dir . "/tmp/sshlogin/" . ::hostname() .
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"/linelen";
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my $cached_limit;
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if(-e $len_cache) {
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@ -11348,7 +11372,7 @@ sub new {
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my $count = shift;
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$id =~ s/([^-_a-z0-9])/unpack("H*",$1)/ige; # Convert non-word chars to hex
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$id = "id-".$id; # To distinguish it from a process id
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my $parallel_locks = $ENV{'PARALLEL_HOME'}."/semaphores";
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my $parallel_locks = $Global::cache_dir . "/semaphores";
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-d $parallel_locks or ::mkdir_or_die($parallel_locks);
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my $lockdir = "$parallel_locks/$id";
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@ -1042,7 +1042,7 @@ B<-l 0> is an alias for B<-l 1>.
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Implies B<-X> unless B<-m>, B<--xargs>, or B<--pipe> is set.
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=item B<--limit> "I<command> I<args>" (alpha testing)
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=item B<--limit> "I<command> I<args>" (beta testing)
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Dynamic job limit. Before starting a new job run I<command> with
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I<args>. The exit value of I<command> determines what GNU B<parallel>
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@ -1085,9 +1085,9 @@ Similar to B<--memfree>.
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=back
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=item B<--line-buffer> (beta testing)
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=item B<--line-buffer>
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=item B<--lb> (beta testing)
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=item B<--lb>
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Buffer output on line basis. B<--group> will keep the output together
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for a whole job. B<--ungroup> allows output to mixup with half a line
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@ -1915,7 +1915,7 @@ You can even use multiple matches:
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See also: B<{= perl expression =}> B<--parens>
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=item B<--rsync-opts> I<options> (alpha testing)
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=item B<--rsync-opts> I<options> (beta testing)
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Options to pass on to B<rsync>. Setting B<--rsync-opts> takes
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precedence over setting the environment variable $PARALLEL_RSYNC_OPTS.
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@ -2188,7 +2188,8 @@ B<ssh-copy-id>, and B<sshpass> may help with that).
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The sshlogin ':' is special, it means 'no ssh' and will therefore run
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on the local computer.
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The sshlogin '..' is special, it read sshlogins from ~/.parallel/sshloginfile
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The sshlogin '..' is special, it read sshlogins from ~/.parallel/sshloginfile or
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$XDG_CONFIG_HOME/parallel/sshloginfile
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The sshlogin '-' is special, too, it read sshlogins from stdin
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(standard input).
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@ -1288,6 +1288,18 @@ 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 coshell
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B<coshell> only accepts full commands on standard input. Any quoting
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needs to be done by the user.
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Commands are run in B<sh> so any B<bash>/B<tcsh>/B<zsh> specific
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syntax will not work.
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Output can be buffered by using B<-d>. Output is buffered in memory,
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so big output can cause swapping and therefore be terrible slow or
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even cause out of memory.
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=head2 Todo
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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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$Global::version = 20170922;
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$Global::version = 20170923;
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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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@ -62,9 +62,9 @@ par_linebuffer_matters_compress_tag() {
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testfunc() {
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linebuffer="$1"
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# Sleep 2 sec to give time to linebuffer-print the first part
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# Sleep 3 sec to give time to linebuffer-print the first part
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parallel -j0 $linebuffer --compress --tag \
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"shuf $randomfile; sleep 2; shuf $randomfile; true" ::: {0..10} |
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"shuf $randomfile; sleep 3; shuf $randomfile; true" ::: {0..10} |
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perl -ne '/^(\S+)\t/ and print "$1\n"' | uniq | sort
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}
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@ -349,13 +349,13 @@ echo '{##} bug #45841: Replacement string for total no of jobs'
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3 3
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parallel -k -S 8/: -X --plus echo {#} {##} ::: {1..15}
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1 15 15
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2 15 15
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3 15 15
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4 15 15
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5 15 15
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6 15 15
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7 15 15
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8 15
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2 14 14
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3 14 14
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4 14 14
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5 14 14
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6 14 14
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7 14 14
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8 14
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echo '**'
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**
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echo 'bug #47002: --tagstring with -d \n\n'
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