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parallel: --tmux works for remote running jobs.
This commit is contained in:
Ole Tange
parent
1a1c0ebe0f
commit
81ff568ce7
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@ -241,6 +241,8 @@ New in this release:
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* The parenthesis around {= perl expression =} can be changed with --parens.
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* --tmux will direct the output to a tmux session instead of files.
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* GNU Parallel was cited in: bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS) http://bioinformatics.oxfordjournals.org/content/early/2014/06/28/bioinformatics.btu410.abstract
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* GNU Parallel was cited in: Molecular ferroelectric contributions to anomalous hysteresis in hybrid perovskite solar cells http://people.bath.ac.uk/aw558/publications/2014/arxiv_hysteresis_14.pdf
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@ -251,10 +253,14 @@ New in this release:
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* Webcast at 2014-08-20 covering GNU Parallel: Data Science at the Command Line http://www.oreilly.com/pub/e/3115
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* GNU Parallel all the things! http://longwayaround.org.uk/notes/gnu-parallel-all-the-things/
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* Shell command composition and dispatch http://lukeluo.blogspot.dk/2014/07/linux-virtual-console6-shell-command.html
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* Parallelising plink (or anything else) the easy way http://chrisladroue.com/2012/03/parallelising-plink-or-anything-else-the-easy-way/
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* Easy and cheap cluster building on AWS https://grapeot.me/easy-and-cheap-cluster-building-on-aws.html
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* Paralelizace běžných činností v konzoli pomocí GNU Parallel http://www.abclinuxu.cz/clanky/paralelizace-beznych-cinnosti-v-konzoli-pomoci-gnu-parallel
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* [原] Ubuntu 下使用 parallel 命令的注意事项 http://blog.ailms.me/2014/06/28/ubuntu-with-parallel.html
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35
src/parallel
35
src/parallel
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@ -5220,8 +5220,9 @@ sub start {
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(cat $tmpfile; rm $tmpfile; cat - ) | } .
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"($command);";
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if($opt::tmux) {
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$command = tmux_wrap($command);
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$command = tmux_wrap($command,$job->replaced());
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}
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# The eval is needed to catch exception from open3
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eval {
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$pid = ::open3($stdin_fh, ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
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@ -5236,7 +5237,7 @@ sub start {
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*IN = *STDIN;
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# The eval is needed to catch exception from open3
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if($opt::tmux) {
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$command = tmux_wrap($command);
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$command = tmux_wrap($command,$job->replaced());
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}
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eval {
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$pid = ::open3("<&IN", ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
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@ -5252,7 +5253,7 @@ sub start {
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*IN = $devtty_fh;
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# The eval is needed to catch exception from open3
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if($opt::tmux) {
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$command = tmux_wrap($command);
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$command = tmux_wrap($command,$job->replaced());
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}
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eval {
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$pid = ::open3("<&IN", ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
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@ -5263,7 +5264,7 @@ sub start {
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};
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} else {
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if($opt::tmux) {
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$command = tmux_wrap($command);
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$command = tmux_wrap($command,$job->replaced());
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}
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eval {
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$pid = ::open3(::gensym, ">&OUT", ">&ERR", $ENV{SHELL}, "-c", $command) ||
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@ -5292,21 +5293,33 @@ sub start {
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}
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sub tmux_wrap {
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my $command = shift;
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# Start tmux seesion as pPID
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# Wrap command with tmux for session pPID
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# Input:
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# $actual_command = the actual command being run (incl ssh wrap)
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# $visual_command = the command the user wants run (= -v)
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my $actual_command = shift;
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my $visual_command = shift;
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# Temporary file name. Used for fifo to communicate exit val
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my ($fh, $tmpfile) = ::tempfile(SUFFIX => ".tmx");
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close $fh;
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unlink $tmpfile;
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my $c = $visual_command;
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# tmux does not like some chars (e.g. ;).
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$c =~ s/[^-<>(),:_+=#a-z0-9 `\\\$\|]//g;
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my $tmux;
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if($Global::total_running == 0) {
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$tmux = "tmux new-session -s p$$ -d";
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if($Global::total_running == 0) {
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$tmux = "tmux new-session -s p$$ -d -n ".
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::shell_quote_scalar($c);
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print $Global::original_stderr "See output with: tmux attach -t p$$\n";
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} else {
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$tmux = "tmux new-window -t p$$";
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$tmux = "tmux new-window -t p$$ -n ".::shell_quote_scalar($c);
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}
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return "mkfifo $tmpfile; $tmux ".
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::shell_quote_scalar("(".$command.');echo $?$status >'.$tmpfile).
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"; ( exit `cat < $tmpfile;rm $tmpfile` )";
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::shell_quote_scalar("(".$actual_command.');echo $?$status >'.$tmpfile.";".
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"echo ".::shell_quote_scalar($visual_command).";".
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"echo \007Job finished at: `date`;sleep 60").
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"; ( exit `cat < $tmpfile;rm $tmpfile` )";
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}
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sub is_already_in_results {
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@ -124,7 +124,7 @@
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.\" ========================================================================
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.\"
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.IX Title "PARALLEL_TUTORIAL 1"
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.TH PARALLEL_TUTORIAL 1 "2014-07-15" "20140711" "parallel"
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.TH PARALLEL_TUTORIAL 1 "2014-07-18" "20140711" "parallel"
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.\" For nroff, turn off justification. Always turn off hyphenation; it makes
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.\" way too many mistakes in technical documents.
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.if n .ad l
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@ -483,8 +483,8 @@ Output (the order may be different):
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.Ve
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.SS "Replacement strings"
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.IX Subsection "Replacement strings"
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\fIThe 7 replacement strings\fR
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.IX Subsection "The 7 replacement strings"
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\fIThe 7 predefined replacement strings\fR
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.IX Subsection "The 7 predefined replacement strings"
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.PP
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\&\s-1GNU\s0 Parallel has several replacement strings. If no replacement
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strings are used the default is to append {}:
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@ -587,8 +587,10 @@ Output (the order may be different):
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\& 2
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\& 1
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.Ve
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.SS "Changing the replacement strings"
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.PP
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\fIChanging the replacement strings\fR
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.IX Subsection "Changing the replacement strings"
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.PP
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The replacement string {} can be changed with \-I:
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.PP
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.Vb 1
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@ -676,8 +678,64 @@ Output (the order may be different):
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\& 2
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\& 1
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.Ve
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.SS "Positional replacement strings"
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.PP
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\fIPerl expression replacement string\fR
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.IX Subsection "Perl expression replacement string"
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.PP
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When predefined replacement strings are not flexible enough a perl
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expression can be used instead. One example is to remove two
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extensions: foo.tar.gz \-> foo
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.PP
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.Vb 1
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\& parallel echo \*(Aq{= s:\e.[^.]+$::;s:\e.[^.]+$::; =}\*(Aq ::: foo.tar.gz
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.Ve
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.PP
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Output:
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.PP
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.Vb 1
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\& foo
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.Ve
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.PP
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If the strings \fB{=\fR and \fB=}\fR cause problems they can be replaced with \-\-parens:
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.PP
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.Vb 1
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\& parallel \-\-parens ,,,, echo \*(Aq,, s:\e.[^.]+$::;s:\e.[^.]+$::; ,,\*(Aq ::: foo.tar.gz
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.Ve
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.PP
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Output: Same as above.
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.PP
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To define a short hand replacement string use \fB\-\-rpl\fR:
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.PP
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.Vb 1
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\& parallel \-\-rpl \*(Aq.. s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq..\*(Aq ::: foo.tar.gz
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.Ve
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.PP
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Output: Same as above.
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.PP
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If the short hand starts with '{' it can be used as a positional
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replacement string, too:
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.PP
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.Vb 1
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\& parallel \-\-rpl \*(Aq{..} s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq{..}\*(Aq ::: foo.tar.gz
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.Ve
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.PP
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Output: Same as above.
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.PP
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\&\s-1GNU\s0 \fBparallel\fR's 7 replacement strings are implemented as:
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.PP
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.Vb 7
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\& \-\-rpl \*(Aq{} \*(Aq
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\& \-\-rpl \*(Aq{#} $_=$job\->seq()\*(Aq
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\& \-\-rpl \*(Aq{%} $_=$job\->slot()\*(Aq
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\& \-\-rpl \*(Aq{/} s:.*/::\*(Aq
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\& \-\-rpl \*(Aq{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);\*(Aq
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\& \-\-rpl \*(Aq{/.} s:.*/::; s:\e.[^/.]+$::;\*(Aq
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\& \-\-rpl \*(Aq{.} s:\e.[^/.]+$::\*(Aq
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.Ve
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.PP
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\fIPositional replacement strings\fR
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.IX Subsection "Positional replacement strings"
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.PP
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With multiple input sources the argument from the individual input
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sources can be access with {number}:
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.PP
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@ -726,8 +784,35 @@ Output (the order may be different):
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\& 1=B 2=D 3=E \-1=E \-2=D \-3=B
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\& 1=B 2=D 3=F \-1=F \-2=D \-3=B
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.Ve
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.SS "Input from columns"
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.PP
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\fIPositional perl expression replacement string\fR
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.IX Subsection "Positional perl expression replacement string"
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.PP
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To use a perl expression as a positional replacement string simply
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prepend the perl expression with number and space:
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.PP
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.Vb 1
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\& parallel echo \*(Aq{=2 s:\e.[^.]+$::;s:\e.[^.]+$::; =} {1}\*(Aq ::: bar ::: foo.tar.gz
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.Ve
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.PP
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Output:
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.PP
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.Vb 1
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\& foo bar
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.Ve
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.PP
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If a defined short hand starts with '{' it can be used as a positional
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replacement string, too:
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.PP
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.Vb 1
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\& parallel \-\-rpl \*(Aq{..} s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq{2..} {1}\*(Aq ::: bar ::: foo.tar.gz
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.Ve
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.PP
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Output: Same as above.
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.PP
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\fIInput from columns\fR
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.IX Subsection "Input from columns"
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.PP
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The columns in a file can be bound to positional replacement strings
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using \-\-colsep. Here the columns are separated with \s-1TAB\s0 (\et):
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.PP
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@ -742,8 +827,10 @@ Output (the order may be different):
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\& 1=A 2=B
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\& 1=C 2=D
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.Ve
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.SS "Header defined replacement strings"
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.PP
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\fIHeader defined replacement strings\fR
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.IX Subsection "Header defined replacement strings"
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.PP
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With \-\-header \s-1GNU\s0 Parallel will use the first value of the input
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source as the name of the replacement string. Only the non-modified
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version {} is supported:
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@ -41,13 +41,15 @@
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<li><a href="#replacement_strings">Replacement strings</a></li>
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<ul>
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<li><a href="#the_7_replacement_strings">The 7 replacement strings</a></li>
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<li><a href="#the_7_predefined_replacement_strings">The 7 predefined replacement strings</a></li>
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<li><a href="#changing_the_replacement_strings">Changing the replacement strings</a></li>
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<li><a href="#perl_expression_replacement_string">Perl expression replacement string</a></li>
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<li><a href="#positional_replacement_strings">Positional replacement strings</a></li>
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<li><a href="#positional_perl_expression_replacement_string">Positional perl expression replacement string</a></li>
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<li><a href="#input_from_columns">Input from columns</a></li>
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<li><a href="#header_defined_replacement_strings">Header defined replacement strings</a></li>
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</ul>
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|
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<li><a href="#changing_the_replacement_strings">Changing the replacement strings</a></li>
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<li><a href="#positional_replacement_strings">Positional replacement strings</a></li>
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<li><a href="#input_from_columns">Input from columns</a></li>
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<li><a href="#header_defined_replacement_strings">Header defined replacement strings</a></li>
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<li><a href="#more_than_one_argument">More than one argument</a></li>
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<li><a href="#quoting">Quoting</a></li>
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<li><a href="#trimming_space">Trimming space</a></li>
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@ -390,7 +392,7 @@ exported using 'export -f':</p>
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<h2><a name="replacement_strings">Replacement strings</a></h2>
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<p>
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</p>
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<h3><a name="the_7_replacement_strings">The 7 replacement strings</a></h3>
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<h3><a name="the_7_predefined_replacement_strings">The 7 predefined replacement strings</a></h3>
|
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<p>GNU Parallel has several replacement strings. If no replacement
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strings are used the default is to append {}:</p>
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<pre>
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@ -447,7 +449,7 @@ number of jobs to run in parallel):</p>
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1</pre>
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<p>
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</p>
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<h2><a name="changing_the_replacement_strings">Changing the replacement strings</a></h2>
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<h3><a name="changing_the_replacement_strings">Changing the replacement strings</a></h3>
|
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<p>The replacement string {} can be changed with -I:</p>
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<pre>
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parallel -I ,, echo ,, ::: A/B.C</pre>
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|
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@ -496,7 +498,40 @@ number of jobs to run in parallel):</p>
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1</pre>
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<p>
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</p>
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<h2><a name="positional_replacement_strings">Positional replacement strings</a></h2>
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<h3><a name="perl_expression_replacement_string">Perl expression replacement string</a></h3>
|
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<p>When predefined replacement strings are not flexible enough a perl
|
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expression can be used instead. One example is to remove two
|
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extensions: foo.tar.gz -> foo</p>
|
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<pre>
|
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parallel echo '{= s:\.[^.]+$::;s:\.[^.]+$::; =}' ::: foo.tar.gz</pre>
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<p>Output:</p>
|
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<pre>
|
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foo</pre>
|
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<p>If the strings <strong>{=</strong> and <strong>=}</strong> cause problems they can be replaced with --parens:</p>
|
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<pre>
|
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parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' ::: foo.tar.gz</pre>
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<p>Output: Same as above.</p>
|
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<p>To define a short hand replacement string use <strong>--rpl</strong>:</p>
|
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<pre>
|
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parallel --rpl '.. s:\.[^.]+$::;s:\.[^.]+$::;' echo '..' ::: foo.tar.gz</pre>
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<p>Output: Same as above.</p>
|
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<p>If the short hand starts with '{' it can be used as a positional
|
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replacement string, too:</p>
|
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<pre>
|
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parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{..}' ::: foo.tar.gz</pre>
|
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<p>Output: Same as above.</p>
|
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<p>GNU <strong>parallel</strong>'s 7 replacement strings are implemented as:</p>
|
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<pre>
|
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--rpl '{} '
|
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--rpl '{#} $_=$job->seq()'
|
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--rpl '{%} $_=$job->slot()'
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--rpl '{/} s:.*/::'
|
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--rpl '{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);'
|
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--rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
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--rpl '{.} s:\.[^/.]+$::'</pre>
|
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<p>
|
||||
</p>
|
||||
<h3><a name="positional_replacement_strings">Positional replacement strings</a></h3>
|
||||
<p>With multiple input sources the argument from the individual input
|
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sources can be access with {number}:</p>
|
||||
<pre>
|
||||
|
|
@ -530,7 +565,22 @@ from behind:</p>
|
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1=B 2=D 3=F -1=F -2=D -3=B</pre>
|
||||
<p>
|
||||
</p>
|
||||
<h2><a name="input_from_columns">Input from columns</a></h2>
|
||||
<h3><a name="positional_perl_expression_replacement_string">Positional perl expression replacement string</a></h3>
|
||||
<p>To use a perl expression as a positional replacement string simply
|
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prepend the perl expression with number and space:</p>
|
||||
<pre>
|
||||
parallel echo '{=2 s:\.[^.]+$::;s:\.[^.]+$::; =} {1}' ::: bar ::: foo.tar.gz</pre>
|
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<p>Output:</p>
|
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<pre>
|
||||
foo bar</pre>
|
||||
<p>If a defined short hand starts with '{' it can be used as a positional
|
||||
replacement string, too:</p>
|
||||
<pre>
|
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parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' ::: bar ::: foo.tar.gz</pre>
|
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<p>Output: Same as above.</p>
|
||||
<p>
|
||||
</p>
|
||||
<h3><a name="input_from_columns">Input from columns</a></h3>
|
||||
<p>The columns in a file can be bound to positional replacement strings
|
||||
using --colsep. Here the columns are separated with TAB (\t):</p>
|
||||
<pre>
|
||||
|
|
@ -542,7 +592,7 @@ using --colsep. Here the columns are separated with TAB (\t):</p>
|
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1=C 2=D</pre>
|
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<p>
|
||||
</p>
|
||||
<h2><a name="header_defined_replacement_strings">Header defined replacement strings</a></h2>
|
||||
<h3><a name="header_defined_replacement_strings">Header defined replacement strings</a></h3>
|
||||
<p>With --header GNU Parallel will use the first value of the input
|
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source as the name of the replacement string. Only the non-modified
|
||||
version {} is supported:</p>
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -300,7 +300,7 @@ Output (the order may be different):
|
|||
|
||||
=head2 Replacement strings
|
||||
|
||||
=head3 The 7 replacement strings
|
||||
=head3 The 7 predefined replacement strings
|
||||
|
||||
GNU Parallel has several replacement strings. If no replacement
|
||||
strings are used the default is to append {}:
|
||||
|
|
@ -372,7 +372,7 @@ Output (the order may be different):
|
|||
2
|
||||
1
|
||||
|
||||
=head2 Changing the replacement strings
|
||||
=head3 Changing the replacement strings
|
||||
|
||||
The replacement string {} can be changed with -I:
|
||||
|
||||
|
|
@ -434,7 +434,48 @@ Output (the order may be different):
|
|||
2
|
||||
1
|
||||
|
||||
=head2 Positional replacement strings
|
||||
=head3 Perl expression replacement string
|
||||
|
||||
When predefined replacement strings are not flexible enough a perl
|
||||
expression can be used instead. One example is to remove two
|
||||
extensions: foo.tar.gz -> foo
|
||||
|
||||
parallel echo '{= s:\.[^.]+$::;s:\.[^.]+$::; =}' ::: foo.tar.gz
|
||||
|
||||
Output:
|
||||
|
||||
foo
|
||||
|
||||
If the strings B<{=> and B<=}> cause problems they can be replaced with --parens:
|
||||
|
||||
parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' ::: foo.tar.gz
|
||||
|
||||
Output: Same as above.
|
||||
|
||||
To define a short hand replacement string use B<--rpl>:
|
||||
|
||||
parallel --rpl '.. s:\.[^.]+$::;s:\.[^.]+$::;' echo '..' ::: foo.tar.gz
|
||||
|
||||
Output: Same as above.
|
||||
|
||||
If the short hand starts with '{' it can be used as a positional
|
||||
replacement string, too:
|
||||
|
||||
parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{..}' ::: foo.tar.gz
|
||||
|
||||
Output: Same as above.
|
||||
|
||||
GNU B<parallel>'s 7 replacement strings are implemented as:
|
||||
|
||||
--rpl '{} '
|
||||
--rpl '{#} $_=$job->seq()'
|
||||
--rpl '{%} $_=$job->slot()'
|
||||
--rpl '{/} s:.*/::'
|
||||
--rpl '{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);'
|
||||
--rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
|
||||
--rpl '{.} s:\.[^/.]+$::'
|
||||
|
||||
=head3 Positional replacement strings
|
||||
|
||||
With multiple input sources the argument from the individual input
|
||||
sources can be access with {number}:
|
||||
|
|
@ -473,7 +514,27 @@ Output (the order may be different):
|
|||
1=B 2=D 3=E -1=E -2=D -3=B
|
||||
1=B 2=D 3=F -1=F -2=D -3=B
|
||||
|
||||
=head2 Input from columns
|
||||
|
||||
=head3 Positional perl expression replacement string
|
||||
|
||||
To use a perl expression as a positional replacement string simply
|
||||
prepend the perl expression with number and space:
|
||||
|
||||
parallel echo '{=2 s:\.[^.]+$::;s:\.[^.]+$::; =} {1}' ::: bar ::: foo.tar.gz
|
||||
|
||||
Output:
|
||||
|
||||
foo bar
|
||||
|
||||
If a defined short hand starts with '{' it can be used as a positional
|
||||
replacement string, too:
|
||||
|
||||
parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' ::: bar ::: foo.tar.gz
|
||||
|
||||
Output: Same as above.
|
||||
|
||||
|
||||
=head3 Input from columns
|
||||
|
||||
The columns in a file can be bound to positional replacement strings
|
||||
using --colsep. Here the columns are separated with TAB (\t):
|
||||
|
|
@ -486,7 +547,7 @@ Output (the order may be different):
|
|||
1=A 2=B
|
||||
1=C 2=D
|
||||
|
||||
=head2 Header defined replacement strings
|
||||
=head3 Header defined replacement strings
|
||||
|
||||
With --header GNU Parallel will use the first value of the input
|
||||
source as the name of the replacement string. Only the non-modified
|
||||
|
|
|
|||
Loading…
Reference in a new issue