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.\" ========================================================================
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.\"
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.IX Title "PARALLEL_TUTORIAL 1"
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2014-07-18 14:18:44 +00:00
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.TH PARALLEL_TUTORIAL 1 "2014-07-18" "20140711" "parallel"
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2013-08-17 16:43:30 +00:00
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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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.nh
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2013-09-20 23:25:06 +00:00
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.SH "GNU Parallel Tutorial"
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.IX Header "GNU Parallel Tutorial"
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2013-08-17 16:43:30 +00:00
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This tutorial shows off much of \s-1GNU\s0 Parallel's functionality. The
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tutorial is meant to learn the options in \s-1GNU\s0 Parallel. The tutorial
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is not to show realistic examples from the real world.
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.PP
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2013-09-18 00:00:10 +00:00
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Spend an hour walking through the tutorial. Your command line will
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love you for it.
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.SH "Prerequisites"
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.IX Header "Prerequisites"
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To run this tutorial you must have the following:
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2014-06-04 00:22:39 +00:00
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.IP "parallel >= version 20140622" 9
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.IX Item "parallel >= version 20140622"
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2013-09-18 00:00:10 +00:00
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Install the newest version with:
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.Sp
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.Vb 1
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2013-09-18 00:00:10 +00:00
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\& (wget \-O \- pi.dk/3 || curl pi.dk/3/) | bash
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.Ve
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2013-09-18 00:00:10 +00:00
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.Sp
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This will also install the newest version of the tutorial:
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.Sp
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.Vb 1
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\& man parallel_tutorial
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.Ve
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.Sp
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Most of the tutorial will work on older versions, too.
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.IP "abc-file:" 9
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.IX Item "abc-file:"
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The file can be generated by:
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.Sp
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.Vb 1
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\& parallel \-k echo ::: A B C > abc\-file
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.Ve
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.IP "def-file:" 9
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.IX Item "def-file:"
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The file can be generated by:
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.Sp
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.Vb 1
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\& parallel \-k echo ::: D E F > def\-file
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.Ve
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.IP "abc0\-file:" 9
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.IX Item "abc0-file:"
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The file can be generated by:
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.Sp
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.Vb 1
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\& perl \-e \*(Aqprintf "A\e0B\e0C\e0"\*(Aq > abc0\-file
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.Ve
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.IX Item "abc_-file:"
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The file can be generated by:
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.Sp
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.Vb 1
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\& perl \-e \*(Aqprintf "A_B_C_"\*(Aq > abc_\-file
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.Ve
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.IP "tsv\-file.tsv" 9
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.IX Item "tsv-file.tsv"
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The file can be generated by:
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.Sp
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.Vb 1
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\& perl \-e \*(Aqprintf "f1\etf2\enA\etB\enC\etD\en"\*(Aq > tsv\-file.tsv
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.Ve
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.IP "num30000" 9
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.IX Item "num30000"
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The file can be generated by:
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.Sp
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.Vb 1
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.Ve
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.IP "num1000000" 9
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.IX Item "num1000000"
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The file can be generated by:
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.Sp
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.Vb 1
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\& perl \-e \*(Aqfor(1..1000000){print "$_\en"}\*(Aq > num1000000
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.Ve
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.IP "num_%header" 9
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.IX Item "num_%header"
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The file can be generated by:
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.Sp
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.Vb 1
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\& (echo %head1; echo %head2; perl \-e \*(Aqfor(1..10){print "$_\en"}\*(Aq) > num_%header
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.Ve
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.ie n .IP "For remote running: ssh login on 2 servers with no password in $SERVER1 and $SERVER2" 9
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.el .IP "For remote running: ssh login on 2 servers with no password in \f(CW$SERVER1\fR and \f(CW$SERVER2\fR" 9
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.IX Item "For remote running: ssh login on 2 servers with no password in $SERVER1 and $SERVER2"
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.Vb 2
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\& SERVER1=server.example.com
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\& SERVER2=server2.example.net
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.Ve
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.Sp
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You must be able to:
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.Sp
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.Vb 2
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\& ssh $SERVER1 echo works
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\& ssh $SERVER2 echo works
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.Ve
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2013-09-18 00:00:10 +00:00
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.Sp
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It can be setup by running 'ssh\-keygen \-t dsa; ssh-copy-id \f(CW$SERVER1\fR'
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and using an empty pass phrase.
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.SH "Input sources"
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.IX Header "Input sources"
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\&\s-1GNU\s0 Parallel reads input from input sources. These can be files, the
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command line, and stdin (standard input or a pipe).
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.SS "A single input source"
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.IX Subsection "A single input source"
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Input can be read from the command line:
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.PP
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.Vb 1
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\& parallel echo ::: A B C
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Output (the order may be different because the jobs are run in
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parallel):
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.PP
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\& A
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\& B
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\& C
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.PP
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The input source can be a file:
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.PP
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.Vb 1
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\& parallel \-a abc\-file echo
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.PP
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Output: Same as above.
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.PP
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\&\s-1STDIN\s0 (standard input) can be the input source:
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.PP
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.Vb 1
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\& cat abc\-file | parallel echo
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.PP
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Output: Same as above.
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.SS "Multiple input sources"
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.IX Subsection "Multiple input sources"
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\&\s-1GNU\s0 Parallel can take multiple input sources given on the command
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line. \s-1GNU\s0 Parallel then generates all combinations of the input
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sources:
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.PP
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.Vb 1
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\& parallel echo ::: A B C ::: D E F
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Output (the order may be different):
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.PP
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\& A D
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\& A E
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\& A F
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\& B D
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\& B E
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\& B F
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\& C D
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|
|
|
\& C E
|
|
|
|
|
\& C F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The input sources can be files:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-a abc\-file \-a def\-file echo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1STDIN\s0 (standard input) can be one of the input sources using '\-':
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat abc\-file | parallel \-a \- \-a def\-file echo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
Instead of \-a files can be given after '::::':
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat abc\-file | parallel echo :::: \- def\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
::: and :::: can be mixed:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo ::: A B C :::: def\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
\fIMatching arguments from all input sources\fR
|
|
|
|
|
.IX Subsection "Matching arguments from all input sources"
|
|
|
|
|
.PP
|
2013-08-22 15:24:36 +00:00
|
|
|
With \-\-xapply you can get one argument from each input source:
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-xapply echo ::: A B C ::: D E F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& A D
|
|
|
|
|
\& B E
|
|
|
|
|
\& C F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If one of the input sources is too short, its values will wrap:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-xapply echo ::: A B C D E ::: F G
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& A F
|
|
|
|
|
\& B G
|
|
|
|
|
\& C F
|
|
|
|
|
\& D G
|
|
|
|
|
\& E F
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Changing the argument separator."
|
|
|
|
|
.IX Subsection "Changing the argument separator."
|
|
|
|
|
\&\s-1GNU\s0 Parallel can use other separators than ::: or ::::. This is
|
|
|
|
|
typically useful if ::: or :::: is used in the command to run:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-arg\-sep ,, echo ,, A B C :::: def\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& A D
|
|
|
|
|
\& A E
|
|
|
|
|
\& A F
|
|
|
|
|
\& B D
|
|
|
|
|
\& B E
|
|
|
|
|
\& B F
|
|
|
|
|
\& C D
|
|
|
|
|
\& C E
|
|
|
|
|
\& C F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Changing the argument file separator:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-arg\-file\-sep // echo ::: A B C // def\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.SS "Changing the argument delimiter"
|
|
|
|
|
.IX Subsection "Changing the argument delimiter"
|
|
|
|
|
\&\s-1GNU\s0 Parallel will normally treat a full line as a single argument: It
|
|
|
|
|
uses \en as argument delimiter. This can be changed with \-d:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-d _ echo :::: abc_\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& A
|
|
|
|
|
\& B
|
|
|
|
|
\& C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1NULL\s0 can be given as \e0:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-d \*(Aq\e0\*(Aq echo :::: abc0\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
A shorthand for \-d '\e0' is \-0 (this will often be used to read files
|
|
|
|
|
from find ... \-print0):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-0 echo :::: abc0\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.SS "End-of-file value for input source"
|
|
|
|
|
.IX Subsection "End-of-file value for input source"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can stop reading when it encounters a certain value:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-E stop echo ::: A B stop C D
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& A
|
|
|
|
|
\& B
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Skipping empty lines"
|
|
|
|
|
.IX Subsection "Skipping empty lines"
|
|
|
|
|
Using \-\-no\-run\-if\-empty \s-1GNU\s0 Parallel will skip empty lines.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& (echo 1; echo; echo 2) | parallel \-\-no\-run\-if\-empty echo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
.Ve
|
|
|
|
|
.SH "Building the command line"
|
|
|
|
|
.IX Header "Building the command line"
|
|
|
|
|
.SS "No command means arguments are commands"
|
|
|
|
|
.IX Subsection "No command means arguments are commands"
|
|
|
|
|
If no command is given after parallel the arguments themselves are
|
|
|
|
|
treated as commands:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel ::: ls \*(Aqecho foo\*(Aq pwd
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& [list of files in current dir]
|
|
|
|
|
\& foo
|
|
|
|
|
\& [/path/to/current/working/dir]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The command can be a script, a binary or a Bash function if the function is
|
|
|
|
|
exported using 'export \-f':
|
|
|
|
|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
.Vb 6
|
|
|
|
|
\& # Only works in Bash and only if $SHELL=.../bash
|
2013-08-17 16:43:30 +00:00
|
|
|
\& my_func() {
|
|
|
|
|
\& echo in my_func $1
|
|
|
|
|
\& }
|
|
|
|
|
\& export \-f my_func
|
|
|
|
|
\& parallel my_func ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& in my_func 1
|
|
|
|
|
\& in my_func 2
|
|
|
|
|
\& in my_func 3
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Replacement strings"
|
|
|
|
|
.IX Subsection "Replacement strings"
|
2014-07-18 14:18:44 +00:00
|
|
|
\fIThe 7 predefined replacement strings\fR
|
|
|
|
|
.IX Subsection "The 7 predefined replacement strings"
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel has several replacement strings. If no replacement
|
|
|
|
|
strings are used the default is to append {}:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The default replacement string is {}:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {} ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {.} removes the extension:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {.} ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A/B
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {/} removes the path:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {/} ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {//} keeps only the path:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {//} ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {/.} removes the path and the extension:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {/.} ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& B
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {#} gives the job number:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {#} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 3
|
|
|
|
|
.Ve
|
2014-05-31 06:42:56 +00:00
|
|
|
.PP
|
|
|
|
|
The replacement string {%} gives the job slot number (between 1 and
|
|
|
|
|
number of jobs to run in parallel):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j 2 echo {%} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 1
|
|
|
|
|
.Ve
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
|
|
|
|
\fIChanging the replacement strings\fR
|
2013-08-17 16:43:30 +00:00
|
|
|
.IX Subsection "Changing the replacement strings"
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
2013-08-17 16:43:30 +00:00
|
|
|
The replacement string {} can be changed with \-I:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-I ,, echo ,, ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {.} can be changed with \-\-extensionreplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-extensionreplace ,, echo ,, ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A/B
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {/} can be replaced with \-\-basenamereplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-basenamereplace ,, echo ,, ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {//} can be changed with \-\-dirnamereplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-dirnamereplace ,, echo ,, ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {/.} can be changed with \-\-basenameextensionreplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-basenameextensionreplace ,, echo ,, ::: A/B.C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& B
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The replacement string {#} can be changed with \-\-seqreplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-seqreplace ,, echo ,, ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 3
|
|
|
|
|
.Ve
|
2014-05-31 06:42:56 +00:00
|
|
|
.PP
|
|
|
|
|
The replacement string {%} can be changed with \-\-slotreplace:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-\-slotreplace ,, echo ,, ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 1
|
|
|
|
|
.Ve
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
|
|
|
|
\fIPerl expression replacement string\fR
|
|
|
|
|
.IX Subsection "Perl expression replacement string"
|
|
|
|
|
.PP
|
|
|
|
|
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
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo \*(Aq{= s:\e.[^.]+$::;s:\e.[^.]+$::; =}\*(Aq ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& foo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If the strings \fB{=\fR and \fB=}\fR cause problems they can be replaced with \-\-parens:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-parens ,,,, echo \*(Aq,, s:\e.[^.]+$::;s:\e.[^.]+$::; ,,\*(Aq ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
To define a short hand replacement string use \fB\-\-rpl\fR:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-rpl \*(Aq.. s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq..\*(Aq ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
If the short hand starts with '{' it can be used as a positional
|
|
|
|
|
replacement string, too:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-rpl \*(Aq{..} s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq{..}\*(Aq ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 \fBparallel\fR's 7 replacement strings are implemented as:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 7
|
|
|
|
|
\& \-\-rpl \*(Aq{} \*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{#} $_=$job\->seq()\*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{%} $_=$job\->slot()\*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{/} s:.*/::\*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);\*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{/.} s:.*/::; s:\e.[^/.]+$::;\*(Aq
|
|
|
|
|
\& \-\-rpl \*(Aq{.} s:\e.[^/.]+$::\*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\fIPositional replacement strings\fR
|
2013-08-17 16:43:30 +00:00
|
|
|
.IX Subsection "Positional replacement strings"
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
2013-08-17 16:43:30 +00:00
|
|
|
With multiple input sources the argument from the individual input
|
|
|
|
|
sources can be access with {number}:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo {1} and {2} ::: A B ::: C D
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& A and C
|
|
|
|
|
\& A and D
|
|
|
|
|
\& B and C
|
|
|
|
|
\& B and D
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The positional replacement strings can also be modified using / // /. and .:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo /={1/} //={1//} /.={1/.} .={1.} ::: A/B.C D/E.F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& /=B.C //=A /.=B .=A/B
|
|
|
|
|
\& /=E.F //=D /.=E .=D/E
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If a position is negative, it will refer to the input source counted
|
|
|
|
|
from behind:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo 1={1} 2={2} 3={3} \-1={\-1} \-2={\-2} \-3={\-3} ::: A B ::: C D ::: E F
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& 1=A 2=C 3=E \-1=E \-2=C \-3=A
|
|
|
|
|
\& 1=A 2=C 3=F \-1=F \-2=C \-3=A
|
|
|
|
|
\& 1=A 2=D 3=E \-1=E \-2=D \-3=A
|
|
|
|
|
\& 1=A 2=D 3=F \-1=F \-2=D \-3=A
|
|
|
|
|
\& 1=B 2=C 3=E \-1=E \-2=C \-3=B
|
|
|
|
|
\& 1=B 2=C 3=F \-1=F \-2=C \-3=B
|
|
|
|
|
\& 1=B 2=D 3=E \-1=E \-2=D \-3=B
|
|
|
|
|
\& 1=B 2=D 3=F \-1=F \-2=D \-3=B
|
|
|
|
|
.Ve
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
|
|
|
|
\fIPositional perl expression replacement string\fR
|
|
|
|
|
.IX Subsection "Positional perl expression replacement string"
|
|
|
|
|
.PP
|
|
|
|
|
To use a perl expression as a positional replacement string simply
|
|
|
|
|
prepend the perl expression with number and space:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel echo \*(Aq{=2 s:\e.[^.]+$::;s:\e.[^.]+$::; =} {1}\*(Aq ::: bar ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If a defined short hand starts with '{' it can be used as a positional
|
|
|
|
|
replacement string, too:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-rpl \*(Aq{..} s:\e.[^.]+$::;s:\e.[^.]+$::;\*(Aq echo \*(Aq{2..} {1}\*(Aq ::: bar ::: foo.tar.gz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
\fIInput from columns\fR
|
2013-08-17 16:43:30 +00:00
|
|
|
.IX Subsection "Input from columns"
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
2013-08-17 16:43:30 +00:00
|
|
|
The columns in a file can be bound to positional replacement strings
|
|
|
|
|
using \-\-colsep. Here the columns are separated with \s-1TAB\s0 (\et):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-colsep \*(Aq\et\*(Aq echo 1={1} 2={2} :::: tsv\-file.tsv
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1=f1 2=f2
|
|
|
|
|
\& 1=A 2=B
|
|
|
|
|
\& 1=C 2=D
|
|
|
|
|
.Ve
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
|
|
|
|
\fIHeader defined replacement strings\fR
|
2013-08-17 16:43:30 +00:00
|
|
|
.IX Subsection "Header defined replacement strings"
|
2014-07-18 14:18:44 +00:00
|
|
|
.PP
|
2013-08-17 16:43:30 +00:00
|
|
|
With \-\-header \s-1GNU\s0 Parallel will use the first value of the input
|
|
|
|
|
source as the name of the replacement string. Only the non-modified
|
|
|
|
|
version {} is supported:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-header : echo f1={f1} f2={f2} ::: f1 A B ::: f2 C D
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& f1=A f2=C
|
|
|
|
|
\& f1=A f2=D
|
|
|
|
|
\& f1=B f2=C
|
|
|
|
|
\& f1=B f2=D
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
It is useful with \-\-colsep for processing files with \s-1TAB\s0 separated values:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-header : \-\-colsep \*(Aq\et\*(Aq echo f1={f1} f2={f2} :::: tsv\-file.tsv
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& f1=A f2=B
|
|
|
|
|
\& f1=C f2=D
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "More than one argument"
|
|
|
|
|
.IX Subsection "More than one argument"
|
|
|
|
|
With \-\-xargs will \s-1GNU\s0 Parallel fit as many arguments as possible on a
|
|
|
|
|
single line:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num30000 | parallel \-\-xargs echo | wc \-l
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& 2
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The 30000 arguments fitted on 2 lines.
|
|
|
|
|
.PP
|
|
|
|
|
The maximal length of a single line can be set with \-s. With a maximal
|
|
|
|
|
line length of 10000 chars 17 commands will be run:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num30000 | parallel \-\-xargs \-s 10000 echo | wc \-l
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& 17
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
For better parallelism \s-1GNU\s0 Parallel can distribute the arguments
|
|
|
|
|
between all the parallel jobs when end of file is met.
|
|
|
|
|
.PP
|
2014-01-22 01:54:18 +00:00
|
|
|
Below \s-1GNU\s0 Parallel reads the last argument when generating the second
|
|
|
|
|
job. When \s-1GNU\s0 Parallel reads the last argument, it spreads all the
|
|
|
|
|
arguments for the second job over 4 jobs instead, as 4 parallel jobs
|
|
|
|
|
are requested.
|
|
|
|
|
.PP
|
|
|
|
|
The first job will be the same as the \-\-xargs example above, but the
|
|
|
|
|
second job will be split into 4 evenly sized jobs, resulting in a
|
|
|
|
|
total of 5 jobs:
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num30000 | parallel \-\-jobs 4 \-m echo | wc \-l
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& 5
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
2014-01-22 01:54:18 +00:00
|
|
|
This is even more visible when running 4 jobs with 10 arguments. The
|
|
|
|
|
10 arguments are being spread over 4 jobs:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-jobs 4 \-m echo ::: {1..10}
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& 1 2 3
|
|
|
|
|
\& 4 5 6
|
|
|
|
|
\& 7 8 9
|
|
|
|
|
\& 10
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
2013-08-17 16:43:30 +00:00
|
|
|
A replacement string can be part of a word. \-m will not repeat the context:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-jobs 4 \-m echo pre\-{}\-post ::: A B C D E F G
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& pre\-A B\-post
|
|
|
|
|
\& pre\-C D\-post
|
|
|
|
|
\& pre\-E F\-post
|
|
|
|
|
\& pre\-G\-post
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To repeat the context use \-X which otherwise works like \-m:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-jobs 4 \-X echo pre\-{}\-post ::: A B C D E F G
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& pre\-A\-post pre\-B\-post
|
|
|
|
|
\& pre\-C\-post pre\-D\-post
|
|
|
|
|
\& pre\-E\-post pre\-F\-post
|
|
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|
|
\& pre\-G\-post
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To limit the number of arguments use \-N:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-N3 echo ::: A B C D E F G H
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
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|
|
.PP
|
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|
|
.Vb 3
|
|
|
|
|
\& A B C
|
|
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|
|
\& D E F
|
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|
|
\& G H
|
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|
.Ve
|
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|
.PP
|
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|
|
\&\-N also sets the positional replacement strings:
|
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|
|
|
.PP
|
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|
|
.Vb 1
|
|
|
|
|
\& parallel \-N3 echo 1={1} 2={2} 3={3} ::: A B C D E F G H
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
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|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1=A 2=B 3=C
|
|
|
|
|
\& 1=D 2=E 3=F
|
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|
|
\& 1=G 2=H 3=
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.Ve
|
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.PP
|
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|
|
\&\-N0 reads 1 argument but inserts none:
|
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|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-N0 echo foo ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
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|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& foo
|
|
|
|
|
\& foo
|
|
|
|
|
\& foo
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Quoting"
|
|
|
|
|
.IX Subsection "Quoting"
|
|
|
|
|
Command lines that contain special characters may need to be protected from the shell.
|
|
|
|
|
.PP
|
|
|
|
|
The perl program 'print \*(L"@ARGV\en\*(R"' basically works like echo.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& perl \-e \*(Aqprint "@ARGV\en"\*(Aq A
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& A
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To run that in parallel the command needs to be quoted:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel perl \-e \*(Aqprint "@ARGV\en"\*(Aq ::: This wont work
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& [Nothing]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To quote the command use \-q:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-q perl \-e \*(Aqprint "@ARGV\en"\*(Aq ::: This works
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& This
|
|
|
|
|
\& works
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Or you can quote the critical part using \e':
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel perl \-e \e\*(Aq\*(Aqprint "@ARGV\en"\*(Aq\e\*(Aq ::: This works, too
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& This
|
|
|
|
|
\& works,
|
|
|
|
|
\& too
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can also \e\-quote full lines. Simply run:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& parallel \-\-shellquote
|
|
|
|
|
\& parallel: Warning: Input is read from the terminal. Only experts do this on purpose. Press CTRL\-D to exit.
|
|
|
|
|
\& perl \-e \*(Aqprint "@ARGV\en"\*(Aq
|
|
|
|
|
\& [CTRL\-D]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& perl\e \-e\e \e\*(Aqprint\e \e"@ARGV\e\en\e"\e\*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
This can then be used as the command:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel perl\e \-e\e \e\*(Aqprint\e \e"@ARGV\e\en\e"\e\*(Aq ::: This also works
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& This
|
|
|
|
|
\& also
|
|
|
|
|
\& works
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Trimming space"
|
|
|
|
|
.IX Subsection "Trimming space"
|
|
|
|
|
Space can be trimmed on the arguments using \-\-trim:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-trim r echo pre\-{}\-post ::: \*(Aq A \*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& pre\- A\-post
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To trim on the left side:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-trim l echo pre\-{}\-post ::: \*(Aq A \*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& pre\-A \-post
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To trim on the both sides:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-trim lr echo pre\-{}\-post ::: \*(Aq A \*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& pre\-A\-post
|
|
|
|
|
.Ve
|
|
|
|
|
.SH "Controling the output"
|
|
|
|
|
.IX Header "Controling the output"
|
|
|
|
|
The output can prefixed with the argument:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-tag echo foo\-{} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& A foo\-A
|
|
|
|
|
\& B foo\-B
|
|
|
|
|
\& C foo\-C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To prefix it with another string use \-\-tagstring:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-tagstring {}\-bar echo foo\-{} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& A\-bar foo\-A
|
|
|
|
|
\& B\-bar foo\-B
|
|
|
|
|
\& C\-bar foo\-C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To see what commands will be run without running them:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-dryrun echo {} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& echo A
|
|
|
|
|
\& echo B
|
|
|
|
|
\& echo C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To print the command before running them use \-\-verbose:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-verbose echo {} ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 6
|
|
|
|
|
\& echo A
|
|
|
|
|
\& echo B
|
|
|
|
|
\& A
|
|
|
|
|
\& echo C
|
|
|
|
|
\& B
|
|
|
|
|
\& C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel will postpone the output until the command completes:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \*(Aqprintf "%s\-start\en%s" {} {};sleep {};printf "%s\en" \-middle;echo {}\-end\*(Aq ::: 4 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& 2\-start
|
|
|
|
|
\& 2\-middle
|
|
|
|
|
\& 2\-end
|
|
|
|
|
\& 1\-start
|
|
|
|
|
\& 1\-middle
|
|
|
|
|
\& 1\-end
|
|
|
|
|
\& 4\-start
|
|
|
|
|
\& 4\-middle
|
|
|
|
|
\& 4\-end
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To get the output immediately use \-\-ungroup:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-\-ungroup \*(Aqprintf "%s\-start\en%s" {} {};sleep {};printf "%s\en" \-middle;echo {}\-end\*(Aq ::: 4 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& 4\-start
|
|
|
|
|
\& 42\-start
|
|
|
|
|
\& 2\-middle
|
|
|
|
|
\& 2\-end
|
|
|
|
|
\& 1\-start
|
|
|
|
|
\& 1\-middle
|
|
|
|
|
\& 1\-end
|
|
|
|
|
\& \-middle
|
|
|
|
|
\& 4\-end
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\-\-ungroup is fast, but can cause half a line from one job to be mixed
|
|
|
|
|
with half a line of another job. That has happend in the second line,
|
|
|
|
|
where the line '4\-middle' is mixed with '2\-start'.
|
|
|
|
|
.PP
|
2014-06-04 00:22:39 +00:00
|
|
|
To avoid this use \-\-linebuffer:
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-\-linebuffer \*(Aqprintf "%s\-start\en%s" {} {};sleep {};printf "%s\en" \-middle;echo {}\-end\*(Aq ::: 4 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& 4\-start
|
|
|
|
|
\& 2\-start
|
|
|
|
|
\& 2\-middle
|
|
|
|
|
\& 2\-end
|
|
|
|
|
\& 1\-start
|
|
|
|
|
\& 1\-middle
|
|
|
|
|
\& 1\-end
|
|
|
|
|
\& 4\-middle
|
|
|
|
|
\& 4\-end
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To force the output in the same order as the arguments use \-\-keep\-order/\-k:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-k \*(Aqprintf "%s\-start\en%s" {} {};sleep {};printf "%s\en" \-middle;echo {}\-end\*(Aq ::: 4 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& 4\-start
|
|
|
|
|
\& 4\-middle
|
|
|
|
|
\& 4\-end
|
|
|
|
|
\& 2\-start
|
|
|
|
|
\& 2\-middle
|
|
|
|
|
\& 2\-end
|
|
|
|
|
\& 1\-start
|
|
|
|
|
\& 1\-middle
|
|
|
|
|
\& 1\-end
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Saving output into files"
|
|
|
|
|
.IX Subsection "Saving output into files"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can save the output of each job into files:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-files ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output will be similar to:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& /tmp/pAh6uWuQCg.par
|
|
|
|
|
\& /tmp/opjhZCzAX4.par
|
|
|
|
|
\& /tmp/W0AT_Rph2o.par
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
By default \s-1GNU\s0 Parallel will cache the output in files in /tmp. This
|
|
|
|
|
can be changed by setting \f(CW$TMPDIR\fR or \-\-tmpdir:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-tmpdir /var/tmp \-\-files ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output will be similar to:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& /var/tmp/N_vk7phQRc.par
|
|
|
|
|
\& /var/tmp/7zA4Ccf3wZ.par
|
|
|
|
|
\& /var/tmp/LIuKgF_2LP.par
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Or:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& TMPDIR=/var/tmp parallel \-\-files ::: A B C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
The output files can be saved in a structured way using \-\-results:
|
|
|
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|
.PP
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.Vb 1
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|
\& parallel \-\-results outdir echo ::: A B C
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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 3
|
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|
|
\& A
|
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|
\& B
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|
\& C
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.Ve
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|
.PP
|
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|
but also these files were generated containing the standard output
|
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(stdout) and standard error (stderr):
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|
.PP
|
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|
.Vb 6
|
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|
|
\& outdir/1/A/stderr
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|
\& outdir/1/A/stdout
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|
\& outdir/1/B/stderr
|
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|
\& outdir/1/B/stdout
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|
\& outdir/1/C/stderr
|
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|
\& outdir/1/C/stdout
|
|
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|
.Ve
|
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|
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|
.PP
|
|
|
|
|
This is useful if you are running multiple variables:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-header : \-\-results outdir echo ::: f1 A B ::: f2 C D
|
|
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|
.Ve
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|
.PP
|
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|
|
Generated files:
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|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& outdir/f1/A/f2/C/stderr
|
|
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|
\& outdir/f1/A/f2/C/stdout
|
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|
\& outdir/f1/A/f2/D/stderr
|
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|
\& outdir/f1/A/f2/D/stdout
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|
|
\& outdir/f1/B/f2/C/stderr
|
|
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|
|
\& outdir/f1/B/f2/C/stdout
|
|
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|
|
\& outdir/f1/B/f2/D/stderr
|
|
|
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|
\& outdir/f1/B/f2/D/stdout
|
|
|
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|
.Ve
|
|
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|
.PP
|
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|
|
The directories are named after the variables and their values.
|
|
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|
|
.SH "Control the execution"
|
|
|
|
|
.IX Header "Control the execution"
|
|
|
|
|
.SS "Number of simultaneous jobs"
|
|
|
|
|
.IX Subsection "Number of simultaneous jobs"
|
|
|
|
|
The number of concurrent jobs is given with \-\-jobs/\-j:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& /usr/bin/time parallel \-N0 \-j64 sleep 1 ::: {1..128}
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
With 64 jobs in parallel the 128 sleeps will take 2\-8 seconds to run \-
|
|
|
|
|
depending on how fast your machine is.
|
|
|
|
|
.PP
|
|
|
|
|
By default \-\-jobs is the same as the number of \s-1CPU\s0 cores. So this:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& /usr/bin/time parallel \-N0 sleep 1 ::: {1..128}
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
should take twice the time of running 2 jobs per \s-1CPU\s0 core:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& /usr/bin/time parallel \-N0 \-\-jobs 200% sleep 1 ::: {1..128}
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\-\-jobs 0 will run as many jobs in parallel as possible:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& /usr/bin/time parallel \-N0 \-\-jobs 0 sleep 1 ::: {1..128}
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
which should take 1\-7 seconds depending on how fast your machine is.
|
|
|
|
|
.PP
|
|
|
|
|
\&\-\-jobs can read from a file which is re-read when a job finishes:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& echo 50% > my_jobs
|
|
|
|
|
\& /usr/bin/time parallel \-N0 \-\-jobs my_jobs sleep 1 ::: {1..128} &
|
|
|
|
|
\& sleep 1
|
|
|
|
|
\& echo 0 > my_jobs
|
|
|
|
|
\& wait
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The first second only 50% of the \s-1CPU\s0 cores will run a job. The '0' is
|
|
|
|
|
put into my_jobs and then the rest of the jobs will be started in
|
|
|
|
|
parallel.
|
|
|
|
|
.PP
|
|
|
|
|
Instead of basing the percentage on the number of \s-1CPU\s0 cores
|
|
|
|
|
\&\s-1GNU\s0 Parallel can base it on the number of CPUs:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-use\-cpus\-instead\-of\-cores \-N0 sleep 1 ::: {1..128}
|
|
|
|
|
.Ve
|
2014-06-04 19:48:24 +00:00
|
|
|
.SS "Interactivity"
|
|
|
|
|
.IX Subsection "Interactivity"
|
2013-08-17 16:43:30 +00:00
|
|
|
\&\s-1GNU\s0 Parallel can ask the user if a command should be run using \-\-interactive:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-interactive echo ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& echo 1 ?...y
|
|
|
|
|
\& echo 2 ?...n
|
|
|
|
|
\& 1
|
|
|
|
|
\& echo 3 ?...y
|
|
|
|
|
\& 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can be used to put arguments on the command line for an
|
|
|
|
|
interactive command such as emacs to edit one file at a time:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-tty emacs ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Or give multiple argument in one go to open multiple files:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-X \-\-tty vi ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Timing"
|
|
|
|
|
.IX Subsection "Timing"
|
|
|
|
|
Some jobs do heavy I/O when they start. To avoid a thundering herd \s-1GNU\s0
|
|
|
|
|
Parallel can delay starting new jobs. \-\-delay X will make sure there is
|
|
|
|
|
at least X seconds between each start:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-delay 2.5 echo Starting {}\e;date ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 6
|
|
|
|
|
\& Starting 1
|
|
|
|
|
\& Thu Aug 15 16:24:33 CEST 2013
|
|
|
|
|
\& Starting 2
|
|
|
|
|
\& Thu Aug 15 16:24:35 CEST 2013
|
|
|
|
|
\& Starting 3
|
|
|
|
|
\& Thu Aug 15 16:24:38 CEST 2013
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If jobs taking more than a certain amount of time are known to fail,
|
|
|
|
|
they can be stopped with \-\-timeout:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-timeout 2.1 sleep {}\e; echo {} ::: 1 2 3 4
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can compute the median runtime for jobs and kill those
|
|
|
|
|
that take more than 200% of the median runtime:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-timeout 200% sleep {}\e; echo {} ::: 2.1 2.2 3 7 2.3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& 2.1
|
|
|
|
|
\& 2.2
|
|
|
|
|
\& 3
|
|
|
|
|
\& 2.3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Based on the runtime of completed jobs \s-1GNU\s0 Parallel can estimate the
|
|
|
|
|
total runtime:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-eta sleep ::: 1 3 2 2 1 3 3 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& Computers / CPU cores / Max jobs to run
|
|
|
|
|
\& 1:local / 2 / 2
|
|
|
|
|
\&
|
|
|
|
|
\& Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
|
|
|
|
|
\& ETA: 2s 0left 1.11avg local:0/9/100%/1.1s
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Progress"
|
|
|
|
|
.IX Subsection "Progress"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can give progress information with \-\-progress:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-progress sleep ::: 1 3 2 2 1 3 3 2 1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& Computers / CPU cores / Max jobs to run
|
|
|
|
|
\& 1:local / 2 / 2
|
|
|
|
|
\&
|
|
|
|
|
\& Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
|
|
|
|
|
\& local:0/9/100%/1.1s
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
A logfile of the jobs completed so far can be generated with \-\-joblog:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& parallel \-\-joblog /tmp/log exit ::: 1 2 3 0
|
|
|
|
|
\& cat /tmp/log
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& Seq Host Starttime Runtime Send Receive Exitval Signal Command
|
|
|
|
|
\& 1 : 1376577364.974 0.008 0 0 1 0 exit 1
|
|
|
|
|
\& 2 : 1376577364.982 0.013 0 0 2 0 exit 2
|
|
|
|
|
\& 3 : 1376577364.990 0.013 0 0 3 0 exit 3
|
|
|
|
|
\& 4 : 1376577365.003 0.003 0 0 0 0 exit 0
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The log contains the job sequence, which host the job was run on, the
|
|
|
|
|
start time and run time, how much data was transferred if the job was
|
|
|
|
|
run on a remote host, the exit value, the signal that killed the job,
|
|
|
|
|
and finally the command being run.
|
|
|
|
|
.PP
|
|
|
|
|
With a joblog \s-1GNU\s0 Parallel can be stopped and later pickup where it
|
|
|
|
|
left off. It it important that the input of the completed jobs is
|
|
|
|
|
unchanged.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& parallel \-\-joblog /tmp/log exit ::: 1 2 3 0
|
|
|
|
|
\& cat /tmp/log
|
|
|
|
|
\& parallel \-\-resume \-\-joblog /tmp/log exit ::: 1 2 3 0 0 0
|
|
|
|
|
\& cat /tmp/log
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& Seq Host Starttime Runtime Send Receive Exitval Signal Command
|
|
|
|
|
\& 1 : 1376580069.544 0.008 0 0 1 0 exit 1
|
|
|
|
|
\& 2 : 1376580069.552 0.009 0 0 2 0 exit 2
|
|
|
|
|
\& 3 : 1376580069.560 0.012 0 0 3 0 exit 3
|
|
|
|
|
\& 4 : 1376580069.571 0.005 0 0 0 0 exit 0
|
|
|
|
|
\&
|
|
|
|
|
\& Seq Host Starttime Runtime Send Receive Exitval Signal Command
|
|
|
|
|
\& 1 : 1376580069.544 0.008 0 0 1 0 exit 1
|
|
|
|
|
\& 2 : 1376580069.552 0.009 0 0 2 0 exit 2
|
|
|
|
|
\& 3 : 1376580069.560 0.012 0 0 3 0 exit 3
|
|
|
|
|
\& 4 : 1376580069.571 0.005 0 0 0 0 exit 0
|
|
|
|
|
\& 5 : 1376580070.028 0.009 0 0 0 0 exit 0
|
|
|
|
|
\& 6 : 1376580070.038 0.007 0 0 0 0 exit 0
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Note how the start time of the last 2 jobs is clearly from the second run.
|
|
|
|
|
.PP
|
|
|
|
|
With \-\-resume\-failed \s-1GNU\s0 Parallel will re-run the jobs that failed:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& parallel \-\-resume\-failed \-\-joblog /tmp/log exit ::: 1 2 3 0 0 0
|
|
|
|
|
\& cat /tmp/log
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 10
|
|
|
|
|
\& Seq Host Starttime Runtime Send Receive Exitval Signal Command
|
|
|
|
|
\& 1 : 1376580069.544 0.008 0 0 1 0 exit 1
|
|
|
|
|
\& 2 : 1376580069.552 0.009 0 0 2 0 exit 2
|
|
|
|
|
\& 3 : 1376580069.560 0.012 0 0 3 0 exit 3
|
|
|
|
|
\& 4 : 1376580069.571 0.005 0 0 0 0 exit 0
|
|
|
|
|
\& 5 : 1376580070.028 0.009 0 0 0 0 exit 0
|
|
|
|
|
\& 6 : 1376580070.038 0.007 0 0 0 0 exit 0
|
|
|
|
|
\& 1 : 1376580154.433 0.010 0 0 1 0 exit 1
|
|
|
|
|
\& 2 : 1376580154.444 0.022 0 0 2 0 exit 2
|
|
|
|
|
\& 3 : 1376580154.466 0.005 0 0 3 0 exit 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Note how seq 1 2 3 have been repeated because they had exit value != 0.
|
|
|
|
|
.SS "Termination"
|
|
|
|
|
.IX Subsection "Termination"
|
|
|
|
|
For certain jobs there is no need to continue if one of the jobs fails
|
|
|
|
|
and has an exit code != 0. \s-1GNU\s0 Parallel will stop spawning new jobs
|
|
|
|
|
with \-\-halt 1:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-\-halt 1 echo {}\e; exit {} ::: 0 0 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& 0
|
|
|
|
|
\& 0
|
|
|
|
|
\& 1
|
|
|
|
|
\& parallel: Starting no more jobs. Waiting for 2 jobs to finish. This job failed:
|
|
|
|
|
\& echo 1; exit 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& parallel: Starting no more jobs. Waiting for 1 jobs to finish. This job failed:
|
|
|
|
|
\& echo 2; exit 2
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
With \-\-halt 2 the running jobs will be killed immediately:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-j2 \-\-halt 2 echo {}\e; exit {} ::: 0 0 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
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.Vb 5
|
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|
\& 0
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|
\& 0
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\& 1
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|
|
\& parallel: This job failed:
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|
|
\& echo 1; exit 1
|
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|
.Ve
|
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.PP
|
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|
|
\&\s-1GNU\s0 Parallel can retry the command with \-\-retries. This is useful if a
|
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|
|
command fails for unkown reasons now and then.
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|
.PP
|
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|
.Vb 2
|
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|
|
\& parallel \-k \-\-retries 3 \*(Aqecho tried {} >>/tmp/runs; echo completed {}; exit {}\*(Aq ::: 1 2 0
|
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|
|
\& cat /tmp/runs
|
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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 3
|
|
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|
|
\& completed 1
|
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|
\& completed 2
|
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|
\& completed 0
|
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|
|
\&
|
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|
|
\& tried 1
|
|
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|
|
\& tried 2
|
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|
|
\& tried 1
|
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|
\& tried 2
|
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|
|
\& tried 1
|
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|
|
\& tried 2
|
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|
|
\& tried 0
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|
.Ve
|
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|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
Note how job 1 and 2 were tried 3 times, but 0 was not retried because it had exit code 0.
|
2013-08-17 16:43:30 +00:00
|
|
|
.SS "Limiting the ressources"
|
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|
|
|
.IX Subsection "Limiting the ressources"
|
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|
|
To avoid overloading systems \s-1GNU\s0 Parallel can look at the system load
|
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|
|
before starting another job:
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.PP
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|
.Vb 1
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|
\& parallel \-\-load 100% echo load is less than {} job per cpu ::: 1
|
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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 2
|
|
|
|
|
\& [when then load is less than the number of cpu cores]
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|
|
\& load is less than 1 job per cpu
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|
.Ve
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.PP
|
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|
|
\&\s-1GNU\s0 Parallel can also check if the system is swapping.
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|
.PP
|
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|
|
.Vb 1
|
|
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|
|
\& parallel \-\-noswap echo the system is not swapping ::: now
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|
.Ve
|
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|
.PP
|
|
|
|
|
Output:
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|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& [when then system is not swapping]
|
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|
|
\& the system is not swapping now
|
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|
.Ve
|
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|
.PP
|
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|
|
\&\s-1GNU\s0 Parallel can run the jobs with a nice value. This will work both
|
|
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|
|
locally and remotely.
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|
.PP
|
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|
.Vb 1
|
|
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|
|
\& parallel \-\-nice 17 echo this is being run with nice \-n ::: 17
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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
|
|
|
|
|
\& this is being run with nice \-n 17
|
|
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|
.Ve
|
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|
|
.SH "Remote execution"
|
|
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|
|
.IX Header "Remote execution"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can run jobs on remote servers. It uses ssh to
|
|
|
|
|
communicate with the remote machines.
|
|
|
|
|
.SS "Sshlogin"
|
|
|
|
|
.IX Subsection "Sshlogin"
|
|
|
|
|
The most basic sshlogin is \-S host:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S $SERVER1 echo running on ::: $SERVER1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& running on [$SERVER1]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To use a different username prepend the server with username@
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S username@$SERVER1 echo running on ::: username@$SERVER1
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& running on [username@$SERVER1]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The special sshlogin ':' is the local machine:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S : echo running on ::: the_local_machine
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& running on the_local_machine
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If ssh is not in \f(CW$PATH\fR it can be prepended to \f(CW$SERVER1:\fR
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S \*(Aq/usr/bin/ssh \*(Aq$SERVER1 echo custom ::: ssh
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& custom ssh
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Several servers can be given using multiple \-S:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S $SERVER1 \-S $SERVER2 echo ::: running on more hosts
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& running
|
|
|
|
|
\& on
|
|
|
|
|
\& more
|
|
|
|
|
\& hosts
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Or they can be separated by ,:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S $SERVER1,$SERVER2 echo ::: running on more hosts
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
The can also be read from a file (replace user@ with the user on \f(CW$SERVER2\fR):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& echo $SERVER1 > nodefile
|
|
|
|
|
\& # Force 4 cores, special ssh\-command, username
|
|
|
|
|
\& echo 4//usr/bin/ssh user@$SERVER2 >> nodefile
|
|
|
|
|
\& parallel \-\-sshloginfile nodefile echo ::: running on more hosts
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
The special \-\-sshloginfile '..' reads from ~/.parallel/sshloginfile.
|
|
|
|
|
.PP
|
|
|
|
|
To force \s-1GNU\s0 Parallel to treat a server having a given number of \s-1CPU\s0
|
|
|
|
|
cores prepend #/ to the sshlogin:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S 4/$SERVER1 echo force {} cpus on server ::: 4
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& force 4 cpus on server
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Transferring files"
|
|
|
|
|
.IX Subsection "Transferring files"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can transfer the files to be processed to the remote
|
|
|
|
|
host. It does that using rsync.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& echo This is input_file > input_file
|
|
|
|
|
\& parallel \-S $SERVER1 \-\-transfer cat ::: input_file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& This is input_file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If the files is processed into another file, the resulting file can be
|
|
|
|
|
transferred back:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& echo This is input_file > input_file
|
|
|
|
|
\& parallel \-S $SERVER1 \-\-transfer \-\-return {}.out cat {} ">"{}.out ::: input_file
|
|
|
|
|
\& cat input_file.out
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
To remove the input and output file on the remote server use \-\-cleanup:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& echo This is input_file > input_file
|
|
|
|
|
\& parallel \-S $SERVER1 \-\-transfer \-\-return {}.out \-\-cleanup cat {} ">"{}.out ::: input_file
|
|
|
|
|
\& cat input_file.out
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
There is a short hand for \-\-transfer \-\-return \-\-cleanup called \-\-trc:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& echo This is input_file > input_file
|
|
|
|
|
\& parallel \-S $SERVER1 \-\-trc {}.out cat {} ">"{}.out ::: input_file
|
|
|
|
|
\& cat input_file.out
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.PP
|
|
|
|
|
Some jobs need a common database for all jobs. \s-1GNU\s0 Parallel can
|
|
|
|
|
transfer that using \-\-basefile which will transfer the file before the
|
|
|
|
|
first job:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& echo common data > common_file
|
|
|
|
|
\& parallel \-\-basefile common_file \-S $SERVER1 cat common_file\e; echo {} ::: foo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& common data
|
|
|
|
|
\& foo
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
To remove it from the remote host after the last job use \-\-cleanup.
|
|
|
|
|
.SS "Working dir"
|
|
|
|
|
.IX Subsection "Working dir"
|
|
|
|
|
The default working dir on the remote machines is the login dir. This
|
|
|
|
|
can be changed with \-\-workdir \fImydir\fR.
|
|
|
|
|
.PP
|
2013-08-22 15:24:36 +00:00
|
|
|
Files transferred using \-\-transfer and \-\-return will be relative
|
2013-08-17 16:43:30 +00:00
|
|
|
to \fImydir\fR on remote computers, and the command will be executed in
|
|
|
|
|
the dir \fImydir\fR.
|
|
|
|
|
.PP
|
2013-08-22 15:24:36 +00:00
|
|
|
The special \fImydir\fR value ... will create working dirs under
|
|
|
|
|
~/.parallel/tmp/ on the remote computers. If \-\-cleanup is given
|
2013-08-17 16:43:30 +00:00
|
|
|
these dirs will be removed.
|
|
|
|
|
.PP
|
2013-08-22 15:24:36 +00:00
|
|
|
The special \fImydir\fR value . uses the current working dir. If the
|
|
|
|
|
current working dir is beneath your home dir, the value . is
|
2013-08-17 16:43:30 +00:00
|
|
|
treated as the relative path to your home dir. This means that if your
|
|
|
|
|
home dir is different on remote computers (e.g. if your login is
|
|
|
|
|
different) the relative path will still be relative to your home dir.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& parallel \-S $SERVER1 pwd ::: ""
|
|
|
|
|
\& parallel \-\-workdir . \-S $SERVER1 pwd ::: ""
|
|
|
|
|
\& parallel \-\-workdir ... \-S $SERVER1 pwd ::: ""
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& [the login dir on $SERVER1]
|
|
|
|
|
\& [current dir relative on $SERVER1]
|
|
|
|
|
\& [a dir in ~/.parallel/tmp/...]
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Avoid overloading sshd"
|
|
|
|
|
.IX Subsection "Avoid overloading sshd"
|
|
|
|
|
If many jobs are started on the same server, sshd can be
|
|
|
|
|
overloaded. \s-1GNU\s0 Parallel can insert a delay between each job run on
|
|
|
|
|
the same server:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-S $SERVER1 \-\-sshdelay 0.2 echo ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Sshd will be less overloaded if using \-\-controlmaster, which will
|
|
|
|
|
multiplex ssh connections:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-controlmaster \-S $SERVER1 echo ::: 1 2 3
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.SS "Ignore hosts that are down"
|
|
|
|
|
.IX Subsection "Ignore hosts that are down"
|
|
|
|
|
In clusters with many hosts a few of the are often down. \s-1GNU\s0 Parallel
|
|
|
|
|
can ignore those hosts. In this case the host 173.194.32.46 is down:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-filter\-hosts \-S 173.194.32.46,$SERVER1 echo ::: bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& bar
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Running the same commands on all hosts"
|
|
|
|
|
.IX Subsection "Running the same commands on all hosts"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can run the same command on all the hosts:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-onall \-S $SERVER1,$SERVER2 echo ::: foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& foo
|
|
|
|
|
\& bar
|
|
|
|
|
\& foo
|
|
|
|
|
\& bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Often you will just want to run a single command on all hosts with out
|
|
|
|
|
arguments. \-\-nonall is a no argument \-\-onall:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-nonall \-S $SERVER1,$SERVER2 echo foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& foo bar
|
|
|
|
|
\& foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
When \-\-tag is used with \-\-nonall and \-\-onall the \-\-tagstring is the host:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-\-nonall \-\-tag \-S $SERVER1,$SERVER2 echo foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& $SERVER1 foo bar
|
|
|
|
|
\& $SERVER2 foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\-\-jobs sets the number of servers to log in to in parallel.
|
|
|
|
|
.SS "Transfer environment variables and functions"
|
|
|
|
|
.IX Subsection "Transfer environment variables and functions"
|
|
|
|
|
Using \-\-env \s-1GNU\s0 Parallel can transfer an environment variable to the
|
|
|
|
|
remote system.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& MYVAR=\*(Aqfoo bar\*(Aq
|
|
|
|
|
\& export MYVAR
|
|
|
|
|
\& parallel \-\-env MYVAR \-S $SERVER1 echo \*(Aq$MYVAR\*(Aq ::: baz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& foo bar baz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
This works for functions too if your shell is Bash:
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
.Vb 6
|
|
|
|
|
\& # This only works in Bash
|
2013-08-17 16:43:30 +00:00
|
|
|
\& my_func() {
|
|
|
|
|
\& echo in my_func $1
|
|
|
|
|
\& }
|
|
|
|
|
\& export \-f my_func
|
|
|
|
|
\& parallel \-\-env my_func \-S $SERVER1 my_func ::: baz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& in my_func baz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can copy all defined variables and functions to the
|
2013-12-04 16:12:09 +00:00
|
|
|
remote system. It just needs to record which ones to ignore in
|
2013-08-17 16:43:30 +00:00
|
|
|
~/.parallel/ignored_vars. Do that by running this once:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& parallel \-\-record\-env
|
|
|
|
|
\& cat ~/.parallel/ignored_vars
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& [list of variables to ignore \- including $PATH and $HOME]
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Now all new variables and functions defined will be copied when using
|
|
|
|
|
\&\-\-env _:
|
|
|
|
|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
.Vb 7
|
|
|
|
|
\& # The function is only copied if using Bash
|
2013-08-17 16:43:30 +00:00
|
|
|
\& my_func2() {
|
|
|
|
|
\& echo in my_func2 $VAR $1
|
|
|
|
|
\& }
|
|
|
|
|
\& export \-f my_func2
|
|
|
|
|
\& VAR=foo
|
|
|
|
|
\& export VAR
|
|
|
|
|
\&
|
2013-09-28 13:59:03 +00:00
|
|
|
\& parallel \-\-env _ \-S $SERVER1 \*(Aqecho $VAR; my_func2\*(Aq ::: bar
|
2013-08-17 16:43:30 +00:00
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
2013-09-28 13:59:03 +00:00
|
|
|
.Vb 2
|
|
|
|
|
\& foo
|
2013-08-17 16:43:30 +00:00
|
|
|
\& in my_func2 foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Showing what is actually run"
|
|
|
|
|
.IX Subsection "Showing what is actually run"
|
|
|
|
|
\&\-\-verbose will show the command that would be run on the local
|
|
|
|
|
machine. When a job is run on a remote machine this is wrapped with
|
|
|
|
|
ssh and possibly transferring files and environment variables, setting
|
|
|
|
|
the workdir, and setting \-\-nice value. \-vv shows all of this.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel \-vv \-S $SERVER1 echo ::: bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& ssh \-tt \-oLogLevel=quiet lo \*(Aqeval \`echo $SHELL | grep "/t\e{0,1\e}csh" > /dev/null && echo setenv PARALLEL_SEQ \*(Aq$PARALLEL_SEQ\*(Aq\e; setenv PARALLEL_PID \*(Aq$PARALLEL_PID\*(Aq || echo PARALLEL_SEQ=\*(Aq$PARALLEL_SEQ\*(Aq\e;export PARALLEL_SEQ\e; PARALLEL_PID=\*(Aq$PARALLEL_PID\*(Aq\e;export PARALLEL_PID\` ;\*(Aq tty\e \e>/dev/null\e \e&\e&\e stty\e isig\e \-onlcr\e \-echo\e;echo\e bar;
|
|
|
|
|
\& bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
When the command gets more complex, the output is so hard to read, that it is only useful for debugging:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& my_func3() {
|
|
|
|
|
\& echo in my_func $1 > $1.out
|
|
|
|
|
\& }
|
|
|
|
|
\& export \-f my_func3
|
|
|
|
|
\& parallel \-vv \-\-workdir ... \-\-nice 17 \-\-env _ \-\-trc {}.out \-S $SERVER1 my_func3 {} ::: abc\-file
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output will be similar to:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& ssh server mkdir \-p .parallel/tmp/hk\-31483\-1; rsync \-rlDzR \-essh ./abc\-file server:.parallel/tmp/hk\-31483\-1;ssh \-tt \-oLogLevel=quiet server \*(Aqeval \`echo $SHELL | grep "/t\e{0,1\e}csh" > /dev/null && echo setenv PARALLEL_SEQ \*(Aq$PARALLEL_SEQ\*(Aq\e; setenv PARALLEL_PID \*(Aq$PARALLEL_PID\*(Aq || echo PARALLEL_SEQ=\*(Aq$PARALLEL_SEQ\*(Aq\e;export PARALLEL_SEQ\e; PARALLEL_PID=\*(Aq$PARALLEL_PID\*(Aq\e;export PARALLEL_PID\` ;\*(Aq tty\e \e>/dev/null\e \e&\e&\e stty\e isig\e \-onlcr\e \-echo\e;mkdir\e \-p\e .parallel/tmp/hk\-31483\-1\e;\e cd\e .parallel/tmp/hk\-31483\-1\e \e&\e&\e echo\e \e$SHELL\e \e|\e grep\e \e"/t\e\e\e{0,1\e\e\e}csh\e"\e \e>\e /dev/null\e \e&\e&\e setenv\e my_func3\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e\e\e \e\e\e>\e\e\e \e\e\e$1.out\e"\*(Aq
|
|
|
|
|
\& \*(Aq\e"\e\e\e}\e \e&\e&\e setenv\e VAR\e foo\e \e&\e&\e setenv\e my_func2\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
|
|
|
|
|
\& \*(Aq\e"\e\e\e}\e \e|\e|\e export\e my_func3=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e\e\e \e\e\e>\e\e\e \e\e\e$1.out\e"\*(Aq
|
|
|
|
|
\& \*(Aq\e"\e\e\e}\e \e&\e&\e export\e VAR=foo\e \e&\e&\e export\e my_func2=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
|
|
|
|
|
\& \*(Aq\e"\e\e\e}\e \e&\e&\e eval\e my_func3\e"\e$my_func3\e"\e \e&\e&\e eval\e my_func2\e"\e$my_func2\e"\e;\e\enice\e \-n17\e /bin/bash\e \-c\e my_func3\e\e\e abc\-file;_EXIT_status=$?; mkdir \-p .; rsync \-\-rsync\-path=cd\e .parallel/tmp/hk\-31483\-1/.\e;\e rsync \-rlDzR \-essh server:abc\-file.out .;ssh server rm\e \-f\e .parallel/tmp/hk\-31483\-1/abc\-file\e;rm\e \-f\e .parallel/tmp/hk\-31483\-1/abc\-file.out\e;rm \-rf .parallel/tmp/hk\-31483\-1\e;; exit $_EXIT_status;
|
|
|
|
|
.Ve
|
|
|
|
|
.SH "\-\-pipe"
|
|
|
|
|
.IX Header "--pipe"
|
|
|
|
|
The \-\-pipe functionality puts \s-1GNU\s0 Parallel in a different mode:
|
2013-08-22 15:24:36 +00:00
|
|
|
Instead of treating the data on stdin (standard input) as arguments
|
|
|
|
|
for a command to run, the data will be sent to stdin (standard input)
|
|
|
|
|
of the command.
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
2013-08-22 15:24:36 +00:00
|
|
|
The typical situation is:
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& command_A | command_B | command_C
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
where command_B is slow, and you want to speed up command_B.
|
|
|
|
|
.SS "Chunk size"
|
|
|
|
|
.IX Subsection "Chunk size"
|
|
|
|
|
By default \s-1GNU\s0 Parallel will start an instance of command_B, read a
|
|
|
|
|
chunk of 1 \s-1MB\s0, and pass that to the instance. Then start another
|
|
|
|
|
instance, read another chunk, and pass that to the second instance.
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num1000000 | parallel \-\-pipe wc
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 7
|
|
|
|
|
\& 165668 165668 1048571
|
|
|
|
|
\& 149797 149797 1048579
|
|
|
|
|
\& 149796 149796 1048572
|
|
|
|
|
\& 149797 149797 1048579
|
|
|
|
|
\& 149797 149797 1048579
|
|
|
|
|
\& 149796 149796 1048572
|
|
|
|
|
\& 85349 85349 597444
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The size of the chunk is not exactly 1 \s-1MB\s0 because \s-1GNU\s0 Parallel only
|
|
|
|
|
passes full lines \- never half a line, thus the blocksize is only
|
|
|
|
|
average 1 \s-1MB\s0. You can change the block size to 2 \s-1MB\s0 with \-\-block:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num1000000 | parallel \-\-pipe \-\-block 2M wc
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& 315465 315465 2097150
|
|
|
|
|
\& 299593 299593 2097151
|
|
|
|
|
\& 299593 299593 2097151
|
|
|
|
|
\& 85349 85349 597444
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel treats each line as a record. If the order of record is
|
|
|
|
|
unimportant (e.g. you need all lines processed, but you do not care
|
|
|
|
|
which is processed first), then you can use \-\-round\-robin. Without
|
|
|
|
|
\&\-\-round\-robin \s-1GNU\s0 Parallel will start a command per block; with
|
|
|
|
|
\&\-\-round\-robin only the requested number of jobs will be started
|
|
|
|
|
(\-\-jobs). The records will then be distributed between the running
|
|
|
|
|
jobs:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num1000000 | parallel \-\-pipe \-j4 \-\-round\-robin wc
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output will be similar to:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& 149797 149797 1048579
|
|
|
|
|
\& 299593 299593 2097151
|
|
|
|
|
\& 315465 315465 2097150
|
|
|
|
|
\& 235145 235145 1646016
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
One of the 4 instances got a single record, 2 instances got 2 full
|
|
|
|
|
records each, and one instance got 1 full and 1 partial record.
|
|
|
|
|
.SS "Records"
|
|
|
|
|
.IX Subsection "Records"
|
|
|
|
|
\&\s-1GNU\s0 Parallel sees the input as records. The default record is a single
|
|
|
|
|
line.
|
|
|
|
|
.PP
|
|
|
|
|
Using \-N140000 \s-1GNU\s0 Parallel will read 140000 records at a time:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num1000000 | parallel \-\-pipe \-N140000 wc
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& 140000 140000 868895
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 140000 140000 980000
|
|
|
|
|
\& 20000 20000 140001
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
2013-12-04 16:12:09 +00:00
|
|
|
Notice that the last job could not get the full 140000 lines, but only
|
|
|
|
|
20000 lines.
|
2013-08-17 16:43:30 +00:00
|
|
|
.PP
|
|
|
|
|
If a record is 75 lines \-L can be used:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num1000000 | parallel \-\-pipe \-L75 wc
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& 165600 165600 1048095
|
|
|
|
|
\& 149850 149850 1048950
|
|
|
|
|
\& 149775 149775 1048425
|
|
|
|
|
\& 149775 149775 1048425
|
|
|
|
|
\& 149850 149850 1048950
|
|
|
|
|
\& 149775 149775 1048425
|
|
|
|
|
\& 85350 85350 597450
|
|
|
|
|
\& 25 25 176
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Notice \s-1GNU\s0 Parallel still reads a block of around 1 \s-1MB\s0; but instead of
|
|
|
|
|
passing full lines to 'wc' it passes full 75 lines at a time. This
|
|
|
|
|
of course does not hold for the last job (which in this case got 25
|
|
|
|
|
lines).
|
|
|
|
|
.SS "Record separators"
|
|
|
|
|
.IX Subsection "Record separators"
|
|
|
|
|
\&\s-1GNU\s0 Parallel uses separators to determine where two record split.
|
|
|
|
|
.PP
|
|
|
|
|
\&\-\-recstart gives the string that starts a record; \-\-recend gives the
|
|
|
|
|
string that ends a record. The default is \-\-recend '\en' (newline).
|
|
|
|
|
.PP
|
|
|
|
|
If both \-\-recend and \-\-recstart are given, then the record will only
|
|
|
|
|
split if the recend string is immediately followed by the recstart
|
|
|
|
|
string.
|
|
|
|
|
.PP
|
|
|
|
|
Here the \-\-recend is set to ', ':
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& echo /foo, bar/, /baz, qux/, | parallel \-kN1 \-\-recend \*(Aq, \*(Aq \-\-pipe echo JOB{#}\e;cat\e;echo END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& JOB1
|
|
|
|
|
\& /foo, END
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& bar/, END
|
|
|
|
|
\& JOB3
|
|
|
|
|
\& /baz, END
|
|
|
|
|
\& JOB4
|
|
|
|
|
\& qux/,
|
|
|
|
|
\& END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Here the \-\-recstart is set to '/':
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& echo /foo, bar/, /baz, qux/, | parallel \-kN1 \-\-recstart \*(Aq/\*(Aq \-\-pipe echo JOB{#}\e;cat\e;echo END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 9
|
|
|
|
|
\& JOB1
|
|
|
|
|
\& /foo, barEND
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& /, END
|
|
|
|
|
\& JOB3
|
|
|
|
|
\& /baz, quxEND
|
|
|
|
|
\& JOB4
|
|
|
|
|
\& /,
|
|
|
|
|
\& END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Here both \-\-recend and \-\-recstart are set:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& echo /foo, bar/, /baz, qux/, | parallel \-kN1 \-\-recend \*(Aq, \*(Aq \-\-recstart \*(Aq/\*(Aq \-\-pipe echo JOB{#}\e;cat\e;echo END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& JOB1
|
|
|
|
|
\& /foo, bar/, END
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& /baz, qux/,
|
|
|
|
|
\& END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Note the difference between setting one string and setting both strings.
|
|
|
|
|
.PP
|
|
|
|
|
With \-\-regexp the \-\-recend and \-\-recstart will be treated as a regular expression:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& echo foo,bar,_baz,_\|_qux, | parallel \-kN1 \-\-regexp \-\-recend \*(Aq,_+\*(Aq \-\-pipe echo JOB{#}\e;cat\e;echo END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 7
|
|
|
|
|
\& JOB1
|
|
|
|
|
\& foo,bar,_END
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& baz,_\|_END
|
|
|
|
|
\& JOB3
|
|
|
|
|
\& qux,
|
|
|
|
|
\& END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can remove the record separators with \-\-remove\-rec\-sep/\-\-rrs:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& echo foo,bar,_baz,_\|_qux, | parallel \-kN1 \-\-rrs \-\-regexp \-\-recend \*(Aq,_+\*(Aq \-\-pipe echo JOB{#}\e;cat\e;echo END
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 7
|
|
|
|
|
\& JOB1
|
|
|
|
|
\& foo,barEND
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& bazEND
|
|
|
|
|
\& JOB3
|
|
|
|
|
\& qux,
|
|
|
|
|
\& END
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Header"
|
|
|
|
|
.IX Subsection "Header"
|
|
|
|
|
If the input data has a header, the header can be repeated for each
|
|
|
|
|
job by matching the header with \-\-header. If headers start with \f(CW%:\fR
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num_%header | parallel \-\-header \*(Aq(%.*\en)*\*(Aq \-\-pipe \-N3 echo JOB{#}\e;cat
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 10
|
2014-01-25 22:29:25 +00:00
|
|
|
\& JOB1
|
2013-08-17 16:43:30 +00:00
|
|
|
\& %head1
|
|
|
|
|
\& %head2
|
|
|
|
|
\& 1
|
|
|
|
|
\& 2
|
|
|
|
|
\& 3
|
|
|
|
|
\& JOB2
|
|
|
|
|
\& %head1
|
|
|
|
|
\& %head2
|
|
|
|
|
\& 4
|
|
|
|
|
\& 5
|
|
|
|
|
\& 6
|
|
|
|
|
\& JOB3
|
|
|
|
|
\& %head1
|
|
|
|
|
\& %head2
|
|
|
|
|
\& 7
|
|
|
|
|
\& 8
|
|
|
|
|
\& 9
|
|
|
|
|
\& JOB4
|
|
|
|
|
\& %head1
|
|
|
|
|
\& %head2
|
|
|
|
|
\& 10
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If the header is 2 lines, \-\-header 2 will work:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat num_%header | parallel \-\-header 2 \-\-pipe \-N3 echo JOB{#}\e;cat
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output: Same as above.
|
|
|
|
|
.SH "Shebang"
|
|
|
|
|
.IX Header "Shebang"
|
|
|
|
|
.SS "Input data and parallel command in the same file"
|
|
|
|
|
.IX Subsection "Input data and parallel command in the same file"
|
|
|
|
|
\&\s-1GNU\s0 Parallel is often called as:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& cat input_file | parallel command
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
With \-\-shebang the input_file and parallel can be combined into the same script.
|
|
|
|
|
.PP
|
|
|
|
|
UNIX-scripts start with a shebang line like:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& #!/bin/bash
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
\&\s-1GNU\s0 Parallel can do that, too. With \-\-shebang the arguments can be
|
|
|
|
|
listed in the file. The parallel command is the first line of the
|
|
|
|
|
script:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& #!/usr/bin/parallel \-\-shebang \-r echo
|
|
|
|
|
\&
|
|
|
|
|
\& foo
|
|
|
|
|
\& bar
|
|
|
|
|
\& baz
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 3
|
|
|
|
|
\& foo
|
|
|
|
|
\& bar
|
|
|
|
|
\& baz
|
|
|
|
|
.Ve
|
|
|
|
|
.SS "Parallelizing existing scripts"
|
|
|
|
|
.IX Subsection "Parallelizing existing scripts"
|
|
|
|
|
\&\s-1GNU\s0 Parallel is often called as:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& cat input_file | parallel command
|
|
|
|
|
\& parallel command ::: foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
If command is a script parallel can be combined into a single file so:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& cat input_file | command
|
|
|
|
|
\& command foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
will run the script in parallel.
|
|
|
|
|
.PP
|
|
|
|
|
This perl script perl_echo works like echo:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& #!/usr/bin/perl
|
|
|
|
|
\&
|
|
|
|
|
\& print "@ARGV\en"
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
It can be called as:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& parallel perl_echo ::: foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
By changing the #!\-line it can be run in parallel
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& #!/usr/bin/parallel \-\-shebang\-wrap /usr/bin/perl
|
|
|
|
|
\&
|
|
|
|
|
\& print "@ARGV\en"
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Thus this will work:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& perl_echo foo bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output (the order may be different):
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 2
|
|
|
|
|
\& foo
|
|
|
|
|
\& bar
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
This technique can be used for:
|
|
|
|
|
.IP "Perl:" 9
|
|
|
|
|
.IX Item "Perl:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap /usr/bin/perl
|
|
|
|
|
.IP "Python:" 9
|
|
|
|
|
.IX Item "Python:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap /usr/bin/python
|
|
|
|
|
.IP "Bash:" 9
|
|
|
|
|
.IX Item "Bash:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap /bin/bash
|
|
|
|
|
.IP "R:" 9
|
|
|
|
|
.IX Item "R:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap /usr/bin/Rscript \-\-vanilla \-\-slave
|
|
|
|
|
.IP "GNUplot:" 9
|
|
|
|
|
.IX Item "GNUplot:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap ARG={} /usr/bin/gnuplot
|
|
|
|
|
.IP "Ruby:" 9
|
|
|
|
|
.IX Item "Ruby:"
|
|
|
|
|
#!/usr/bin/parallel \-\-shebang\-wrap /usr/bin/ruby
|
|
|
|
|
.SH "Semaphore"
|
|
|
|
|
.IX Header "Semaphore"
|
|
|
|
|
\&\s-1GNU\s0 Parallel can work as a counting semaphore. This is slower and less
|
|
|
|
|
efficient than its normal mode.
|
|
|
|
|
.PP
|
|
|
|
|
An alias for 'parallel \-\-semaphore' is 'sem'. The default is to allow
|
|
|
|
|
only one program to run at a time (technically called a mutex). The
|
|
|
|
|
program is started in the background. Use \-\-wait for all 'sem's to
|
|
|
|
|
finish:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& sem \*(Aqsleep 1; echo The first finished\*(Aq &&
|
|
|
|
|
\& echo The first is now running in the background &&
|
|
|
|
|
\& sem \*(Aqsleep 1; echo The second finished\*(Aq &&
|
|
|
|
|
\& echo The second is now running in the background
|
|
|
|
|
\& sem \-\-wait
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 4
|
|
|
|
|
\& The first is now running in the background
|
|
|
|
|
\& The first finished
|
|
|
|
|
\& The second is now running in the background
|
|
|
|
|
\& The second finished
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The command can be run in the foreground with \-\-fg:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& sem \-\-fg \*(Aqsleep 1; echo The first finished\*(Aq &&
|
|
|
|
|
\& echo The first finished running in the foreground &&
|
|
|
|
|
\& sem \-\-fg \*(Aqsleep 1; echo The second finished\*(Aq &&
|
|
|
|
|
\& echo The second finished running in the foreground
|
|
|
|
|
\& sem \-\-wait
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
The difference between this and just running the command, is that a
|
|
|
|
|
mutex is set, so if other sems were running in the background only one
|
|
|
|
|
would run at the same time.
|
|
|
|
|
.PP
|
|
|
|
|
To tell the difference between which semaphore is used, use
|
|
|
|
|
\&\-\-semaphorename/\-\-id. Run this in one terminal:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& sem \-\-id my_id \-u \*(Aqecho First started; sleep 10; echo The first finished\*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
and simultaneously this in another terminal:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 1
|
|
|
|
|
\& sem \-\-id my_id \-u \*(Aqecho Second started; sleep 10; echo The second finished\*(Aq
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Note how the second will only be started when the first has finished.
|
|
|
|
|
.SS "Counting semaphore"
|
|
|
|
|
.IX Subsection "Counting semaphore"
|
|
|
|
|
A mutex is like having a single toilet: When it is in use everyone
|
|
|
|
|
else will have to wait. A counting semaphore is like having multiple
|
|
|
|
|
toilets: Several people can use the toilets, but when they all are in
|
|
|
|
|
use, everyone else will have to wait.
|
|
|
|
|
.PP
|
|
|
|
|
sem can emulate a counting semaphore. Use \-\-jobs to set the number of
|
|
|
|
|
toilets:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 5
|
|
|
|
|
\& sem \-\-jobs 3 \-\-id my_id \-u \*(Aqecho First started; sleep 5; echo The first finished\*(Aq &&
|
|
|
|
|
\& sem \-\-jobs 3 \-\-id my_id \-u \*(Aqecho Second started; sleep 6; echo The second finished\*(Aq &&
|
|
|
|
|
\& sem \-\-jobs 3 \-\-id my_id \-u \*(Aqecho Third started; sleep 7; echo The third finished\*(Aq &&
|
|
|
|
|
\& sem \-\-jobs 3 \-\-id my_id \-u \*(Aqecho Fourth started; sleep 8; echo The fourth finished\*(Aq &&
|
|
|
|
|
\& sem \-\-wait \-\-id my_id
|
|
|
|
|
.Ve
|
|
|
|
|
.PP
|
|
|
|
|
Output:
|
|
|
|
|
.PP
|
|
|
|
|
.Vb 8
|
|
|
|
|
\& First started
|
|
|
|
|
\& Second started
|
|
|
|
|
\& Third started
|
|
|
|
|
\& The first finished
|
|
|
|
|
\& Fourth started
|
|
|
|
|
\& The second finished
|
|
|
|
|
\& The third finished
|
|
|
|
|
\& The fourth finished
|
|
|
|
|
.Ve
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.SH "Informational"
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.IX Header "Informational"
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\&\s-1GNU\s0 Parallel has some options to give short information about the
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configuration.
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\&\-\-help will print a summary of the most important options:
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.Vb 1
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\& parallel \-\-help
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Output:
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.Vb 4
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\& Usage:
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\& parallel [options] [command [arguments]] < list_of_arguments
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\& parallel [options] [command [arguments]] (::: arguments|:::: argfile(s))...
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\& cat ... | parallel \-\-pipe [options] [command [arguments]]
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\&
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\& \-j n Run n jobs in parallel
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\& \-k Keep same order
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\& \-X Multiple arguments with context replace
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\& \-\-colsep regexp Split input on regexp for positional replacements
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\& {} {.} {/} {/.} {#} Replacement strings
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\& {3} {3.} {3/} {3/.} Positional replacement strings
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\&
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\& \-S sshlogin Example: foo@server.example.com
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\& \-\-slf .. Use ~/.parallel/sshloginfile as the list of sshlogins
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\& \-\-trc {}.bar Shorthand for \-\-transfer \-\-return {}.bar \-\-cleanup
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\& \-\-onall Run the given command with argument on all sshlogins
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\& \-\-nonall Run the given command with no arguments on all sshlogins
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\&
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\& \-\-pipe Split stdin (standard input) to multiple jobs.
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\& \-\-recend str Record end separator for \-\-pipe.
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\& \-\-recstart str Record start separator for \-\-pipe.
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\&
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\& See \*(Aqman parallel\*(Aq for details
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\&
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\& When using GNU Parallel for a publication please cite:
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\&
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\& O. Tange (2011): GNU Parallel \- The Command\-Line Power Tool,
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\& ;login: The USENIX Magazine, February 2011:42\-47.
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.Ve
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When asking for help, always report the full output of:
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.Vb 1
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\& parallel \-\-version
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Output:
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.PP
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.Vb 5
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\& GNU parallel 20130822
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\& Copyright (C) 2007,2008,2009,2010,2011,2012,2013 Ole Tange and Free Software Foundation, Inc.
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\& License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
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\& This is free software: you are free to change and redistribute it.
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\& GNU parallel comes with no warranty.
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\&
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\& Web site: http://www.gnu.org/software/parallel
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\&
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\& When using GNU Parallel for a publication please cite:
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\&
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\& O. Tange (2011): GNU Parallel \- The Command\-Line Power Tool,
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\& ;login: The USENIX Magazine, February 2011:42\-47.
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.Ve
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In scripts \-\-minversion can be used to ensure the user has at least
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this version:
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.Vb 1
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\& parallel \-\-minversion 20130722 && echo Your version is at least 20130722.
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.Ve
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Output:
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.PP
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.Vb 2
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\& 20130722
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\& Your version is at least 20130722.
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.Ve
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.PP
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If using \s-1GNU\s0 Parallel for research the BibTeX citation can be
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generated using \-\-bibtex.
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.PP
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.Vb 1
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\& parallel \-\-bibtex
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Output:
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.Vb 12
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\& @article{Tange2011a,
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\& title = {GNU Parallel \- The Command\-Line Power Tool},
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\& author = {O. Tange},
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\& address = {Frederiksberg, Denmark},
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\& journal = {;login: The USENIX Magazine},
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\& month = {Feb},
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\& number = {1},
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\& volume = {36},
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\& url = {http://www.gnu.org/s/parallel},
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\& year = {2011},
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\& pages = {42\-47}
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\& }
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.Ve
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With \-\-max\-line\-length\-allowed \s-1GNU\s0 Parallel will report the maximal
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size of the command line:
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.PP
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.Vb 1
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\& parallel \-\-max\-line\-length\-allowed
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Output (may vary on different systems):
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.PP
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.Vb 1
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\& 131071
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.Ve
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.PP
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\&\-\-number\-of\-cpus and \-\-number\-of\-cores run system specific code to
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determine the number of CPUs and \s-1CPU\s0 cores on the system. On
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unsupported platforms they will return 1:
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.PP
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.Vb 2
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\& parallel \-\-number\-of\-cpus
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\& parallel \-\-number\-of\-cores
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Output (may vary on different systems):
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.PP
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.Vb 2
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\& 4
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\& 64
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.Ve
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.SH "Profiles"
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.IX Header "Profiles"
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The defaults for \s-1GNU\s0 Parallel can be changed systemwise by putting the
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command line options in /etc/parallel/config. They can be changed for
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a user by putting them in ~/.parallel/config.
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.PP
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Profiles work the same way, but have to be referred to with \-\-profile:
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.PP
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.Vb 6
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\& echo \*(Aq\-S :,\*(Aq$SERVER1 > ~/.parallel/cluster
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\& echo \*(Aq\-\-nice 17\*(Aq >> ~/.parallel/cluster
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\& echo \*(Aq\-\-filter\-hosts\*(Aq >> ~/.parallel/cluster
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\& echo \*(Aq\-\-timeout 300%\*(Aq >> ~/.parallel/cluster
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\& echo \*(Aq\-\-env _\*(Aq >> ~/.parallel/cluster
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\& parallel \-\-profile cluster echo ::: A B C
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Output:
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.Vb 3
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\& A
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\& B
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\& C
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Profiles can be combined:
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.PP
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.Vb 2
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\& echo \*(Aq\-vv \-\-dry\-run\*(Aq > ~/.parallel/dryverbose
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\& parallel \-\-profile dryverbose \-\-profile cluster echo ::: A B C
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Output:
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.PP
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.Vb 10
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\& ssh \-tt \-oLogLevel=quiet lo \*(Aqeval \`echo $SHELL | grep "/t\e{0,1\e}csh" > /dev/null && echo setenv PARALLEL_SEQ \*(Aq$PARALLEL_SEQ\*(Aq\e; setenv PARALLEL_PID \*(Aq$PARALLEL_PID\*(Aq || echo PARALLEL_SEQ=\*(Aq$PARALLEL_SEQ\*(Aq\e;export PARALLEL_SEQ\e; PARALLEL_PID=\*(Aq$PARALLEL_PID\*(Aq\e;export PARALLEL_PID\` ;\*(Aq tty\e \e>/dev/null\e \e&\e&\e stty\e isig\e \-onlcr\e \-echo\e;echo\e \e$SHELL\e \e|\e grep\e \e"/t\e\e\e{0,1\e\e\e}csh\e"\e \e>\e /dev/null\e \e&\e&\e setenv\e SERVER1\e lo\e \e&\e&\e setenv\e MYVAR\e foo\e\e\e bar\e \e&\e&\e setenv\e VAR\e foo\e \e&\e&\e setenv\e my_func\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e setenv\e my_func2\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e|\e|\e export\e SERVER1=lo\e \e&\e&\e export\e MYVAR=foo\e\e\e bar\e \e&\e&\e export\e VAR=foo\e \e&\e&\e export\e my_func=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e export\e my_func2=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e eval\e my_func\e"\e$my_func\e"\e \e&\e&\e eval\e my_func2\e"\e$my_func2\e"\e;\e\enice\e \-n17\e /bin/bash\e \-c\e echo\e\e\e A;
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\& ssh \-tt \-oLogLevel=quiet lo \*(Aqeval \`echo $SHELL | grep "/t\e{0,1\e}csh" > /dev/null && echo setenv PARALLEL_SEQ \*(Aq$PARALLEL_SEQ\*(Aq\e; setenv PARALLEL_PID \*(Aq$PARALLEL_PID\*(Aq || echo PARALLEL_SEQ=\*(Aq$PARALLEL_SEQ\*(Aq\e;export PARALLEL_SEQ\e; PARALLEL_PID=\*(Aq$PARALLEL_PID\*(Aq\e;export PARALLEL_PID\` ;\*(Aq tty\e \e>/dev/null\e \e&\e&\e stty\e isig\e \-onlcr\e \-echo\e;echo\e \e$SHELL\e \e|\e grep\e \e"/t\e\e\e{0,1\e\e\e}csh\e"\e \e>\e /dev/null\e \e&\e&\e setenv\e SERVER1\e lo\e \e&\e&\e setenv\e MYVAR\e foo\e\e\e bar\e \e&\e&\e setenv\e VAR\e foo\e \e&\e&\e setenv\e my_func\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e setenv\e my_func2\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e|\e|\e export\e SERVER1=lo\e \e&\e&\e export\e MYVAR=foo\e\e\e bar\e \e&\e&\e export\e VAR=foo\e \e&\e&\e export\e my_func=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e export\e my_func2=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e eval\e my_func\e"\e$my_func\e"\e \e&\e&\e eval\e my_func2\e"\e$my_func2\e"\e;\e\enice\e \-n17\e /bin/bash\e \-c\e echo\e\e\e B;
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\& ssh \-tt \-oLogLevel=quiet lo \*(Aqeval \`echo $SHELL | grep "/t\e{0,1\e}csh" > /dev/null && echo setenv PARALLEL_SEQ \*(Aq$PARALLEL_SEQ\*(Aq\e; setenv PARALLEL_PID \*(Aq$PARALLEL_PID\*(Aq || echo PARALLEL_SEQ=\*(Aq$PARALLEL_SEQ\*(Aq\e;export PARALLEL_SEQ\e; PARALLEL_PID=\*(Aq$PARALLEL_PID\*(Aq\e;export PARALLEL_PID\` ;\*(Aq tty\e \e>/dev/null\e \e&\e&\e stty\e isig\e \-onlcr\e \-echo\e;echo\e \e$SHELL\e \e|\e grep\e \e"/t\e\e\e{0,1\e\e\e}csh\e"\e \e>\e /dev/null\e \e&\e&\e setenv\e SERVER1\e lo\e \e&\e&\e setenv\e MYVAR\e foo\e\e\e bar\e \e&\e&\e setenv\e VAR\e foo\e \e&\e&\e setenv\e my_func\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e setenv\e my_func2\e \e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e|\e|\e export\e SERVER1=lo\e \e&\e&\e export\e MYVAR=foo\e\e\e bar\e \e&\e&\e export\e VAR=foo\e \e&\e&\e export\e my_func=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e export\e my_func2=\e\e\e(\e\e\e)\e\e\e \e\e\e{\e\e\e \e\e\e echo\e\e\e in\e\e\e my_func2\e\e\e \e\e\e$VAR\e\e\e \e\e\e$1\e"\*(Aq
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\& \*(Aq\e"\e\e\e}\e \e&\e&\e eval\e my_func\e"\e$my_func\e"\e \e&\e&\e eval\e my_func2\e"\e$my_func2\e"\e;\e\enice\e \-n17\e /bin/bash\e \-c\e echo\e\e\e C;
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.Ve
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.SH "Spread the word"
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.IX Header "Spread the word"
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I hope you have learned something from this tutorial.
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.PP
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If you like \s-1GNU\s0 Parallel:
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.IP "\(bu" 2
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Give a demo at your local user group/team/colleagues
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.IP "\(bu" 2
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Post the intro videos and the tutorial on Reddit, Diaspora*,
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forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin,
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mailing lists
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.IP "\(bu" 2
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Request or write a review for your favourite blog or magazine
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.IP "\(bu" 2
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Invite me for your next conference
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.PP
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If you use \s-1GNU\s0 Parallel for research:
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.IP "\(bu" 2
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Please cite \s-1GNU\s0 Parallel in you publications (use \-\-bibtex)
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.PP
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If \s-1GNU\s0 Parallel saves you money:
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.IP "\(bu" 2
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(Have your company) donate to \s-1FSF\s0 https://my.fsf.org/donate/
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.PP
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2014-06-04 00:22:39 +00:00
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(C) 20140622 Ole Tange GPLv3
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