xref: /dports/sysutils/parallel/parallel-20211122/src/parallel_tutorial.rst

*********************
GNU Parallel Tutorial
*********************


This tutorial shows off much of GNU \ **parallel**\ 's functionality. The
tutorial is meant to learn the options in and syntax of GNU
\ **parallel**\ .  The tutorial is \ **not**\  to show realistic examples from the
real world.

Reader's guide
==============


If you prefer reading a book buy \ **GNU Parallel 2018**\  at
https://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
or download it at: https://doi.org/10.5281/zenodo.1146014

Otherwise start by watching the intro videos for a quick introduction:
https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

Then browse through the \ **EXAMPLE**\ s after the list of \ **OPTIONS**\  in
\ **man parallel**\  (Use \ **LESS=+/EXAMPLE: man parallel**\ ). That will give
you an idea of what GNU \ **parallel**\  is capable of.

If you want to dive even deeper: spend a couple of hours walking
through the tutorial (\ **man parallel_tutorial**\ ). Your command line
will love you for it.

Finally you may want to look at the rest of the manual (\ **man
parallel**\ ) if you have special needs not already covered.

If you want to know the design decisions behind GNU \ **parallel**\ , try:
\ **man parallel_design**\ . This is also a good intro if you intend to
change GNU \ **parallel**\ .



*************
Prerequisites
*************


To run this tutorial you must have the following:


- parallel >= version 20160822

 Install the newest version using your package manager (recommended for
 security reasons), the way described in README, or with this command:


 .. code-block:: perl

    $ (wget -O - pi.dk/3 || lynx -source pi.dk/3 || curl pi.dk/3/ || \
       fetch -o - http://pi.dk/3 ) > install.sh
    $ sha1sum install.sh
    12345678 3374ec53 bacb199b 245af2dd a86df6c9
    $ md5sum install.sh
    029a9ac0 6e8b5bc6 052eac57 b2c3c9ca
    $ sha512sum install.sh
    40f53af6 9e20dae5 713ba06c f517006d 9897747b ed8a4694 b1acba1b 1464beb4
    60055629 3f2356f3 3e9c4e3c 76e3f3af a9db4b32 bd33322b 975696fc e6b23cfb
    $ bash install.sh


 This will also install the newest version of the tutorial which you
 can see by running this:


 .. code-block:: perl

    man parallel_tutorial


 Most of the tutorial will work on older versions, too.



- abc-file:

 The file can be generated by this command:


 .. code-block:: perl

    parallel -k echo ::: A B C > abc-file




- def-file:

 The file can be generated by this command:


 .. code-block:: perl

    parallel -k echo ::: D E F > def-file




- abc0-file:

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'printf "A\0B\0C\0"' > abc0-file




- abc_-file:

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'printf "A_B_C_"' > abc_-file




- tsv-file.tsv

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'printf "f1\tf2\nA\tB\nC\tD\n"' > tsv-file.tsv




- num8

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'for(1..8){print "$_\n"}' > num8




- num128

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'for(1..128){print "$_\n"}' > num128




- num30000

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'for(1..30000){print "$_\n"}' > num30000




- num1000000

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'for(1..1000000){print "$_\n"}' > num1000000




- num_%header

 The file can be generated by this command:


 .. code-block:: perl

    (echo %head1; echo %head2; \
     perl -e 'for(1..10){print "$_\n"}') > num_%header




- fixedlen

 The file can be generated by this command:


 .. code-block:: perl

    perl -e 'print "HHHHAAABBBCCC"' > fixedlen




- For remote running: ssh login on 2 servers with no password in $SERVER1 and $SERVER2 must work.


 .. code-block:: perl

    SERVER1=server.example.com
    SERVER2=server2.example.net


 So you must be able to do this without entering a password:


 .. code-block:: perl

    ssh $SERVER1 echo works
    ssh $SERVER2 echo works


 It can be setup by running 'ssh-keygen -t dsa; ssh-copy-id $SERVER1'
 and using an empty passphrase, or you can use \ **ssh-agent**\ .




*************
Input sources
*************


GNU \ **parallel**\  reads input from input sources. These can be files, the
command line, and stdin (standard input or a pipe).

A single input source
=====================


Input can be read from the command line:


.. code-block:: perl

   parallel echo ::: A B C


Output (the order may be different because the jobs are run in
parallel):


.. code-block:: perl

   A
   B
   C


The input source can be a file:


.. code-block:: perl

   parallel -a abc-file echo


Output: Same as above.

STDIN (standard input) can be the input source:


.. code-block:: perl

   cat abc-file | parallel echo


Output: Same as above.


Multiple input sources
======================


GNU \ **parallel**\  can take multiple input sources given on the command
line. GNU \ **parallel**\  then generates all combinations of the input
sources:


.. code-block:: perl

   parallel echo ::: A B C ::: D E F


Output (the order may be different):


.. code-block:: perl

   A D
   A E
   A F
   B D
   B E
   B F
   C D
   C E
   C F


The input sources can be files:


.. code-block:: perl

   parallel -a abc-file -a def-file echo


Output: Same as above.

STDIN (standard input) can be one of the input sources using \ **-**\ :


.. code-block:: perl

   cat abc-file | parallel -a - -a def-file echo


Output: Same as above.

Instead of \ **-a**\  files can be given after \ **::::**\ :


.. code-block:: perl

   cat abc-file | parallel echo :::: - def-file


Output: Same as above.

::: and :::: can be mixed:


.. code-block:: perl

   parallel echo ::: A B C :::: def-file


Output: Same as above.

Linking arguments from input sources
------------------------------------


With \ **--link**\  you can link the input sources and get one argument
from each input source:


.. code-block:: perl

   parallel --link echo ::: A B C ::: D E F


Output (the order may be different):


.. code-block:: perl

   A D
   B E
   C F


If one of the input sources is too short, its values will wrap:


.. code-block:: perl

   parallel --link echo ::: A B C D E ::: F G


Output (the order may be different):


.. code-block:: perl

   A F
   B G
   C F
   D G
   E F


For more flexible linking you can use \ **:::+**\  and \ **::::+**\ . They work
like \ **:::**\  and \ **::::**\  except they link the previous input source to
this input source.

This will link ABC to GHI:


.. code-block:: perl

   parallel echo :::: abc-file :::+ G H I :::: def-file


Output (the order may be different):


.. code-block:: perl

   A G D
   A G E
   A G F
   B H D
   B H E
   B H F
   C I D
   C I E
   C I F


This will link GHI to DEF:


.. code-block:: perl

   parallel echo :::: abc-file ::: G H I ::::+ def-file


Output (the order may be different):


.. code-block:: perl

   A G D
   A H E
   A I F
   B G D
   B H E
   B I F
   C G D
   C H E
   C I F


If one of the input sources is too short when using \ **:::+**\  or
\ **::::+**\ , the rest will be ignored:


.. code-block:: perl

   parallel echo ::: A B C D E :::+ F G


Output (the order may be different):


.. code-block:: perl

   A F
   B G




Changing the argument separator.
================================


GNU \ **parallel**\  can use other separators than \ **:::**\  or \ **::::**\ . This is
typically useful if \ **:::**\  or \ **::::**\  is used in the command to run:


.. code-block:: perl

   parallel --arg-sep ,, echo ,, A B C :::: def-file


Output (the order may be different):


.. code-block:: perl

   A D
   A E
   A F
   B D
   B E
   B F
   C D
   C E
   C F


Changing the argument file separator:


.. code-block:: perl

   parallel --arg-file-sep // echo ::: A B C // def-file


Output: Same as above.


Changing the argument delimiter
===============================


GNU \ **parallel**\  will normally treat a full line as a single argument: It
uses \ **\n**\  as argument delimiter. This can be changed with \ **-d**\ :


.. code-block:: perl

   parallel -d _ echo :::: abc_-file


Output (the order may be different):


.. code-block:: perl

   A
   B
   C


NUL can be given as \ **\0**\ :


.. code-block:: perl

   parallel -d '\0' echo :::: abc0-file


Output: Same as above.

A shorthand for \ **-d '\0'**\  is \ **-0**\  (this will often be used to read files
from \ **find ... -print0**\ ):


.. code-block:: perl

   parallel -0 echo :::: abc0-file


Output: Same as above.


End-of-file value for input source
==================================


GNU \ **parallel**\  can stop reading when it encounters a certain value:


.. code-block:: perl

   parallel -E stop echo ::: A B stop C D


Output:


.. code-block:: perl

   A
   B



Skipping empty lines
====================


Using \ **--no-run-if-empty**\  GNU \ **parallel**\  will skip empty lines.


.. code-block:: perl

   (echo 1; echo; echo 2) | parallel --no-run-if-empty echo


Output:


.. code-block:: perl

   1
   2




*************************
Building the command line
*************************


No command means arguments are commands
=======================================


If no command is given after parallel the arguments themselves are
treated as commands:


.. code-block:: perl

   parallel ::: ls 'echo foo' pwd


Output (the order may be different):


.. code-block:: perl

   [list of files in current dir]
   foo
   [/path/to/current/working/dir]


The command can be a script, a binary or a Bash function if the function is
exported using \ **export -f**\ :


.. code-block:: perl

   # Only works in Bash
   my_func() {
     echo in my_func $1
   }
   export -f my_func
   parallel my_func ::: 1 2 3


Output (the order may be different):


.. code-block:: perl

   in my_func 1
   in my_func 2
   in my_func 3



Replacement strings
===================


The 7 predefined replacement strings
------------------------------------


GNU \ **parallel**\  has several replacement strings. If no replacement
strings are used the default is to append \ **{}**\ :


.. code-block:: perl

   parallel echo ::: A/B.C


Output:


.. code-block:: perl

   A/B.C


The default replacement string is \ **{}**\ :


.. code-block:: perl

   parallel echo {} ::: A/B.C


Output:


.. code-block:: perl

   A/B.C


The replacement string \ **{.}**\  removes the extension:


.. code-block:: perl

   parallel echo {.} ::: A/B.C


Output:


.. code-block:: perl

   A/B


The replacement string \ **{/}**\  removes the path:


.. code-block:: perl

   parallel echo {/} ::: A/B.C


Output:


.. code-block:: perl

   B.C


The replacement string \ **{//}**\  keeps only the path:


.. code-block:: perl

   parallel echo {//} ::: A/B.C


Output:


.. code-block:: perl

   A


The replacement string \ **{/.}**\  removes the path and the extension:


.. code-block:: perl

   parallel echo {/.} ::: A/B.C


Output:


.. code-block:: perl

   B


The replacement string \ **{#}**\  gives the job number:


.. code-block:: perl

   parallel echo {#} ::: A B C


Output (the order may be different):


.. code-block:: perl

   1
   2
   3


The replacement string \ **{%}**\  gives the job slot number (between 1 and
number of jobs to run in parallel):


.. code-block:: perl

   parallel -j 2 echo {%} ::: A B C


Output (the order may be different and 1 and 2 may be swapped):


.. code-block:: perl

   1
   2
   1



Changing the replacement strings
--------------------------------


The replacement string \ **{}**\  can be changed with \ **-I**\ :


.. code-block:: perl

   parallel -I ,, echo ,, ::: A/B.C


Output:


.. code-block:: perl

   A/B.C


The replacement string \ **{.}**\  can be changed with \ **--extensionreplace**\ :


.. code-block:: perl

   parallel --extensionreplace ,, echo ,, ::: A/B.C


Output:


.. code-block:: perl

   A/B


The replacement string \ **{/}**\  can be replaced with \ **--basenamereplace**\ :


.. code-block:: perl

   parallel --basenamereplace ,, echo ,, ::: A/B.C


Output:


.. code-block:: perl

   B.C


The replacement string \ **{//}**\  can be changed with \ **--dirnamereplace**\ :


.. code-block:: perl

   parallel --dirnamereplace ,, echo ,, ::: A/B.C


Output:


.. code-block:: perl

   A


The replacement string \ **{/.}**\  can be changed with \ **--basenameextensionreplace**\ :


.. code-block:: perl

   parallel --basenameextensionreplace ,, echo ,, ::: A/B.C


Output:


.. code-block:: perl

   B


The replacement string \ **{#}**\  can be changed with \ **--seqreplace**\ :


.. code-block:: perl

   parallel --seqreplace ,, echo ,, ::: A B C


Output (the order may be different):


.. code-block:: perl

   1
   2
   3


The replacement string \ **{%}**\  can be changed with \ **--slotreplace**\ :


.. code-block:: perl

   parallel -j2 --slotreplace ,, echo ,, ::: A B C


Output (the order may be different and 1 and 2 may be swapped):


.. code-block:: perl

   1
   2
   1



Perl expression replacement string
----------------------------------


When predefined replacement strings are not flexible enough a perl
expression can be used instead. One example is to remove two
extensions: foo.tar.gz becomes foo


.. code-block:: perl

   parallel echo '{= s:\.[^.]+$::;s:\.[^.]+$::; =}' ::: foo.tar.gz


Output:


.. code-block:: perl

   foo


In \ **{= =}**\  you can access all of GNU \ **parallel**\ 's internal functions
and variables. A few are worth mentioning.

\ **total_jobs()**\  returns the total number of jobs:


.. code-block:: perl

   parallel echo Job {#} of {= '$_=total_jobs()' =} ::: {1..5}


Output:


.. code-block:: perl

   Job 1 of 5
   Job 2 of 5
   Job 3 of 5
   Job 4 of 5
   Job 5 of 5


\ **Q(...)**\  shell quotes the string:


.. code-block:: perl

   parallel echo {} shell quoted is {= '$_=Q($_)' =} ::: '*/!#$'


Output:


.. code-block:: perl

   */!#$ shell quoted is \*/\!\#\$


\ **skip()**\  skips the job:


.. code-block:: perl

   parallel echo {= 'if($_==3) { skip() }' =} ::: {1..5}


Output:


.. code-block:: perl

   1
   2
   4
   5


\ **@arg**\  contains the input source variables:


.. code-block:: perl

   parallel echo {= 'if($arg[1]==$arg[2]) { skip() }' =} \
     ::: {1..3} ::: {1..3}


Output:


.. code-block:: perl

   1 2
   1 3
   2 1
   2 3
   3 1
   3 2


If the strings \ **{=**\  and \ **=}**\  cause problems they can be replaced with \ **--parens**\ :


.. code-block:: perl

   parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' \
     ::: foo.tar.gz


Output:


.. code-block:: perl

   foo


To define a shorthand replacement string use \ **--rpl**\ :


.. code-block:: perl

   parallel --rpl '.. s:\.[^.]+$::;s:\.[^.]+$::;' echo '..' \
     ::: foo.tar.gz


Output: Same as above.

If the shorthand starts with \ **{**\  it can be used as a positional
replacement string, too:


.. code-block:: perl

   parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{..}'
     ::: foo.tar.gz


Output: Same as above.

If the shorthand contains matching parenthesis the replacement string
becomes a dynamic replacement string and the string in the parenthesis
can be accessed as $$1. If there are multiple matching parenthesis,
the matched strings can be accessed using $$2, $$3 and so on.

You can think of this as giving arguments to the replacement
string. Here we give the argument \ **.tar.gz**\  to the replacement string
\ **{%\ \*string\*\ }**\  which removes \ *string*\ :


.. code-block:: perl

   parallel --rpl '{%(.+?)} s/$$1$//;' echo {%.tar.gz}.zip ::: foo.tar.gz


Output:


.. code-block:: perl

   foo.zip


Here we give the two arguments \ **tar.gz**\  and \ **zip**\  to the replacement
string \ **{/\ \*string1\*\ /\ \*string2\*\ }**\  which replaces \ *string1*\  with
\ *string2*\ :


.. code-block:: perl

   parallel --rpl '{/(.+?)/(.*?)} s/$$1/$$2/;' echo {/tar.gz/zip} \
     ::: foo.tar.gz


Output:


.. code-block:: perl

   foo.zip


GNU \ **parallel**\ 's 7 replacement strings are implemented as this:


.. code-block:: perl

   --rpl '{} '
   --rpl '{#} $_=$job->seq()'
   --rpl '{%} $_=$job->slot()'
   --rpl '{/} s:.*/::'
   --rpl '{//} $Global::use{"File::Basename"} ||=
            eval "use File::Basename; 1;"; $_ = dirname($_);'
   --rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
   --rpl '{.} s:\.[^/.]+$::'



Positional replacement strings
------------------------------


With multiple input sources the argument from the individual input
sources can be accessed with \ **{**\ number\ **}**\ :


.. code-block:: perl

   parallel echo {1} and {2} ::: A B ::: C D


Output (the order may be different):


.. code-block:: perl

   A and C
   A and D
   B and C
   B and D


The positional replacement strings can also be modified using \ **/**\ , \ **//**\ , \ **/.**\ , and  \ **.**\ :


.. code-block:: perl

   parallel echo /={1/} //={1//} /.={1/.} .={1.} ::: A/B.C D/E.F


Output (the order may be different):


.. code-block:: perl

   /=B.C //=A /.=B .=A/B
   /=E.F //=D /.=E .=D/E


If a position is negative, it will refer to the input source counted
from behind:


.. code-block:: perl

   parallel echo 1={1} 2={2} 3={3} -1={-1} -2={-2} -3={-3} \
     ::: A B ::: C D ::: E F


Output (the order may be different):


.. code-block:: perl

   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



Positional perl expression replacement string
---------------------------------------------


To use a perl expression as a positional replacement string simply
prepend the perl expression with number and space:


.. code-block:: perl

   parallel echo '{=2 s:\.[^.]+$::;s:\.[^.]+$::; =} {1}' \
     ::: bar ::: foo.tar.gz


Output:


.. code-block:: perl

   foo bar


If a shorthand defined using \ **--rpl**\  starts with \ **{**\  it can be used as
a positional replacement string, too:


.. code-block:: perl

   parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' \
     ::: bar ::: foo.tar.gz


Output: Same as above.


Input from columns
------------------


The columns in a file can be bound to positional replacement strings
using \ **--colsep**\ . Here the columns are separated by TAB (\t):


.. code-block:: perl

   parallel --colsep '\t' echo 1={1} 2={2} :::: tsv-file.tsv


Output (the order may be different):


.. code-block:: perl

   1=f1 2=f2
   1=A 2=B
   1=C 2=D



Header defined replacement strings
----------------------------------


With \ **--header**\  GNU \ **parallel**\  will use the first value of the input
source as the name of the replacement string. Only the non-modified
version \ **{}**\  is supported:


.. code-block:: perl

   parallel --header : echo f1={f1} f2={f2} ::: f1 A B ::: f2 C D


Output (the order may be different):


.. code-block:: perl

   f1=A f2=C
   f1=A f2=D
   f1=B f2=C
   f1=B f2=D


It is useful with \ **--colsep**\  for processing files with TAB separated values:


.. code-block:: perl

   parallel --header : --colsep '\t' echo f1={f1} f2={f2} \
     :::: tsv-file.tsv


Output (the order may be different):


.. code-block:: perl

   f1=A f2=B
   f1=C f2=D



More pre-defined replacement strings with --plus
------------------------------------------------


\ **--plus**\  adds the replacement strings \ **{+/} {+.} {+..} {+...} {..}  {...}
{/..} {/...} {##}**\ . The idea being that \ **{+foo}**\  matches the opposite of \ **{foo}**\
and \ **{}**\  = \ **{+/}**\ /\ **{/}**\  = \ **{.}**\ .\ **{+.}**\  = \ **{+/}**\ /\ **{/.}**\ .\ **{+.}**\  = \ **{..}**\ .\ **{+..}**\  =
\ **{+/}**\ /\ **{/..}**\ .\ **{+..}**\  = \ **{...}**\ .\ **{+...}**\  = \ **{+/}**\ /\ **{/...}**\ .\ **{+...}**\ .


.. code-block:: perl

   parallel --plus echo {} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {+/}/{/} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {.}.{+.} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {+/}/{/.}.{+.} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {..}.{+..} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {+/}/{/..}.{+..} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {...}.{+...} ::: dir/sub/file.ex1.ex2.ex3
   parallel --plus echo {+/}/{/...}.{+...} ::: dir/sub/file.ex1.ex2.ex3


Output:


.. code-block:: perl

   dir/sub/file.ex1.ex2.ex3


\ **{##}**\  is simply the number of jobs:


.. code-block:: perl

   parallel --plus echo Job {#} of {##} ::: {1..5}


Output:


.. code-block:: perl

   Job 1 of 5
   Job 2 of 5
   Job 3 of 5
   Job 4 of 5
   Job 5 of 5



Dynamic replacement strings with --plus
---------------------------------------


\ **--plus**\  also defines these dynamic replacement strings:


- \ **{:-\ \*string\*\ }**\

 Default value is \ *string*\  if the argument is empty.



- \ **{:\ \*number\*\ }**\

 Substring from \ *number*\  till end of string.



- \ **{:\ \*number1\*\ :\ \*number2\*\ }**\

 Substring from \ *number1*\  to \ *number2*\ .



- \ **{#\ \*string\*\ }**\

 If the argument starts with \ *string*\ , remove it.



- \ **{%\ \*string\*\ }**\

 If the argument ends with \ *string*\ , remove it.



- \ **{/\ \*string1\*\ /\ \*string2\*\ }**\

 Replace \ *string1*\  with \ *string2*\ .



- \ **{^\ \*string\*\ }**\

 If the argument starts with \ *string*\ , upper case it. \ *string*\  must
 be a single letter.



- \ **{^^\ \*string\*\ }**\

 If the argument contains \ *string*\ , upper case it. \ *string*\  must be a
 single letter.



- \ **{,\ \*string\*\ }**\

 If the argument starts with \ *string*\ , lower case it. \ *string*\  must
 be a single letter.



- \ **{,,\ \*string\*\ }**\

 If the argument contains \ *string*\ , lower case it. \ *string*\  must be a
 single letter.



They are inspired from \ **Bash**\ :


.. code-block:: perl

   unset myvar
   echo ${myvar:-myval}
   parallel --plus echo {:-myval} ::: "$myvar"

   myvar=abcAaAdef
   echo ${myvar:2}
   parallel --plus echo {:2} ::: "$myvar"

   echo ${myvar:2:3}
   parallel --plus echo {:2:3} ::: "$myvar"

   echo ${myvar#bc}
   parallel --plus echo {#bc} ::: "$myvar"
   echo ${myvar#abc}
   parallel --plus echo {#abc} ::: "$myvar"

   echo ${myvar%de}
   parallel --plus echo {%de} ::: "$myvar"
   echo ${myvar%def}
   parallel --plus echo {%def} ::: "$myvar"

   echo ${myvar/def/ghi}
   parallel --plus echo {/def/ghi} ::: "$myvar"

   echo ${myvar^a}
   parallel --plus echo {^a} ::: "$myvar"
   echo ${myvar^^a}
   parallel --plus echo {^^a} ::: "$myvar"

   myvar=AbcAaAdef
   echo ${myvar,A}
   parallel --plus echo '{,A}' ::: "$myvar"
   echo ${myvar,,A}
   parallel --plus echo '{,,A}' ::: "$myvar"


Output:


.. code-block:: perl

   myval
   myval
   cAaAdef
   cAaAdef
   cAa
   cAa
   abcAaAdef
   abcAaAdef
   AaAdef
   AaAdef
   abcAaAdef
   abcAaAdef
   abcAaA
   abcAaA
   abcAaAghi
   abcAaAghi
   AbcAaAdef
   AbcAaAdef
   AbcAAAdef
   AbcAAAdef
   abcAaAdef
   abcAaAdef
   abcaaadef
   abcaaadef




More than one argument
======================


With \ **--xargs**\  GNU \ **parallel**\  will fit as many arguments as possible on a
single line:


.. code-block:: perl

   cat num30000 | parallel --xargs echo | wc -l


Output (if you run this under Bash on GNU/Linux):


.. code-block:: perl

   2


The 30000 arguments fitted on 2 lines.

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:


.. code-block:: perl

   cat num30000 | parallel --xargs -s 10000 echo | wc -l


Output:


.. code-block:: perl

   17


For better parallelism GNU \ **parallel**\  can distribute the arguments
between all the parallel jobs when end of file is met.

Below GNU \ **parallel**\  reads the last argument when generating the second
job. When GNU \ **parallel**\  reads the last argument, it spreads all the
arguments for the second job over 4 jobs instead, as 4 parallel jobs
are requested.

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:


.. code-block:: perl

   cat num30000 | parallel --jobs 4 -m echo | wc -l


Output (if you run this under Bash on GNU/Linux):


.. code-block:: perl

   5


This is even more visible when running 4 jobs with 10 arguments. The
10 arguments are being spread over 4 jobs:


.. code-block:: perl

   parallel --jobs 4 -m echo ::: 1 2 3 4 5 6 7 8 9 10


Output:


.. code-block:: perl

   1 2 3
   4 5 6
   7 8 9
   10


A replacement string can be part of a word. \ **-m**\  will not repeat the context:


.. code-block:: perl

   parallel --jobs 4 -m echo pre-{}-post ::: A B C D E F G


Output (the order may be different):


.. code-block:: perl

   pre-A B-post
   pre-C D-post
   pre-E F-post
   pre-G-post


To repeat the context use \ **-X**\  which otherwise works like \ **-m**\ :


.. code-block:: perl

   parallel --jobs 4 -X echo pre-{}-post ::: A B C D E F G


Output (the order may be different):


.. code-block:: perl

   pre-A-post pre-B-post
   pre-C-post pre-D-post
   pre-E-post pre-F-post
   pre-G-post


To limit the number of arguments use \ **-N**\ :


.. code-block:: perl

   parallel -N3 echo ::: A B C D E F G H


Output (the order may be different):


.. code-block:: perl

   A B C
   D E F
   G H


\ **-N**\  also sets the positional replacement strings:


.. code-block:: perl

   parallel -N3 echo 1={1} 2={2} 3={3} ::: A B C D E F G H


Output (the order may be different):


.. code-block:: perl

   1=A 2=B 3=C
   1=D 2=E 3=F
   1=G 2=H 3=


\ **-N0**\  reads 1 argument but inserts none:


.. code-block:: perl

   parallel -N0 echo foo ::: 1 2 3


Output:


.. code-block:: perl

   foo
   foo
   foo



Quoting
=======


Command lines that contain special characters may need to be protected from the shell.

The \ **perl**\  program \ **print "@ARGV\n"**\  basically works like \ **echo**\ .


.. code-block:: perl

   perl -e 'print "@ARGV\n"' A


Output:


.. code-block:: perl

   A


To run that in parallel the command needs to be quoted:


.. code-block:: perl

   parallel perl -e 'print "@ARGV\n"' ::: This wont work


Output:


.. code-block:: perl

   [Nothing]


To quote the command use \ **-q**\ :


.. code-block:: perl

   parallel -q perl -e 'print "@ARGV\n"' ::: This works


Output (the order may be different):


.. code-block:: perl

   This
   works


Or you can quote the critical part using \ **\'**\ :


.. code-block:: perl

   parallel perl -e \''print "@ARGV\n"'\' ::: This works, too


Output (the order may be different):


.. code-block:: perl

   This
   works,
   too


GNU \ **parallel**\  can also \-quote full lines. Simply run this:


.. code-block:: perl

   parallel --shellquote
   Warning: Input is read from the terminal. You either know what you
   Warning: are doing (in which case: YOU ARE AWESOME!) or you forgot
   Warning: ::: or :::: or to pipe data into parallel. If so
   Warning: consider going through the tutorial: man parallel_tutorial
   Warning: Press CTRL-D to exit.
   perl -e 'print "@ARGV\n"'
   [CTRL-D]


Output:


.. code-block:: perl

   perl\ -e\ \'print\ \"@ARGV\\n\"\'


This can then be used as the command:


.. code-block:: perl

   parallel perl\ -e\ \'print\ \"@ARGV\\n\"\' ::: This also works


Output (the order may be different):


.. code-block:: perl

   This
   also
   works



Trimming space
==============


Space can be trimmed on the arguments using \ **--trim**\ :


.. code-block:: perl

   parallel --trim r echo pre-{}-post ::: ' A '


Output:


.. code-block:: perl

   pre- A-post


To trim on the left side:


.. code-block:: perl

   parallel --trim l echo pre-{}-post ::: ' A '


Output:


.. code-block:: perl

   pre-A -post


To trim on the both sides:


.. code-block:: perl

   parallel --trim lr echo pre-{}-post ::: ' A '


Output:


.. code-block:: perl

   pre-A-post



Respecting the shell
====================


This tutorial uses Bash as the shell. GNU \ **parallel**\  respects which
shell you are using, so in \ **zsh**\  you can do:


.. code-block:: perl

   parallel echo \={} ::: zsh bash ls


Output:


.. code-block:: perl

   /usr/bin/zsh
   /bin/bash
   /bin/ls


In \ **csh**\  you can do:


.. code-block:: perl

   parallel 'set a="{}"; if( { test -d "$a" } ) echo "$a is a dir"' ::: *


Output:


.. code-block:: perl

   [somedir] is a dir


This also becomes useful if you use GNU \ **parallel**\  in a shell script:
GNU \ **parallel**\  will use the same shell as the shell script.



**********************
Controlling the output
**********************


The output can prefixed with the argument:


.. code-block:: perl

   parallel --tag echo foo-{} ::: A B C


Output (the order may be different):


.. code-block:: perl

   A       foo-A
   B       foo-B
   C       foo-C


To prefix it with another string use \ **--tagstring**\ :


.. code-block:: perl

   parallel --tagstring {}-bar echo foo-{} ::: A B C


Output (the order may be different):


.. code-block:: perl

   A-bar   foo-A
   B-bar   foo-B
   C-bar   foo-C


To see what commands will be run without running them use \ **--dryrun**\ :


.. code-block:: perl

   parallel --dryrun echo {} ::: A B C


Output (the order may be different):


.. code-block:: perl

   echo A
   echo B
   echo C


To print the command before running them use \ **--verbose**\ :


.. code-block:: perl

   parallel --verbose echo {} ::: A B C


Output (the order may be different):


.. code-block:: perl

   echo A
   echo B
   A
   echo C
   B
   C


GNU \ **parallel**\  will postpone the output until the command completes:


.. code-block:: perl

   parallel -j2 'printf "%s-start\n%s" {} {};
     sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1


Output:


.. code-block:: perl

   2-start
   2-middle
   2-end
   1-start
   1-middle
   1-end
   4-start
   4-middle
   4-end


To get the output immediately use \ **--ungroup**\ :


.. code-block:: perl

   parallel -j2 --ungroup 'printf "%s-start\n%s" {} {};
     sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1


Output:


.. code-block:: perl

   4-start
   42-start
   2-middle
   2-end
   1-start
   1-middle
   1-end
   -middle
   4-end


\ **--ungroup**\  is fast, but can cause half a line from one job to be mixed
with half a line of another job. That has happened in the second line,
where the line '4-middle' is mixed with '2-start'.

To avoid this use \ **--linebuffer**\ :


.. code-block:: perl

   parallel -j2 --linebuffer 'printf "%s-start\n%s" {} {};
     sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1


Output:


.. code-block:: perl

   4-start
   2-start
   2-middle
   2-end
   1-start
   1-middle
   1-end
   4-middle
   4-end


To force the output in the same order as the arguments use \ **--keep-order**\ /\ **-k**\ :


.. code-block:: perl

   parallel -j2 -k 'printf "%s-start\n%s" {} {};
     sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1


Output:


.. code-block:: perl

   4-start
   4-middle
   4-end
   2-start
   2-middle
   2-end
   1-start
   1-middle
   1-end


Saving output into files
========================


GNU \ **parallel**\  can save the output of each job into files:


.. code-block:: perl

   parallel --files echo ::: A B C


Output will be similar to this:


.. code-block:: perl

   /tmp/pAh6uWuQCg.par
   /tmp/opjhZCzAX4.par
   /tmp/W0AT_Rph2o.par


By default GNU \ **parallel**\  will cache the output in files in \ **/tmp**\ . This
can be changed by setting \ **$TMPDIR**\  or \ **--tmpdir**\ :


.. code-block:: perl

   parallel --tmpdir /var/tmp --files echo ::: A B C


Output will be similar to this:


.. code-block:: perl

   /var/tmp/N_vk7phQRc.par
   /var/tmp/7zA4Ccf3wZ.par
   /var/tmp/LIuKgF_2LP.par


Or:


.. code-block:: perl

   TMPDIR=/var/tmp parallel --files echo ::: A B C


Output: Same as above.

The output files can be saved in a structured way using \ **--results**\ :


.. code-block:: perl

   parallel --results outdir echo ::: A B C


Output:


.. code-block:: perl

   A
   B
   C


These files were also generated containing the standard output
(stdout), standard error (stderr), and the sequence number (seq):


.. code-block:: perl

   outdir/1/A/seq
   outdir/1/A/stderr
   outdir/1/A/stdout
   outdir/1/B/seq
   outdir/1/B/stderr
   outdir/1/B/stdout
   outdir/1/C/seq
   outdir/1/C/stderr
   outdir/1/C/stdout


\ **--header :**\  will take the first value as name and use that in the
directory structure. This is useful if you are using multiple input
sources:


.. code-block:: perl

   parallel --header : --results outdir echo ::: f1 A B ::: f2 C D


Generated files:


.. code-block:: perl

   outdir/f1/A/f2/C/seq
   outdir/f1/A/f2/C/stderr
   outdir/f1/A/f2/C/stdout
   outdir/f1/A/f2/D/seq
   outdir/f1/A/f2/D/stderr
   outdir/f1/A/f2/D/stdout
   outdir/f1/B/f2/C/seq
   outdir/f1/B/f2/C/stderr
   outdir/f1/B/f2/C/stdout
   outdir/f1/B/f2/D/seq
   outdir/f1/B/f2/D/stderr
   outdir/f1/B/f2/D/stdout


The directories are named after the variables and their values.



*************************
Controlling the execution
*************************


Number of simultaneous jobs
===========================


The number of concurrent jobs is given with \ **--jobs**\ /\ **-j**\ :


.. code-block:: perl

   /usr/bin/time parallel -N0 -j64 sleep 1 :::: num128


With 64 jobs in parallel the 128 \ **sleep**\ s will take 2-8 seconds to run -
depending on how fast your machine is.

By default \ **--jobs**\  is the same as the number of CPU cores. So this:


.. code-block:: perl

   /usr/bin/time parallel -N0 sleep 1 :::: num128


should take twice the time of running 2 jobs per CPU core:


.. code-block:: perl

   /usr/bin/time parallel -N0 --jobs 200% sleep 1 :::: num128


\ **--jobs 0**\  will run as many jobs in parallel as possible:


.. code-block:: perl

   /usr/bin/time parallel -N0 --jobs 0 sleep 1 :::: num128


which should take 1-7 seconds depending on how fast your machine is.

\ **--jobs**\  can read from a file which is re-read when a job finishes:


.. code-block:: perl

   echo 50% > my_jobs
   /usr/bin/time parallel -N0 --jobs my_jobs sleep 1 :::: num128 &
   sleep 1
   echo 0 > my_jobs
   wait


The first second only 50% of the CPU cores will run a job. Then \ **0**\  is
put into \ **my_jobs**\  and then the rest of the jobs will be started in
parallel.

Instead of basing the percentage on the number of CPU cores
GNU \ **parallel**\  can base it on the number of CPUs:


.. code-block:: perl

   parallel --use-cpus-instead-of-cores -N0 sleep 1 :::: num8



Shuffle job order
=================


If you have many jobs (e.g. by multiple combinations of input
sources), it can be handy to shuffle the jobs, so you get different
values run. Use \ **--shuf**\  for that:


.. code-block:: perl

   parallel --shuf echo ::: 1 2 3 ::: a b c ::: A B C


Output:


.. code-block:: perl

   All combinations but different order for each run.



Interactivity
=============


GNU \ **parallel**\  can ask the user if a command should be run using \ **--interactive**\ :


.. code-block:: perl

   parallel --interactive echo ::: 1 2 3


Output:


.. code-block:: perl

   echo 1 ?...y
   echo 2 ?...n
   1
   echo 3 ?...y
   3


GNU \ **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:


.. code-block:: perl

   parallel --tty emacs ::: 1 2 3


Or give multiple argument in one go to open multiple files:


.. code-block:: perl

   parallel -X --tty vi ::: 1 2 3



A terminal for every job
========================


Using \ **--tmux**\  GNU \ **parallel**\  can start a terminal for every job run:


.. code-block:: perl

   seq 10 20 | parallel --tmux 'echo start {}; sleep {}; echo done {}'


This will tell you to run something similar to:


.. code-block:: perl

   tmux -S /tmp/tmsrPrO0 attach


Using normal \ **tmux**\  keystrokes (CTRL-b n or CTRL-b p) you can cycle
between windows of the running jobs. When a job is finished it will
pause for 10 seconds before closing the window.


Timing
======


Some jobs do heavy I/O when they start. To avoid a thundering herd GNU
\ **parallel**\  can delay starting new jobs. \ **--delay**\  \ *X*\  will make
sure there is at least \ *X*\  seconds between each start:


.. code-block:: perl

   parallel --delay 2.5 echo Starting {}\;date ::: 1 2 3


Output:


.. code-block:: perl

   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


If jobs taking more than a certain amount of time are known to fail,
they can be stopped with \ **--timeout**\ . The accuracy of \ **--timeout**\  is
2 seconds:


.. code-block:: perl

   parallel --timeout 4.1 sleep {}\; echo {} ::: 2 4 6 8


Output:


.. code-block:: perl

   2
   4


GNU \ **parallel**\  can compute the median runtime for jobs and kill those
that take more than 200% of the median runtime:


.. code-block:: perl

   parallel --timeout 200% sleep {}\; echo {} ::: 2.1 2.2 3 7 2.3


Output:


.. code-block:: perl

   2.1
   2.2
   3
   2.3



Progress information
====================


Based on the runtime of completed jobs GNU \ **parallel**\  can estimate the
total runtime:


.. code-block:: perl

   parallel --eta sleep ::: 1 3 2 2 1 3 3 2 1


Output:


.. code-block:: perl

   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


GNU \ **parallel**\  can give progress information with \ **--progress**\ :


.. code-block:: perl

   parallel --progress sleep ::: 1 3 2 2 1 3 3 2 1


Output:


.. code-block:: perl

   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


A progress bar can be shown with \ **--bar**\ :


.. code-block:: perl

   parallel --bar sleep ::: 1 3 2 2 1 3 3 2 1


And a graphic bar can be shown with \ **--bar**\  and \ **zenity**\ :


.. code-block:: perl

   seq 1000 | parallel -j10 --bar '(echo -n {};sleep 0.1)' \
     2> >(perl -pe 'BEGIN{$/="\r";$|=1};s/\r/\n/g' |
          zenity --progress --auto-kill --auto-close)


A logfile of the jobs completed so far can be generated with \ **--joblog**\ :


.. code-block:: perl

   parallel --joblog /tmp/log exit  ::: 1 2 3 0
   cat /tmp/log


Output:


.. code-block:: perl

   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


The log contains the job sequence, which host the job was run on, the
start time and run time, how much data was transferred, the exit
value, the signal that killed the job, and finally the command being
run.

With a joblog GNU \ **parallel**\  can be stopped and later pickup where it
left off. It it important that the input of the completed jobs is
unchanged.


.. code-block:: perl

   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


Output:


.. code-block:: perl

   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


Note how the start time of the last 2 jobs is clearly different from the second run.

With \ **--resume-failed**\  GNU \ **parallel**\  will re-run the jobs that failed:


.. code-block:: perl

   parallel --resume-failed --joblog /tmp/log exit  ::: 1 2 3 0 0 0
   cat /tmp/log


Output:


.. code-block:: perl

   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


Note how seq 1 2 3 have been repeated because they had exit value
different from 0.

\ **--retry-failed**\  does almost the same as \ **--resume-failed**\ . Where
\ **--resume-failed**\  reads the commands from the command line (and
ignores the commands in the joblog), \ **--retry-failed**\  ignores the
command line and reruns the commands mentioned in the joblog.


.. code-block:: perl

   parallel --retry-failed --joblog /tmp/log
   cat /tmp/log


Output:


.. code-block:: perl

   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
   1   :    1376580164.633 0.010   0    0       1       0      exit 1
   2   :    1376580164.644 0.022   0    0       2       0      exit 2
   3   :    1376580164.666 0.005   0    0       3       0      exit 3



Termination
===========


Unconditional termination
-------------------------


By default GNU \ **parallel**\  will wait for all jobs to finish before exiting.

If you send GNU \ **parallel**\  the \ **TERM**\  signal, GNU \ **parallel**\  will
stop spawning new jobs and wait for the remaining jobs to finish. If
you send GNU \ **parallel**\  the \ **TERM**\  signal again, GNU \ **parallel**\
will kill all running jobs and exit.


Termination dependent on job status
-----------------------------------


For certain jobs there is no need to continue if one of the jobs fails
and has an exit code different from 0. GNU \ **parallel**\  will stop spawning new jobs
with \ **--halt soon,fail=1**\ :


.. code-block:: perl

   parallel -j2 --halt soon,fail=1 echo {}\; exit {} ::: 0 0 1 2 3


Output:


.. code-block:: perl

   0
   0
   1
   parallel: This job failed:
   echo 1; exit 1
   parallel: Starting no more jobs. Waiting for 1 jobs to finish.
   2


With \ **--halt now,fail=1**\  the running jobs will be killed immediately:


.. code-block:: perl

   parallel -j2 --halt now,fail=1 echo {}\; exit {} ::: 0 0 1 2 3


Output:


.. code-block:: perl

   0
   0
   1
   parallel: This job failed:
   echo 1; exit 1


If \ **--halt**\  is given a percentage this percentage of the jobs must fail
before GNU \ **parallel**\  stops spawning more jobs:


.. code-block:: perl

   parallel -j2 --halt soon,fail=20% echo {}\; exit {} \
     ::: 0 1 2 3 4 5 6 7 8 9


Output:


.. code-block:: perl

   0
   1
   parallel: This job failed:
   echo 1; exit 1
   2
   parallel: This job failed:
   echo 2; exit 2
   parallel: Starting no more jobs. Waiting for 1 jobs to finish.
   3
   parallel: This job failed:
   echo 3; exit 3


If you are looking for success instead of failures, you can use
\ **success**\ . This will finish as soon as the first job succeeds:


.. code-block:: perl

   parallel -j2 --halt now,success=1 echo {}\; exit {} ::: 1 2 3 0 4 5 6


Output:


.. code-block:: perl

   1
   2
   3
   0
   parallel: This job succeeded:
   echo 0; exit 0


GNU \ **parallel**\  can retry the command with \ **--retries**\ . This is useful if a
command fails for unknown reasons now and then.


.. code-block:: perl

   parallel -k --retries 3 \
     'echo tried {} >>/tmp/runs; echo completed {}; exit {}' ::: 1 2 0
   cat /tmp/runs


Output:


.. code-block:: perl

   completed 1
   completed 2
   completed 0

   tried 1
   tried 2
   tried 1
   tried 2
   tried 1
   tried 2
   tried 0


Note how job 1 and 2 were tried 3 times, but 0 was not retried because it had exit code 0.


Termination signals (advanced)
------------------------------


Using \ **--termseq**\  you can control which signals are sent when killing
children. Normally children will be killed by sending them \ **SIGTERM**\ ,
waiting 200 ms, then another \ **SIGTERM**\ , waiting 100 ms, then another
\ **SIGTERM**\ , waiting 50 ms, then a \ **SIGKILL**\ , finally waiting 25 ms
before giving up. It looks like this:


.. code-block:: perl

   show_signals() {
     perl -e 'for(keys %SIG) {
         $SIG{$_} = eval "sub { print \"Got $_\\n\"; }";
       }
       while(1){sleep 1}'
   }
   export -f show_signals
   echo | parallel --termseq TERM,200,TERM,100,TERM,50,KILL,25 \
     -u --timeout 1 show_signals


Output:


.. code-block:: perl

   Got TERM
   Got TERM
   Got TERM


Or just:


.. code-block:: perl

   echo | parallel -u --timeout 1 show_signals


Output: Same as above.

You can change this to \ **SIGINT**\ , \ **SIGTERM**\ , \ **SIGKILL**\ :


.. code-block:: perl

   echo | parallel --termseq INT,200,TERM,100,KILL,25 \
     -u --timeout 1 show_signals


Output:


.. code-block:: perl

   Got INT
   Got TERM


The \ **SIGKILL**\  does not show because it cannot be caught, and thus the
child dies.



Limiting the resources
======================


To avoid overloading systems GNU \ **parallel**\  can look at the system load
before starting another job:


.. code-block:: perl

   parallel --load 100% echo load is less than {} job per cpu ::: 1


Output:


.. code-block:: perl

   [when then load is less than the number of cpu cores]
   load is less than 1 job per cpu


GNU \ **parallel**\  can also check if the system is swapping.


.. code-block:: perl

   parallel --noswap echo the system is not swapping ::: now


Output:


.. code-block:: perl

   [when then system is not swapping]
   the system is not swapping now


Some jobs need a lot of memory, and should only be started when there
is enough memory free. Using \ **--memfree**\  GNU \ **parallel**\  can check if
there is enough memory free. Additionally, GNU \ **parallel**\  will kill
off the youngest job if the memory free falls below 50% of the
size. The killed job will put back on the queue and retried later.


.. code-block:: perl

   parallel --memfree 1G echo will run if more than 1 GB is ::: free


GNU \ **parallel**\  can run the jobs with a nice value. This will work both
locally and remotely.


.. code-block:: perl

   parallel --nice 17 echo this is being run with nice -n ::: 17


Output:


.. code-block:: perl

   this is being run with nice -n 17




****************
Remote execution
****************


GNU \ **parallel**\  can run jobs on remote servers. It uses \ **ssh**\  to
communicate with the remote machines.

Sshlogin
========


The most basic sshlogin is \ **-S**\  \ *host*\ :


.. code-block:: perl

   parallel -S $SERVER1 echo running on ::: $SERVER1


Output:


.. code-block:: perl

   running on [$SERVER1]


To use a different username prepend the server with \ *username@*\ :


.. code-block:: perl

   parallel -S username@$SERVER1 echo running on ::: username@$SERVER1


Output:


.. code-block:: perl

   running on [username@$SERVER1]


The special sshlogin \ **:**\  is the local machine:


.. code-block:: perl

   parallel -S : echo running on ::: the_local_machine


Output:


.. code-block:: perl

   running on the_local_machine


If \ **ssh**\  is not in $PATH it can be prepended to $SERVER1:


.. code-block:: perl

   parallel -S '/usr/bin/ssh '$SERVER1 echo custom ::: ssh


Output:


.. code-block:: perl

   custom ssh


The \ **ssh**\  command can also be given using \ **--ssh**\ :


.. code-block:: perl

   parallel --ssh /usr/bin/ssh -S $SERVER1 echo custom ::: ssh


or by setting \ **$PARALLEL_SSH**\ :


.. code-block:: perl

   export PARALLEL_SSH=/usr/bin/ssh
   parallel -S $SERVER1 echo custom ::: ssh


Several servers can be given using multiple \ **-S**\ :


.. code-block:: perl

   parallel -S $SERVER1 -S $SERVER2 echo ::: running on more hosts


Output (the order may be different):


.. code-block:: perl

   running
   on
   more
   hosts


Or they can be separated by \ **,**\ :


.. code-block:: perl

   parallel -S $SERVER1,$SERVER2 echo ::: running on more hosts


Output: Same as above.

Or newline:


.. code-block:: perl

   # This gives a \n between $SERVER1 and $SERVER2
   SERVERS="`echo $SERVER1; echo $SERVER2`"
   parallel -S "$SERVERS" echo ::: running on more hosts


They can also be read from a file (replace \ *user@*\  with the user on \ **$SERVER2**\ ):


.. code-block:: perl

   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


Output: Same as above.

Every time a job finished, the \ **--sshloginfile**\  will be re-read, so
it is possible to both add and remove hosts while running.

The special \ **--sshloginfile ..**\  reads from \ **~/.parallel/sshloginfile**\ .

To force GNU \ **parallel**\  to treat a server having a given number of CPU
cores prepend the number of core followed by \ **/**\  to the sshlogin:


.. code-block:: perl

   parallel -S 4/$SERVER1 echo force {} cpus on server ::: 4


Output:


.. code-block:: perl

   force 4 cpus on server


Servers can be put into groups by prepending \ *@groupname*\  to the
server and the group can then be selected by appending \ *@groupname*\  to
the argument if using \ **--hostgroup**\ :


.. code-block:: perl

   parallel --hostgroup -S @grp1/$SERVER1 -S @grp2/$SERVER2 echo {} \
     ::: run_on_grp1@grp1 run_on_grp2@grp2


Output:


.. code-block:: perl

   run_on_grp1
   run_on_grp2


A host can be in multiple groups by separating the groups with \ **+**\ , and
you can force GNU \ **parallel**\  to limit the groups on which the command
can be run with \ **-S**\  \ *@groupname*\ :


.. code-block:: perl

   parallel -S @grp1 -S @grp1+grp2/$SERVER1 -S @grp2/SERVER2 echo {} \
     ::: run_on_grp1 also_grp1


Output:


.. code-block:: perl

   run_on_grp1
   also_grp1



Transferring files
==================


GNU \ **parallel**\  can transfer the files to be processed to the remote
host. It does that using rsync.


.. code-block:: perl

   echo This is input_file > input_file
   parallel -S $SERVER1 --transferfile {} cat ::: input_file


Output:


.. code-block:: perl

   This is input_file


If the files are processed into another file, the resulting file can be
transferred back:


.. code-block:: perl

   echo This is input_file > input_file
   parallel -S $SERVER1 --transferfile {} --return {}.out \
     cat {} ">"{}.out ::: input_file
   cat input_file.out


Output: Same as above.

To remove the input and output file on the remote server use \ **--cleanup**\ :


.. code-block:: perl

   echo This is input_file > input_file
   parallel -S $SERVER1 --transferfile {} --return {}.out --cleanup \
     cat {} ">"{}.out ::: input_file
   cat input_file.out


Output: Same as above.

There is a shorthand for \ **--transferfile {} --return --cleanup**\  called \ **--trc**\ :


.. code-block:: perl

   echo This is input_file > input_file
   parallel -S $SERVER1 --trc {}.out cat {} ">"{}.out ::: input_file
   cat input_file.out


Output: Same as above.

Some jobs need a common database for all jobs. GNU \ **parallel**\  can
transfer that using \ **--basefile**\  which will transfer the file before the
first job:


.. code-block:: perl

   echo common data > common_file
   parallel --basefile common_file -S $SERVER1 \
     cat common_file\; echo {} ::: foo


Output:


.. code-block:: perl

   common data
   foo


To remove it from the remote host after the last job use \ **--cleanup**\ .


Working dir
===========


The default working dir on the remote machines is the login dir. This
can be changed with \ **--workdir**\  \ *mydir*\ .

Files transferred using \ **--transferfile**\  and \ **--return**\  will be relative
to \ *mydir*\  on remote computers, and the command will be executed in
the dir \ *mydir*\ .

The special \ *mydir*\  value \ **...**\  will create working dirs under
\ **~/.parallel/tmp**\  on the remote computers. If \ **--cleanup**\  is given
these dirs will be removed.

The special \ *mydir*\  value \ **.**\  uses the current working dir.  If the
current working dir is beneath your home dir, the value \ **.**\  is
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.


.. code-block:: perl

   parallel -S $SERVER1 pwd ::: ""
   parallel --workdir . -S $SERVER1 pwd ::: ""
   parallel --workdir ... -S $SERVER1 pwd ::: ""


Output:


.. code-block:: perl

   [the login dir on $SERVER1]
   [current dir relative on $SERVER1]
   [a dir in ~/.parallel/tmp/...]



Avoid overloading sshd
======================


If many jobs are started on the same server, \ **sshd**\  can be
overloaded. GNU \ **parallel**\  can insert a delay between each job run on
the same server:


.. code-block:: perl

   parallel -S $SERVER1 --sshdelay 0.2 echo ::: 1 2 3


Output (the order may be different):


.. code-block:: perl

   1
   2
   3


\ **sshd**\  will be less overloaded if using \ **--controlmaster**\ , which will
multiplex ssh connections:


.. code-block:: perl

   parallel --controlmaster -S $SERVER1 echo ::: 1 2 3


Output: Same as above.


Ignore hosts that are down
==========================


In clusters with many hosts a few of them are often down. GNU \ **parallel**\
can ignore those hosts. In this case the host 173.194.32.46 is down:


.. code-block:: perl

   parallel --filter-hosts -S 173.194.32.46,$SERVER1 echo ::: bar


Output:


.. code-block:: perl

   bar



Running the same commands on all hosts
======================================


GNU \ **parallel**\  can run the same command on all the hosts:


.. code-block:: perl

   parallel --onall -S $SERVER1,$SERVER2 echo ::: foo bar


Output (the order may be different):


.. code-block:: perl

   foo
   bar
   foo
   bar


Often you will just want to run a single command on all hosts with out
arguments. \ **--nonall**\  is a no argument \ **--onall**\ :


.. code-block:: perl

   parallel --nonall -S $SERVER1,$SERVER2 echo foo bar


Output:


.. code-block:: perl

   foo bar
   foo bar


When \ **--tag**\  is used with \ **--nonall**\  and \ **--onall**\  the \ **--tagstring**\  is the host:


.. code-block:: perl

   parallel --nonall --tag -S $SERVER1,$SERVER2 echo foo bar


Output (the order may be different):


.. code-block:: perl

   $SERVER1 foo bar
   $SERVER2 foo bar


\ **--jobs**\  sets the number of servers to log in to in parallel.


Transferring environment variables and functions
================================================


\ **env_parallel**\  is a shell function that transfers all aliases,
functions, variables, and arrays. You active it by running:


.. code-block:: perl

   source `which env_parallel.bash`


Replace \ **bash**\  with the shell you use.

Now you can use \ **env_parallel**\  instead of \ **parallel**\  and still have
your environment:


.. code-block:: perl

   alias myecho=echo
   myvar="Joe's var is"
   env_parallel -S $SERVER1 'myecho $myvar' ::: green


Output:


.. code-block:: perl

   Joe's var is green


The disadvantage is that if your environment is huge \ **env_parallel**\
will fail.

When \ **env_parallel**\  fails, you can still use \ **--env**\  to tell GNU
\ **parallel**\  to transfer an environment variable to the remote system.


.. code-block:: perl

   MYVAR='foo bar'
   export MYVAR
   parallel --env MYVAR -S $SERVER1 echo '$MYVAR' ::: baz


Output:


.. code-block:: perl

   foo bar baz


This works for functions, too, if your shell is Bash:


.. code-block:: perl

   # This only works in Bash
   my_func() {
     echo in my_func $1
   }
   export -f my_func
   parallel --env my_func -S $SERVER1 my_func ::: baz


Output:


.. code-block:: perl

   in my_func baz


GNU \ **parallel**\  can copy all user defined variables and functions to
the remote system. It just needs to record which ones to ignore in
\ **~/.parallel/ignored_vars**\ . Do that by running this once:


.. code-block:: perl

   parallel --record-env
   cat ~/.parallel/ignored_vars


Output:


.. code-block:: perl

   [list of variables to ignore - including $PATH and $HOME]


Now all other variables and functions defined will be copied when
using \ **--env _**\ .


.. code-block:: perl

   # The function is only copied if using Bash
   my_func2() {
     echo in my_func2 $VAR $1
   }
   export -f my_func2
   VAR=foo
   export VAR

   parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar


Output:


.. code-block:: perl

   foo
   in my_func2 foo bar


If you use \ **env_parallel**\  the variables, functions, and aliases do
not even need to be exported to be copied:


.. code-block:: perl

   NOT='not exported var'
   alias myecho=echo
   not_ex() {
     myecho in not_exported_func $NOT $1
   }
   env_parallel --env _ -S $SERVER1 'echo $NOT; not_ex' ::: bar


Output:


.. code-block:: perl

   not exported var
   in not_exported_func not exported var bar



Showing what is actually run
============================


\ **--verbose**\  will show the command that would be run on the local
machine.

When using \ **--cat**\ , \ **--pipepart**\ , or when a job is run on a remote
machine, the command is wrapped with helper scripts. \ **-vv**\  shows all
of this.


.. code-block:: perl

   parallel -vv --pipepart --block 1M wc :::: num30000


Output:


.. code-block:: perl

   <num30000 perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die;
   $left = shift; while($read = sysread(STDIN,$buf, ($left > 131072
   ? 131072 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }'
   0 0 0 168894 | (wc)
     30000   30000  168894


When the command gets more complex, the output is so hard to read,
that it is only useful for debugging:


.. code-block:: perl

   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


Output will be similar to:


.. code-block:: perl

   ( ssh server -- mkdir -p ./.parallel/tmp/aspire-1928520-1;rsync
   --protocol 30 -rlDzR -essh ./abc-file
   server:./.parallel/tmp/aspire-1928520-1 );ssh server -- exec perl -e
   \''@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64");
   eval"@GNU_Parallel";my$eval=decode_base64(join"",@ARGV);eval$eval;'\'
   c3lzdGVtKCJta2RpciIsIi1wIiwiLS0iLCIucGFyYWxsZWwvdG1wL2FzcGlyZS0xOTI4N
   TsgY2hkaXIgIi5wYXJhbGxlbC90bXAvYXNwaXJlLTE5Mjg1MjAtMSIgfHxwcmludChTVE
   BhcmFsbGVsOiBDYW5ub3QgY2hkaXIgdG8gLnBhcmFsbGVsL3RtcC9hc3BpcmUtMTkyODU
   iKSAmJiBleGl0IDI1NTskRU5WeyJPTERQV0QifT0iL2hvbWUvdGFuZ2UvcHJpdmF0L3Bh
   IjskRU5WeyJQQVJBTExFTF9QSUQifT0iMTkyODUyMCI7JEVOVnsiUEFSQUxMRUxfU0VRI
   0BiYXNoX2Z1bmN0aW9ucz1xdyhteV9mdW5jMyk7IGlmKCRFTlZ7IlNIRUxMIn09fi9jc2
   ByaW50IFNUREVSUiAiQ1NIL1RDU0ggRE8gTk9UIFNVUFBPUlQgbmV3bGluZXMgSU4gVkF
   TL0ZVTkNUSU9OUy4gVW5zZXQgQGJhc2hfZnVuY3Rpb25zXG4iOyBleGVjICJmYWxzZSI7
   YXNoZnVuYyA9ICJteV9mdW5jMygpIHsgIGVjaG8gaW4gbXlfZnVuYyBcJDEgPiBcJDEub
   Xhwb3J0IC1mIG15X2Z1bmMzID4vZGV2L251bGw7IjtAQVJHVj0ibXlfZnVuYzMgYWJjLW
   RzaGVsbD0iJEVOVntTSEVMTH0iOyR0bXBkaXI9Ii90bXAiOyRuaWNlPTE3O2RveyRFTlZ
   MRUxfVE1QfT0kdG1wZGlyLiIvcGFyIi5qb2luIiIsbWFweygwLi45LCJhIi4uInoiLCJB
   KVtyYW5kKDYyKV19KDEuLjUpO313aGlsZSgtZSRFTlZ7UEFSQUxMRUxfVE1QfSk7JFNJ
   fT1zdWJ7JGRvbmU9MTt9OyRwaWQ9Zm9yazt1bmxlc3MoJHBpZCl7c2V0cGdycDtldmFse
   W9yaXR5KDAsMCwkbmljZSl9O2V4ZWMkc2hlbGwsIi1jIiwoJGJhc2hmdW5jLiJAQVJHVi
   JleGVjOiQhXG4iO31kb3skcz0kczwxPzAuMDAxKyRzKjEuMDM6JHM7c2VsZWN0KHVuZGV
   mLHVuZGVmLCRzKTt9dW50aWwoJGRvbmV8fGdldHBwaWQ9PTEpO2tpbGwoU0lHSFVQLC0k
   dW5sZXNzJGRvbmU7d2FpdDtleGl0KCQ/JjEyNz8xMjgrKCQ/JjEyNyk6MSskPz4+OCk=;
   _EXIT_status=$?; mkdir -p ./.; rsync --protocol 30 --rsync-path=cd\
   ./.parallel/tmp/aspire-1928520-1/./.\;\ rsync -rlDzR -essh
   server:./abc-file.out ./.;ssh server -- \(rm\ -f\
   ./.parallel/tmp/aspire-1928520-1/abc-file\;\ sh\ -c\ \'rmdir\
   ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\ ./.parallel/\
   2\>/dev/null\'\;rm\ -rf\ ./.parallel/tmp/aspire-1928520-1\;\);ssh
   server -- \(rm\ -f\ ./.parallel/tmp/aspire-1928520-1/abc-file.out\;\
   sh\ -c\ \'rmdir\ ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\
   ./.parallel/\ 2\>/dev/null\'\;rm\ -rf\
   ./.parallel/tmp/aspire-1928520-1\;\);ssh server -- rm -rf
   .parallel/tmp/aspire-1928520-1; exit $_EXIT_status;




*******************************************
Saving output to shell variables (advanced)
*******************************************


GNU \ **parset**\  will set shell variables to the output of GNU
\ **parallel**\ . GNU \ **parset**\  has one important limitation: It cannot be
part of a pipe. In particular this means it cannot read anything from
standard input (stdin) or pipe output to another program.

To use GNU \ **parset**\  prepend command with destination variables:


.. code-block:: perl

   parset myvar1,myvar2 echo ::: a b
   echo $myvar1
   echo $myvar2


Output:


.. code-block:: perl

   a
   b


If you only give a single variable, it will be treated as an array:


.. code-block:: perl

   parset myarray seq {} 5 ::: 1 2 3
   echo "${myarray[1]}"


Output:


.. code-block:: perl

   2
   3
   4
   5


The commands to run can be an array:


.. code-block:: perl

   cmd=("echo '<<joe  \"double  space\"  cartoon>>'" "pwd")
   parset data ::: "${cmd[@]}"
   echo "${data[0]}"
   echo "${data[1]}"


Output:


.. code-block:: perl

   <<joe  "double  space"  cartoon>>
   [current dir]



********************************
Saving to an SQL base (advanced)
********************************


GNU \ **parallel**\  can save into an SQL base. Point GNU \ **parallel**\  to a
table and it will put the joblog there together with the variables and
the output each in their own column.

CSV as SQL base
===============


The simplest is to use a CSV file as the storage table:


.. code-block:: perl

   parallel --sqlandworker csv:///%2Ftmp/log.csv \
     seq ::: 10 ::: 12 13 14
   cat /tmp/log.csv


Note how '/' in the path must be written as %2F.

Output will be similar to:


.. code-block:: perl

   Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
     Command,V1,V2,Stdout,Stderr
   1,:,1458254498.254,0.069,0,9,0,0,"seq 10 12",10,12,"10
   11
   12
   ",
   2,:,1458254498.278,0.080,0,12,0,0,"seq 10 13",10,13,"10
   11
   12
   13
   ",
   3,:,1458254498.301,0.083,0,15,0,0,"seq 10 14",10,14,"10
   11
   12
   13
   14
   ",


A proper CSV reader (like LibreOffice or R's read.csv) will read this
format correctly - even with fields containing newlines as above.

If the output is big you may want to put it into files using \ **--results**\ :


.. code-block:: perl

   parallel --results outdir --sqlandworker csv:///%2Ftmp/log2.csv \
     seq ::: 10 ::: 12 13 14
   cat /tmp/log2.csv


Output will be similar to:


.. code-block:: perl

   Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
     Command,V1,V2,Stdout,Stderr
   1,:,1458824738.287,0.029,0,9,0,0,
     "seq 10 12",10,12,outdir/1/10/2/12/stdout,outdir/1/10/2/12/stderr
   2,:,1458824738.298,0.025,0,12,0,0,
     "seq 10 13",10,13,outdir/1/10/2/13/stdout,outdir/1/10/2/13/stderr
   3,:,1458824738.309,0.026,0,15,0,0,
     "seq 10 14",10,14,outdir/1/10/2/14/stdout,outdir/1/10/2/14/stderr



DBURL as table
==============


The CSV file is an example of a DBURL.

GNU \ **parallel**\  uses a DBURL to address the table. A DBURL has this format:


.. code-block:: perl

   vendor://[[user][:password]@][host][:port]/[database[/table]


Example:


.. code-block:: perl

   mysql://scott:tiger@my.example.com/mydatabase/mytable
   postgresql://scott:tiger@pg.example.com/mydatabase/mytable
   sqlite3:///%2Ftmp%2Fmydatabase/mytable
   csv:///%2Ftmp/log.csv


To refer to \ **/tmp/mydatabase**\  with \ **sqlite**\  or \ **csv**\  you need to
encode the \ **/**\  as \ **%2F**\ .

Run a job using \ **sqlite**\  on \ **mytable**\  in \ **/tmp/mydatabase**\ :


.. code-block:: perl

   DBURL=sqlite3:///%2Ftmp%2Fmydatabase
   DBURLTABLE=$DBURL/mytable
   parallel --sqlandworker $DBURLTABLE echo ::: foo bar ::: baz quuz


To see the result:


.. code-block:: perl

   sql $DBURL 'SELECT * FROM mytable ORDER BY Seq;'


Output will be similar to:


.. code-block:: perl

   Seq|Host|Starttime|JobRuntime|Send|Receive|Exitval|_Signal|
     Command|V1|V2|Stdout|Stderr
   1|:|1451619638.903|0.806||8|0|0|echo foo baz|foo|baz|foo baz
   |
   2|:|1451619639.265|1.54||9|0|0|echo foo quuz|foo|quuz|foo quuz
   |
   3|:|1451619640.378|1.43||8|0|0|echo bar baz|bar|baz|bar baz
   |
   4|:|1451619641.473|0.958||9|0|0|echo bar quuz|bar|quuz|bar quuz
   |


The first columns are well known from \ **--joblog**\ . \ **V1**\  and \ **V2**\  are
data from the input sources. \ **Stdout**\  and \ **Stderr**\  are standard
output and standard error, respectively.


Using multiple workers
======================


Using an SQL base as storage costs overhead in the order of 1 second
per job.

One of the situations where it makes sense is if you have multiple
workers.

You can then have a single master machine that submits jobs to the SQL
base (but does not do any of the work):


.. code-block:: perl

   parallel --sqlmaster $DBURLTABLE echo ::: foo bar ::: baz quuz


On the worker machines you run exactly the same command except you
replace \ **--sqlmaster**\  with \ **--sqlworker**\ .


.. code-block:: perl

   parallel --sqlworker $DBURLTABLE echo ::: foo bar ::: baz quuz


To run a master and a worker on the same machine use \ **--sqlandworker**\
as shown earlier.



******
--pipe
******


The \ **--pipe**\  functionality puts GNU \ **parallel**\  in a different mode:
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.

The typical situation is:


.. code-block:: perl

   command_A | command_B | command_C


where command_B is slow, and you want to speed up command_B.

Chunk size
==========


By default GNU \ **parallel**\  will start an instance of command_B, read a
chunk of 1 MB, and pass that to the instance. Then start another
instance, read another chunk, and pass that to the second instance.


.. code-block:: perl

   cat num1000000 | parallel --pipe wc


Output (the order may be different):


.. code-block:: perl

   165668  165668 1048571
   149797  149797 1048579
   149796  149796 1048572
   149797  149797 1048579
   149797  149797 1048579
   149796  149796 1048572
    85349   85349  597444


The size of the chunk is not exactly 1 MB because GNU \ **parallel**\  only
passes full lines - never half a line, thus the blocksize is only
1 MB on average. You can change the block size to 2 MB with \ **--block**\ :


.. code-block:: perl

   cat num1000000 | parallel --pipe --block 2M wc


Output (the order may be different):


.. code-block:: perl

   315465  315465 2097150
   299593  299593 2097151
   299593  299593 2097151
    85349   85349  597444


GNU \ **parallel**\  treats each line as a record. If the order of records
is unimportant (e.g. you need all lines processed, but you do not care
which is processed first), then you can use \ **--roundrobin**\ . Without
\ **--roundrobin**\  GNU \ **parallel**\  will start a command per block; with
\ **--roundrobin**\  only the requested number of jobs will be started
(\ **--jobs**\ ). The records will then be distributed between the running
jobs:


.. code-block:: perl

   cat num1000000 | parallel --pipe -j4 --roundrobin wc


Output will be similar to:


.. code-block:: perl

   149797  149797 1048579
   299593  299593 2097151
   315465  315465 2097150
   235145  235145 1646016


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.


Records
=======


GNU \ **parallel**\  sees the input as records. The default record is a single
line.

Using \ **-N140000**\  GNU \ **parallel**\  will read 140000 records at a time:


.. code-block:: perl

   cat num1000000 | parallel --pipe -N140000 wc


Output (the order may be different):


.. code-block:: perl

   140000  140000  868895
   140000  140000  980000
   140000  140000  980000
   140000  140000  980000
   140000  140000  980000
   140000  140000  980000
   140000  140000  980000
    20000   20000  140001


Note how that the last job could not get the full 140000 lines, but
only 20000 lines.

If a record is 75 lines \ **-L**\  can be used:


.. code-block:: perl

   cat num1000000 | parallel --pipe -L75 wc


Output (the order may be different):


.. code-block:: perl

   165600  165600 1048095
   149850  149850 1048950
   149775  149775 1048425
   149775  149775 1048425
   149850  149850 1048950
   149775  149775 1048425
    85350   85350  597450
       25      25     176


Note how GNU \ **parallel**\  still reads a block of around 1 MB; 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).


Fixed length records
====================


Fixed length records can be processed by setting \ **--recend ''**\  and
\ **--block \ \*recordsize\*\ **\ . A header of size \ *n*\  can be processed with
\ **--header .{\ \*n\*\ }**\ .

Here is how to process a file with a 4-byte header and a 3-byte record
size:


.. code-block:: perl

   cat fixedlen | parallel --pipe --header .{4} --block 3 --recend '' \
     'echo start; cat; echo'


Output:


.. code-block:: perl

   start
   HHHHAAA
   start
   HHHHCCC
   start
   HHHHBBB


It may be more efficient to increase \ **--block**\  to a multiplum of the
record size.


Record separators
=================


GNU \ **parallel**\  uses separators to determine where two records split.

\ **--recstart**\  gives the string that starts a record; \ **--recend**\  gives the
string that ends a record. The default is \ **--recend '\n'**\  (newline).

If both \ **--recend**\  and \ **--recstart**\  are given, then the record will only
split if the recend string is immediately followed by the recstart
string.

Here the \ **--recend**\  is set to \ **', '**\ :


.. code-block:: perl

   echo /foo, bar/, /baz, qux/, | \
     parallel -kN1 --recend ', ' --pipe echo JOB{#}\;cat\;echo END


Output:


.. code-block:: perl

   JOB1
   /foo, END
   JOB2
   bar/, END
   JOB3
   /baz, END
   JOB4
   qux/,
   END


Here the \ **--recstart**\  is set to \ **/**\ :


.. code-block:: perl

   echo /foo, bar/, /baz, qux/, | \
     parallel -kN1 --recstart / --pipe echo JOB{#}\;cat\;echo END


Output:


.. code-block:: perl

   JOB1
   /foo, barEND
   JOB2
   /, END
   JOB3
   /baz, quxEND
   JOB4
   /,
   END


Here both \ **--recend**\  and \ **--recstart**\  are set:


.. code-block:: perl

   echo /foo, bar/, /baz, qux/, | \
     parallel -kN1 --recend ', ' --recstart / --pipe \
     echo JOB{#}\;cat\;echo END


Output:


.. code-block:: perl

   JOB1
   /foo, bar/, END
   JOB2
   /baz, qux/,
   END


Note the difference between setting one string and setting both strings.

With \ **--regexp**\  the \ **--recend**\  and \ **--recstart**\  will be treated as
a regular expression:


.. code-block:: perl

   echo foo,bar,_baz,__qux, | \
     parallel -kN1 --regexp --recend ,_+ --pipe \
     echo JOB{#}\;cat\;echo END


Output:


.. code-block:: perl

   JOB1
   foo,bar,_END
   JOB2
   baz,__END
   JOB3
   qux,
   END


GNU \ **parallel**\  can remove the record separators with
\ **--remove-rec-sep**\ /\ **--rrs**\ :


.. code-block:: perl

   echo foo,bar,_baz,__qux, | \
     parallel -kN1 --rrs --regexp --recend ,_+ --pipe \
     echo JOB{#}\;cat\;echo END


Output:


.. code-block:: perl

   JOB1
   foo,barEND
   JOB2
   bazEND
   JOB3
   qux,
   END



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
\ **%**\  you can do this:


.. code-block:: perl

   cat num_%header | \
     parallel --header '(%.*\n)*' --pipe -N3 echo JOB{#}\;cat


Output (the order may be different):


.. code-block:: perl

   JOB1
   %head1
   %head2
   1
   2
   3
   JOB2
   %head1
   %head2
   4
   5
   6
   JOB3
   %head1
   %head2
   7
   8
   9
   JOB4
   %head1
   %head2
   10


If the header is 2 lines, \ **--header**\  2 will work:


.. code-block:: perl

   cat num_%header | parallel --header 2 --pipe -N3 echo JOB{#}\;cat


Output: Same as above.


--pipepart
==========


\ **--pipe**\  is not very efficient. It maxes out at around 500
MB/s. \ **--pipepart**\  can easily deliver 5 GB/s. But there are a few
limitations. The input has to be a normal file (not a pipe) given by
\ **-a**\  or \ **::::**\  and \ **-L**\ /\ **-l**\ /\ **-N**\  do not work. \ **--recend**\  and
\ **--recstart**\ , however, \ *do*\  work, and records can often be split on
that alone.


.. code-block:: perl

   parallel --pipepart -a num1000000 --block 3m wc


Output (the order may be different):


.. code-block:: perl

  444443  444444 3000002
  428572  428572 3000004
  126985  126984  888890




*******
Shebang
*******


Input data and parallel command in the same file
================================================


GNU \ **parallel**\  is often called as this:


.. code-block:: perl

   cat input_file | parallel command


With \ **--shebang**\  the \ *input_file*\  and \ **parallel**\  can be combined into the same script.

UNIX shell scripts start with a shebang line like this:


.. code-block:: perl

   #!/bin/bash


GNU \ **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:


.. code-block:: perl

   #!/usr/bin/parallel --shebang -r echo

   foo
   bar
   baz


Output (the order may be different):


.. code-block:: perl

   foo
   bar
   baz



Parallelizing existing scripts
==============================


GNU \ **parallel**\  is often called as this:


.. code-block:: perl

   cat input_file | parallel command
   parallel command ::: foo bar


If \ **command**\  is a script, \ **parallel**\  can be combined into a single
file so this will run the script in parallel:


.. code-block:: perl

   cat input_file | command
   command foo bar


This \ **perl**\  script \ **perl_echo**\  works like \ **echo**\ :


.. code-block:: perl

   #!/usr/bin/perl

   print "@ARGV\n"


It can be called as this:


.. code-block:: perl

   parallel perl_echo ::: foo bar


By changing the \ **#!**\ -line it can be run in parallel:


.. code-block:: perl

   #!/usr/bin/parallel --shebang-wrap /usr/bin/perl

   print "@ARGV\n"


Thus this will work:


.. code-block:: perl

   perl_echo foo bar


Output (the order may be different):


.. code-block:: perl

   foo
   bar


This technique can be used for:


- Perl:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/perl

    print "Arguments @ARGV\n";




- Python:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/python

    import sys
    print 'Arguments', str(sys.argv)




- Bash/sh/zsh/Korn shell:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /bin/bash

    echo Arguments "$@"




- csh:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /bin/csh

    echo Arguments "$argv"




- Tcl:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/tclsh

    puts "Arguments $argv"




- R:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/Rscript --vanilla --slave

    args <- commandArgs(trailingOnly = TRUE)
    print(paste("Arguments ",args))




- GNUplot:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap ARG={} /usr/bin/gnuplot

    print "Arguments ", system('echo $ARG')




- Ruby:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/ruby

    print "Arguments "
    puts ARGV




- Octave:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/octave

    printf ("Arguments");
    arg_list = argv ();
    for i = 1:nargin
      printf (" %s", arg_list{i});
    endfor
    printf ("\n");




- Common LISP:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/clisp

    (format t "~&~S~&" 'Arguments)
    (format t "~&~S~&" *args*)




- PHP:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/php
    <?php
    echo "Arguments";
    foreach(array_slice($argv,1) as $v)
    {
      echo " $v";
    }
    echo "\n";
    ?>




- Node.js:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/node

    var myArgs = process.argv.slice(2);
    console.log('Arguments ', myArgs);




- LUA:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap /usr/bin/lua

    io.write "Arguments"
    for a = 1, #arg do
      io.write(" ")
      io.write(arg[a])
    end
    print("")




- C#:


 .. code-block:: perl

    #!/usr/bin/parallel --shebang-wrap ARGV={} /usr/bin/csharp

    var argv = Environment.GetEnvironmentVariable("ARGV");
    print("Arguments "+argv);






*********
Semaphore
*********


GNU \ **parallel**\  can work as a counting semaphore. This is slower and less
efficient than its normal mode.

A counting semaphore is like a row of toilets. People needing a toilet
can use any toilet, but if there are more people than toilets, they
will have to wait for one of the toilets to become available.

An alias for \ **parallel --semaphore**\  is \ **sem**\ .

\ **sem**\  will follow a person to the toilets, wait until a toilet is
available, leave the person in the toilet and exit.

\ **sem --fg**\  will follow a person to the toilets, wait until a toilet is
available, stay with the person in the toilet and exit when the person
exits.

\ **sem --wait**\  will wait for all persons to leave the toilets.

\ **sem**\  does not have a queue discipline, so the next person is chosen
randomly.

\ **-j**\  sets the number of toilets.

Mutex
=====


The default is to have only one toilet (this is called a mutex). The
program is started in the background and \ **sem**\  exits immediately. Use
\ **--wait**\  to wait for all \ **sem**\ s to finish:


.. code-block:: perl

   sem 'sleep 1; echo The first finished' &&
     echo The first is now running in the background &&
     sem 'sleep 1; echo The second finished' &&
     echo The second is now running in the background
   sem --wait


Output:


.. code-block:: perl

   The first is now running in the background
   The first finished
   The second is now running in the background
   The second finished


The command can be run in the foreground with \ **--fg**\ , which will only
exit when the command completes:


.. code-block:: perl

   sem --fg 'sleep 1; echo The first finished' &&
     echo The first finished running in the foreground &&
     sem --fg 'sleep 1; echo The second finished' &&
     echo The second finished running in the foreground
   sem --wait


The difference between this and just running the command, is that a
mutex is set, so if other \ **sem**\ s were running in the background only one
would run at a time.

To control which semaphore is used, use
\ **--semaphorename**\ /\ **--id**\ . Run this in one terminal:


.. code-block:: perl

   sem --id my_id -u 'echo First started; sleep 10; echo First done'


and simultaneously this in another terminal:


.. code-block:: perl

   sem --id my_id -u 'echo Second started; sleep 10; echo Second done'


Note how the second will only be started when the first has finished.


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.

\ **sem**\  can emulate a counting semaphore. Use \ **--jobs**\  to set the
number of toilets like this:


.. code-block:: perl

   sem --jobs 3 --id my_id -u 'echo Start 1; sleep 5; echo 1 done' &&
   sem --jobs 3 --id my_id -u 'echo Start 2; sleep 6; echo 2 done' &&
   sem --jobs 3 --id my_id -u 'echo Start 3; sleep 7; echo 3 done' &&
   sem --jobs 3 --id my_id -u 'echo Start 4; sleep 8; echo 4 done' &&
   sem --wait --id my_id


Output:


.. code-block:: perl

   Start 1
   Start 2
   Start 3
   1 done
   Start 4
   2 done
   3 done
   4 done



Timeout
=======


With \ **--semaphoretimeout**\  you can force running the command anyway after
a period (positive number) or give up (negative number):


.. code-block:: perl

   sem --id foo -u 'echo Slow started; sleep 5; echo Slow ended' &&
   sem --id foo --semaphoretimeout 1 'echo Forced running after 1 sec' &&
   sem --id foo --semaphoretimeout -2 'echo Give up after 2 secs'
   sem --id foo --wait


Output:


.. code-block:: perl

   Slow started
   parallel: Warning: Semaphore timed out. Stealing the semaphore.
   Forced running after 1 sec
   parallel: Warning: Semaphore timed out. Exiting.
   Slow ended


Note how the 'Give up' was not run.



*************
Informational
*************


GNU \ **parallel**\  has some options to give short information about the
configuration.

\ **--help**\  will print a summary of the most important options:


.. code-block:: perl

   parallel --help


Output:


.. code-block:: perl

   Usage:

   parallel [options] [command [arguments]] < list_of_arguments
   parallel [options] [command [arguments]] (::: arguments|:::: argfile(s))...
   cat ... | parallel --pipe [options] [command [arguments]]

   -j n            Run n jobs in parallel
   -k              Keep same order
   -X              Multiple arguments with context replace
   --colsep regexp Split input on regexp for positional replacements
   {} {.} {/} {/.} {#} {%} {= perl code =} Replacement strings
   {3} {3.} {3/} {3/.} {=3 perl code =}    Positional replacement strings
   With --plus:    {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} =
                   {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}

   -S sshlogin     Example: foo@server.example.com
   --slf ..        Use ~/.parallel/sshloginfile as the list of sshlogins
   --trc {}.bar    Shorthand for --transfer --return {}.bar --cleanup
   --onall         Run the given command with argument on all sshlogins
   --nonall        Run the given command with no arguments on all sshlogins

   --pipe          Split stdin (standard input) to multiple jobs.
   --recend str    Record end separator for --pipe.
   --recstart str  Record start separator for --pipe.

   See 'man parallel' for details

   Academic tradition requires you to cite works you base your article on.
   When using programs that use GNU Parallel to process data for publication
   please cite:

     O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
     ;login: The USENIX Magazine, February 2011:42-47.

   This helps funding further development; AND IT WON'T COST YOU A CENT.
   If you pay 10000 EUR you should feel free to use GNU Parallel without citing.


When asking for help, always report the full output of this:


.. code-block:: perl

   parallel --version


Output:


.. code-block:: perl

   GNU parallel 20210122
   Copyright (C) 2007-2021 Ole Tange, http://ole.tange.dk and Free Software
   Foundation, Inc.
   License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>
   This is free software: you are free to change and redistribute it.
   GNU parallel comes with no warranty.

   Web site: https://www.gnu.org/software/parallel

   When using programs that use GNU Parallel to process data for publication
   please cite as described in 'parallel --citation'.


In scripts \ **--minversion**\  can be used to ensure the user has at least
this version:


.. code-block:: perl

   parallel --minversion 20130722 && \
     echo Your version is at least 20130722.


Output:


.. code-block:: perl

   20160322
   Your version is at least 20130722.


If you are using GNU \ **parallel**\  for research the BibTeX citation can be
generated using \ **--citation**\ :


.. code-block:: perl

   parallel --citation


Output:


.. code-block:: perl

   Academic tradition requires you to cite works you base your article on.
   When using programs that use GNU Parallel to process data for publication
   please cite:

   @article{Tange2011a,
     title = {GNU Parallel - The Command-Line Power Tool},
     author = {O. Tange},
     address = {Frederiksberg, Denmark},
     journal = {;login: The USENIX Magazine},
     month = {Feb},
     number = {1},
     volume = {36},
     url = {https://www.gnu.org/s/parallel},
     year = {2011},
     pages = {42-47},
     doi = {10.5281/zenodo.16303}
   }

   (Feel free to use \nocite{Tange2011a})

   This helps funding further development; AND IT WON'T COST YOU A CENT.
   If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

   If you send a copy of your published article to tange@gnu.org, it will be
   mentioned in the release notes of next version of GNU Parallel.


With \ **--max-line-length-allowed**\  GNU \ **parallel**\  will report the maximal
size of the command line:


.. code-block:: perl

   parallel --max-line-length-allowed


Output (may vary on different systems):


.. code-block:: perl

   131071


\ **--number-of-cpus**\  and \ **--number-of-cores**\  run system specific code to
determine the number of CPUs and CPU cores on the system. On
unsupported platforms they will return 1:


.. code-block:: perl

   parallel --number-of-cpus
   parallel --number-of-cores


Output (may vary on different systems):


.. code-block:: perl

   4
   64



********
Profiles
********


The defaults for GNU \ **parallel**\  can be changed systemwide by putting the
command line options in \ **/etc/parallel/config**\ . They can be changed for
a user by putting them in \ **~/.parallel/config**\ .

Profiles work the same way, but have to be referred to with \ **--profile**\ :


.. code-block:: perl

   echo '--nice 17' > ~/.parallel/nicetimeout
   echo '--timeout 300%' >> ~/.parallel/nicetimeout
   parallel --profile nicetimeout echo ::: A B C


Output:


.. code-block:: perl

   A
   B
   C


Profiles can be combined:


.. code-block:: perl

   echo '-vv --dry-run' > ~/.parallel/dryverbose
   parallel --profile dryverbose --profile nicetimeout echo ::: A B C


Output:


.. code-block:: perl

   echo A
   echo B
   echo C



***************
Spread the word
***************


I hope you have learned something from this tutorial.

If you like GNU \ **parallel**\ :


- \*

 (Re-)walk through the tutorial if you have not done so in the past year
 (https://www.gnu.org/software/parallel/parallel_tutorial.html)



- \*

 Give a demo at your local user group/your team/your colleagues



- \*

 Post the intro videos and the tutorial on Reddit, Mastodon, Diaspora\*,
 forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin, and
 mailing lists



- \*

 Request or write a review for your favourite blog or magazine
 (especially if you do something cool with GNU \ **parallel**\ )



- \*

 Invite me for your next conference



If you use GNU \ **parallel**\  for research:


- \*

 Please cite GNU \ **parallel**\  in you publications (use \ **--citation**\ )



If GNU \ **parallel**\  saves you money:


- \*

 (Have your company) donate to FSF or become a member
 https://my.fsf.org/donate/



(C) 2013-2021 Ole Tange, GFDLv1.3+ (See
LICENSES/GFDL-1.3-or-later.txt)