*********************
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 examples (\ **man parallel_examples**\ ). 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 51621b7f 1ee103c0 0783aae4 ef9889f8
$ md5sum install.sh
62eada78 703b5500 241b8e50 baf62758
$ sha512sum install.sh
160d3159 9480cf5c a101512f 150b7ac0 206a65dc 86f2bb6b bdf1a2bc 96bc6d06
7f8237c2 0964b67f bccf8a93 332528fa 11e5ab43 2a6226a6 ceb197ab 7f03c061
$ 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$eval;'\'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=;
_EXIT_status=$?; 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 20230122
Copyright (C) 2007-2023 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) 2013-2023 Ole Tange, GFDLv1.3+ (See LICENSES/GFDL-1.3-or-later.txt)
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