
******************************
Why should you read this book?
******************************


If you write shell scripts to do the same processing for different
input, then GNU \ **parallel**\  will make your life easier and make your
scripts run faster.

The book is written so you get the juicy parts first: The goal is that
you read just enough to get you going. GNU \ **parallel**\  has an
overwhelming amount of special features to help in different
situations, and to avoid overloading you with information, the most
used features are presented first.

All the examples are tested in Bash, and most will work in other
shells, too, but there are a few exceptions. So you are recommended to
use Bash while testing out the examples.


*******************************
Learn GNU Parallel in 5 minutes
*******************************


You just need to run commands in parallel. You do not care about fine
tuning.

To get going please run this to make some example files:


.. code-block:: perl

   # If your system does not have 'seq', replace 'seq' with 'jot'
   seq 5 | parallel seq {} '>' example.{}


Input sources
=============


GNU \ **parallel**\  reads values from input sources. One input source is
the command line. The values are put after \ **:::**\  :


.. code-block:: perl

   parallel echo ::: 1 2 3 4 5


This makes it easy to run the same program on some files:


.. code-block:: perl

   parallel wc ::: example.*


If you give multiple \ **:::**\ s, GNU \ **parallel**\  will generate all
combinations:


.. code-block:: perl

   parallel wc ::: -l -c ::: example.*


GNU \ **parallel**\  can also read the values from stdin (standard input):


.. code-block:: perl

   seq 5 | parallel echo



Building the command line
=========================


The command line is put before the \ **:::**\ . It can contain contain a
command and options for the command:


.. code-block:: perl

   parallel wc -l ::: example.*


The command can contain multiple programs. Just remember to quote
characters that are interpreted by the shell (such as \ **;**\ ):


.. code-block:: perl

   parallel echo counting lines';' wc -l ::: example.*


The value will normally be appended to the command, but can be placed
anywhere by using the replacement string \ **{}**\ :


.. code-block:: perl

   parallel echo counting {}';' wc -l {} ::: example.*


When using multiple input sources you use the positional replacement
strings \ **{1}**\  and \ **{2}**\ :


.. code-block:: perl

   parallel echo count {1} in {2}';' wc {1} {2} ::: -l -c ::: example.*


You can check what will be run with \ **--dry-run**\ :


.. code-block:: perl

   parallel --dry-run echo count {1} in {2}';' wc {1} {2} ::: -l -c ::: example.*


This is a good idea to do for every command until you are comfortable
with GNU \ **parallel**\ .


Controlling the output
======================


The output will be printed as soon as the command completes. This
means the output may come in a different order than the input:


.. code-block:: perl

   parallel sleep {}';' echo {} done ::: 5 4 3 2 1


You can force GNU \ **parallel**\  to print in the order of the values with
\ **--keep-order**\ /\ **-k**\ . This will still run the commands in parallel.
The output of the later jobs will be delayed, until the earlier jobs
are printed:


.. code-block:: perl

   parallel -k sleep {}';' echo {} done ::: 5 4 3 2 1



Controlling the execution
=========================


If your jobs are compute intensive, you will most likely run one job
for each core in the system. This is the default for GNU \ **parallel**\ .

But sometimes you want more jobs running. You control the number of
job slots with \ **-j**\ . Give \ **-j**\  the number of jobs to run in
parallel:


.. code-block:: perl

   parallel -j50 \
     wget https://ftpmirror.gnu.org/parallel/parallel-{1}{2}22.tar.bz2 \
     ::: 2012 2013 2014 2015 2016 \
     ::: 01 02 03 04 05 06 07 08 09 10 11 12



Pipe mode
=========


GNU \ **parallel**\  can also pass blocks of data to commands on stdin
(standard input):


.. code-block:: perl

   seq 1000000 | parallel --pipe wc


This can be used to process big text files. By default GNU \ **parallel**\ 
splits on \n (newline) and passes a block of around 1 MB to each job.


That's it
=========


You have now learned the basic use of GNU \ **parallel**\ . This will
probably cover most cases of your use of GNU \ **parallel**\ .

The rest of this document will go into more details on each of the
sections and cover special use cases.



*****************************
Learn GNU Parallel in an hour
*****************************


In this part we will dive deeper into what you learned in the first 5 minutes.

To get going please run this to make some example files:


.. code-block:: perl

   seq 6 > seq6
   seq 6 -1 1 > seq-6


Input sources
=============


On top of the command line, input sources can also be stdin (standard
input or '-'), files and fifos and they can be mixed. Files are given
after \ **-a**\  or \ **::::**\ . So these all do the same:


.. code-block:: perl

   parallel echo Dice1={1} Dice2={2} ::: 1 2 3 4 5 6 ::: 6 5 4 3 2 1
   parallel echo Dice1={1} Dice2={2} :::: <(seq 6) :::: <(seq 6 -1 1)
   parallel echo Dice1={1} Dice2={2} :::: seq6 seq-6
   parallel echo Dice1={1} Dice2={2} :::: seq6 :::: seq-6
   parallel -a seq6 -a seq-6 echo Dice1={1} Dice2={2}
   parallel -a seq6 echo Dice1={1} Dice2={2} :::: seq-6
   parallel echo Dice1={1} Dice2={2} ::: 1 2 3 4 5 6 :::: seq-6
   cat seq-6 | parallel echo Dice1={1} Dice2={2} :::: seq6 -


If stdin (standard input) is the only input source, you do not need the '-':


.. code-block:: perl

   cat seq6 | parallel echo Dice1={1}


Linking input sources
---------------------


You can link multiple input sources with \ **:::+**\  and \ **::::+**\ :


.. code-block:: perl

   parallel echo {1}={2} ::: I II III IV V VI :::+ 1 2 3 4 5 6
   parallel echo {1}={2} ::: I II III IV V VI ::::+ seq6


The \ **:::+**\  (and \ **::::+**\ ) will link each value to the corresponding
value in the previous input source, so value number 3 from the first
input source will be linked to value number 3 from the second input
source.

You can combine \ **:::+**\  and \ **:::**\ , so you link 2 input sources, but
generate all combinations with other input sources:


.. code-block:: perl

   parallel echo Dice1={1}={2} Dice2={3}={4} ::: I II III IV V VI ::::+ seq6 \
     ::: VI V IV III II I ::::+ seq-6




Building the command line
=========================


The command
-----------


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


.. code-block:: perl

   # Works only in Bash
   my_func() {
     echo in my_func "$1"
   }
   export -f my_func
   parallel my_func ::: 1 2 3


If the command is complex, it often improves readability to make it
into a function.


The replacement strings
-----------------------


GNU \ **parallel**\  has some replacement strings to make it easier to
refer to the input read from the input sources.

If the input is \ **mydir/mysubdir/myfile.myext**\  then:


.. code-block:: perl

   {} = mydir/mysubdir/myfile.myext
   {.} = mydir/mysubdir/myfile
   {/} = myfile.myext
   {//} = mydir/mysubdir
   {/.} = myfile
   {#} = the sequence number of the job
   {%} = the job slot number


When a job is started it gets a sequence number that starts at 1 and
increases by 1 for each new job. The job also gets assigned a slot
number. This number is from 1 to the number of jobs running in
parallel. It is unique between the running jobs, but is re-used as
soon as a job finishes.

The positional replacement strings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


The replacement strings have corresponding positional replacement
strings. If the value from the 3rd input source is
\ **mydir/mysubdir/myfile.myext**\ :


.. code-block:: perl

   {3} = mydir/mysubdir/myfile.myext
   {3.} = mydir/mysubdir/myfile
   {3/} = myfile.myext
   {3//} = mydir/mysubdir
   {3/.} = myfile


So the number of the input source is simply prepended inside the {}'s.





*******************
Replacement strings
*******************


--plus replacement strings

change the replacement string (-I --extensionreplace --basenamereplace --basenamereplace --dirnamereplace --basenameextensionreplace --seqreplace --slotreplace

--header with named replacement string

{= =}

Dynamic replacement strings

Defining replacement strings
============================



Copying environment
===================


env_parallel


Controlling the output
======================


parset
------


\ **parset**\  is a shell function to get the output from GNU \ **parallel**\ 
into shell variables.

\ **parset**\  is fully supported for \ **Bash/Zsh/Ksh**\  and partially supported
for \ **ash/dash**\ . I will assume you run \ **Bash**\ .

To activate \ **parset**\  you have to run:


.. code-block:: perl

   . `which env_parallel.bash`


(replace \ **bash**\  with your shell's name).

Then you can run:


.. code-block:: perl

   parset a,b,c seq ::: 4 5 6
   echo "$c"


or:


.. code-block:: perl

   parset 'a b c' seq ::: 4 5 6
   echo "$c"


If you give a single variable, this will become an array:


.. code-block:: perl

   parset arr seq ::: 4 5 6
   echo "${arr[1]}"


\ **parset**\  has one limitation: If it reads from a pipe, the output will
be lost.


.. code-block:: perl

   echo This will not work | parset myarr echo
   echo Nothing: "${myarr[*]}"


Instead you can do this:


.. code-block:: perl

   echo This will work > tempfile
   parset myarr echo < tempfile
   echo ${myarr[*]}


sql
cvs



Controlling the execution
=========================


--dryrun -v


Remote execution
================


For this section you must have \ **ssh**\  access with no password to 2
servers: \ **$server1**\  and \ **$server2**\ .


.. code-block:: perl

   server1=server.example.com
   server2=server2.example.net


So you must be able to do this:


.. 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**\ .

Workers
-------



--transferfile
--------------


\ **--transferfile**\  \ *filename*\  will transfer \ *filename*\  to the
worker. \ *filename*\  can contain a replacement string:


.. code-block:: perl

   parallel -S $server1,$server2 --transferfile {} wc ::: example.*
   parallel -S $server1,$server2 --transferfile {2} \
      echo count {1} in {2}';' wc {1} {2} ::: -l -c ::: example.*


A shorthand for \ **--transferfile {}**\  is \ **--transfer**\ .


--return
--------



--cleanup
---------


A shorthand for \ **--transfer --return {} --cleanup**\  is \ **--trc {}**\ .



Pipe mode
=========


--pipepart


That's it
=========




**************
Advanced usage
**************


parset fifo, cmd substitution, arrayelements, array with var names and cmds, env_parset

env_parallel

Interfacing with R.

Interfacing with JSON/jq

4dl() {
  board="$(printf -- '%s' "${1}" | cut -d '/' -f4)"
  thread="$(printf -- '%s' "${1}" | cut -d '/' -f6)"
  wget -qO- "https://a.4cdn.org/${board}/thread/${thread}.json" |
    jq -r '
      .posts
      | map(select(.tim != null))
      | map((.tim | tostring) + .ext)
      | map("https://i.4cdn.org/'"${board}"'/"+.)[]
    ' |
      parallel --gnu -j 0 wget -nv
}

Interfacing with XML/?

Interfacing with HTML/?

Controlling the execution
=========================


--termseq


Remote execution
================


seq 10 | parallel --sshlogin 'ssh -i "key.pem" a@b.com' echo

seq 10 | PARALLEL_SSH='ssh -i "key.pem"' parallel --sshlogin a@b.com echo

seq 10 | parallel --ssh 'ssh -i "key.pem"' --sshlogin a@b.com echo

ssh-agent

The sshlogin file format

Check if servers are up


