#!/usr/bin/perl -w =head1 GNU Parallel Tutorial This tutorial shows off much of GNU B's functionality. The tutorial is meant to learn the options in GNU B. The tutorial is not to show realistic examples from the real world. Spend an hour walking through the tutorial. Your command line will love you for it. =head1 Prerequisites To run this tutorial you must have the following: =over 9 =item parallel >= version 20160822 Install the newest version using your package manager (recommended for security reasons) or with this command: (wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash This will also install the newest version of the tutorial which you can see by running this: man parallel_tutorial Most of the tutorial will work on older versions, too. =item abc-file: The file can be generated by this command: parallel -k echo ::: A B C > abc-file =item def-file: The file can be generated by this command: parallel -k echo ::: D E F > def-file =item abc0-file: The file can be generated by this command: perl -e 'printf "A\0B\0C\0"' > abc0-file =item abc_-file: The file can be generated by this command: perl -e 'printf "A_B_C_"' > abc_-file =item tsv-file.tsv The file can be generated by this command: perl -e 'printf "f1\tf2\nA\tB\nC\tD\n"' > tsv-file.tsv =item num8 The file can be generated by this command: perl -e 'for(1..8){print "$_\n"}' > num8 =item num128 The file can be generated by this command: perl -e 'for(1..128){print "$_\n"}' > num128 =item num30000 The file can be generated by this command: perl -e 'for(1..30000){print "$_\n"}' > num30000 =item num1000000 The file can be generated by this command: perl -e 'for(1..1000000){print "$_\n"}' > num1000000 =item num_%header The file can be generated by this command: (echo %head1; echo %head2; perl -e 'for(1..10){print "$_\n"}') > num_%header =item For remote running: ssh login on 2 servers with no password in $SERVER1 and $SERVER2 must work. SERVER1=server.example.com SERVER2=server2.example.net So you must be able to do this: 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 pass phrase. =back =head1 Input sources GNU B reads input from input sources. These can be files, the command line, and stdin (standard input or a pipe). =head2 A single input source Input can be read from the command line: parallel echo ::: A B C Output (the order may be different because the jobs are run in parallel): A B C The input source can be a file: parallel -a abc-file echo Output: Same as above. STDIN (standard input) can be the input source: cat abc-file | parallel echo Output: Same as above. =head2 Multiple input sources GNU B can take multiple input sources given on the command line. GNU B then generates all combinations of the input sources: parallel echo ::: A B C ::: D E F Output (the order may be different): A D A E A F B D B E B F C D C E C F The input sources can be files: parallel -a abc-file -a def-file echo Output: Same as above. STDIN (standard input) can be one of the input sources using B<->: cat abc-file | parallel -a - -a def-file echo Output: Same as above. Instead of B<-a> files can be given after B<::::>: cat abc-file | parallel echo :::: - def-file Output: Same as above. ::: and :::: can be mixed: parallel echo ::: A B C :::: def-file Output: Same as above. =head3 Linking arguments from input sources With B<--link> you can link the input sources and get one argument from each input source: parallel --link echo ::: A B C ::: D E F Output (the order may be different): A D B E C F If one of the input sources is too short, its values will wrap: parallel --link echo ::: A B C D E ::: F G Output (the order may be different): A F B G C F D G E F For more flexible linking you can use B<:::+> and B<::::+>. They work like B<:::> and B<::::> except they link the previous input source to this input source. This will link ABC to GHI: parallel echo :::: abc-file :::+ G H I :::: def-file Output (the order may be different): 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: parallel echo :::: abc-file ::: G H I ::::+ def-file Output (the order may be different): 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 B<:::+> or B<::::+>, the rest will be ignored: parallel echo ::: A B C D E :::+ F G Output (the order may be different): A F B G =head2 Changing the argument separator. GNU B can use other separators than B<:::> or B<::::>. This is typically useful if B<:::> or B<::::> is used in the command to run: parallel --arg-sep ,, echo ,, A B C :::: def-file Output (the order may be different): A D A E A F B D B E B F C D C E C F Changing the argument file separator: parallel --arg-file-sep // echo ::: A B C // def-file Output: Same as above. =head2 Changing the argument delimiter GNU B will normally treat a full line as a single argument: It uses B<\n> as argument delimiter. This can be changed with B<-d>: parallel -d _ echo :::: abc_-file Output (the order may be different): A B C NUL can be given as B<\0>: parallel -d '\0' echo :::: abc0-file Output: Same as above. A shorthand for B<-d '\0'> is B<-0> (this will often be used to read files from B): parallel -0 echo :::: abc0-file Output: Same as above. =head2 End-of-file value for input source GNU B can stop reading when it encounters a certain value: parallel -E stop echo ::: A B stop C D Output: A B =head2 Skipping empty lines Using B<--no-run-if-empty> GNU B will skip empty lines. (echo 1; echo; echo 2) | parallel --no-run-if-empty echo Output: 1 2 =head1 Building the command line =head2 No command means arguments are commands If no command is given after parallel the arguments themselves are treated as commands: parallel ::: ls 'echo foo' pwd Output (the order may be different): [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 B: # 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): in my_func 1 in my_func 2 in my_func 3 =head2 Replacement strings =head3 The 7 predefined replacement strings GNU B has several replacement strings. If no replacement strings are used the default is to append B<{}>: parallel echo ::: A/B.C Output: A/B.C The default replacement string is B<{}>: parallel echo {} ::: A/B.C Output: A/B.C The replacement string B<{.}> removes the extension: parallel echo {.} ::: A/B.C Output: A/B The replacement string B<{/}> removes the path: parallel echo {/} ::: A/B.C Output: B.C The replacement string B<{//}> keeps only the path: parallel echo {//} ::: A/B.C Output: A The replacement string B<{/.}> removes the path and the extension: parallel echo {/.} ::: A/B.C Output: B The replacement string B<{#}> gives the job number: parallel echo {#} ::: A B C Output (the order may be different): 1 2 3 The replacement string B<{%}> gives the job slot number (between 1 and number of jobs to run in parallel): parallel -j 2 echo {%} ::: A B C Output (the order may be different and 1 and 2 may be swapped): 1 2 1 =head3 Changing the replacement strings The replacement string B<{}> can be changed with B<-I>: parallel -I ,, echo ,, ::: A/B.C Output: A/B.C The replacement string B<{.}> can be changed with B<--extensionreplace>: parallel --extensionreplace ,, echo ,, ::: A/B.C Output: A/B The replacement string B<{/}> can be replaced with B<--basenamereplace>: parallel --basenamereplace ,, echo ,, ::: A/B.C Output: B.C The replacement string B<{//}> can be changed with B<--dirnamereplace>: parallel --dirnamereplace ,, echo ,, ::: A/B.C Output: A The replacement string B<{/.}> can be changed with B<--basenameextensionreplace>: parallel --basenameextensionreplace ,, echo ,, ::: A/B.C Output: B The replacement string B<{#}> can be changed with B<--seqreplace>: parallel --seqreplace ,, echo ,, ::: A B C Output (the order may be different): 1 2 3 The replacement string B<{%}> can be changed with B<--slotreplace>: parallel -j2 --slotreplace ,, echo ,, ::: A B C Output (the order may be different and 1 and 2 may be swapped): 1 2 1 =head3 Perl expression replacement string When predefined replacement strings are not flexible enough a perl expression can be used instead. One example is to remove two extensions: foo.tar.gz becomes foo parallel echo '{= s:\.[^.]+$::;s:\.[^.]+$::; =}' ::: foo.tar.gz Output: foo In B<{= =}> you can access all of GNU B's internal functions and variables. A few are worth mentioning. B returns the total number of jobs: parallel echo Job {#} of {= '$_=total_jobs()' =} ::: {1..5} Output: Job 1 of 5 Job 2 of 5 Job 3 of 5 Job 4 of 5 Job 5 of 5 B shell quotes the string: parallel echo {} shell quoted is {= '$_=Q($_)' =} ::: '*/!#$' Output: */!#$ shell quoted is \*/\!\#\$ B skips the job: parallel echo {= 'if($_==3) { skip() }' =} ::: {1..5} Output: 1 2 4 5 B<@arg> contains the input source variables: parallel echo {= 'if($arg[1]==$arg[2]) { skip() }' =} ::: {1..3} ::: {1..3} Output: 1 2 1 3 2 1 2 3 3 1 3 2 If the strings B<{=> and B<=}> cause problems they can be replaced with B<--parens>: parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' ::: foo.tar.gz Output: foo To define a shorthand replacement string use B<--rpl>: parallel --rpl '.. s:\.[^.]+$::;s:\.[^.]+$::;' echo '..' ::: foo.tar.gz Output: Same as above. If the shorthand starts with B<{> it can be used as a positional replacement string, too: parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{..}' ::: foo.tar.gz Output: Same as above. GNU B's 7 replacement strings are implemented as this: --rpl '{} ' --rpl '{#} $_=$job->seq()' --rpl '{%} $_=$job->slot()' --rpl '{/} s:.*/::' --rpl '{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);' --rpl '{/.} s:.*/::; s:\.[^/.]+$::;' --rpl '{.} s:\.[^/.]+$::' =head3 Positional replacement strings With multiple input sources the argument from the individual input sources can be accessed with B<{>numberB<}>: parallel echo {1} and {2} ::: A B ::: C D Output (the order may be different): A and C A and D B and C B and D The positional replacement strings can also be modified using B, B, B, and B<.>: parallel echo /={1/} //={1//} /.={1/.} .={1.} ::: A/B.C D/E.F Output (the order may be different): /=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: 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): 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 =head3 Positional perl expression replacement string To use a perl expression as a positional replacement string simply prepend the perl expression with number and space: parallel echo '{=2 s:\.[^.]+$::;s:\.[^.]+$::; =} {1}' ::: bar ::: foo.tar.gz Output: foo bar If a shorthand defined using B<--rpl> starts with B<{> it can be used as a positional replacement string, too: parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' ::: bar ::: foo.tar.gz Output: Same as above. =head3 Input from columns The columns in a file can be bound to positional replacement strings using B<--colsep>. Here the columns are separated by TAB (\t): parallel --colsep '\t' echo 1={1} 2={2} :::: tsv-file.tsv Output (the order may be different): 1=f1 2=f2 1=A 2=B 1=C 2=D =head3 Header defined replacement strings With B<--header> GNU B will use the first value of the input source as the name of the replacement string. Only the non-modified version B<{}> is supported: parallel --header : echo f1={f1} f2={f2} ::: f1 A B ::: f2 C D Output (the order may be different): f1=A f2=C f1=A f2=D f1=B f2=C f1=B f2=D It is useful with B<--colsep> for processing files with TAB separated values: parallel --header : --colsep '\t' echo f1={f1} f2={f2} :::: tsv-file.tsv Output (the order may be different): f1=A f2=B f1=C f2=D =head3 More pre-defined replacement strings B<--plus> adds the replacement strings B<{+/} {+.} {+..} {+...} {..} {...} {/..} {/...} {##}>. The idea being that B<{+foo}> matches the opposite of B<{foo}> and B<{}> = B<{+/}>/B<{/}> = B<{.}>.B<{+.}> = B<{+/}>/B<{/.}>.B<{+.}> = B<{..}>.B<{+..}> = B<{+/}>/B<{/..}>.B<{+..}> = B<{...}>.B<{+...}> = B<{+/}>/B<{/...}>.B<{+...}>. parallel --plus echo {} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {+/}/{/} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {.}.{+.} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {+/}/{/.}.{+.} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {..}.{+..} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {+/}/{/..}.{+..} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {...}.{+...} ::: dir/sub/file.ext1.ext2.ext3 parallel --plus echo {+/}/{/...}.{+...} ::: dir/sub/file.ext1.ext2.ext3 Output: dir/sub/file.ext1.ext2.ext3 B<{##}> is simply the number of jobs: parallel --plus echo Job {#} of {##} ::: {1..5} Output: Job 1 of 5 Job 2 of 5 Job 3 of 5 Job 4 of 5 Job 5 of 5 =head2 More than one argument With B<--xargs> GNU B will fit as many arguments as possible on a single line: cat num30000 | parallel --xargs echo | wc -l Output (if you run this under Bash on GNU/Linux): 2 The 30000 arguments fitted on 2 lines. The maximal length of a single line can be set with B<-s>. With a maximal line length of 10000 chars 17 commands will be run: cat num30000 | parallel --xargs -s 10000 echo | wc -l Output: 17 For better parallelism GNU B can distribute the arguments between all the parallel jobs when end of file is met. Below GNU B reads the last argument when generating the second job. When GNU B 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 B<--xargs> example above, but the second job will be split into 4 evenly sized jobs, resulting in a total of 5 jobs: cat num30000 | parallel --jobs 4 -m echo | wc -l Output (if you run this under Bash on GNU/Linux): 5 This is even more visible when running 4 jobs with 10 arguments. The 10 arguments are being spread over 4 jobs: parallel --jobs 4 -m echo ::: 1 2 3 4 5 6 7 8 9 10 Output: 1 2 3 4 5 6 7 8 9 10 A replacement string can be part of a word. B<-m> will not repeat the context: parallel --jobs 4 -m echo pre-{}-post ::: A B C D E F G Output (the order may be different): pre-A B-post pre-C D-post pre-E F-post pre-G-post To repeat the context use B<-X> which otherwise works like B<-m>: parallel --jobs 4 -X echo pre-{}-post ::: A B C D E F G Output (the order may be different): 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 B<-N>: parallel -N3 echo ::: A B C D E F G H Output (the order may be different): A B C D E F G H B<-N> also sets the positional replacement strings: parallel -N3 echo 1={1} 2={2} 3={3} ::: A B C D E F G H Output (the order may be different): 1=A 2=B 3=C 1=D 2=E 3=F 1=G 2=H 3= B<-N0> reads 1 argument but inserts none: parallel -N0 echo foo ::: 1 2 3 Output: foo foo foo =head2 Quoting Command lines that contain special characters may need to be protected from the shell. The B program B basically works like B. perl -e 'print "@ARGV\n"' A Output: A To run that in parallel the command needs to be quoted: parallel perl -e 'print "@ARGV\n"' ::: This wont work Output: [Nothing] To quote the command use B<-q>: parallel -q perl -e 'print "@ARGV\n"' ::: This works Output (the order may be different): This works Or you can quote the critical part using B<\'>: parallel perl -e \''print "@ARGV\n"'\' ::: This works, too Output (the order may be different): This works, too GNU B can also \-quote full lines. Simply run this: parallel --shellquote parallel: Warning: Input is read from the terminal. You either know what you parallel: Warning: are doing (in which case: YOU ARE AWESOME!) or you forgot parallel: Warning: ::: or :::: or to pipe data into parallel. If so parallel: Warning: consider going through the tutorial: man parallel_tutorial parallel: Warning: Press CTRL-D to exit. perl -e 'print "@ARGV\n"' [CTRL-D] Output: perl\ -e\ \'print\ \"@ARGV\\n\"\' This can then be used as the command: parallel perl\ -e\ \'print\ \"@ARGV\\n\"\' ::: This also works Output (the order may be different): This also works =head2 Trimming space Space can be trimmed on the arguments using B<--trim>: parallel --trim r echo pre-{}-post ::: ' A ' Output: pre- A-post To trim on the left side: parallel --trim l echo pre-{}-post ::: ' A ' Output: pre-A -post To trim on the both sides: parallel --trim lr echo pre-{}-post ::: ' A ' Output: pre-A-post =head2 Respecting the shell This tutorial uses Bash as the shell. GNU B respects which shell you are using, so in B you can do: parallel echo \={} ::: zsh bash ls Output: /usr/bin/zsh /bin/bash /bin/ls In B you can do: parallel 'set a="{}"; if( { test -d "$a" } ) echo "$a is a dir"' ::: * Output: [somedir] is a dir This also becomes useful if you use GNU B in a shell script: GNU B will use the same shell as the shell script. =head1 Controlling the output The output can prefixed with the argument: parallel --tag echo foo-{} ::: A B C Output (the order may be different): A foo-A B foo-B C foo-C To prefix it with another string use B<--tagstring>: parallel --tagstring {}-bar echo foo-{} ::: A B C Output (the order may be different): A-bar foo-A B-bar foo-B C-bar foo-C To see what commands will be run without running them use B<--dryrun>: parallel --dryrun echo {} ::: A B C Output (the order may be different): echo A echo B echo C To print the command before running them use B<--verbose>: parallel --verbose echo {} ::: A B C Output (the order may be different): echo A echo B A echo C B C GNU B will postpone the output until the command completes: parallel -j2 'printf "%s-start\n%s" {} {};sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1 Output: 2-start 2-middle 2-end 1-start 1-middle 1-end 4-start 4-middle 4-end To get the output immediately use B<--ungroup>: parallel -j2 --ungroup 'printf "%s-start\n%s" {} {};sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1 Output: 4-start 42-start 2-middle 2-end 1-start 1-middle 1-end -middle 4-end B<--ungroup> is fast, but can cause half a line from one job to be mixed with half a line of another job. That has happend in the second line, where the line '4-middle' is mixed with '2-start'. To avoid this use B<--linebuffer>: parallel -j2 --linebuffer 'printf "%s-start\n%s" {} {};sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1 Output: 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 B<--keep-order>/B<-k>: parallel -j2 -k 'printf "%s-start\n%s" {} {};sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1 Output: 4-start 4-middle 4-end 2-start 2-middle 2-end 1-start 1-middle 1-end =head2 Saving output into files GNU B can save the output of each job into files: parallel --files echo ::: A B C Output will be similar to this: /tmp/pAh6uWuQCg.par /tmp/opjhZCzAX4.par /tmp/W0AT_Rph2o.par By default GNU B will cache the output in files in B. This can be changed by setting B<$TMPDIR> or B<--tmpdir>: parallel --tmpdir /var/tmp --files echo ::: A B C Output will be similar to this: /var/tmp/N_vk7phQRc.par /var/tmp/7zA4Ccf3wZ.par /var/tmp/LIuKgF_2LP.par Or: TMPDIR=/var/tmp parallel --files echo ::: A B C Output: Same as above. The output files can be saved in a structured way using B<--results>: parallel --results outdir echo ::: A B C Output: A B C These files were also generated containing the standard output (stdout), standard error (stderr), and the sequence number (seq): 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 B<--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: parallel --header : --results outdir echo ::: f1 A B ::: f2 C D Generated files: 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. =head1 Controlling the execution =head2 Number of simultaneous jobs The number of concurrent jobs is given with B<--jobs>/B<-j>: /usr/bin/time parallel -N0 -j64 sleep 1 :::: num128 With 64 jobs in parallel the 128 Bs will take 2-8 seconds to run - depending on how fast your machine is. By default B<--jobs> is the same as the number of CPU cores. So this: /usr/bin/time parallel -N0 sleep 1 :::: num128 should take twice the time of running 2 jobs per CPU core: /usr/bin/time parallel -N0 --jobs 200% sleep 1 :::: num128 B<--jobs 0> will run as many jobs in parallel as possible: /usr/bin/time parallel -N0 --jobs 0 sleep 1 :::: num128 which should take 1-7 seconds depending on how fast your machine is. B<--jobs> can read from a file which is re-read when a job finishes: 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 B<0> is put into B and then the rest of the jobs will be started in parallel. Instead of basing the percentage on the number of CPU cores GNU B can base it on the number of CPUs: parallel --use-cpus-instead-of-cores -N0 sleep 1 :::: num8 =head2 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 B<--shuf> for that: parallel --shuf echo ::: 1 2 3 ::: a b c ::: A B C Output: All combinations but different order for each run. =head2 Interactivity GNU B can ask the user if a command should be run using B<--interactive>: parallel --interactive echo ::: 1 2 3 Output: echo 1 ?...y echo 2 ?...n 1 echo 3 ?...y 3 GNU B can be used to put arguments on the command line for an interactive command such as B to edit one file at a time: parallel --tty emacs ::: 1 2 3 Or give multiple argument in one go to open multiple files: parallel -X --tty vi ::: 1 2 3 =head2 A terminal for every job Using B<--tmux> GNU B can start a terminal for every job run: seq 10 20 | parallel --tmux 'echo start {}; sleep {}; echo done {}' This will tell you to run something similar to: tmux -S /tmp/tmsrPrO0 attach Using normal B 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. =head2 Timing Some jobs do heavy I/O when they start. To avoid a thundering herd GNU B can delay starting new jobs. B<--delay> I will make sure there is at least I seconds between each start: parallel --delay 2.5 echo Starting {}\;date ::: 1 2 3 Output: 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 B<--timeout>. The accuracy of B<--timeout> is 2 seconds: parallel --timeout 4.1 sleep {}\; echo {} ::: 2 4 6 8 Output: 2 4 GNU B can compute the median runtime for jobs and kill those that take more than 200% of the median runtime: parallel --timeout 200% sleep {}\; echo {} ::: 2.1 2.2 3 7 2.3 Output: 2.1 2.2 3 2.3 =head2 Progress information Based on the runtime of completed jobs GNU B can estimate the total runtime: parallel --eta sleep ::: 1 3 2 2 1 3 3 2 1 Output: 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 B can give progress information with B<--progress>: parallel --progress sleep ::: 1 3 2 2 1 3 3 2 1 Output: 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 B<--bar>: parallel --bar sleep ::: 1 3 2 2 1 3 3 2 1 And a graphic bar can be shown with B<--bar> and B: seq 1000 | parallel -j10 --bar '(echo -n {};sleep 0.1)' 2> >(zenity --progress --auto-kill --auto-close) A logfile of the jobs completed so far can be generated with B<--joblog>: parallel --joblog /tmp/log exit ::: 1 2 3 0 cat /tmp/log Output: 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 B can be stopped and later pickup where it left off. It it important that the input of the completed jobs is unchanged. 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: 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 B<--resume-failed> GNU B will re-run the jobs that failed: parallel --resume-failed --joblog /tmp/log exit ::: 1 2 3 0 0 0 cat /tmp/log Output: 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. B<--retry-failed> does almost the same as B<--resume-failed>. Where B<--resume-failed> reads the commands from the command line (and ignores the commands in the joblog), B<--retry-failed> ignores the command line and reruns the commands mentioned in the joblog. parallel --retry-failed --joblog /tmp/log cat /tmp/log Output: 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 =head2 Termination For certain jobs there is no need to continue if one of the jobs fails and has an exit code different from 0. GNU B will stop spawning new jobs with B<--halt soon,fail=1>: parallel -j2 --halt soon,fail=1 echo {}\; exit {} ::: 0 0 1 2 3 Output: 0 0 1 parallel: Starting no more jobs. Waiting for 2 jobs to finish. This job failed: echo 1; exit 1 2 parallel: Starting no more jobs. Waiting for 1 jobs to finish. This job failed: echo 2; exit 2 With B<--halt now,fail=1> the running jobs will be killed immediately: parallel -j2 --halt now,fail=1 echo {}\; exit {} ::: 0 0 1 2 3 Output: 0 0 1 parallel: This job failed: echo 1; exit 1 If B<--halt> is given a percentage this percentage of the jobs must fail before GNU B stops spawning more jobs: parallel -j2 --halt soon,fail=20% echo {}\; exit {} ::: 0 1 2 3 4 5 6 7 8 9 Output: 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 B. This will finish as soon as the first job succeeds: parallel -j2 --halt now,success=1 echo {}\; exit {} ::: 1 2 3 0 4 5 6 Output: 1 2 3 0 parallel: This job succeeded: echo 0; exit 0 GNU B can retry the command with B<--retries>. This is useful if a command fails for unknown reasons now and then. parallel -k --retries 3 'echo tried {} >>/tmp/runs; echo completed {}; exit {}' ::: 1 2 0 cat /tmp/runs Output: 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. =head3 Termination signals (advanced) Using B<--termseq> you can control which signals are sent when killing children. Normally children will be killed by sending them B, waiting 200 ms, then another B, waiting 100 ms, then another B, waiting 50 ms, then a B, finally waiting 25 ms before giving up. It looks like this: 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: Got TERM Got TERM Got TERM Or just: echo | parallel -u --timeout 1 show_signals Output: Same as above. You can change this to B, B, B: echo | parallel --termseq INT,200,TERM,100,KILL,25 -u --timeout 1 show_signals Output: Got INT Got TERM The B does not show because it cannot be caught, and thus the child dies. =head2 Limiting the resources To avoid overloading systems GNU B can look at the system load before starting another job: parallel --load 100% echo load is less than {} job per cpu ::: 1 Output: [when then load is less than the number of cpu cores] load is less than 1 job per cpu GNU B can also check if the system is swapping. parallel --noswap echo the system is not swapping ::: now Output: [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 B<--memfree> GNU B can check if there is enough memory free. Additionally, GNU B 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. parallel --memfree 1G echo will run if more than 1 GB is ::: free GNU B can run the jobs with a nice value. This will work both locally and remotely. parallel --nice 17 echo this is being run with nice -n ::: 17 Output: this is being run with nice -n 17 =head1 Remote execution GNU B can run jobs on remote servers. It uses B to communicate with the remote machines. =head2 Sshlogin The most basic sshlogin is B<-S> I: parallel -S $SERVER1 echo running on ::: $SERVER1 Output: running on [$SERVER1] To use a different username prepend the server with I: parallel -S username@$SERVER1 echo running on ::: username@$SERVER1 Output: running on [username@$SERVER1] The special sshlogin B<:> is the local machine: parallel -S : echo running on ::: the_local_machine Output: running on the_local_machine If B is not in $PATH it can be prepended to $SERVER1: parallel -S '/usr/bin/ssh '$SERVER1 echo custom ::: ssh Output: custom ssh The B command can also be given using B<--ssh>: parallel --ssh /usr/bin/ssh -S $SERVER1 echo custom ::: ssh or by setting B<$PARALLEL_SSH>: export PARALLEL_SSH=/usr/bin/ssh parallel -S $SERVER1 echo custom ::: ssh Several servers can be given using multiple B<-S>: parallel -S $SERVER1 -S $SERVER2 echo ::: running on more hosts Output (the order may be different): running on more hosts Or they can be separated by B<,>: parallel -S $SERVER1,$SERVER2 echo ::: running on more hosts Output: Same as above. Or newline: # 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 I with the user on B<$SERVER2>): 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 B<--sshloginfile> will be re-read, so it is possible to both add and remove hosts while running. The special B<--sshloginfile ..> reads from B<~/.parallel/sshloginfile>. To force GNU B to treat a server having a given number of CPU cores prepend the number of core followed by B to the sshlogin: parallel -S 4/$SERVER1 echo force {} cpus on server ::: 4 Output: force 4 cpus on server Servers can be put into groups by prepending I<@groupname> to the server and the group can then be selected by appending I<@groupname> to the argument if using B<--hostgroup>: parallel --hostgroup -S @grp1/$SERVER1 -S @grp2/$SERVER2 echo {} ::: \ run_on_grp1@grp1 run_on_grp2@grp2 Output: run_on_grp1 run_on_grp2 A host can be in multiple groups by separating the groups with B<+>, and you can force GNU B to limit the groups on which the command can be run with B<-S> I<@groupname>: parallel -S @grp1 -S @grp1+grp2/$SERVER1 -S @grp2/SERVER2 echo {} ::: \ run_on_grp1 also_grp1 Output: run_on_grp1 also_grp1 =head2 Transferring files GNU B can transfer the files to be processed to the remote host. It does that using rsync. echo This is input_file > input_file parallel -S $SERVER1 --transferfile {} cat ::: input_file Output: This is input_file If the files are processed into another file, the resulting file can be transferred back: 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 B<--cleanup>: 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 B<--transferfile {} --return --cleanup> called B<--trc>: 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 B can transfer that using B<--basefile> which will transfer the file before the first job: echo common data > common_file parallel --basefile common_file -S $SERVER1 cat common_file\; echo {} ::: foo Output: common data foo To remove it from the remote host after the last job use B<--cleanup>. =head2 Working dir The default working dir on the remote machines is the login dir. This can be changed with B<--workdir> I. Files transferred using B<--transferfile> and B<--return> will be relative to I on remote computers, and the command will be executed in the dir I. The special I value B<...> will create working dirs under B<~/.parallel/tmp> on the remote computers. If B<--cleanup> is given these dirs will be removed. The special I value B<.> uses the current working dir. If the current working dir is beneath your home dir, the value B<.> 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. parallel -S $SERVER1 pwd ::: "" parallel --workdir . -S $SERVER1 pwd ::: "" parallel --workdir ... -S $SERVER1 pwd ::: "" Output: [the login dir on $SERVER1] [current dir relative on $SERVER1] [a dir in ~/.parallel/tmp/...] =head2 Avoid overloading sshd If many jobs are started on the same server, B can be overloaded. GNU B can insert a delay between each job run on the same server: parallel -S $SERVER1 --sshdelay 0.2 echo ::: 1 2 3 Output (the order may be different): 1 2 3 B will be less overloaded if using B<--controlmaster>, which will multiplex ssh connections: parallel --controlmaster -S $SERVER1 echo ::: 1 2 3 Output: Same as above. =head2 Ignore hosts that are down In clusters with many hosts a few of them are often down. GNU B can ignore those hosts. In this case the host 173.194.32.46 is down: parallel --filter-hosts -S 173.194.32.46,$SERVER1 echo ::: bar Output: bar =head2 Running the same commands on all hosts GNU B can run the same command on all the hosts: parallel --onall -S $SERVER1,$SERVER2 echo ::: foo bar Output (the order may be different): foo bar foo bar Often you will just want to run a single command on all hosts with out arguments. B<--nonall> is a no argument B<--onall>: parallel --nonall -S $SERVER1,$SERVER2 echo foo bar Output: foo bar foo bar When B<--tag> is used with B<--nonall> and B<--onall> the B<--tagstring> is the host: parallel --nonall --tag -S $SERVER1,$SERVER2 echo foo bar Output (the order may be different): $SERVER1 foo bar $SERVER2 foo bar B<--jobs> sets the number of servers to log in to in parallel. =head2 Transferring environment variables and functions B is a shell function that transfers all aliases, functions, variables, and arrays. You active it by running: source `which env_parallel.bash` Replace B with the shell you use. Now you can use B instead of B and still have your environment: alias myecho=echo myvar="Joe's var is" env_parallel -S $SERVER1 'myecho $myvar' ::: green Output: Joe's var is green The disadvantage is that if your environment is huge B will fail. When B fails, you can still use B<--env> to tell GNU B to transfer an environment variable to the remote system. MYVAR='foo bar' export MYVAR parallel --env MYVAR -S $SERVER1 echo '$MYVAR' ::: baz Output: foo bar baz This works for functions, too, if your shell is Bash: # 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: in my_func baz GNU B can copy all defined variables and functions to the remote system. It just needs to record which ones to ignore in B<~/.parallel/ignored_vars>. Do that by running this once: parallel --record-env cat ~/.parallel/ignored_vars Output: [list of variables to ignore - including $PATH and $HOME] Now all new variables and functions defined will be copied when using B<--env _>: # 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: foo in my_func2 foo bar =head2 Showing what is actually run B<--verbose> will show the command that would be run on the local machine. When using B<--cat>, B<--pipepart>, or when a job is run on a remote machine, the command is wrapped with helper scripts. B<-vv> shows all of this. parallel -vv --pipepart --block 1M wc :::: num30000 Output: 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: my_func3() { echo in my_func $1 > $1.out } export -f my_func3 parallel -vv --workdir ... --nice 17 --env _ --trc {}.out -S $SERVER1 my_func3 {} ::: abc-file Output will be similar to: ( ssh server -- mkdir -p ./.parallel/tmp/aspire-1928520-1;rsync --protocol 30 -rlDzR -essh ./abc-file server:./.parallel/tmp/aspire-1928520-1 );ssh server -- exec perl -e \''@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64"); eval"@GNU_Parallel";my$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 $_EXIT_status; =head1 Saving to an SQL base (advanced) GNU B can save into an SQL base. Point GNU B to a table and it will put the joblog there together with the variables and the output each in their own column. =head2 CSV as SQL base The simplest is to use a CSV file as the storage table: parallel --sqlandworker csv:////%2Ftmp%2Flog.csv seq ::: 10 ::: 12 13 14 cat /tmp/log.csv Note how '/' in the path must be written as %2F. Output will be similar to: Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,Command,V1,V2,Stdout,Stderr 1,:,1458254498.254,0.069,0,9,0,0,"seq 10 12",10,12,"10 11 12 ", 2,:,1458254498.278,0.080,0,12,0,0,"seq 10 13",10,13,"10 11 12 13 ", 3,:,1458254498.301,0.083,0,15,0,0,"seq 10 14",10,14,"10 11 12 13 14 ", A proper CSV reader (like LibreOffice or R's read.csv) will read this format correctly - even with fields containing newlines as above. If the output is big you may want to put it into files using B<--results>: parallel --results outdir --sqlandworker csv:////%2Ftmp%2Flog2.csv seq ::: 10 ::: 12 13 14 cat /tmp/log2.csv Output will be similar to: Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,Command,V1,V2,Stdout,Stderr 1,:,1458824738.287,0.029,0,9,0,0,"seq 10 12",10,12,outdir/1/10/2/12/stdout,outdir/1/10/2/12/stderr 2,:,1458824738.298,0.025,0,12,0,0,"seq 10 13",10,13,outdir/1/10/2/13/stdout,outdir/1/10/2/13/stderr 3,:,1458824738.309,0.026,0,15,0,0,"seq 10 14",10,14,outdir/1/10/2/14/stdout,outdir/1/10/2/14/stderr =head2 DBURL as table The CSV file is an example of a DBURL. GNU B uses a DBURL to address the table. A DBURL has this format: vendor://[[user][:password]@][host][:port]/[database[/table] Example: mysql://scott:tiger@my.example.com/mydatabase/mytable postgresql://scott:tiger@pg.example.com/mydatabase/mytable sqlite3:///%2Ftmp%2Fmydatabase/mytable csv:////%2Ftmp%2Flog.csv To refer to B with B or B you need to encode the B as B<%2F>. Run a job using B on B in B: DBURL=sqlite3:///%2Ftmp%2Fmydatabase DBURLTABLE=$DBURL/mytable parallel --sqlandworker $DBURLTABLE echo ::: foo bar ::: baz quuz To see the result: sql $DBURL 'SELECT * FROM mytable ORDER BY Seq;' Output will be similar to: 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 B<--joblog>. B and B are data from the input sources. B and B are standard output and standard error, respectively. =head2 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): parallel --sqlmaster $DBURLTABLE echo ::: foo bar ::: baz quuz On the worker machines you run exactly the same command except you replace B<--sqlmaster> with B<--sqlworker>. parallel --sqlworker $DBURLTABLE echo ::: foo bar ::: baz quuz To run a master and a worker on the same machine use B<--sqlandworker> as shown earlier. =head1 --pipe The B<--pipe> functionality puts GNU B 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: command_A | command_B | command_C where command_B is slow, and you want to speed up command_B. =head2 Chunk size By default GNU B 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. cat num1000000 | parallel --pipe wc Output (the order may be different): 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 B 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 B<--block>: cat num1000000 | parallel --pipe --block 2M wc Output (the order may be different): 315465 315465 2097150 299593 299593 2097151 299593 299593 2097151 85349 85349 597444 GNU B 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 B<--round-robin>. Without B<--round-robin> GNU B will start a command per block; with B<--round-robin> only the requested number of jobs will be started (B<--jobs>). The records will then be distributed between the running jobs: cat num1000000 | parallel --pipe -j4 --round-robin wc Output will be similar to: 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. =head2 Records GNU B sees the input as records. The default record is a single line. Using B<-N140000> GNU B will read 140000 records at a time: cat num1000000 | parallel --pipe -N140000 wc Output (the order may be different): 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 B<-L> can be used: cat num1000000 | parallel --pipe -L75 wc Output (the order may be different): 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 B still reads a block of around 1 MB; but instead of passing full lines to B 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). =head2 Record separators GNU B uses separators to determine where two records split. B<--recstart> gives the string that starts a record; B<--recend> gives the string that ends a record. The default is B<--recend '\n'> (newline). If both B<--recend> and B<--recstart> are given, then the record will only split if the recend string is immediately followed by the recstart string. Here the B<--recend> is set to B<', '>: echo /foo, bar/, /baz, qux/, | parallel -kN1 --recend ', ' --pipe echo JOB{#}\;cat\;echo END Output: JOB1 /foo, END JOB2 bar/, END JOB3 /baz, END JOB4 qux/, END Here the B<--recstart> is set to B: echo /foo, bar/, /baz, qux/, | parallel -kN1 --recstart / --pipe echo JOB{#}\;cat\;echo END Output: JOB1 /foo, barEND JOB2 /, END JOB3 /baz, quxEND JOB4 /, END Here both B<--recend> and B<--recstart> are set: echo /foo, bar/, /baz, qux/, | parallel -kN1 --recend ', ' --recstart / --pipe echo JOB{#}\;cat\;echo END Output: JOB1 /foo, bar/, END JOB2 /baz, qux/, END Note the difference between setting one string and setting both strings. With B<--regexp> the B<--recend> and B<--recstart> will be treated as a regular expression: echo foo,bar,_baz,__qux, | parallel -kN1 --regexp --recend ,_+ --pipe echo JOB{#}\;cat\;echo END Output: JOB1 foo,bar,_END JOB2 baz,__END JOB3 qux, END GNU B can remove the record separators with B<--remove-rec-sep>/B<--rrs>: echo foo,bar,_baz,__qux, | parallel -kN1 --rrs --regexp --recend ,_+ --pipe echo JOB{#}\;cat\;echo END Output: JOB1 foo,barEND JOB2 bazEND JOB3 qux, END =head2 Header If the input data has a header, the header can be repeated for each job by matching the header with B<--header>. If headers start with B<%> you can do this: cat num_%header | parallel --header '(%.*\n)*' --pipe -N3 echo JOB{#}\;cat Output (the order may be different): 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, B<--header> 2 will work: cat num_%header | parallel --header 2 --pipe -N3 echo JOB{#}\;cat Output: Same as above. =head2 --pipepart B<--pipe> is not very efficient. It maxes out at around 500 MB/s. B<--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 B<-a> or B<::::> and B<-L>/B<-l>/B<-N> do not work. B<--recend> and B<--recstart>, however, I work, and records can often be split on that alone. parallel --pipepart -a num1000000 --block 3m wc Output (the order may be different): 444443 444444 3000002 428572 428572 3000004 126985 126984 888890 =head1 Shebang =head2 Input data and parallel command in the same file GNU B is often called as this: cat input_file | parallel command With B<--shebang> the I and B can be combined into the same script. UNIX shell scripts start with a shebang line like this: #!/bin/bash GNU B can do that, too. With B<--shebang> the arguments can be listed in the file. The B command is the first line of the script: #!/usr/bin/parallel --shebang -r echo foo bar baz Output (the order may be different): foo bar baz =head2 Parallelizing existing scripts GNU B is often called as this: cat input_file | parallel command parallel command ::: foo bar If B is a script, B can be combined into a single file so this will run the script in parallel: cat input_file | command command foo bar This B script B works like B: #!/usr/bin/perl print "@ARGV\n" It can be called as this: parallel perl_echo ::: foo bar By changing the B<#!>-line it can be run in parallel: #!/usr/bin/parallel --shebang-wrap /usr/bin/perl print "@ARGV\n" Thus this will work: perl_echo foo bar Output (the order may be different): foo bar This technique can be used for: =over 9 =item Perl: #!/usr/bin/parallel --shebang-wrap /usr/bin/perl print "Arguments @ARGV\n"; =item Python: #!/usr/bin/parallel --shebang-wrap /usr/bin/python import sys print 'Arguments', str(sys.argv) =item Bash/sh/zsh/Korn shell: #!/usr/bin/parallel --shebang-wrap /bin/bash echo Arguments "$@" =item csh: #!/usr/bin/parallel --shebang-wrap /bin/csh echo Arguments "$argv" =item Tcl: #!/usr/bin/parallel --shebang-wrap /usr/bin/tclsh puts "Arguments $argv" =item R: #!/usr/bin/parallel --shebang-wrap /usr/bin/Rscript --vanilla --slave args <- commandArgs(trailingOnly = TRUE) print(paste("Arguments ",args)) =item GNUplot: #!/usr/bin/parallel --shebang-wrap ARG={} /usr/bin/gnuplot print "Arguments ", system('echo $ARG') =item Ruby: #!/usr/bin/parallel --shebang-wrap /usr/bin/ruby print "Arguments " puts ARGV =item Octave: #!/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"); =item Common LISP: #!/usr/bin/parallel --shebang-wrap /usr/bin/clisp (format t "~&~S~&" 'Arguments) (format t "~&~S~&" *args*) =item PHP: #!/usr/bin/parallel --shebang-wrap /usr/bin/php =item Node.js: #!/usr/bin/parallel --shebang-wrap /usr/bin/node var myArgs = process.argv.slice(2); console.log('Arguments ', myArgs); =item LUA: #!/usr/bin/parallel --shebang-wrap /usr/bin/lua io.write "Arguments" for a = 1, #arg do io.write(" ") io.write(arg[a]) end print("") =item C#: #!/usr/bin/parallel --shebang-wrap ARGV={} /usr/bin/csharp var argv = Environment.GetEnvironmentVariable("ARGV"); print("Arguments "+argv); =back =head1 Semaphore GNU B 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 B is B. B will follow a person to the toilets, wait until a toilet is available, leave the person in the toilet and exit. B 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. B will wait for all persons to leave the toilets. B does not have a queue discipline, so the next person is chosen randomly. B<-j> sets the number of toilets. =head2 Mutex The default is to have only one toilet (this is called a mutex). The program is started in the background and B exits immediately. Use B<--wait> to wait for all Bs to finish: 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: 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 B<--fg>, which will only exit when the command completes: 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 Bs were running in the background only one would run at a time. To control which semaphore is used, use B<--semaphorename>/B<--id>. Run this in one terminal: sem --id my_id -u 'echo First started; sleep 10; echo The first finished' and simultaneously this in another terminal: sem --id my_id -u 'echo Second started; sleep 10; echo The second finished' Note how the second will only be started when the first has finished. =head2 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. B can emulate a counting semaphore. Use B<--jobs> to set the number of toilets like this: sem --jobs 3 --id my_id -u 'echo First started; sleep 5; echo The first finished' && sem --jobs 3 --id my_id -u 'echo Second started; sleep 6; echo The second finished' && sem --jobs 3 --id my_id -u 'echo Third started; sleep 7; echo The third finished' && sem --jobs 3 --id my_id -u 'echo Fourth started; sleep 8; echo The fourth finished' && sem --wait --id my_id Output: First started Second started Third started The first finished Fourth started The second finished The third finished The fourth finished =head2 Timeout With B<--semaphoretimeout> you can force running the command anyway after a period (postive number) or give up (negative number): sem --id foo -u 'echo Slow started; sleep 5; echo Slow ended' && sem --id foo --semaphoretimeout 1 'echo Force this running after 1 sec' && sem --id foo --semaphoretimeout -2 'echo Give up after 1 sec' sem --id foo --wait Output: Slow started parallel: Warning: Semaphore timed out. Stealing the semaphore. Force this running after 1 sec Slow ended parallel: Warning: Semaphore timed out. Exiting. Note how the 'Give up' was not run. =head1 Informational GNU B has some options to give short information about the configuration. B<--help> will print a summary of the most important options: parallel --help Output: 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: parallel --version Output: GNU parallel 20160323 Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017 Ole Tange and Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. GNU parallel comes with no warranty. Web site: http://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 B<--minversion> can be used to ensure the user has at least this version: parallel --minversion 20130722 && echo Your version is at least 20130722. Output: 20160322 Your version is at least 20130722. If you are using GNU B for research the BibTeX citation can be generated using B<--citation>: parallel --citation Output: 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 = {http://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 B<--max-line-length-allowed> GNU B will report the maximal size of the command line: parallel --max-line-length-allowed Output (may vary on different systems): 131071 B<--number-of-cpus> and B<--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: parallel --number-of-cpus parallel --number-of-cores Output (may vary on different systems): 4 64 =head1 Profiles The defaults for GNU B can be changed systemwide by putting the command line options in B. They can be changed for a user by putting them in B<~/.parallel/config>. Profiles work the same way, but have to be referred to with B<--profile>: echo '--nice 17' > ~/.parallel/nicetimeout echo '--timeout 300%' >> ~/.parallel/nicetimeout parallel --profile nicetimeout echo ::: A B C Output: A B C Profiles can be combined: echo '-vv --dry-run' > ~/.parallel/dryverbose parallel --profile dryverbose --profile nicetimeout echo ::: A B C Output: echo A echo B echo C =head1 Spread the word I hope you have learned something from this tutorial. If you like GNU B: =over 2 =item * (Re-)walk through the tutorial if you have not done so in the past year (http://www.gnu.org/software/parallel/parallel_tutorial.html) =item * Give a demo at your local user group/your team/your colleagues =item * Post the intro videos and the tutorial on Reddit, Diaspora*, forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin, and mailing lists =item * Request or write a review for your favourite blog or magazine (especially if you do something cool with GNU B) =item * Invite me for your next conference =back If you use GNU B for research: =over 2 =item * Please cite GNU B in you publications (use B<--citation>) =back If GNU B saves you money: =over 2 =item * (Have your company) donate to FSF or become a member https://my.fsf.org/donate/ =back (C) 2013,2014,2015,2016,2017 Ole Tange, GPLv3 =cut