1PARALLEL_TUTORIAL(7) parallel PARALLEL_TUTORIAL(7)
2
6 This tutorial shows off much of GNU parallel's functionality. The
7 tutorial is meant to learn the options in and syntax of GNU parallel.
8 The tutorial is not to show realistic examples from the real world.
9 Reader's guide
11 If you prefer reading a book buy GNU Parallel 2018 at
12 http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
13 or download it at: https://doi.org/10.5281/zenodo.1146014
14 Otherwise start by watching the intro videos for a quick introduction:
16 http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
17 Then browse through the EXAMPLEs after the list of OPTIONS in man
19 parallel (Use LESS=+/EXAMPLE: man parallel). That will give you an idea
20 of what GNU parallel is capable of.
21 If you want to dive even deeper: spend a couple of hours walking
23 through the tutorial (man parallel_tutorial). Your command line will
24 love you for it.
25 Finally you may want to look at the rest of the manual (man parallel)
27 if you have special needs not already covered.
28 If you want to know the design decisions behind GNU parallel, try: man
30 parallel_design. This is also a good intro if you intend to change GNU
31 parallel.
32
34 To run this tutorial you must have the following:
35 parallel >= version 20160822
37 Install the newest version using your package manager
38 (recommended for security reasons), the way described in
39 README, or with this command:
40 $ (wget -O - pi.dk/3 || lynx -source pi.dk/3 || curl pi.dk/3/ || \
42 fetch -o - http://pi.dk/3 ) > install.sh
43 $ sha1sum install.sh
44 12345678 3374ec53 bacb199b 245af2dd a86df6c9
45 $ md5sum install.sh
46 029a9ac0 6e8b5bc6 052eac57 b2c3c9ca
47 $ sha512sum install.sh
48 40f53af6 9e20dae5 713ba06c f517006d 9897747b ed8a4694 b1acba1b 1464beb4
49 60055629 3f2356f3 3e9c4e3c 76e3f3af a9db4b32 bd33322b 975696fc e6b23cfb
50 $ bash install.sh
51 This will also install the newest version of the tutorial
53 which you can see by running this:
54 man parallel_tutorial
56 Most of the tutorial will work on older versions, too.
58 abc-file:
60 The file can be generated by this command:
61 parallel -k echo ::: A B C > abc-file
63 def-file:
65 The file can be generated by this command:
66 parallel -k echo ::: D E F > def-file
68 abc0-file:
70 The file can be generated by this command:
71 perl -e 'printf "A\0B\0C\0"' > abc0-file
73 abc_-file:
75 The file can be generated by this command:
76 perl -e 'printf "A_B_C_"' > abc_-file
78 tsv-file.tsv
80 The file can be generated by this command:
81 perl -e 'printf "f1\tf2\nA\tB\nC\tD\n"' > tsv-file.tsv
83 num8 The file can be generated by this command:
85 perl -e 'for(1..8){print "$_\n"}' > num8
87 num128 The file can be generated by this command:
89 perl -e 'for(1..128){print "$_\n"}' > num128
91 num30000 The file can be generated by this command:
93 perl -e 'for(1..30000){print "$_\n"}' > num30000
95 num1000000
97 The file can be generated by this command:
98 perl -e 'for(1..1000000){print "$_\n"}' > num1000000
100 num_%header
102 The file can be generated by this command:
103 (echo %head1; echo %head2; \
105 perl -e 'for(1..10){print "$_\n"}') > num_%header
106 fixedlen The file can be generated by this command:
108 perl -e 'print "HHHHAAABBBCCC"' > fixedlen
110 For remote running: ssh login on 2 servers with no password in $SERVER1
112 and $SERVER2 must work.
113 SERVER1=server.example.com
114 SERVER2=server2.example.net
115 So you must be able to do this without entering a password:
117 ssh $SERVER1 echo works
119 ssh $SERVER2 echo works
120 It can be setup by running 'ssh-keygen -t dsa; ssh-copy-id
122 $SERVER1' and using an empty passphrase, or you can use ssh-
123 agent.
124
126 GNU parallel reads input from input sources. These can be files, the
127 command line, and stdin (standard input or a pipe).
128 A single input source
130 Input can be read from the command line:
131 parallel echo ::: A B C
133 Output (the order may be different because the jobs are run in
135 parallel):
136 A
138 B
139 C
140 The input source can be a file:
142 parallel -a abc-file echo
144 Output: Same as above.
146 STDIN (standard input) can be the input source:
148 cat abc-file | parallel echo
150 Output: Same as above.
152 Multiple input sources
154 GNU parallel can take multiple input sources given on the command line.
155 GNU parallel then generates all combinations of the input sources:
156 parallel echo ::: A B C ::: D E F
158 Output (the order may be different):
160 A D
162 A E
163 A F
164 B D
165 B E
166 B F
167 C D
168 C E
169 C F
170 The input sources can be files:
172 parallel -a abc-file -a def-file echo
174 Output: Same as above.
176 STDIN (standard input) can be one of the input sources using -:
178 cat abc-file | parallel -a - -a def-file echo
180 Output: Same as above.
182 Instead of -a files can be given after :::::
184 cat abc-file | parallel echo :::: - def-file
186 Output: Same as above.
188 ::: and :::: can be mixed:
190 parallel echo ::: A B C :::: def-file
192 Output: Same as above.
194 Linking arguments from input sources
196 With --link you can link the input sources and get one argument from
198 each input source:
199 parallel --link echo ::: A B C ::: D E F
201 Output (the order may be different):
203 A D
205 B E
206 C F
207 If one of the input sources is too short, its values will wrap:
209 parallel --link echo ::: A B C D E ::: F G
211 Output (the order may be different):
213 A F
215 B G
216 C F
217 D G
218 E F
219 For more flexible linking you can use :::+ and ::::+. They work like
221 ::: and :::: except they link the previous input source to this input
222 source.
223 This will link ABC to GHI:
225 parallel echo :::: abc-file :::+ G H I :::: def-file
227 Output (the order may be different):
229 A G D
231 A G E
232 A G F
233 B H D
234 B H E
235 B H F
236 C I D
237 C I E
238 C I F
239 This will link GHI to DEF:
241 parallel echo :::: abc-file ::: G H I ::::+ def-file
243 Output (the order may be different):
245 A G D
247 A H E
248 A I F
249 B G D
250 B H E
251 B I F
252 C G D
253 C H E
254 C I F
255 If one of the input sources is too short when using :::+ or ::::+, the
257 rest will be ignored:
258 parallel echo ::: A B C D E :::+ F G
260 Output (the order may be different):
262 A F
264 B G
265 Changing the argument separator.
267 GNU parallel can use other separators than ::: or ::::. This is
268 typically useful if ::: or :::: is used in the command to run:
269 parallel --arg-sep ,, echo ,, A B C :::: def-file
271 Output (the order may be different):
273 A D
275 A E
276 A F
277 B D
278 B E
279 B F
280 C D
281 C E
282 C F
283 Changing the argument file separator:
285 parallel --arg-file-sep // echo ::: A B C // def-file
287 Output: Same as above.
289 Changing the argument delimiter
291 GNU parallel will normally treat a full line as a single argument: It
292 uses \n as argument delimiter. This can be changed with -d:
293 parallel -d _ echo :::: abc_-file
295 Output (the order may be different):
297 A
299 B
300 C
301 NUL can be given as \0:
303 parallel -d '\0' echo :::: abc0-file
305 Output: Same as above.
307 A shorthand for -d '\0' is -0 (this will often be used to read files
309 from find ... -print0):
310 parallel -0 echo :::: abc0-file
312 Output: Same as above.
314 End-of-file value for input source
316 GNU parallel can stop reading when it encounters a certain value:
317 parallel -E stop echo ::: A B stop C D
319 Output:
321 A
323 B
324 Skipping empty lines
326 Using --no-run-if-empty GNU parallel will skip empty lines.
327 (echo 1; echo; echo 2) | parallel --no-run-if-empty echo
329 Output:
331 1
333 2
334
336 No command means arguments are commands
337 If no command is given after parallel the arguments themselves are
338 treated as commands:
339 parallel ::: ls 'echo foo' pwd
341 Output (the order may be different):
343 [list of files in current dir]
345 foo
346 [/path/to/current/working/dir]
347 The command can be a script, a binary or a Bash function if the
349 function is exported using export -f:
350 # Only works in Bash
352 my_func() {
353 echo in my_func $1
354 }
355 export -f my_func
356 parallel my_func ::: 1 2 3
357 Output (the order may be different):
359 in my_func 1
361 in my_func 2
362 in my_func 3
363 Replacement strings
365 The 7 predefined replacement strings
366 GNU parallel has several replacement strings. If no replacement strings
368 are used the default is to append {}:
369 parallel echo ::: A/B.C
371 Output:
373 A/B.C
375 The default replacement string is {}:
377 parallel echo {} ::: A/B.C
379 Output:
381 A/B.C
383 The replacement string {.} removes the extension:
385 parallel echo {.} ::: A/B.C
387 Output:
389 A/B
391 The replacement string {/} removes the path:
393 parallel echo {/} ::: A/B.C
395 Output:
397 B.C
399 The replacement string {//} keeps only the path:
401 parallel echo {//} ::: A/B.C
403 Output:
405 A
407 The replacement string {/.} removes the path and the extension:
409 parallel echo {/.} ::: A/B.C
411 Output:
413 B
415 The replacement string {#} gives the job number:
417 parallel echo {#} ::: A B C
419 Output (the order may be different):
421 1
423 2
424 3
425 The replacement string {%} gives the job slot number (between 1 and
427 number of jobs to run in parallel):
428 parallel -j 2 echo {%} ::: A B C
430 Output (the order may be different and 1 and 2 may be swapped):
432 1
434 2
435 1
436 Changing the replacement strings
438 The replacement string {} can be changed with -I:
440 parallel -I ,, echo ,, ::: A/B.C
442 Output:
444 A/B.C
446 The replacement string {.} can be changed with --extensionreplace:
448 parallel --extensionreplace ,, echo ,, ::: A/B.C
450 Output:
452 A/B
454 The replacement string {/} can be replaced with --basenamereplace:
456 parallel --basenamereplace ,, echo ,, ::: A/B.C
458 Output:
460 B.C
462 The replacement string {//} can be changed with --dirnamereplace:
464 parallel --dirnamereplace ,, echo ,, ::: A/B.C
466 Output:
468 A
470 The replacement string {/.} can be changed with
472 --basenameextensionreplace:
473 parallel --basenameextensionreplace ,, echo ,, ::: A/B.C
475 Output:
477 B
479 The replacement string {#} can be changed with --seqreplace:
481 parallel --seqreplace ,, echo ,, ::: A B C
483 Output (the order may be different):
485 1
487 2
488 3
489 The replacement string {%} can be changed with --slotreplace:
491 parallel -j2 --slotreplace ,, echo ,, ::: A B C
493 Output (the order may be different and 1 and 2 may be swapped):
495 1
497 2
498 1
499 Perl expression replacement string
501 When predefined replacement strings are not flexible enough a perl
503 expression can be used instead. One example is to remove two
504 extensions: foo.tar.gz becomes foo
505 parallel echo '{= s:\.[^.]+$::;s:\.[^.]+$::; =}' ::: foo.tar.gz
507 Output:
509 foo
511 In {= =} you can access all of GNU parallel's internal functions and
513 variables. A few are worth mentioning.
514 total_jobs() returns the total number of jobs:
516 parallel echo Job {#} of {= '$_=total_jobs()' =} ::: {1..5}
518 Output:
520 Job 1 of 5
522 Job 2 of 5
523 Job 3 of 5
524 Job 4 of 5
525 Job 5 of 5
526 Q(...) shell quotes the string:
528 parallel echo {} shell quoted is {= '$_=Q($_)' =} ::: '*/!#$'
530 Output:
532 */!#$ shell quoted is \*/\!\#\$
534 skip() skips the job:
536 parallel echo {= 'if($_==3) { skip() }' =} ::: {1..5}
538 Output:
540 1
542 2
543 4
544 5
545 @arg contains the input source variables:
547 parallel echo {= 'if($arg[1]==$arg[2]) { skip() }' =} \
549 ::: {1..3} ::: {1..3}
550 Output:
552 1 2
554 1 3
555 2 1
556 2 3
557 3 1
558 3 2
559 If the strings {= and =} cause problems they can be replaced with
561 --parens:
562 parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' \
564 ::: foo.tar.gz
565 Output:
567 foo
569 To define a shorthand replacement string use --rpl:
571 parallel --rpl '.. s:\.[^.]+$::;s:\.[^.]+$::;' echo '..' \
573 ::: foo.tar.gz
574 Output: Same as above.
576 If the shorthand starts with { it can be used as a positional
578 replacement string, too:
579 parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{..}'
581 ::: foo.tar.gz
582 Output: Same as above.
584 If the shorthand contains matching parenthesis the replacement string
586 becomes a dynamic replacement string and the string in the parenthesis
587 can be accessed as $$1. If there are multiple matching parenthesis, the
588 matched strings can be accessed using $$2, $$3 and so on.
589 You can think of this as giving arguments to the replacement string.
591 Here we give the argument .tar.gz to the replacement string {%string}
592 which removes string:
593 parallel --rpl '{%(.+?)} s/$$1$//;' echo {%.tar.gz}.zip ::: foo.tar.gz
595 Output:
597 foo.zip
599 Here we give the two arguments tar.gz and zip to the replacement string
601 {/string1/string2} which replaces string1 with string2:
602 parallel --rpl '{/(.+?)/(.*?)} s/$$1/$$2/;' echo {/tar.gz/zip} \
604 ::: foo.tar.gz
605 Output:
607 foo.zip
609 GNU parallel's 7 replacement strings are implemented as this:
611 --rpl '{} '
613 --rpl '{#} $_=$job->seq()'
614 --rpl '{%} $_=$job->slot()'
615 --rpl '{/} s:.*/::'
616 --rpl '{//} $Global::use{"File::Basename"} ||=
617 eval "use File::Basename; 1;"; $_ = dirname($_);'
618 --rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
619 --rpl '{.} s:\.[^/.]+$::'
620 Positional replacement strings
622 With multiple input sources the argument from the individual input
624 sources can be accessed with {number}:
625 parallel echo {1} and {2} ::: A B ::: C D
627 Output (the order may be different):
629 A and C
631 A and D
632 B and C
633 B and D
634 The positional replacement strings can also be modified using /, //,
636 /., and .:
637 parallel echo /={1/} //={1//} /.={1/.} .={1.} ::: A/B.C D/E.F
639 Output (the order may be different):
641 /=B.C //=A /.=B .=A/B
643 /=E.F //=D /.=E .=D/E
644 If a position is negative, it will refer to the input source counted
646 from behind:
647 parallel echo 1={1} 2={2} 3={3} -1={-1} -2={-2} -3={-3} \
649 ::: A B ::: C D ::: E F
650 Output (the order may be different):
652 1=A 2=C 3=E -1=E -2=C -3=A
654 1=A 2=C 3=F -1=F -2=C -3=A
655 1=A 2=D 3=E -1=E -2=D -3=A
656 1=A 2=D 3=F -1=F -2=D -3=A
657 1=B 2=C 3=E -1=E -2=C -3=B
658 1=B 2=C 3=F -1=F -2=C -3=B
659 1=B 2=D 3=E -1=E -2=D -3=B
660 1=B 2=D 3=F -1=F -2=D -3=B
661 Positional perl expression replacement string
663 To use a perl expression as a positional replacement string simply
665 prepend the perl expression with number and space:
666 parallel echo '{=2 s:\.[^.]+$::;s:\.[^.]+$::; =} {1}' \
668 ::: bar ::: foo.tar.gz
669 Output:
671 foo bar
673 If a shorthand defined using --rpl starts with { it can be used as a
675 positional replacement string, too:
676 parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' \
678 ::: bar ::: foo.tar.gz
679 Output: Same as above.
681 Input from columns
683 The columns in a file can be bound to positional replacement strings
685 using --colsep. Here the columns are separated by TAB (\t):
686 parallel --colsep '\t' echo 1={1} 2={2} :::: tsv-file.tsv
688 Output (the order may be different):
690 1=f1 2=f2
692 1=A 2=B
693 1=C 2=D
694 Header defined replacement strings
696 With --header GNU parallel will use the first value of the input source
698 as the name of the replacement string. Only the non-modified version {}
699 is supported:
700 parallel --header : echo f1={f1} f2={f2} ::: f1 A B ::: f2 C D
702 Output (the order may be different):
704 f1=A f2=C
706 f1=A f2=D
707 f1=B f2=C
708 f1=B f2=D
709 It is useful with --colsep for processing files with TAB separated
711 values:
712 parallel --header : --colsep '\t' echo f1={f1} f2={f2} \
714 :::: tsv-file.tsv
715 Output (the order may be different):
717 f1=A f2=B
719 f1=C f2=D
720 More pre-defined replacement strings with --plus
722 --plus adds the replacement strings {+/} {+.} {+..} {+...} {..} {...}
724 {/..} {/...} {##}. The idea being that {+foo} matches the opposite of
725 {foo} and {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} =
726 {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}.
727 parallel --plus echo {} ::: dir/sub/file.ex1.ex2.ex3
729 parallel --plus echo {+/}/{/} ::: dir/sub/file.ex1.ex2.ex3
730 parallel --plus echo {.}.{+.} ::: dir/sub/file.ex1.ex2.ex3
731 parallel --plus echo {+/}/{/.}.{+.} ::: dir/sub/file.ex1.ex2.ex3
732 parallel --plus echo {..}.{+..} ::: dir/sub/file.ex1.ex2.ex3
733 parallel --plus echo {+/}/{/..}.{+..} ::: dir/sub/file.ex1.ex2.ex3
734 parallel --plus echo {...}.{+...} ::: dir/sub/file.ex1.ex2.ex3
735 parallel --plus echo {+/}/{/...}.{+...} ::: dir/sub/file.ex1.ex2.ex3
736 Output:
738 dir/sub/file.ex1.ex2.ex3
740 {##} is simply the number of jobs:
742 parallel --plus echo Job {#} of {##} ::: {1..5}
744 Output:
746 Job 1 of 5
748 Job 2 of 5
749 Job 3 of 5
750 Job 4 of 5
751 Job 5 of 5
752 Dynamic replacement strings with --plus
754 --plus also defines these dynamic replacement strings:
756 {:-string} Default value is string if the argument is empty.
758 {:number} Substring from number till end of string.
760 {:number1:number2} Substring from number1 to number2.
762 {#string} If the argument starts with string, remove it.
764 {%string} If the argument ends with string, remove it.
766 {/string1/string2} Replace string1 with string2.
768 {^string} If the argument starts with string, upper case it.
770 string must be a single letter.
771 {^^string} If the argument contains string, upper case it.
773 string must be a single letter.
774 {,string} If the argument starts with string, lower case it.
776 string must be a single letter.
777 {,,string} If the argument contains string, lower case it.
779 string must be a single letter.
780 They are inspired from Bash:
782 unset myvar
784 echo ${myvar:-myval}
785 parallel --plus echo {:-myval} ::: "$myvar"
786 myvar=abcAaAdef
788 echo ${myvar:2}
789 parallel --plus echo {:2} ::: "$myvar"
790 echo ${myvar:2:3}
792 parallel --plus echo {:2:3} ::: "$myvar"
793 echo ${myvar#bc}
795 parallel --plus echo {#bc} ::: "$myvar"
796 echo ${myvar#abc}
797 parallel --plus echo {#abc} ::: "$myvar"
798 echo ${myvar%de}
800 parallel --plus echo {%de} ::: "$myvar"
801 echo ${myvar%def}
802 parallel --plus echo {%def} ::: "$myvar"
803 echo ${myvar/def/ghi}
805 parallel --plus echo {/def/ghi} ::: "$myvar"
806 echo ${myvar^a}
808 parallel --plus echo {^a} ::: "$myvar"
809 echo ${myvar^^a}
810 parallel --plus echo {^^a} ::: "$myvar"
811 myvar=AbcAaAdef
813 echo ${myvar,A}
814 parallel --plus echo '{,A}' ::: "$myvar"
815 echo ${myvar,,A}
816 parallel --plus echo '{,,A}' ::: "$myvar"
817 Output:
819 myval
821 myval
822 cAaAdef
823 cAaAdef
824 cAa
825 cAa
826 abcAaAdef
827 abcAaAdef
828 AaAdef
829 AaAdef
830 abcAaAdef
831 abcAaAdef
832 abcAaA
833 abcAaA
834 abcAaAghi
835 abcAaAghi
836 AbcAaAdef
837 AbcAaAdef
838 AbcAAAdef
839 AbcAAAdef
840 abcAaAdef
841 abcAaAdef
842 abcaaadef
843 abcaaadef
844 More than one argument
846 With --xargs GNU parallel will fit as many arguments as possible on a
847 single line:
848 cat num30000 | parallel --xargs echo | wc -l
850 Output (if you run this under Bash on GNU/Linux):
852 2
854 The 30000 arguments fitted on 2 lines.
856 The maximal length of a single line can be set with -s. With a maximal
858 line length of 10000 chars 17 commands will be run:
859 cat num30000 | parallel --xargs -s 10000 echo | wc -l
861 Output:
863 17
865 For better parallelism GNU parallel can distribute the arguments
867 between all the parallel jobs when end of file is met.
868 Below GNU parallel reads the last argument when generating the second
870 job. When GNU parallel reads the last argument, it spreads all the
871 arguments for the second job over 4 jobs instead, as 4 parallel jobs
872 are requested.
873 The first job will be the same as the --xargs example above, but the
875 second job will be split into 4 evenly sized jobs, resulting in a total
876 of 5 jobs:
877 cat num30000 | parallel --jobs 4 -m echo | wc -l
879 Output (if you run this under Bash on GNU/Linux):
881 5
883 This is even more visible when running 4 jobs with 10 arguments. The 10
885 arguments are being spread over 4 jobs:
886 parallel --jobs 4 -m echo ::: 1 2 3 4 5 6 7 8 9 10
888 Output:
890 1 2 3
892 4 5 6
893 7 8 9
894 10
895 A replacement string can be part of a word. -m will not repeat the
897 context:
898 parallel --jobs 4 -m echo pre-{}-post ::: A B C D E F G
900 Output (the order may be different):
902 pre-A B-post
904 pre-C D-post
905 pre-E F-post
906 pre-G-post
907 To repeat the context use -X which otherwise works like -m:
909 parallel --jobs 4 -X echo pre-{}-post ::: A B C D E F G
911 Output (the order may be different):
913 pre-A-post pre-B-post
915 pre-C-post pre-D-post
916 pre-E-post pre-F-post
917 pre-G-post
918 To limit the number of arguments use -N:
920 parallel -N3 echo ::: A B C D E F G H
922 Output (the order may be different):
924 A B C
926 D E F
927 G H
928 -N also sets the positional replacement strings:
930 parallel -N3 echo 1={1} 2={2} 3={3} ::: A B C D E F G H
932 Output (the order may be different):
934 1=A 2=B 3=C
936 1=D 2=E 3=F
937 1=G 2=H 3=
938 -N0 reads 1 argument but inserts none:
940 parallel -N0 echo foo ::: 1 2 3
942 Output:
944 foo
946 foo
947 foo
948 Quoting
950 Command lines that contain special characters may need to be protected
951 from the shell.
952 The perl program print "@ARGV\n" basically works like echo.
954 perl -e 'print "@ARGV\n"' A
956 Output:
958 A
960 To run that in parallel the command needs to be quoted:
962 parallel perl -e 'print "@ARGV\n"' ::: This wont work
964 Output:
966 [Nothing]
968 To quote the command use -q:
970 parallel -q perl -e 'print "@ARGV\n"' ::: This works
972 Output (the order may be different):
974 This
976 works
977 Or you can quote the critical part using \':
979 parallel perl -e \''print "@ARGV\n"'\' ::: This works, too
981 Output (the order may be different):
983 This
985 works,
986 too
987 GNU parallel can also \-quote full lines. Simply run this:
989 parallel --shellquote
991 Warning: Input is read from the terminal. You either know what you
992 Warning: are doing (in which case: YOU ARE AWESOME!) or you forgot
993 Warning: ::: or :::: or to pipe data into parallel. If so
994 Warning: consider going through the tutorial: man parallel_tutorial
995 Warning: Press CTRL-D to exit.
996 perl -e 'print "@ARGV\n"'
997 [CTRL-D]
998 Output:
1000 perl\ -e\ \'print\ \"@ARGV\\n\"\'
1002 This can then be used as the command:
1004 parallel perl\ -e\ \'print\ \"@ARGV\\n\"\' ::: This also works
1006 Output (the order may be different):
1008 This
1010 also
1011 works
1012 Trimming space
1014 Space can be trimmed on the arguments using --trim:
1015 parallel --trim r echo pre-{}-post ::: ' A '
1017 Output:
1019 pre- A-post
1021 To trim on the left side:
1023 parallel --trim l echo pre-{}-post ::: ' A '
1025 Output:
1027 pre-A -post
1029 To trim on the both sides:
1031 parallel --trim lr echo pre-{}-post ::: ' A '
1033 Output:
1035 pre-A-post
1037 Respecting the shell
1039 This tutorial uses Bash as the shell. GNU parallel respects which shell
1040 you are using, so in zsh you can do:
1041 parallel echo \={} ::: zsh bash ls
1043 Output:
1045 /usr/bin/zsh
1047 /bin/bash
1048 /bin/ls
1049 In csh you can do:
1051 parallel 'set a="{}"; if( { test -d "$a" } ) echo "$a is a dir"' ::: *
1053 Output:
1055 [somedir] is a dir
1057 This also becomes useful if you use GNU parallel in a shell script: GNU
1059 parallel will use the same shell as the shell script.
1060
1062 The output can prefixed with the argument:
1063 parallel --tag echo foo-{} ::: A B C
1065 Output (the order may be different):
1067 A foo-A
1069 B foo-B
1070 C foo-C
1071 To prefix it with another string use --tagstring:
1073 parallel --tagstring {}-bar echo foo-{} ::: A B C
1075 Output (the order may be different):
1077 A-bar foo-A
1079 B-bar foo-B
1080 C-bar foo-C
1081 To see what commands will be run without running them use --dryrun:
1083 parallel --dryrun echo {} ::: A B C
1085 Output (the order may be different):
1087 echo A
1089 echo B
1090 echo C
1091 To print the command before running them use --verbose:
1093 parallel --verbose echo {} ::: A B C
1095 Output (the order may be different):
1097 echo A
1099 echo B
1100 A
1101 echo C
1102 B
1103 C
1104 GNU parallel will postpone the output until the command completes:
1106 parallel -j2 'printf "%s-start\n%s" {} {};
1108 sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1
1109 Output:
1111 2-start
1113 2-middle
1114 2-end
1115 1-start
1116 1-middle
1117 1-end
1118 4-start
1119 4-middle
1120 4-end
1121 To get the output immediately use --ungroup:
1123 parallel -j2 --ungroup 'printf "%s-start\n%s" {} {};
1125 sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1
1126 Output:
1128 4-start
1130 42-start
1131 2-middle
1132 2-end
1133 1-start
1134 1-middle
1135 1-end
1136 -middle
1137 4-end
1138 --ungroup is fast, but can cause half a line from one job to be mixed
1140 with half a line of another job. That has happened in the second line,
1141 where the line '4-middle' is mixed with '2-start'.
1142 To avoid this use --linebuffer:
1144 parallel -j2 --linebuffer 'printf "%s-start\n%s" {} {};
1146 sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1
1147 Output:
1149 4-start
1151 2-start
1152 2-middle
1153 2-end
1154 1-start
1155 1-middle
1156 1-end
1157 4-middle
1158 4-end
1159 To force the output in the same order as the arguments use
1161 --keep-order/-k:
1162 parallel -j2 -k 'printf "%s-start\n%s" {} {};
1164 sleep {};printf "%s\n" -middle;echo {}-end' ::: 4 2 1
1165 Output:
1167 4-start
1169 4-middle
1170 4-end
1171 2-start
1172 2-middle
1173 2-end
1174 1-start
1175 1-middle
1176 1-end
1177 Saving output into files
1179 GNU parallel can save the output of each job into files:
1180 parallel --files echo ::: A B C
1182 Output will be similar to this:
1184 /tmp/pAh6uWuQCg.par
1186 /tmp/opjhZCzAX4.par
1187 /tmp/W0AT_Rph2o.par
1188 By default GNU parallel will cache the output in files in /tmp. This
1190 can be changed by setting $TMPDIR or --tmpdir:
1191 parallel --tmpdir /var/tmp --files echo ::: A B C
1193 Output will be similar to this:
1195 /var/tmp/N_vk7phQRc.par
1197 /var/tmp/7zA4Ccf3wZ.par
1198 /var/tmp/LIuKgF_2LP.par
1199 Or:
1201 TMPDIR=/var/tmp parallel --files echo ::: A B C
1203 Output: Same as above.
1205 The output files can be saved in a structured way using --results:
1207 parallel --results outdir echo ::: A B C
1209 Output:
1211 A
1213 B
1214 C
1215 These files were also generated containing the standard output
1217 (stdout), standard error (stderr), and the sequence number (seq):
1218 outdir/1/A/seq
1220 outdir/1/A/stderr
1221 outdir/1/A/stdout
1222 outdir/1/B/seq
1223 outdir/1/B/stderr
1224 outdir/1/B/stdout
1225 outdir/1/C/seq
1226 outdir/1/C/stderr
1227 outdir/1/C/stdout
1228 --header : will take the first value as name and use that in the
1230 directory structure. This is useful if you are using multiple input
1231 sources:
1232 parallel --header : --results outdir echo ::: f1 A B ::: f2 C D
1234 Generated files:
1236 outdir/f1/A/f2/C/seq
1238 outdir/f1/A/f2/C/stderr
1239 outdir/f1/A/f2/C/stdout
1240 outdir/f1/A/f2/D/seq
1241 outdir/f1/A/f2/D/stderr
1242 outdir/f1/A/f2/D/stdout
1243 outdir/f1/B/f2/C/seq
1244 outdir/f1/B/f2/C/stderr
1245 outdir/f1/B/f2/C/stdout
1246 outdir/f1/B/f2/D/seq
1247 outdir/f1/B/f2/D/stderr
1248 outdir/f1/B/f2/D/stdout
1249 The directories are named after the variables and their values.
1251
1253 Number of simultaneous jobs
1254 The number of concurrent jobs is given with --jobs/-j:
1255 /usr/bin/time parallel -N0 -j64 sleep 1 :::: num128
1257 With 64 jobs in parallel the 128 sleeps will take 2-8 seconds to run -
1259 depending on how fast your machine is.
1260 By default --jobs is the same as the number of CPU cores. So this:
1262 /usr/bin/time parallel -N0 sleep 1 :::: num128
1264 should take twice the time of running 2 jobs per CPU core:
1266 /usr/bin/time parallel -N0 --jobs 200% sleep 1 :::: num128
1268 --jobs 0 will run as many jobs in parallel as possible:
1270 /usr/bin/time parallel -N0 --jobs 0 sleep 1 :::: num128
1272 which should take 1-7 seconds depending on how fast your machine is.
1274 --jobs can read from a file which is re-read when a job finishes:
1276 echo 50% > my_jobs
1278 /usr/bin/time parallel -N0 --jobs my_jobs sleep 1 :::: num128 &
1279 sleep 1
1280 echo 0 > my_jobs
1281 wait
1282 The first second only 50% of the CPU cores will run a job. Then 0 is
1284 put into my_jobs and then the rest of the jobs will be started in
1285 parallel.
1286 Instead of basing the percentage on the number of CPU cores GNU
1288 parallel can base it on the number of CPUs:
1289 parallel --use-cpus-instead-of-cores -N0 sleep 1 :::: num8
1291 Shuffle job order
1293 If you have many jobs (e.g. by multiple combinations of input sources),
1294 it can be handy to shuffle the jobs, so you get different values run.
1295 Use --shuf for that:
1296 parallel --shuf echo ::: 1 2 3 ::: a b c ::: A B C
1298 Output:
1300 All combinations but different order for each run.
1302 Interactivity
1304 GNU parallel can ask the user if a command should be run using
1305 --interactive:
1306 parallel --interactive echo ::: 1 2 3
1308 Output:
1310 echo 1 ?...y
1312 echo 2 ?...n
1313 1
1314 echo 3 ?...y
1315 3
1316 GNU parallel can be used to put arguments on the command line for an
1318 interactive command such as emacs to edit one file at a time:
1319 parallel --tty emacs ::: 1 2 3
1321 Or give multiple argument in one go to open multiple files:
1323 parallel -X --tty vi ::: 1 2 3
1325 A terminal for every job
1327 Using --tmux GNU parallel can start a terminal for every job run:
1328 seq 10 20 | parallel --tmux 'echo start {}; sleep {}; echo done {}'
1330 This will tell you to run something similar to:
1332 tmux -S /tmp/tmsrPrO0 attach
1334 Using normal tmux keystrokes (CTRL-b n or CTRL-b p) you can cycle
1336 between windows of the running jobs. When a job is finished it will
1337 pause for 10 seconds before closing the window.
1338 Timing
1340 Some jobs do heavy I/O when they start. To avoid a thundering herd GNU
1341 parallel can delay starting new jobs. --delay X will make sure there is
1342 at least X seconds between each start:
1343 parallel --delay 2.5 echo Starting {}\;date ::: 1 2 3
1345 Output:
1347 Starting 1
1349 Thu Aug 15 16:24:33 CEST 2013
1350 Starting 2
1351 Thu Aug 15 16:24:35 CEST 2013
1352 Starting 3
1353 Thu Aug 15 16:24:38 CEST 2013
1354 If jobs taking more than a certain amount of time are known to fail,
1356 they can be stopped with --timeout. The accuracy of --timeout is 2
1357 seconds:
1358 parallel --timeout 4.1 sleep {}\; echo {} ::: 2 4 6 8
1360 Output:
1362 2
1364 4
1365 GNU parallel can compute the median runtime for jobs and kill those
1367 that take more than 200% of the median runtime:
1368 parallel --timeout 200% sleep {}\; echo {} ::: 2.1 2.2 3 7 2.3
1370 Output:
1372 2.1
1374 2.2
1375 3
1376 2.3
1377 Progress information
1379 Based on the runtime of completed jobs GNU parallel can estimate the
1380 total runtime:
1381 parallel --eta sleep ::: 1 3 2 2 1 3 3 2 1
1383 Output:
1385 Computers / CPU cores / Max jobs to run
1387 1:local / 2 / 2
1388 Computer:jobs running/jobs completed/%of started jobs/
1390 Average seconds to complete
1391 ETA: 2s 0left 1.11avg local:0/9/100%/1.1s
1392 GNU parallel can give progress information with --progress:
1394 parallel --progress sleep ::: 1 3 2 2 1 3 3 2 1
1396 Output:
1398 Computers / CPU cores / Max jobs to run
1400 1:local / 2 / 2
1401 Computer:jobs running/jobs completed/%of started jobs/
1403 Average seconds to complete
1404 local:0/9/100%/1.1s
1405 A progress bar can be shown with --bar:
1407 parallel --bar sleep ::: 1 3 2 2 1 3 3 2 1
1409 And a graphic bar can be shown with --bar and zenity:
1411 seq 1000 | parallel -j10 --bar '(echo -n {};sleep 0.1)' \
1413 2> >(zenity --progress --auto-kill --auto-close)
1414 A logfile of the jobs completed so far can be generated with --joblog:
1416 parallel --joblog /tmp/log exit ::: 1 2 3 0
1418 cat /tmp/log
1419 Output:
1421 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1423 1 : 1376577364.974 0.008 0 0 1 0 exit 1
1424 2 : 1376577364.982 0.013 0 0 2 0 exit 2
1425 3 : 1376577364.990 0.013 0 0 3 0 exit 3
1426 4 : 1376577365.003 0.003 0 0 0 0 exit 0
1427 The log contains the job sequence, which host the job was run on, the
1429 start time and run time, how much data was transferred, the exit value,
1430 the signal that killed the job, and finally the command being run.
1431 With a joblog GNU parallel can be stopped and later pickup where it
1433 left off. It it important that the input of the completed jobs is
1434 unchanged.
1435 parallel --joblog /tmp/log exit ::: 1 2 3 0
1437 cat /tmp/log
1438 parallel --resume --joblog /tmp/log exit ::: 1 2 3 0 0 0
1439 cat /tmp/log
1440 Output:
1442 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1444 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1445 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1446 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1447 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1448 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1450 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1451 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1452 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1453 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1454 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1455 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1456 Note how the start time of the last 2 jobs is clearly different from
1458 the second run.
1459 With --resume-failed GNU parallel will re-run the jobs that failed:
1461 parallel --resume-failed --joblog /tmp/log exit ::: 1 2 3 0 0 0
1463 cat /tmp/log
1464 Output:
1466 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1468 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1469 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1470 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1471 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1472 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1473 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1474 1 : 1376580154.433 0.010 0 0 1 0 exit 1
1475 2 : 1376580154.444 0.022 0 0 2 0 exit 2
1476 3 : 1376580154.466 0.005 0 0 3 0 exit 3
1477 Note how seq 1 2 3 have been repeated because they had exit value
1479 different from 0.
1480 --retry-failed does almost the same as --resume-failed. Where
1482 --resume-failed reads the commands from the command line (and ignores
1483 the commands in the joblog), --retry-failed ignores the command line
1484 and reruns the commands mentioned in the joblog.
1485 parallel --retry-failed --joblog /tmp/log
1487 cat /tmp/log
1488 Output:
1490 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1492 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1493 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1494 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1495 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1496 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1497 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1498 1 : 1376580154.433 0.010 0 0 1 0 exit 1
1499 2 : 1376580154.444 0.022 0 0 2 0 exit 2
1500 3 : 1376580154.466 0.005 0 0 3 0 exit 3
1501 1 : 1376580164.633 0.010 0 0 1 0 exit 1
1502 2 : 1376580164.644 0.022 0 0 2 0 exit 2
1503 3 : 1376580164.666 0.005 0 0 3 0 exit 3
1504 Termination
1506 Unconditional termination
1507 By default GNU parallel will wait for all jobs to finish before
1509 exiting.
1510 If you send GNU parallel the TERM signal, GNU parallel will stop
1512 spawning new jobs and wait for the remaining jobs to finish. If you
1513 send GNU parallel the TERM signal again, GNU parallel will kill all
1514 running jobs and exit.
1515 Termination dependent on job status
1517 For certain jobs there is no need to continue if one of the jobs fails
1519 and has an exit code different from 0. GNU parallel will stop spawning
1520 new jobs with --halt soon,fail=1:
1521 parallel -j2 --halt soon,fail=1 echo {}\; exit {} ::: 0 0 1 2 3
1523 Output:
1525 0
1527 0
1528 1
1529 parallel: This job failed:
1530 echo 1; exit 1
1531 parallel: Starting no more jobs. Waiting for 1 jobs to finish.
1532 2
1533 With --halt now,fail=1 the running jobs will be killed immediately:
1535 parallel -j2 --halt now,fail=1 echo {}\; exit {} ::: 0 0 1 2 3
1537 Output:
1539 0
1541 0
1542 1
1543 parallel: This job failed:
1544 echo 1; exit 1
1545 If --halt is given a percentage this percentage of the jobs must fail
1547 before GNU parallel stops spawning more jobs:
1548 parallel -j2 --halt soon,fail=20% echo {}\; exit {} \
1550 ::: 0 1 2 3 4 5 6 7 8 9
1551 Output:
1553 0
1555 1
1556 parallel: This job failed:
1557 echo 1; exit 1
1558 2
1559 parallel: This job failed:
1560 echo 2; exit 2
1561 parallel: Starting no more jobs. Waiting for 1 jobs to finish.
1562 3
1563 parallel: This job failed:
1564 echo 3; exit 3
1565 If you are looking for success instead of failures, you can use
1567 success. This will finish as soon as the first job succeeds:
1568 parallel -j2 --halt now,success=1 echo {}\; exit {} ::: 1 2 3 0 4 5 6
1570 Output:
1572 1
1574 2
1575 3
1576 0
1577 parallel: This job succeeded:
1578 echo 0; exit 0
1579 GNU parallel can retry the command with --retries. This is useful if a
1581 command fails for unknown reasons now and then.
1582 parallel -k --retries 3 \
1584 'echo tried {} >>/tmp/runs; echo completed {}; exit {}' ::: 1 2 0
1585 cat /tmp/runs
1586 Output:
1588 completed 1
1590 completed 2
1591 completed 0
1592 tried 1
1594 tried 2
1595 tried 1
1596 tried 2
1597 tried 1
1598 tried 2
1599 tried 0
1600 Note how job 1 and 2 were tried 3 times, but 0 was not retried because
1602 it had exit code 0.
1603 Termination signals (advanced)
1605 Using --termseq you can control which signals are sent when killing
1607 children. Normally children will be killed by sending them SIGTERM,
1608 waiting 200 ms, then another SIGTERM, waiting 100 ms, then another
1609 SIGTERM, waiting 50 ms, then a SIGKILL, finally waiting 25 ms before
1610 giving up. It looks like this:
1611 show_signals() {
1613 perl -e 'for(keys %SIG) {
1614 $SIG{$_} = eval "sub { print \"Got $_\\n\"; }";
1615 }
1616 while(1){sleep 1}'
1617 }
1618 export -f show_signals
1619 echo | parallel --termseq TERM,200,TERM,100,TERM,50,KILL,25 \
1620 -u --timeout 1 show_signals
1621 Output:
1623 Got TERM
1625 Got TERM
1626 Got TERM
1627 Or just:
1629 echo | parallel -u --timeout 1 show_signals
1631 Output: Same as above.
1633 You can change this to SIGINT, SIGTERM, SIGKILL:
1635 echo | parallel --termseq INT,200,TERM,100,KILL,25 \
1637 -u --timeout 1 show_signals
1638 Output:
1640 Got INT
1642 Got TERM
1643 The SIGKILL does not show because it cannot be caught, and thus the
1645 child dies.
1646 Limiting the resources
1648 To avoid overloading systems GNU parallel can look at the system load
1649 before starting another job:
1650 parallel --load 100% echo load is less than {} job per cpu ::: 1
1652 Output:
1654 [when then load is less than the number of cpu cores]
1656 load is less than 1 job per cpu
1657 GNU parallel can also check if the system is swapping.
1659 parallel --noswap echo the system is not swapping ::: now
1661 Output:
1663 [when then system is not swapping]
1665 the system is not swapping now
1666 Some jobs need a lot of memory, and should only be started when there
1668 is enough memory free. Using --memfree GNU parallel can check if there
1669 is enough memory free. Additionally, GNU parallel will kill off the
1670 youngest job if the memory free falls below 50% of the size. The killed
1671 job will put back on the queue and retried later.
1672 parallel --memfree 1G echo will run if more than 1 GB is ::: free
1674 GNU parallel can run the jobs with a nice value. This will work both
1676 locally and remotely.
1677 parallel --nice 17 echo this is being run with nice -n ::: 17
1679 Output:
1681 this is being run with nice -n 17
1683
1685 GNU parallel can run jobs on remote servers. It uses ssh to communicate
1686 with the remote machines.
1687 Sshlogin
1689 The most basic sshlogin is -S host:
1690 parallel -S $SERVER1 echo running on ::: $SERVER1
1692 Output:
1694 running on [$SERVER1]
1696 To use a different username prepend the server with username@:
1698 parallel -S username@$SERVER1 echo running on ::: username@$SERVER1
1700 Output:
1702 running on [username@$SERVER1]
1704 The special sshlogin : is the local machine:
1706 parallel -S : echo running on ::: the_local_machine
1708 Output:
1710 running on the_local_machine
1712 If ssh is not in $PATH it can be prepended to $SERVER1:
1714 parallel -S '/usr/bin/ssh '$SERVER1 echo custom ::: ssh
1716 Output:
1718 custom ssh
1720 The ssh command can also be given using --ssh:
1722 parallel --ssh /usr/bin/ssh -S $SERVER1 echo custom ::: ssh
1724 or by setting $PARALLEL_SSH:
1726 export PARALLEL_SSH=/usr/bin/ssh
1728 parallel -S $SERVER1 echo custom ::: ssh
1729 Several servers can be given using multiple -S:
1731 parallel -S $SERVER1 -S $SERVER2 echo ::: running on more hosts
1733 Output (the order may be different):
1735 running
1737 on
1738 more
1739 hosts
1740 Or they can be separated by ,:
1742 parallel -S $SERVER1,$SERVER2 echo ::: running on more hosts
1744 Output: Same as above.
1746 Or newline:
1748 # This gives a \n between $SERVER1 and $SERVER2
1750 SERVERS="`echo $SERVER1; echo $SERVER2`"
1751 parallel -S "$SERVERS" echo ::: running on more hosts
1752 They can also be read from a file (replace user@ with the user on
1754 $SERVER2):
1755 echo $SERVER1 > nodefile
1757 # Force 4 cores, special ssh-command, username
1758 echo 4//usr/bin/ssh user@$SERVER2 >> nodefile
1759 parallel --sshloginfile nodefile echo ::: running on more hosts
1760 Output: Same as above.
1762 Every time a job finished, the --sshloginfile will be re-read, so it is
1764 possible to both add and remove hosts while running.
1765 The special --sshloginfile .. reads from ~/.parallel/sshloginfile.
1767 To force GNU parallel to treat a server having a given number of CPU
1769 cores prepend the number of core followed by / to the sshlogin:
1770 parallel -S 4/$SERVER1 echo force {} cpus on server ::: 4
1772 Output:
1774 force 4 cpus on server
1776 Servers can be put into groups by prepending @groupname to the server
1778 and the group can then be selected by appending @groupname to the
1779 argument if using --hostgroup:
1780 parallel --hostgroup -S @grp1/$SERVER1 -S @grp2/$SERVER2 echo {} \
1782 ::: run_on_grp1@grp1 run_on_grp2@grp2
1783 Output:
1785 run_on_grp1
1787 run_on_grp2
1788 A host can be in multiple groups by separating the groups with +, and
1790 you can force GNU parallel to limit the groups on which the command can
1791 be run with -S @groupname:
1792 parallel -S @grp1 -S @grp1+grp2/$SERVER1 -S @grp2/SERVER2 echo {} \
1794 ::: run_on_grp1 also_grp1
1795 Output:
1797 run_on_grp1
1799 also_grp1
1800 Transferring files
1802 GNU parallel can transfer the files to be processed to the remote host.
1803 It does that using rsync.
1804 echo This is input_file > input_file
1806 parallel -S $SERVER1 --transferfile {} cat ::: input_file
1807 Output:
1809 This is input_file
1811 If the files are processed into another file, the resulting file can be
1813 transferred back:
1814 echo This is input_file > input_file
1816 parallel -S $SERVER1 --transferfile {} --return {}.out \
1817 cat {} ">"{}.out ::: input_file
1818 cat input_file.out
1819 Output: Same as above.
1821 To remove the input and output file on the remote server use --cleanup:
1823 echo This is input_file > input_file
1825 parallel -S $SERVER1 --transferfile {} --return {}.out --cleanup \
1826 cat {} ">"{}.out ::: input_file
1827 cat input_file.out
1828 Output: Same as above.
1830 There is a shorthand for --transferfile {} --return --cleanup called
1832 --trc:
1833 echo This is input_file > input_file
1835 parallel -S $SERVER1 --trc {}.out cat {} ">"{}.out ::: input_file
1836 cat input_file.out
1837 Output: Same as above.
1839 Some jobs need a common database for all jobs. GNU parallel can
1841 transfer that using --basefile which will transfer the file before the
1842 first job:
1843 echo common data > common_file
1845 parallel --basefile common_file -S $SERVER1 \
1846 cat common_file\; echo {} ::: foo
1847 Output:
1849 common data
1851 foo
1852 To remove it from the remote host after the last job use --cleanup.
1854 Working dir
1856 The default working dir on the remote machines is the login dir. This
1857 can be changed with --workdir mydir.
1858 Files transferred using --transferfile and --return will be relative to
1860 mydir on remote computers, and the command will be executed in the dir
1861 mydir.
1862 The special mydir value ... will create working dirs under
1864 ~/.parallel/tmp on the remote computers. If --cleanup is given these
1865 dirs will be removed.
1866 The special mydir value . uses the current working dir. If the current
1868 working dir is beneath your home dir, the value . is treated as the
1869 relative path to your home dir. This means that if your home dir is
1870 different on remote computers (e.g. if your login is different) the
1871 relative path will still be relative to your home dir.
1872 parallel -S $SERVER1 pwd ::: ""
1874 parallel --workdir . -S $SERVER1 pwd ::: ""
1875 parallel --workdir ... -S $SERVER1 pwd ::: ""
1876 Output:
1878 [the login dir on $SERVER1]
1880 [current dir relative on $SERVER1]
1881 [a dir in ~/.parallel/tmp/...]
1882 Avoid overloading sshd
1884 If many jobs are started on the same server, sshd can be overloaded.
1885 GNU parallel can insert a delay between each job run on the same
1886 server:
1887 parallel -S $SERVER1 --sshdelay 0.2 echo ::: 1 2 3
1889 Output (the order may be different):
1891 1
1893 2
1894 3
1895 sshd will be less overloaded if using --controlmaster, which will
1897 multiplex ssh connections:
1898 parallel --controlmaster -S $SERVER1 echo ::: 1 2 3
1900 Output: Same as above.
1902 Ignore hosts that are down
1904 In clusters with many hosts a few of them are often down. GNU parallel
1905 can ignore those hosts. In this case the host 173.194.32.46 is down:
1906 parallel --filter-hosts -S 173.194.32.46,$SERVER1 echo ::: bar
1908 Output:
1910 bar
1912 Running the same commands on all hosts
1914 GNU parallel can run the same command on all the hosts:
1915 parallel --onall -S $SERVER1,$SERVER2 echo ::: foo bar
1917 Output (the order may be different):
1919 foo
1921 bar
1922 foo
1923 bar
1924 Often you will just want to run a single command on all hosts with out
1926 arguments. --nonall is a no argument --onall:
1927 parallel --nonall -S $SERVER1,$SERVER2 echo foo bar
1929 Output:
1931 foo bar
1933 foo bar
1934 When --tag is used with --nonall and --onall the --tagstring is the
1936 host:
1937 parallel --nonall --tag -S $SERVER1,$SERVER2 echo foo bar
1939 Output (the order may be different):
1941 $SERVER1 foo bar
1943 $SERVER2 foo bar
1944 --jobs sets the number of servers to log in to in parallel.
1946 Transferring environment variables and functions
1948 env_parallel is a shell function that transfers all aliases, functions,
1949 variables, and arrays. You active it by running:
1950 source `which env_parallel.bash`
1952 Replace bash with the shell you use.
1954 Now you can use env_parallel instead of parallel and still have your
1956 environment:
1957 alias myecho=echo
1959 myvar="Joe's var is"
1960 env_parallel -S $SERVER1 'myecho $myvar' ::: green
1961 Output:
1963 Joe's var is green
1965 The disadvantage is that if your environment is huge env_parallel will
1967 fail.
1968 When env_parallel fails, you can still use --env to tell GNU parallel
1970 to transfer an environment variable to the remote system.
1971 MYVAR='foo bar'
1973 export MYVAR
1974 parallel --env MYVAR -S $SERVER1 echo '$MYVAR' ::: baz
1975 Output:
1977 foo bar baz
1979 This works for functions, too, if your shell is Bash:
1981 # This only works in Bash
1983 my_func() {
1984 echo in my_func $1
1985 }
1986 export -f my_func
1987 parallel --env my_func -S $SERVER1 my_func ::: baz
1988 Output:
1990 in my_func baz
1992 GNU parallel can copy all user defined variables and functions to the
1994 remote system. It just needs to record which ones to ignore in
1995 ~/.parallel/ignored_vars. Do that by running this once:
1996 parallel --record-env
1998 cat ~/.parallel/ignored_vars
1999 Output:
2001 [list of variables to ignore - including $PATH and $HOME]
2003 Now all other variables and functions defined will be copied when using
2005 --env _.
2006 # The function is only copied if using Bash
2008 my_func2() {
2009 echo in my_func2 $VAR $1
2010 }
2011 export -f my_func2
2012 VAR=foo
2013 export VAR
2014 parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar
2016 Output:
2018 foo
2020 in my_func2 foo bar
2021 If you use env_parallel the variables, functions, and aliases do not
2023 even need to be exported to be copied:
2024 NOT='not exported var'
2026 alias myecho=echo
2027 not_ex() {
2028 myecho in not_exported_func $NOT $1
2029 }
2030 env_parallel --env _ -S $SERVER1 'echo $NOT; not_ex' ::: bar
2031 Output:
2033 not exported var
2035 in not_exported_func not exported var bar
2036 Showing what is actually run
2038 --verbose will show the command that would be run on the local machine.
2039 When using --cat, --pipepart, or when a job is run on a remote machine,
2041 the command is wrapped with helper scripts. -vv shows all of this.
2042 parallel -vv --pipepart --block 1M wc :::: num30000
2044 Output:
2046 <num30000 perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die;
2048 $left = shift; while($read = sysread(STDIN,$buf, ($left > 131072
2049 ? 131072 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }'
2050 0 0 0 168894 | (wc)
2051 30000 30000 168894
2052 When the command gets more complex, the output is so hard to read, that
2054 it is only useful for debugging:
2055 my_func3() {
2057 echo in my_func $1 > $1.out
2058 }
2059 export -f my_func3
2060 parallel -vv --workdir ... --nice 17 --env _ --trc {}.out \
2061 -S $SERVER1 my_func3 {} ::: abc-file
2062 Output will be similar to:
2064 ( ssh server -- mkdir -p ./.parallel/tmp/aspire-1928520-1;rsync
2066 --protocol 30 -rlDzR -essh ./abc-file
2067 server:./.parallel/tmp/aspire-1928520-1 );ssh server -- exec perl -e
2068 \''@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64");
2069 eval"@GNU_Parallel";my$eval=decode_base64(join"",@ARGV);eval$eval;'\'
2070 c3lzdGVtKCJta2RpciIsIi1wIiwiLS0iLCIucGFyYWxsZWwvdG1wL2FzcGlyZS0xOTI4N
2071 TsgY2hkaXIgIi5wYXJhbGxlbC90bXAvYXNwaXJlLTE5Mjg1MjAtMSIgfHxwcmludChTVE
2072 BhcmFsbGVsOiBDYW5ub3QgY2hkaXIgdG8gLnBhcmFsbGVsL3RtcC9hc3BpcmUtMTkyODU
2073 iKSAmJiBleGl0IDI1NTskRU5WeyJPTERQV0QifT0iL2hvbWUvdGFuZ2UvcHJpdmF0L3Bh
2074 IjskRU5WeyJQQVJBTExFTF9QSUQifT0iMTkyODUyMCI7JEVOVnsiUEFSQUxMRUxfU0VRI
2075 0BiYXNoX2Z1bmN0aW9ucz1xdyhteV9mdW5jMyk7IGlmKCRFTlZ7IlNIRUxMIn09fi9jc2
2076 ByaW50IFNUREVSUiAiQ1NIL1RDU0ggRE8gTk9UIFNVUFBPUlQgbmV3bGluZXMgSU4gVkF
2077 TL0ZVTkNUSU9OUy4gVW5zZXQgQGJhc2hfZnVuY3Rpb25zXG4iOyBleGVjICJmYWxzZSI7
2078 YXNoZnVuYyA9ICJteV9mdW5jMygpIHsgIGVjaG8gaW4gbXlfZnVuYyBcJDEgPiBcJDEub
2079 Xhwb3J0IC1mIG15X2Z1bmMzID4vZGV2L251bGw7IjtAQVJHVj0ibXlfZnVuYzMgYWJjLW
2080 RzaGVsbD0iJEVOVntTSEVMTH0iOyR0bXBkaXI9Ii90bXAiOyRuaWNlPTE3O2RveyRFTlZ
2081 MRUxfVE1QfT0kdG1wZGlyLiIvcGFyIi5qb2luIiIsbWFweygwLi45LCJhIi4uInoiLCJB
2082 KVtyYW5kKDYyKV19KDEuLjUpO313aGlsZSgtZSRFTlZ7UEFSQUxMRUxfVE1QfSk7JFNJ
2083 fT1zdWJ7JGRvbmU9MTt9OyRwaWQ9Zm9yazt1bmxlc3MoJHBpZCl7c2V0cGdycDtldmFse
2084 W9yaXR5KDAsMCwkbmljZSl9O2V4ZWMkc2hlbGwsIi1jIiwoJGJhc2hmdW5jLiJAQVJHVi
2085 JleGVjOiQhXG4iO31kb3skcz0kczwxPzAuMDAxKyRzKjEuMDM6JHM7c2VsZWN0KHVuZGV
2086 mLHVuZGVmLCRzKTt9dW50aWwoJGRvbmV8fGdldHBwaWQ9PTEpO2tpbGwoU0lHSFVQLC0k
2087 dW5sZXNzJGRvbmU7d2FpdDtleGl0KCQ/JjEyNz8xMjgrKCQ/JjEyNyk6MSskPz4+OCk=;
2088 _EXIT_status=$?; mkdir -p ./.; rsync --protocol 30 --rsync-path=cd\
2089 ./.parallel/tmp/aspire-1928520-1/./.\;\ rsync -rlDzR -essh
2090 server:./abc-file.out ./.;ssh server -- \(rm\ -f\
2091 ./.parallel/tmp/aspire-1928520-1/abc-file\;\ sh\ -c\ \'rmdir\
2092 ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\ ./.parallel/\
2093 2\>/dev/null\'\;rm\ -rf\ ./.parallel/tmp/aspire-1928520-1\;\);ssh
2094 server -- \(rm\ -f\ ./.parallel/tmp/aspire-1928520-1/abc-file.out\;\
2095 sh\ -c\ \'rmdir\ ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\
2096 ./.parallel/\ 2\>/dev/null\'\;rm\ -rf\
2097 ./.parallel/tmp/aspire-1928520-1\;\);ssh server -- rm -rf
2098 .parallel/tmp/aspire-1928520-1; exit $_EXIT_status;
2099
2101 GNU parset will set shell variables to the output of GNU parallel. GNU
2102 parset has one important limitation: It cannot be part of a pipe. In
2103 particular this means it cannot read anything from standard input
2104 (stdin) or pipe output to another program.
2105 To use GNU parset prepend command with destination variables:
2107 parset myvar1,myvar2 echo ::: a b
2109 echo $myvar1
2110 echo $myvar2
2111 Output:
2113 a
2115 b
2116 If you only give a single variable, it will be treated as an array:
2118 parset myarray seq {} 5 ::: 1 2 3
2120 echo "${myarray[1]}"
2121 Output:
2123 2
2125 3
2126 4
2127 5
2128 The commands to run can be an array:
2130 cmd=("echo '<<joe \"double space\" cartoon>>'" "pwd")
2132 parset data ::: "${cmd[@]}"
2133 echo "${data[0]}"
2134 echo "${data[1]}"
2135 Output:
2137 <<joe "double space" cartoon>>
2139 [current dir]
2140
2142 GNU parallel can save into an SQL base. Point GNU parallel to a table
2143 and it will put the joblog there together with the variables and the
2144 output each in their own column.
2145 CSV as SQL base
2147 The simplest is to use a CSV file as the storage table:
2148 parallel --sqlandworker csv:///%2Ftmp/log.csv \
2150 seq ::: 10 ::: 12 13 14
2151 cat /tmp/log.csv
2152 Note how '/' in the path must be written as %2F.
2154 Output will be similar to:
2156 Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
2158 Command,V1,V2,Stdout,Stderr
2159 1,:,1458254498.254,0.069,0,9,0,0,"seq 10 12",10,12,"10
2160 11
2161 12
2162 ",
2163 2,:,1458254498.278,0.080,0,12,0,0,"seq 10 13",10,13,"10
2164 11
2165 12
2166 13
2167 ",
2168 3,:,1458254498.301,0.083,0,15,0,0,"seq 10 14",10,14,"10
2169 11
2170 12
2171 13
2172 14
2173 ",
2174 A proper CSV reader (like LibreOffice or R's read.csv) will read this
2176 format correctly - even with fields containing newlines as above.
2177 If the output is big you may want to put it into files using --results:
2179 parallel --results outdir --sqlandworker csv:///%2Ftmp/log2.csv \
2181 seq ::: 10 ::: 12 13 14
2182 cat /tmp/log2.csv
2183 Output will be similar to:
2185 Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
2187 Command,V1,V2,Stdout,Stderr
2188 1,:,1458824738.287,0.029,0,9,0,0,
2189 "seq 10 12",10,12,outdir/1/10/2/12/stdout,outdir/1/10/2/12/stderr
2190 2,:,1458824738.298,0.025,0,12,0,0,
2191 "seq 10 13",10,13,outdir/1/10/2/13/stdout,outdir/1/10/2/13/stderr
2192 3,:,1458824738.309,0.026,0,15,0,0,
2193 "seq 10 14",10,14,outdir/1/10/2/14/stdout,outdir/1/10/2/14/stderr
2194 DBURL as table
2196 The CSV file is an example of a DBURL.
2197 GNU parallel uses a DBURL to address the table. A DBURL has this
2199 format:
2200 vendor://[[user][:password]@][host][:port]/[database[/table]
2202 Example:
2204 mysql://scott:tiger@my.example.com/mydatabase/mytable
2206 postgresql://scott:tiger@pg.example.com/mydatabase/mytable
2207 sqlite3:///%2Ftmp%2Fmydatabase/mytable
2208 csv:///%2Ftmp/log.csv
2209 To refer to /tmp/mydatabase with sqlite or csv you need to encode the /
2211 as %2F.
2212 Run a job using sqlite on mytable in /tmp/mydatabase:
2214 DBURL=sqlite3:///%2Ftmp%2Fmydatabase
2216 DBURLTABLE=$DBURL/mytable
2217 parallel --sqlandworker $DBURLTABLE echo ::: foo bar ::: baz quuz
2218 To see the result:
2220 sql $DBURL 'SELECT * FROM mytable ORDER BY Seq;'
2222 Output will be similar to:
2224 Seq|Host|Starttime|JobRuntime|Send|Receive|Exitval|_Signal|
2226 Command|V1|V2|Stdout|Stderr
2227 1|:|1451619638.903|0.806||8|0|0|echo foo baz|foo|baz|foo baz
2228 |
2229 2|:|1451619639.265|1.54||9|0|0|echo foo quuz|foo|quuz|foo quuz
2230 |
2231 3|:|1451619640.378|1.43||8|0|0|echo bar baz|bar|baz|bar baz
2232 |
2233 4|:|1451619641.473|0.958||9|0|0|echo bar quuz|bar|quuz|bar quuz
2234 |
2235 The first columns are well known from --joblog. V1 and V2 are data from
2237 the input sources. Stdout and Stderr are standard output and standard
2238 error, respectively.
2239 Using multiple workers
2241 Using an SQL base as storage costs overhead in the order of 1 second
2242 per job.
2243 One of the situations where it makes sense is if you have multiple
2245 workers.
2246 You can then have a single master machine that submits jobs to the SQL
2248 base (but does not do any of the work):
2249 parallel --sqlmaster $DBURLTABLE echo ::: foo bar ::: baz quuz
2251 On the worker machines you run exactly the same command except you
2253 replace --sqlmaster with --sqlworker.
2254 parallel --sqlworker $DBURLTABLE echo ::: foo bar ::: baz quuz
2256 To run a master and a worker on the same machine use --sqlandworker as
2258 shown earlier.
2259
2261 The --pipe functionality puts GNU parallel in a different mode: Instead
2262 of treating the data on stdin (standard input) as arguments for a
2263 command to run, the data will be sent to stdin (standard input) of the
2264 command.
2265 The typical situation is:
2267 command_A | command_B | command_C
2269 where command_B is slow, and you want to speed up command_B.
2271 Chunk size
2273 By default GNU parallel will start an instance of command_B, read a
2274 chunk of 1 MB, and pass that to the instance. Then start another
2275 instance, read another chunk, and pass that to the second instance.
2276 cat num1000000 | parallel --pipe wc
2278 Output (the order may be different):
2280 165668 165668 1048571
2282 149797 149797 1048579
2283 149796 149796 1048572
2284 149797 149797 1048579
2285 149797 149797 1048579
2286 149796 149796 1048572
2287 85349 85349 597444
2288 The size of the chunk is not exactly 1 MB because GNU parallel only
2290 passes full lines - never half a line, thus the blocksize is only 1 MB
2291 on average. You can change the block size to 2 MB with --block:
2292 cat num1000000 | parallel --pipe --block 2M wc
2294 Output (the order may be different):
2296 315465 315465 2097150
2298 299593 299593 2097151
2299 299593 299593 2097151
2300 85349 85349 597444
2301 GNU parallel treats each line as a record. If the order of records is
2303 unimportant (e.g. you need all lines processed, but you do not care
2304 which is processed first), then you can use --roundrobin. Without
2305 --roundrobin GNU parallel will start a command per block; with
2306 --roundrobin only the requested number of jobs will be started
2307 (--jobs). The records will then be distributed between the running
2308 jobs:
2309 cat num1000000 | parallel --pipe -j4 --roundrobin wc
2311 Output will be similar to:
2313 149797 149797 1048579
2315 299593 299593 2097151
2316 315465 315465 2097150
2317 235145 235145 1646016
2318 One of the 4 instances got a single record, 2 instances got 2 full
2320 records each, and one instance got 1 full and 1 partial record.
2321 Records
2323 GNU parallel sees the input as records. The default record is a single
2324 line.
2325 Using -N140000 GNU parallel will read 140000 records at a time:
2327 cat num1000000 | parallel --pipe -N140000 wc
2329 Output (the order may be different):
2331 140000 140000 868895
2333 140000 140000 980000
2334 140000 140000 980000
2335 140000 140000 980000
2336 140000 140000 980000
2337 140000 140000 980000
2338 140000 140000 980000
2339 20000 20000 140001
2340 Note how that the last job could not get the full 140000 lines, but
2342 only 20000 lines.
2343 If a record is 75 lines -L can be used:
2345 cat num1000000 | parallel --pipe -L75 wc
2347 Output (the order may be different):
2349 165600 165600 1048095
2351 149850 149850 1048950
2352 149775 149775 1048425
2353 149775 149775 1048425
2354 149850 149850 1048950
2355 149775 149775 1048425
2356 85350 85350 597450
2357 25 25 176
2358 Note how GNU parallel still reads a block of around 1 MB; but instead
2360 of passing full lines to wc it passes full 75 lines at a time. This of
2361 course does not hold for the last job (which in this case got 25
2362 lines).
2363 Fixed length records
2365 Fixed length records can be processed by setting --recend '' and
2366 --block recordsize. A header of size n can be processed with --header
2367 .{n}.
2368 Here is how to process a file with a 4-byte header and a 3-byte record
2370 size:
2371 cat fixedlen | parallel --pipe --header .{4} --block 3 --recend '' \
2373 'echo start; cat; echo'
2374 Output:
2376 start
2378 HHHHAAA
2379 start
2380 HHHHCCC
2381 start
2382 HHHHBBB
2383 It may be more efficient to increase --block to a multiplum of the
2385 record size.
2386 Record separators
2388 GNU parallel uses separators to determine where two records split.
2389 --recstart gives the string that starts a record; --recend gives the
2391 string that ends a record. The default is --recend '\n' (newline).
2392 If both --recend and --recstart are given, then the record will only
2394 split if the recend string is immediately followed by the recstart
2395 string.
2396 Here the --recend is set to ', ':
2398 echo /foo, bar/, /baz, qux/, | \
2400 parallel -kN1 --recend ', ' --pipe echo JOB{#}\;cat\;echo END
2401 Output:
2403 JOB1
2405 /foo, END
2406 JOB2
2407 bar/, END
2408 JOB3
2409 /baz, END
2410 JOB4
2411 qux/,
2412 END
2413 Here the --recstart is set to /:
2415 echo /foo, bar/, /baz, qux/, | \
2417 parallel -kN1 --recstart / --pipe echo JOB{#}\;cat\;echo END
2418 Output:
2420 JOB1
2422 /foo, barEND
2423 JOB2
2424 /, END
2425 JOB3
2426 /baz, quxEND
2427 JOB4
2428 /,
2429 END
2430 Here both --recend and --recstart are set:
2432 echo /foo, bar/, /baz, qux/, | \
2434 parallel -kN1 --recend ', ' --recstart / --pipe \
2435 echo JOB{#}\;cat\;echo END
2436 Output:
2438 JOB1
2440 /foo, bar/, END
2441 JOB2
2442 /baz, qux/,
2443 END
2444 Note the difference between setting one string and setting both
2446 strings.
2447 With --regexp the --recend and --recstart will be treated as a regular
2449 expression:
2450 echo foo,bar,_baz,__qux, | \
2452 parallel -kN1 --regexp --recend ,_+ --pipe \
2453 echo JOB{#}\;cat\;echo END
2454 Output:
2456 JOB1
2458 foo,bar,_END
2459 JOB2
2460 baz,__END
2461 JOB3
2462 qux,
2463 END
2464 GNU parallel can remove the record separators with
2466 --remove-rec-sep/--rrs:
2467 echo foo,bar,_baz,__qux, | \
2469 parallel -kN1 --rrs --regexp --recend ,_+ --pipe \
2470 echo JOB{#}\;cat\;echo END
2471 Output:
2473 JOB1
2475 foo,barEND
2476 JOB2
2477 bazEND
2478 JOB3
2479 qux,
2480 END
2481 Header
2483 If the input data has a header, the header can be repeated for each job
2484 by matching the header with --header. If headers start with % you can
2485 do this:
2486 cat num_%header | \
2488 parallel --header '(%.*\n)*' --pipe -N3 echo JOB{#}\;cat
2489 Output (the order may be different):
2491 JOB1
2493 %head1
2494 %head2
2495 1
2496 2
2497 3
2498 JOB2
2499 %head1
2500 %head2
2501 4
2502 5
2503 6
2504 JOB3
2505 %head1
2506 %head2
2507 7
2508 8
2509 9
2510 JOB4
2511 %head1
2512 %head2
2513 10
2514 If the header is 2 lines, --header 2 will work:
2516 cat num_%header | parallel --header 2 --pipe -N3 echo JOB{#}\;cat
2518 Output: Same as above.
2520 --pipepart
2522 --pipe is not very efficient. It maxes out at around 500 MB/s.
2523 --pipepart can easily deliver 5 GB/s. But there are a few limitations.
2524 The input has to be a normal file (not a pipe) given by -a or :::: and
2525 -L/-l/-N do not work. --recend and --recstart, however, do work, and
2526 records can often be split on that alone.
2527 parallel --pipepart -a num1000000 --block 3m wc
2529 Output (the order may be different):
2531 444443 444444 3000002
2533 428572 428572 3000004
2534 126985 126984 888890
2535
2537 Input data and parallel command in the same file
2538 GNU parallel is often called as this:
2539 cat input_file | parallel command
2541 With --shebang the input_file and parallel can be combined into the
2543 same script.
2544 UNIX shell scripts start with a shebang line like this:
2546 #!/bin/bash
2548 GNU parallel can do that, too. With --shebang the arguments can be
2550 listed in the file. The parallel command is the first line of the
2551 script:
2552 #!/usr/bin/parallel --shebang -r echo
2554 foo
2556 bar
2557 baz
2558 Output (the order may be different):
2560 foo
2562 bar
2563 baz
2564 Parallelizing existing scripts
2566 GNU parallel is often called as this:
2567 cat input_file | parallel command
2569 parallel command ::: foo bar
2570 If command is a script, parallel can be combined into a single file so
2572 this will run the script in parallel:
2573 cat input_file | command
2575 command foo bar
2576 This perl script perl_echo works like echo:
2578 #!/usr/bin/perl
2580 print "@ARGV\n"
2582 It can be called as this:
2584 parallel perl_echo ::: foo bar
2586 By changing the #!-line it can be run in parallel:
2588 #!/usr/bin/parallel --shebang-wrap /usr/bin/perl
2590 print "@ARGV\n"
2592 Thus this will work:
2594 perl_echo foo bar
2596 Output (the order may be different):
2598 foo
2600 bar
2601 This technique can be used for:
2603 Perl:
2605 #!/usr/bin/parallel --shebang-wrap /usr/bin/perl
2606 print "Arguments @ARGV\n";
2608 Python:
2610 #!/usr/bin/parallel --shebang-wrap /usr/bin/python
2611 import sys
2613 print 'Arguments', str(sys.argv)
2614 Bash/sh/zsh/Korn shell:
2616 #!/usr/bin/parallel --shebang-wrap /bin/bash
2617 echo Arguments "$@"
2619 csh:
2621 #!/usr/bin/parallel --shebang-wrap /bin/csh
2622 echo Arguments "$argv"
2624 Tcl:
2626 #!/usr/bin/parallel --shebang-wrap /usr/bin/tclsh
2627 puts "Arguments $argv"
2629 R:
2631 #!/usr/bin/parallel --shebang-wrap /usr/bin/Rscript --vanilla --slave
2632 args <- commandArgs(trailingOnly = TRUE)
2634 print(paste("Arguments ",args))
2635 GNUplot:
2637 #!/usr/bin/parallel --shebang-wrap ARG={} /usr/bin/gnuplot
2638 print "Arguments ", system('echo $ARG')
2640 Ruby:
2642 #!/usr/bin/parallel --shebang-wrap /usr/bin/ruby
2643 print "Arguments "
2645 puts ARGV
2646 Octave:
2648 #!/usr/bin/parallel --shebang-wrap /usr/bin/octave
2649 printf ("Arguments");
2651 arg_list = argv ();
2652 for i = 1:nargin
2653 printf (" %s", arg_list{i});
2654 endfor
2655 printf ("\n");
2656 Common LISP:
2658 #!/usr/bin/parallel --shebang-wrap /usr/bin/clisp
2659 (format t "~&~S~&" 'Arguments)
2661 (format t "~&~S~&" *args*)
2662 PHP:
2664 #!/usr/bin/parallel --shebang-wrap /usr/bin/php
2665 <?php
2666 echo "Arguments";
2667 foreach(array_slice($argv,1) as $v)
2668 {
2669 echo " $v";
2670 }
2671 echo "\n";
2672 ?>
2673 Node.js:
2675 #!/usr/bin/parallel --shebang-wrap /usr/bin/node
2676 var myArgs = process.argv.slice(2);
2678 console.log('Arguments ', myArgs);
2679 LUA:
2681 #!/usr/bin/parallel --shebang-wrap /usr/bin/lua
2682 io.write "Arguments"
2684 for a = 1, #arg do
2685 io.write(" ")
2686 io.write(arg[a])
2687 end
2688 print("")
2689 C#:
2691 #!/usr/bin/parallel --shebang-wrap ARGV={} /usr/bin/csharp
2692 var argv = Environment.GetEnvironmentVariable("ARGV");
2694 print("Arguments "+argv);
2695
2697 GNU parallel can work as a counting semaphore. This is slower and less
2698 efficient than its normal mode.
2699 A counting semaphore is like a row of toilets. People needing a toilet
2701 can use any toilet, but if there are more people than toilets, they
2702 will have to wait for one of the toilets to become available.
2703 An alias for parallel --semaphore is sem.
2705 sem will follow a person to the toilets, wait until a toilet is
2707 available, leave the person in the toilet and exit.
2708 sem --fg will follow a person to the toilets, wait until a toilet is
2710 available, stay with the person in the toilet and exit when the person
2711 exits.
2712 sem --wait will wait for all persons to leave the toilets.
2714 sem does not have a queue discipline, so the next person is chosen
2716 randomly.
2717 -j sets the number of toilets.
2719 Mutex
2721 The default is to have only one toilet (this is called a mutex). The
2722 program is started in the background and sem exits immediately. Use
2723 --wait to wait for all sems to finish:
2724 sem 'sleep 1; echo The first finished' &&
2726 echo The first is now running in the background &&
2727 sem 'sleep 1; echo The second finished' &&
2728 echo The second is now running in the background
2729 sem --wait
2730 Output:
2732 The first is now running in the background
2734 The first finished
2735 The second is now running in the background
2736 The second finished
2737 The command can be run in the foreground with --fg, which will only
2739 exit when the command completes:
2740 sem --fg 'sleep 1; echo The first finished' &&
2742 echo The first finished running in the foreground &&
2743 sem --fg 'sleep 1; echo The second finished' &&
2744 echo The second finished running in the foreground
2745 sem --wait
2746 The difference between this and just running the command, is that a
2748 mutex is set, so if other sems were running in the background only one
2749 would run at a time.
2750 To control which semaphore is used, use --semaphorename/--id. Run this
2752 in one terminal:
2753 sem --id my_id -u 'echo First started; sleep 10; echo First done'
2755 and simultaneously this in another terminal:
2757 sem --id my_id -u 'echo Second started; sleep 10; echo Second done'
2759 Note how the second will only be started when the first has finished.
2761 Counting semaphore
2763 A mutex is like having a single toilet: When it is in use everyone else
2764 will have to wait. A counting semaphore is like having multiple
2765 toilets: Several people can use the toilets, but when they all are in
2766 use, everyone else will have to wait.
2767 sem can emulate a counting semaphore. Use --jobs to set the number of
2769 toilets like this:
2770 sem --jobs 3 --id my_id -u 'echo Start 1; sleep 5; echo 1 done' &&
2772 sem --jobs 3 --id my_id -u 'echo Start 2; sleep 6; echo 2 done' &&
2773 sem --jobs 3 --id my_id -u 'echo Start 3; sleep 7; echo 3 done' &&
2774 sem --jobs 3 --id my_id -u 'echo Start 4; sleep 8; echo 4 done' &&
2775 sem --wait --id my_id
2776 Output:
2778 Start 1
2780 Start 2
2781 Start 3
2782 1 done
2783 Start 4
2784 2 done
2785 3 done
2786 4 done
2787 Timeout
2789 With --semaphoretimeout you can force running the command anyway after
2790 a period (positive number) or give up (negative number):
2791 sem --id foo -u 'echo Slow started; sleep 5; echo Slow ended' &&
2793 sem --id foo --semaphoretimeout 1 'echo Forced running after 1 sec' &&
2794 sem --id foo --semaphoretimeout -2 'echo Give up after 2 secs'
2795 sem --id foo --wait
2796 Output:
2798 Slow started
2800 parallel: Warning: Semaphore timed out. Stealing the semaphore.
2801 Forced running after 1 sec
2802 parallel: Warning: Semaphore timed out. Exiting.
2803 Slow ended
2804 Note how the 'Give up' was not run.
2806
2808 GNU parallel has some options to give short information about the
2809 configuration.
2810 --help will print a summary of the most important options:
2812 parallel --help
2814 Output:
2816 Usage:
2818 parallel [options] [command [arguments]] < list_of_arguments
2820 parallel [options] [command [arguments]] (::: arguments|:::: argfile(s))...
2821 cat ... | parallel --pipe [options] [command [arguments]]
2822 -j n Run n jobs in parallel
2824 -k Keep same order
2825 -X Multiple arguments with context replace
2826 --colsep regexp Split input on regexp for positional replacements
2827 {} {.} {/} {/.} {#} {%} {= perl code =} Replacement strings
2828 {3} {3.} {3/} {3/.} {=3 perl code =} Positional replacement strings
2829 With --plus: {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} =
2830 {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}
2831 -S sshlogin Example: foo@server.example.com
2833 --slf .. Use ~/.parallel/sshloginfile as the list of sshlogins
2834 --trc {}.bar Shorthand for --transfer --return {}.bar --cleanup
2835 --onall Run the given command with argument on all sshlogins
2836 --nonall Run the given command with no arguments on all sshlogins
2837 --pipe Split stdin (standard input) to multiple jobs.
2839 --recend str Record end separator for --pipe.
2840 --recstart str Record start separator for --pipe.
2841 See 'man parallel' for details
2843 Academic tradition requires you to cite works you base your article on.
2845 When using programs that use GNU Parallel to process data for publication
2846 please cite:
2847 O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
2849 ;login: The USENIX Magazine, February 2011:42-47.
2850 This helps funding further development; AND IT WON'T COST YOU A CENT.
2852 If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
2853 When asking for help, always report the full output of this:
2855 parallel --version
2857 Output:
2859 GNU parallel 20200122
2861 Copyright (C) 2007-2020 Ole Tange, http://ole.tange.dk and Free Software
2862 Foundation, Inc.
2863 License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
2864 This is free software: you are free to change and redistribute it.
2865 GNU parallel comes with no warranty.
2866 Web site: http://www.gnu.org/software/parallel
2868 When using programs that use GNU Parallel to process data for publication
2870 please cite as described in 'parallel --citation'.
2871 In scripts --minversion can be used to ensure the user has at least
2873 this version:
2874 parallel --minversion 20130722 && \
2876 echo Your version is at least 20130722.
2877 Output:
2879 20160322
2881 Your version is at least 20130722.
2882 If you are using GNU parallel for research the BibTeX citation can be
2884 generated using --citation:
2885 parallel --citation
2887 Output:
2889 Academic tradition requires you to cite works you base your article on.
2891 When using programs that use GNU Parallel to process data for publication
2892 please cite:
2893 @article{Tange2011a,
2895 title = {GNU Parallel - The Command-Line Power Tool},
2896 author = {O. Tange},
2897 address = {Frederiksberg, Denmark},
2898 journal = {;login: The USENIX Magazine},
2899 month = {Feb},
2900 number = {1},
2901 volume = {36},
2902 url = {http://www.gnu.org/s/parallel},
2903 year = {2011},
2904 pages = {42-47},
2905 doi = {10.5281/zenodo.16303}
2906 }
2907 (Feel free to use \nocite{Tange2011a})
2909 This helps funding further development; AND IT WON'T COST YOU A CENT.
2911 If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
2912 If you send a copy of your published article to tange@gnu.org, it will be
2914 mentioned in the release notes of next version of GNU Parallel.
2915 With --max-line-length-allowed GNU parallel will report the maximal
2917 size of the command line:
2918 parallel --max-line-length-allowed
2920 Output (may vary on different systems):
2922 131071
2924 --number-of-cpus and --number-of-cores run system specific code to
2926 determine the number of CPUs and CPU cores on the system. On
2927 unsupported platforms they will return 1:
2928 parallel --number-of-cpus
2930 parallel --number-of-cores
2931 Output (may vary on different systems):
2933 4
2935 64
2936
2938 The defaults for GNU parallel can be changed systemwide by putting the
2939 command line options in /etc/parallel/config. They can be changed for a
2940 user by putting them in ~/.parallel/config.
2941 Profiles work the same way, but have to be referred to with --profile:
2943 echo '--nice 17' > ~/.parallel/nicetimeout
2945 echo '--timeout 300%' >> ~/.parallel/nicetimeout
2946 parallel --profile nicetimeout echo ::: A B C
2947 Output:
2949 A
2951 B
2952 C
2953 Profiles can be combined:
2955 echo '-vv --dry-run' > ~/.parallel/dryverbose
2957 parallel --profile dryverbose --profile nicetimeout echo ::: A B C
2958 Output:
2960 echo A
2962 echo B
2963 echo C
2964
2966 I hope you have learned something from this tutorial.
2967 If you like GNU parallel:
2969 · (Re-)walk through the tutorial if you have not done so in the past
2971 year (http://www.gnu.org/software/parallel/parallel_tutorial.html)
2972 · Give a demo at your local user group/your team/your colleagues
2974 · Post the intro videos and the tutorial on Reddit, Mastodon,
2976 Diaspora*, forums, blogs, Identi.ca, Google+, Twitter, Facebook,
2977 Linkedin, and mailing lists
2978 · Request or write a review for your favourite blog or magazine
2980 (especially if you do something cool with GNU parallel)
2981 · Invite me for your next conference
2983 If you use GNU parallel for research:
2985 · Please cite GNU parallel in you publications (use --citation)
2987 If GNU parallel saves you money:
2989 · (Have your company) donate to FSF or become a member
2991 https://my.fsf.org/donate/
2992 (C) 2013-2020 Ole Tange, FDLv1.3 (See fdl.txt)
299420200322 2020-04-22 PARALLEL_TUTORIAL(7)