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 https://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 https://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> >(perl -pe 'BEGIN{$/="\r";$|=1};s/\r/\n/g' |
1414 zenity --progress --auto-kill --auto-close)
1415 A logfile of the jobs completed so far can be generated with --joblog:
1417 parallel --joblog /tmp/log exit ::: 1 2 3 0
1419 cat /tmp/log
1420 Output:
1422 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1424 1 : 1376577364.974 0.008 0 0 1 0 exit 1
1425 2 : 1376577364.982 0.013 0 0 2 0 exit 2
1426 3 : 1376577364.990 0.013 0 0 3 0 exit 3
1427 4 : 1376577365.003 0.003 0 0 0 0 exit 0
1428 The log contains the job sequence, which host the job was run on, the
1430 start time and run time, how much data was transferred, the exit value,
1431 the signal that killed the job, and finally the command being run.
1432 With a joblog GNU parallel can be stopped and later pickup where it
1434 left off. It it important that the input of the completed jobs is
1435 unchanged.
1436 parallel --joblog /tmp/log exit ::: 1 2 3 0
1438 cat /tmp/log
1439 parallel --resume --joblog /tmp/log exit ::: 1 2 3 0 0 0
1440 cat /tmp/log
1441 Output:
1443 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1445 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1446 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1447 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1448 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1449 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1451 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1452 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1453 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1454 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1455 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1456 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1457 Note how the start time of the last 2 jobs is clearly different from
1459 the second run.
1460 With --resume-failed GNU parallel will re-run the jobs that failed:
1462 parallel --resume-failed --joblog /tmp/log exit ::: 1 2 3 0 0 0
1464 cat /tmp/log
1465 Output:
1467 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1469 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1470 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1471 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1472 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1473 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1474 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1475 1 : 1376580154.433 0.010 0 0 1 0 exit 1
1476 2 : 1376580154.444 0.022 0 0 2 0 exit 2
1477 3 : 1376580154.466 0.005 0 0 3 0 exit 3
1478 Note how seq 1 2 3 have been repeated because they had exit value
1480 different from 0.
1481 --retry-failed does almost the same as --resume-failed. Where
1483 --resume-failed reads the commands from the command line (and ignores
1484 the commands in the joblog), --retry-failed ignores the command line
1485 and reruns the commands mentioned in the joblog.
1486 parallel --retry-failed --joblog /tmp/log
1488 cat /tmp/log
1489 Output:
1491 Seq Host Starttime Runtime Send Receive Exitval Signal Command
1493 1 : 1376580069.544 0.008 0 0 1 0 exit 1
1494 2 : 1376580069.552 0.009 0 0 2 0 exit 2
1495 3 : 1376580069.560 0.012 0 0 3 0 exit 3
1496 4 : 1376580069.571 0.005 0 0 0 0 exit 0
1497 5 : 1376580070.028 0.009 0 0 0 0 exit 0
1498 6 : 1376580070.038 0.007 0 0 0 0 exit 0
1499 1 : 1376580154.433 0.010 0 0 1 0 exit 1
1500 2 : 1376580154.444 0.022 0 0 2 0 exit 2
1501 3 : 1376580154.466 0.005 0 0 3 0 exit 3
1502 1 : 1376580164.633 0.010 0 0 1 0 exit 1
1503 2 : 1376580164.644 0.022 0 0 2 0 exit 2
1504 3 : 1376580164.666 0.005 0 0 3 0 exit 3
1505 Termination
1507 Unconditional termination
1508 By default GNU parallel will wait for all jobs to finish before
1510 exiting.
1511 If you send GNU parallel the TERM signal, GNU parallel will stop
1513 spawning new jobs and wait for the remaining jobs to finish. If you
1514 send GNU parallel the TERM signal again, GNU parallel will kill all
1515 running jobs and exit.
1516 Termination dependent on job status
1518 For certain jobs there is no need to continue if one of the jobs fails
1520 and has an exit code different from 0. GNU parallel will stop spawning
1521 new jobs with --halt soon,fail=1:
1522 parallel -j2 --halt soon,fail=1 echo {}\; exit {} ::: 0 0 1 2 3
1524 Output:
1526 0
1528 0
1529 1
1530 parallel: This job failed:
1531 echo 1; exit 1
1532 parallel: Starting no more jobs. Waiting for 1 jobs to finish.
1533 2
1534 With --halt now,fail=1 the running jobs will be killed immediately:
1536 parallel -j2 --halt now,fail=1 echo {}\; exit {} ::: 0 0 1 2 3
1538 Output:
1540 0
1542 0
1543 1
1544 parallel: This job failed:
1545 echo 1; exit 1
1546 If --halt is given a percentage this percentage of the jobs must fail
1548 before GNU parallel stops spawning more jobs:
1549 parallel -j2 --halt soon,fail=20% echo {}\; exit {} \
1551 ::: 0 1 2 3 4 5 6 7 8 9
1552 Output:
1554 0
1556 1
1557 parallel: This job failed:
1558 echo 1; exit 1
1559 2
1560 parallel: This job failed:
1561 echo 2; exit 2
1562 parallel: Starting no more jobs. Waiting for 1 jobs to finish.
1563 3
1564 parallel: This job failed:
1565 echo 3; exit 3
1566 If you are looking for success instead of failures, you can use
1568 success. This will finish as soon as the first job succeeds:
1569 parallel -j2 --halt now,success=1 echo {}\; exit {} ::: 1 2 3 0 4 5 6
1571 Output:
1573 1
1575 2
1576 3
1577 0
1578 parallel: This job succeeded:
1579 echo 0; exit 0
1580 GNU parallel can retry the command with --retries. This is useful if a
1582 command fails for unknown reasons now and then.
1583 parallel -k --retries 3 \
1585 'echo tried {} >>/tmp/runs; echo completed {}; exit {}' ::: 1 2 0
1586 cat /tmp/runs
1587 Output:
1589 completed 1
1591 completed 2
1592 completed 0
1593 tried 1
1595 tried 2
1596 tried 1
1597 tried 2
1598 tried 1
1599 tried 2
1600 tried 0
1601 Note how job 1 and 2 were tried 3 times, but 0 was not retried because
1603 it had exit code 0.
1604 Termination signals (advanced)
1606 Using --termseq you can control which signals are sent when killing
1608 children. Normally children will be killed by sending them SIGTERM,
1609 waiting 200 ms, then another SIGTERM, waiting 100 ms, then another
1610 SIGTERM, waiting 50 ms, then a SIGKILL, finally waiting 25 ms before
1611 giving up. It looks like this:
1612 show_signals() {
1614 perl -e 'for(keys %SIG) {
1615 $SIG{$_} = eval "sub { print \"Got $_\\n\"; }";
1616 }
1617 while(1){sleep 1}'
1618 }
1619 export -f show_signals
1620 echo | parallel --termseq TERM,200,TERM,100,TERM,50,KILL,25 \
1621 -u --timeout 1 show_signals
1622 Output:
1624 Got TERM
1626 Got TERM
1627 Got TERM
1628 Or just:
1630 echo | parallel -u --timeout 1 show_signals
1632 Output: Same as above.
1634 You can change this to SIGINT, SIGTERM, SIGKILL:
1636 echo | parallel --termseq INT,200,TERM,100,KILL,25 \
1638 -u --timeout 1 show_signals
1639 Output:
1641 Got INT
1643 Got TERM
1644 The SIGKILL does not show because it cannot be caught, and thus the
1646 child dies.
1647 Limiting the resources
1649 To avoid overloading systems GNU parallel can look at the system load
1650 before starting another job:
1651 parallel --load 100% echo load is less than {} job per cpu ::: 1
1653 Output:
1655 [when then load is less than the number of cpu cores]
1657 load is less than 1 job per cpu
1658 GNU parallel can also check if the system is swapping.
1660 parallel --noswap echo the system is not swapping ::: now
1662 Output:
1664 [when then system is not swapping]
1666 the system is not swapping now
1667 Some jobs need a lot of memory, and should only be started when there
1669 is enough memory free. Using --memfree GNU parallel can check if there
1670 is enough memory free. Additionally, GNU parallel will kill off the
1671 youngest job if the memory free falls below 50% of the size. The killed
1672 job will put back on the queue and retried later.
1673 parallel --memfree 1G echo will run if more than 1 GB is ::: free
1675 GNU parallel can run the jobs with a nice value. This will work both
1677 locally and remotely.
1678 parallel --nice 17 echo this is being run with nice -n ::: 17
1680 Output:
1682 this is being run with nice -n 17
1684
1686 GNU parallel can run jobs on remote servers. It uses ssh to communicate
1687 with the remote machines.
1688 Sshlogin
1690 The most basic sshlogin is -S host:
1691 parallel -S $SERVER1 echo running on ::: $SERVER1
1693 Output:
1695 running on [$SERVER1]
1697 To use a different username prepend the server with username@:
1699 parallel -S username@$SERVER1 echo running on ::: username@$SERVER1
1701 Output:
1703 running on [username@$SERVER1]
1705 The special sshlogin : is the local machine:
1707 parallel -S : echo running on ::: the_local_machine
1709 Output:
1711 running on the_local_machine
1713 If ssh is not in $PATH it can be prepended to $SERVER1:
1715 parallel -S '/usr/bin/ssh '$SERVER1 echo custom ::: ssh
1717 Output:
1719 custom ssh
1721 The ssh command can also be given using --ssh:
1723 parallel --ssh /usr/bin/ssh -S $SERVER1 echo custom ::: ssh
1725 or by setting $PARALLEL_SSH:
1727 export PARALLEL_SSH=/usr/bin/ssh
1729 parallel -S $SERVER1 echo custom ::: ssh
1730 Several servers can be given using multiple -S:
1732 parallel -S $SERVER1 -S $SERVER2 echo ::: running on more hosts
1734 Output (the order may be different):
1736 running
1738 on
1739 more
1740 hosts
1741 Or they can be separated by ,:
1743 parallel -S $SERVER1,$SERVER2 echo ::: running on more hosts
1745 Output: Same as above.
1747 Or newline:
1749 # This gives a \n between $SERVER1 and $SERVER2
1751 SERVERS="`echo $SERVER1; echo $SERVER2`"
1752 parallel -S "$SERVERS" echo ::: running on more hosts
1753 They can also be read from a file (replace user@ with the user on
1755 $SERVER2):
1756 echo $SERVER1 > nodefile
1758 # Force 4 cores, special ssh-command, username
1759 echo 4//usr/bin/ssh user@$SERVER2 >> nodefile
1760 parallel --sshloginfile nodefile echo ::: running on more hosts
1761 Output: Same as above.
1763 Every time a job finished, the --sshloginfile will be re-read, so it is
1765 possible to both add and remove hosts while running.
1766 The special --sshloginfile .. reads from ~/.parallel/sshloginfile.
1768 To force GNU parallel to treat a server having a given number of CPU
1770 cores prepend the number of core followed by / to the sshlogin:
1771 parallel -S 4/$SERVER1 echo force {} cpus on server ::: 4
1773 Output:
1775 force 4 cpus on server
1777 Servers can be put into groups by prepending @groupname to the server
1779 and the group can then be selected by appending @groupname to the
1780 argument if using --hostgroup:
1781 parallel --hostgroup -S @grp1/$SERVER1 -S @grp2/$SERVER2 echo {} \
1783 ::: run_on_grp1@grp1 run_on_grp2@grp2
1784 Output:
1786 run_on_grp1
1788 run_on_grp2
1789 A host can be in multiple groups by separating the groups with +, and
1791 you can force GNU parallel to limit the groups on which the command can
1792 be run with -S @groupname:
1793 parallel -S @grp1 -S @grp1+grp2/$SERVER1 -S @grp2/SERVER2 echo {} \
1795 ::: run_on_grp1 also_grp1
1796 Output:
1798 run_on_grp1
1800 also_grp1
1801 Transferring files
1803 GNU parallel can transfer the files to be processed to the remote host.
1804 It does that using rsync.
1805 echo This is input_file > input_file
1807 parallel -S $SERVER1 --transferfile {} cat ::: input_file
1808 Output:
1810 This is input_file
1812 If the files are processed into another file, the resulting file can be
1814 transferred back:
1815 echo This is input_file > input_file
1817 parallel -S $SERVER1 --transferfile {} --return {}.out \
1818 cat {} ">"{}.out ::: input_file
1819 cat input_file.out
1820 Output: Same as above.
1822 To remove the input and output file on the remote server use --cleanup:
1824 echo This is input_file > input_file
1826 parallel -S $SERVER1 --transferfile {} --return {}.out --cleanup \
1827 cat {} ">"{}.out ::: input_file
1828 cat input_file.out
1829 Output: Same as above.
1831 There is a shorthand for --transferfile {} --return --cleanup called
1833 --trc:
1834 echo This is input_file > input_file
1836 parallel -S $SERVER1 --trc {}.out cat {} ">"{}.out ::: input_file
1837 cat input_file.out
1838 Output: Same as above.
1840 Some jobs need a common database for all jobs. GNU parallel can
1842 transfer that using --basefile which will transfer the file before the
1843 first job:
1844 echo common data > common_file
1846 parallel --basefile common_file -S $SERVER1 \
1847 cat common_file\; echo {} ::: foo
1848 Output:
1850 common data
1852 foo
1853 To remove it from the remote host after the last job use --cleanup.
1855 Working dir
1857 The default working dir on the remote machines is the login dir. This
1858 can be changed with --workdir mydir.
1859 Files transferred using --transferfile and --return will be relative to
1861 mydir on remote computers, and the command will be executed in the dir
1862 mydir.
1863 The special mydir value ... will create working dirs under
1865 ~/.parallel/tmp on the remote computers. If --cleanup is given these
1866 dirs will be removed.
1867 The special mydir value . uses the current working dir. If the current
1869 working dir is beneath your home dir, the value . is treated as the
1870 relative path to your home dir. This means that if your home dir is
1871 different on remote computers (e.g. if your login is different) the
1872 relative path will still be relative to your home dir.
1873 parallel -S $SERVER1 pwd ::: ""
1875 parallel --workdir . -S $SERVER1 pwd ::: ""
1876 parallel --workdir ... -S $SERVER1 pwd ::: ""
1877 Output:
1879 [the login dir on $SERVER1]
1881 [current dir relative on $SERVER1]
1882 [a dir in ~/.parallel/tmp/...]
1883 Avoid overloading sshd
1885 If many jobs are started on the same server, sshd can be overloaded.
1886 GNU parallel can insert a delay between each job run on the same
1887 server:
1888 parallel -S $SERVER1 --sshdelay 0.2 echo ::: 1 2 3
1890 Output (the order may be different):
1892 1
1894 2
1895 3
1896 sshd will be less overloaded if using --controlmaster, which will
1898 multiplex ssh connections:
1899 parallel --controlmaster -S $SERVER1 echo ::: 1 2 3
1901 Output: Same as above.
1903 Ignore hosts that are down
1905 In clusters with many hosts a few of them are often down. GNU parallel
1906 can ignore those hosts. In this case the host 173.194.32.46 is down:
1907 parallel --filter-hosts -S 173.194.32.46,$SERVER1 echo ::: bar
1909 Output:
1911 bar
1913 Running the same commands on all hosts
1915 GNU parallel can run the same command on all the hosts:
1916 parallel --onall -S $SERVER1,$SERVER2 echo ::: foo bar
1918 Output (the order may be different):
1920 foo
1922 bar
1923 foo
1924 bar
1925 Often you will just want to run a single command on all hosts with out
1927 arguments. --nonall is a no argument --onall:
1928 parallel --nonall -S $SERVER1,$SERVER2 echo foo bar
1930 Output:
1932 foo bar
1934 foo bar
1935 When --tag is used with --nonall and --onall the --tagstring is the
1937 host:
1938 parallel --nonall --tag -S $SERVER1,$SERVER2 echo foo bar
1940 Output (the order may be different):
1942 $SERVER1 foo bar
1944 $SERVER2 foo bar
1945 --jobs sets the number of servers to log in to in parallel.
1947 Transferring environment variables and functions
1949 env_parallel is a shell function that transfers all aliases, functions,
1950 variables, and arrays. You active it by running:
1951 source `which env_parallel.bash`
1953 Replace bash with the shell you use.
1955 Now you can use env_parallel instead of parallel and still have your
1957 environment:
1958 alias myecho=echo
1960 myvar="Joe's var is"
1961 env_parallel -S $SERVER1 'myecho $myvar' ::: green
1962 Output:
1964 Joe's var is green
1966 The disadvantage is that if your environment is huge env_parallel will
1968 fail.
1969 When env_parallel fails, you can still use --env to tell GNU parallel
1971 to transfer an environment variable to the remote system.
1972 MYVAR='foo bar'
1974 export MYVAR
1975 parallel --env MYVAR -S $SERVER1 echo '$MYVAR' ::: baz
1976 Output:
1978 foo bar baz
1980 This works for functions, too, if your shell is Bash:
1982 # This only works in Bash
1984 my_func() {
1985 echo in my_func $1
1986 }
1987 export -f my_func
1988 parallel --env my_func -S $SERVER1 my_func ::: baz
1989 Output:
1991 in my_func baz
1993 GNU parallel can copy all user defined variables and functions to the
1995 remote system. It just needs to record which ones to ignore in
1996 ~/.parallel/ignored_vars. Do that by running this once:
1997 parallel --record-env
1999 cat ~/.parallel/ignored_vars
2000 Output:
2002 [list of variables to ignore - including $PATH and $HOME]
2004 Now all other variables and functions defined will be copied when using
2006 --env _.
2007 # The function is only copied if using Bash
2009 my_func2() {
2010 echo in my_func2 $VAR $1
2011 }
2012 export -f my_func2
2013 VAR=foo
2014 export VAR
2015 parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar
2017 Output:
2019 foo
2021 in my_func2 foo bar
2022 If you use env_parallel the variables, functions, and aliases do not
2024 even need to be exported to be copied:
2025 NOT='not exported var'
2027 alias myecho=echo
2028 not_ex() {
2029 myecho in not_exported_func $NOT $1
2030 }
2031 env_parallel --env _ -S $SERVER1 'echo $NOT; not_ex' ::: bar
2032 Output:
2034 not exported var
2036 in not_exported_func not exported var bar
2037 Showing what is actually run
2039 --verbose will show the command that would be run on the local machine.
2040 When using --cat, --pipepart, or when a job is run on a remote machine,
2042 the command is wrapped with helper scripts. -vv shows all of this.
2043 parallel -vv --pipepart --block 1M wc :::: num30000
2045 Output:
2047 <num30000 perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die;
2049 $left = shift; while($read = sysread(STDIN,$buf, ($left > 131072
2050 ? 131072 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }'
2051 0 0 0 168894 | (wc)
2052 30000 30000 168894
2053 When the command gets more complex, the output is so hard to read, that
2055 it is only useful for debugging:
2056 my_func3() {
2058 echo in my_func $1 > $1.out
2059 }
2060 export -f my_func3
2061 parallel -vv --workdir ... --nice 17 --env _ --trc {}.out \
2062 -S $SERVER1 my_func3 {} ::: abc-file
2063 Output will be similar to:
2065 ( ssh server -- mkdir -p ./.parallel/tmp/aspire-1928520-1;rsync
2067 --protocol 30 -rlDzR -essh ./abc-file
2068 server:./.parallel/tmp/aspire-1928520-1 );ssh server -- exec perl -e
2069 \''@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64");
2070 eval"@GNU_Parallel";my$eval=decode_base64(join"",@ARGV);eval$eval;'\'
2071 c3lzdGVtKCJta2RpciIsIi1wIiwiLS0iLCIucGFyYWxsZWwvdG1wL2FzcGlyZS0xOTI4N
2072 TsgY2hkaXIgIi5wYXJhbGxlbC90bXAvYXNwaXJlLTE5Mjg1MjAtMSIgfHxwcmludChTVE
2073 BhcmFsbGVsOiBDYW5ub3QgY2hkaXIgdG8gLnBhcmFsbGVsL3RtcC9hc3BpcmUtMTkyODU
2074 iKSAmJiBleGl0IDI1NTskRU5WeyJPTERQV0QifT0iL2hvbWUvdGFuZ2UvcHJpdmF0L3Bh
2075 IjskRU5WeyJQQVJBTExFTF9QSUQifT0iMTkyODUyMCI7JEVOVnsiUEFSQUxMRUxfU0VRI
2076 0BiYXNoX2Z1bmN0aW9ucz1xdyhteV9mdW5jMyk7IGlmKCRFTlZ7IlNIRUxMIn09fi9jc2
2077 ByaW50IFNUREVSUiAiQ1NIL1RDU0ggRE8gTk9UIFNVUFBPUlQgbmV3bGluZXMgSU4gVkF
2078 TL0ZVTkNUSU9OUy4gVW5zZXQgQGJhc2hfZnVuY3Rpb25zXG4iOyBleGVjICJmYWxzZSI7
2079 YXNoZnVuYyA9ICJteV9mdW5jMygpIHsgIGVjaG8gaW4gbXlfZnVuYyBcJDEgPiBcJDEub
2080 Xhwb3J0IC1mIG15X2Z1bmMzID4vZGV2L251bGw7IjtAQVJHVj0ibXlfZnVuYzMgYWJjLW
2081 RzaGVsbD0iJEVOVntTSEVMTH0iOyR0bXBkaXI9Ii90bXAiOyRuaWNlPTE3O2RveyRFTlZ
2082 MRUxfVE1QfT0kdG1wZGlyLiIvcGFyIi5qb2luIiIsbWFweygwLi45LCJhIi4uInoiLCJB
2083 KVtyYW5kKDYyKV19KDEuLjUpO313aGlsZSgtZSRFTlZ7UEFSQUxMRUxfVE1QfSk7JFNJ
2084 fT1zdWJ7JGRvbmU9MTt9OyRwaWQ9Zm9yazt1bmxlc3MoJHBpZCl7c2V0cGdycDtldmFse
2085 W9yaXR5KDAsMCwkbmljZSl9O2V4ZWMkc2hlbGwsIi1jIiwoJGJhc2hmdW5jLiJAQVJHVi
2086 JleGVjOiQhXG4iO31kb3skcz0kczwxPzAuMDAxKyRzKjEuMDM6JHM7c2VsZWN0KHVuZGV
2087 mLHVuZGVmLCRzKTt9dW50aWwoJGRvbmV8fGdldHBwaWQ9PTEpO2tpbGwoU0lHSFVQLC0k
2088 dW5sZXNzJGRvbmU7d2FpdDtleGl0KCQ/JjEyNz8xMjgrKCQ/JjEyNyk6MSskPz4+OCk=;
2089 _EXIT_status=$?; mkdir -p ./.; rsync --protocol 30 --rsync-path=cd\
2090 ./.parallel/tmp/aspire-1928520-1/./.\;\ rsync -rlDzR -essh
2091 server:./abc-file.out ./.;ssh server -- \(rm\ -f\
2092 ./.parallel/tmp/aspire-1928520-1/abc-file\;\ sh\ -c\ \'rmdir\
2093 ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\ ./.parallel/\
2094 2\>/dev/null\'\;rm\ -rf\ ./.parallel/tmp/aspire-1928520-1\;\);ssh
2095 server -- \(rm\ -f\ ./.parallel/tmp/aspire-1928520-1/abc-file.out\;\
2096 sh\ -c\ \'rmdir\ ./.parallel/tmp/aspire-1928520-1/\ ./.parallel/tmp/\
2097 ./.parallel/\ 2\>/dev/null\'\;rm\ -rf\
2098 ./.parallel/tmp/aspire-1928520-1\;\);ssh server -- rm -rf
2099 .parallel/tmp/aspire-1928520-1; exit $_EXIT_status;
2100
2102 GNU parset will set shell variables to the output of GNU parallel. GNU
2103 parset has one important limitation: It cannot be part of a pipe. In
2104 particular this means it cannot read anything from standard input
2105 (stdin) or pipe output to another program.
2106 To use GNU parset prepend command with destination variables:
2108 parset myvar1,myvar2 echo ::: a b
2110 echo $myvar1
2111 echo $myvar2
2112 Output:
2114 a
2116 b
2117 If you only give a single variable, it will be treated as an array:
2119 parset myarray seq {} 5 ::: 1 2 3
2121 echo "${myarray[1]}"
2122 Output:
2124 2
2126 3
2127 4
2128 5
2129 The commands to run can be an array:
2131 cmd=("echo '<<joe \"double space\" cartoon>>'" "pwd")
2133 parset data ::: "${cmd[@]}"
2134 echo "${data[0]}"
2135 echo "${data[1]}"
2136 Output:
2138 <<joe "double space" cartoon>>
2140 [current dir]
2141
2143 GNU parallel can save into an SQL base. Point GNU parallel to a table
2144 and it will put the joblog there together with the variables and the
2145 output each in their own column.
2146 CSV as SQL base
2148 The simplest is to use a CSV file as the storage table:
2149 parallel --sqlandworker csv:///%2Ftmp/log.csv \
2151 seq ::: 10 ::: 12 13 14
2152 cat /tmp/log.csv
2153 Note how '/' in the path must be written as %2F.
2155 Output will be similar to:
2157 Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
2159 Command,V1,V2,Stdout,Stderr
2160 1,:,1458254498.254,0.069,0,9,0,0,"seq 10 12",10,12,"10
2161 11
2162 12
2163 ",
2164 2,:,1458254498.278,0.080,0,12,0,0,"seq 10 13",10,13,"10
2165 11
2166 12
2167 13
2168 ",
2169 3,:,1458254498.301,0.083,0,15,0,0,"seq 10 14",10,14,"10
2170 11
2171 12
2172 13
2173 14
2174 ",
2175 A proper CSV reader (like LibreOffice or R's read.csv) will read this
2177 format correctly - even with fields containing newlines as above.
2178 If the output is big you may want to put it into files using --results:
2180 parallel --results outdir --sqlandworker csv:///%2Ftmp/log2.csv \
2182 seq ::: 10 ::: 12 13 14
2183 cat /tmp/log2.csv
2184 Output will be similar to:
2186 Seq,Host,Starttime,JobRuntime,Send,Receive,Exitval,_Signal,
2188 Command,V1,V2,Stdout,Stderr
2189 1,:,1458824738.287,0.029,0,9,0,0,
2190 "seq 10 12",10,12,outdir/1/10/2/12/stdout,outdir/1/10/2/12/stderr
2191 2,:,1458824738.298,0.025,0,12,0,0,
2192 "seq 10 13",10,13,outdir/1/10/2/13/stdout,outdir/1/10/2/13/stderr
2193 3,:,1458824738.309,0.026,0,15,0,0,
2194 "seq 10 14",10,14,outdir/1/10/2/14/stdout,outdir/1/10/2/14/stderr
2195 DBURL as table
2197 The CSV file is an example of a DBURL.
2198 GNU parallel uses a DBURL to address the table. A DBURL has this
2200 format:
2201 vendor://[[user][:password]@][host][:port]/[database[/table]
2203 Example:
2205 mysql://scott:tiger@my.example.com/mydatabase/mytable
2207 postgresql://scott:tiger@pg.example.com/mydatabase/mytable
2208 sqlite3:///%2Ftmp%2Fmydatabase/mytable
2209 csv:///%2Ftmp/log.csv
2210 To refer to /tmp/mydatabase with sqlite or csv you need to encode the /
2212 as %2F.
2213 Run a job using sqlite on mytable in /tmp/mydatabase:
2215 DBURL=sqlite3:///%2Ftmp%2Fmydatabase
2217 DBURLTABLE=$DBURL/mytable
2218 parallel --sqlandworker $DBURLTABLE echo ::: foo bar ::: baz quuz
2219 To see the result:
2221 sql $DBURL 'SELECT * FROM mytable ORDER BY Seq;'
2223 Output will be similar to:
2225 Seq|Host|Starttime|JobRuntime|Send|Receive|Exitval|_Signal|
2227 Command|V1|V2|Stdout|Stderr
2228 1|:|1451619638.903|0.806||8|0|0|echo foo baz|foo|baz|foo baz
2229 |
2230 2|:|1451619639.265|1.54||9|0|0|echo foo quuz|foo|quuz|foo quuz
2231 |
2232 3|:|1451619640.378|1.43||8|0|0|echo bar baz|bar|baz|bar baz
2233 |
2234 4|:|1451619641.473|0.958||9|0|0|echo bar quuz|bar|quuz|bar quuz
2235 |
2236 The first columns are well known from --joblog. V1 and V2 are data from
2238 the input sources. Stdout and Stderr are standard output and standard
2239 error, respectively.
2240 Using multiple workers
2242 Using an SQL base as storage costs overhead in the order of 1 second
2243 per job.
2244 One of the situations where it makes sense is if you have multiple
2246 workers.
2247 You can then have a single master machine that submits jobs to the SQL
2249 base (but does not do any of the work):
2250 parallel --sqlmaster $DBURLTABLE echo ::: foo bar ::: baz quuz
2252 On the worker machines you run exactly the same command except you
2254 replace --sqlmaster with --sqlworker.
2255 parallel --sqlworker $DBURLTABLE echo ::: foo bar ::: baz quuz
2257 To run a master and a worker on the same machine use --sqlandworker as
2259 shown earlier.
2260
2262 The --pipe functionality puts GNU parallel in a different mode: Instead
2263 of treating the data on stdin (standard input) as arguments for a
2264 command to run, the data will be sent to stdin (standard input) of the
2265 command.
2266 The typical situation is:
2268 command_A | command_B | command_C
2270 where command_B is slow, and you want to speed up command_B.
2272 Chunk size
2274 By default GNU parallel will start an instance of command_B, read a
2275 chunk of 1 MB, and pass that to the instance. Then start another
2276 instance, read another chunk, and pass that to the second instance.
2277 cat num1000000 | parallel --pipe wc
2279 Output (the order may be different):
2281 165668 165668 1048571
2283 149797 149797 1048579
2284 149796 149796 1048572
2285 149797 149797 1048579
2286 149797 149797 1048579
2287 149796 149796 1048572
2288 85349 85349 597444
2289 The size of the chunk is not exactly 1 MB because GNU parallel only
2291 passes full lines - never half a line, thus the blocksize is only 1 MB
2292 on average. You can change the block size to 2 MB with --block:
2293 cat num1000000 | parallel --pipe --block 2M wc
2295 Output (the order may be different):
2297 315465 315465 2097150
2299 299593 299593 2097151
2300 299593 299593 2097151
2301 85349 85349 597444
2302 GNU parallel treats each line as a record. If the order of records is
2304 unimportant (e.g. you need all lines processed, but you do not care
2305 which is processed first), then you can use --roundrobin. Without
2306 --roundrobin GNU parallel will start a command per block; with
2307 --roundrobin only the requested number of jobs will be started
2308 (--jobs). The records will then be distributed between the running
2309 jobs:
2310 cat num1000000 | parallel --pipe -j4 --roundrobin wc
2312 Output will be similar to:
2314 149797 149797 1048579
2316 299593 299593 2097151
2317 315465 315465 2097150
2318 235145 235145 1646016
2319 One of the 4 instances got a single record, 2 instances got 2 full
2321 records each, and one instance got 1 full and 1 partial record.
2322 Records
2324 GNU parallel sees the input as records. The default record is a single
2325 line.
2326 Using -N140000 GNU parallel will read 140000 records at a time:
2328 cat num1000000 | parallel --pipe -N140000 wc
2330 Output (the order may be different):
2332 140000 140000 868895
2334 140000 140000 980000
2335 140000 140000 980000
2336 140000 140000 980000
2337 140000 140000 980000
2338 140000 140000 980000
2339 140000 140000 980000
2340 20000 20000 140001
2341 Note how that the last job could not get the full 140000 lines, but
2343 only 20000 lines.
2344 If a record is 75 lines -L can be used:
2346 cat num1000000 | parallel --pipe -L75 wc
2348 Output (the order may be different):
2350 165600 165600 1048095
2352 149850 149850 1048950
2353 149775 149775 1048425
2354 149775 149775 1048425
2355 149850 149850 1048950
2356 149775 149775 1048425
2357 85350 85350 597450
2358 25 25 176
2359 Note how GNU parallel still reads a block of around 1 MB; but instead
2361 of passing full lines to wc it passes full 75 lines at a time. This of
2362 course does not hold for the last job (which in this case got 25
2363 lines).
2364 Fixed length records
2366 Fixed length records can be processed by setting --recend '' and
2367 --block recordsize. A header of size n can be processed with --header
2368 .{n}.
2369 Here is how to process a file with a 4-byte header and a 3-byte record
2371 size:
2372 cat fixedlen | parallel --pipe --header .{4} --block 3 --recend '' \
2374 'echo start; cat; echo'
2375 Output:
2377 start
2379 HHHHAAA
2380 start
2381 HHHHCCC
2382 start
2383 HHHHBBB
2384 It may be more efficient to increase --block to a multiplum of the
2386 record size.
2387 Record separators
2389 GNU parallel uses separators to determine where two records split.
2390 --recstart gives the string that starts a record; --recend gives the
2392 string that ends a record. The default is --recend '\n' (newline).
2393 If both --recend and --recstart are given, then the record will only
2395 split if the recend string is immediately followed by the recstart
2396 string.
2397 Here the --recend is set to ', ':
2399 echo /foo, bar/, /baz, qux/, | \
2401 parallel -kN1 --recend ', ' --pipe echo JOB{#}\;cat\;echo END
2402 Output:
2404 JOB1
2406 /foo, END
2407 JOB2
2408 bar/, END
2409 JOB3
2410 /baz, END
2411 JOB4
2412 qux/,
2413 END
2414 Here the --recstart is set to /:
2416 echo /foo, bar/, /baz, qux/, | \
2418 parallel -kN1 --recstart / --pipe echo JOB{#}\;cat\;echo END
2419 Output:
2421 JOB1
2423 /foo, barEND
2424 JOB2
2425 /, END
2426 JOB3
2427 /baz, quxEND
2428 JOB4
2429 /,
2430 END
2431 Here both --recend and --recstart are set:
2433 echo /foo, bar/, /baz, qux/, | \
2435 parallel -kN1 --recend ', ' --recstart / --pipe \
2436 echo JOB{#}\;cat\;echo END
2437 Output:
2439 JOB1
2441 /foo, bar/, END
2442 JOB2
2443 /baz, qux/,
2444 END
2445 Note the difference between setting one string and setting both
2447 strings.
2448 With --regexp the --recend and --recstart will be treated as a regular
2450 expression:
2451 echo foo,bar,_baz,__qux, | \
2453 parallel -kN1 --regexp --recend ,_+ --pipe \
2454 echo JOB{#}\;cat\;echo END
2455 Output:
2457 JOB1
2459 foo,bar,_END
2460 JOB2
2461 baz,__END
2462 JOB3
2463 qux,
2464 END
2465 GNU parallel can remove the record separators with
2467 --remove-rec-sep/--rrs:
2468 echo foo,bar,_baz,__qux, | \
2470 parallel -kN1 --rrs --regexp --recend ,_+ --pipe \
2471 echo JOB{#}\;cat\;echo END
2472 Output:
2474 JOB1
2476 foo,barEND
2477 JOB2
2478 bazEND
2479 JOB3
2480 qux,
2481 END
2482 Header
2484 If the input data has a header, the header can be repeated for each job
2485 by matching the header with --header. If headers start with % you can
2486 do this:
2487 cat num_%header | \
2489 parallel --header '(%.*\n)*' --pipe -N3 echo JOB{#}\;cat
2490 Output (the order may be different):
2492 JOB1
2494 %head1
2495 %head2
2496 1
2497 2
2498 3
2499 JOB2
2500 %head1
2501 %head2
2502 4
2503 5
2504 6
2505 JOB3
2506 %head1
2507 %head2
2508 7
2509 8
2510 9
2511 JOB4
2512 %head1
2513 %head2
2514 10
2515 If the header is 2 lines, --header 2 will work:
2517 cat num_%header | parallel --header 2 --pipe -N3 echo JOB{#}\;cat
2519 Output: Same as above.
2521 --pipepart
2523 --pipe is not very efficient. It maxes out at around 500 MB/s.
2524 --pipepart can easily deliver 5 GB/s. But there are a few limitations.
2525 The input has to be a normal file (not a pipe) given by -a or :::: and
2526 -L/-l/-N do not work. --recend and --recstart, however, do work, and
2527 records can often be split on that alone.
2528 parallel --pipepart -a num1000000 --block 3m wc
2530 Output (the order may be different):
2532 444443 444444 3000002
2534 428572 428572 3000004
2535 126985 126984 888890
2536
2538 Input data and parallel command in the same file
2539 GNU parallel is often called as this:
2540 cat input_file | parallel command
2542 With --shebang the input_file and parallel can be combined into the
2544 same script.
2545 UNIX shell scripts start with a shebang line like this:
2547 #!/bin/bash
2549 GNU parallel can do that, too. With --shebang the arguments can be
2551 listed in the file. The parallel command is the first line of the
2552 script:
2553 #!/usr/bin/parallel --shebang -r echo
2555 foo
2557 bar
2558 baz
2559 Output (the order may be different):
2561 foo
2563 bar
2564 baz
2565 Parallelizing existing scripts
2567 GNU parallel is often called as this:
2568 cat input_file | parallel command
2570 parallel command ::: foo bar
2571 If command is a script, parallel can be combined into a single file so
2573 this will run the script in parallel:
2574 cat input_file | command
2576 command foo bar
2577 This perl script perl_echo works like echo:
2579 #!/usr/bin/perl
2581 print "@ARGV\n"
2583 It can be called as this:
2585 parallel perl_echo ::: foo bar
2587 By changing the #!-line it can be run in parallel:
2589 #!/usr/bin/parallel --shebang-wrap /usr/bin/perl
2591 print "@ARGV\n"
2593 Thus this will work:
2595 perl_echo foo bar
2597 Output (the order may be different):
2599 foo
2601 bar
2602 This technique can be used for:
2604 Perl:
2606 #!/usr/bin/parallel --shebang-wrap /usr/bin/perl
2607 print "Arguments @ARGV\n";
2609 Python:
2611 #!/usr/bin/parallel --shebang-wrap /usr/bin/python
2612 import sys
2614 print 'Arguments', str(sys.argv)
2615 Bash/sh/zsh/Korn shell:
2617 #!/usr/bin/parallel --shebang-wrap /bin/bash
2618 echo Arguments "$@"
2620 csh:
2622 #!/usr/bin/parallel --shebang-wrap /bin/csh
2623 echo Arguments "$argv"
2625 Tcl:
2627 #!/usr/bin/parallel --shebang-wrap /usr/bin/tclsh
2628 puts "Arguments $argv"
2630 R:
2632 #!/usr/bin/parallel --shebang-wrap /usr/bin/Rscript --vanilla --slave
2633 args <- commandArgs(trailingOnly = TRUE)
2635 print(paste("Arguments ",args))
2636 GNUplot:
2638 #!/usr/bin/parallel --shebang-wrap ARG={} /usr/bin/gnuplot
2639 print "Arguments ", system('echo $ARG')
2641 Ruby:
2643 #!/usr/bin/parallel --shebang-wrap /usr/bin/ruby
2644 print "Arguments "
2646 puts ARGV
2647 Octave:
2649 #!/usr/bin/parallel --shebang-wrap /usr/bin/octave
2650 printf ("Arguments");
2652 arg_list = argv ();
2653 for i = 1:nargin
2654 printf (" %s", arg_list{i});
2655 endfor
2656 printf ("\n");
2657 Common LISP:
2659 #!/usr/bin/parallel --shebang-wrap /usr/bin/clisp
2660 (format t "~&~S~&" 'Arguments)
2662 (format t "~&~S~&" *args*)
2663 PHP:
2665 #!/usr/bin/parallel --shebang-wrap /usr/bin/php
2666 <?php
2667 echo "Arguments";
2668 foreach(array_slice($argv,1) as $v)
2669 {
2670 echo " $v";
2671 }
2672 echo "\n";
2673 ?>
2674 Node.js:
2676 #!/usr/bin/parallel --shebang-wrap /usr/bin/node
2677 var myArgs = process.argv.slice(2);
2679 console.log('Arguments ', myArgs);
2680 LUA:
2682 #!/usr/bin/parallel --shebang-wrap /usr/bin/lua
2683 io.write "Arguments"
2685 for a = 1, #arg do
2686 io.write(" ")
2687 io.write(arg[a])
2688 end
2689 print("")
2690 C#:
2692 #!/usr/bin/parallel --shebang-wrap ARGV={} /usr/bin/csharp
2693 var argv = Environment.GetEnvironmentVariable("ARGV");
2695 print("Arguments "+argv);
2696
2698 GNU parallel can work as a counting semaphore. This is slower and less
2699 efficient than its normal mode.
2700 A counting semaphore is like a row of toilets. People needing a toilet
2702 can use any toilet, but if there are more people than toilets, they
2703 will have to wait for one of the toilets to become available.
2704 An alias for parallel --semaphore is sem.
2706 sem will follow a person to the toilets, wait until a toilet is
2708 available, leave the person in the toilet and exit.
2709 sem --fg will follow a person to the toilets, wait until a toilet is
2711 available, stay with the person in the toilet and exit when the person
2712 exits.
2713 sem --wait will wait for all persons to leave the toilets.
2715 sem does not have a queue discipline, so the next person is chosen
2717 randomly.
2718 -j sets the number of toilets.
2720 Mutex
2722 The default is to have only one toilet (this is called a mutex). The
2723 program is started in the background and sem exits immediately. Use
2724 --wait to wait for all sems to finish:
2725 sem 'sleep 1; echo The first finished' &&
2727 echo The first is now running in the background &&
2728 sem 'sleep 1; echo The second finished' &&
2729 echo The second is now running in the background
2730 sem --wait
2731 Output:
2733 The first is now running in the background
2735 The first finished
2736 The second is now running in the background
2737 The second finished
2738 The command can be run in the foreground with --fg, which will only
2740 exit when the command completes:
2741 sem --fg 'sleep 1; echo The first finished' &&
2743 echo The first finished running in the foreground &&
2744 sem --fg 'sleep 1; echo The second finished' &&
2745 echo The second finished running in the foreground
2746 sem --wait
2747 The difference between this and just running the command, is that a
2749 mutex is set, so if other sems were running in the background only one
2750 would run at a time.
2751 To control which semaphore is used, use --semaphorename/--id. Run this
2753 in one terminal:
2754 sem --id my_id -u 'echo First started; sleep 10; echo First done'
2756 and simultaneously this in another terminal:
2758 sem --id my_id -u 'echo Second started; sleep 10; echo Second done'
2760 Note how the second will only be started when the first has finished.
2762 Counting semaphore
2764 A mutex is like having a single toilet: When it is in use everyone else
2765 will have to wait. A counting semaphore is like having multiple
2766 toilets: Several people can use the toilets, but when they all are in
2767 use, everyone else will have to wait.
2768 sem can emulate a counting semaphore. Use --jobs to set the number of
2770 toilets like this:
2771 sem --jobs 3 --id my_id -u 'echo Start 1; sleep 5; echo 1 done' &&
2773 sem --jobs 3 --id my_id -u 'echo Start 2; sleep 6; echo 2 done' &&
2774 sem --jobs 3 --id my_id -u 'echo Start 3; sleep 7; echo 3 done' &&
2775 sem --jobs 3 --id my_id -u 'echo Start 4; sleep 8; echo 4 done' &&
2776 sem --wait --id my_id
2777 Output:
2779 Start 1
2781 Start 2
2782 Start 3
2783 1 done
2784 Start 4
2785 2 done
2786 3 done
2787 4 done
2788 Timeout
2790 With --semaphoretimeout you can force running the command anyway after
2791 a period (positive number) or give up (negative number):
2792 sem --id foo -u 'echo Slow started; sleep 5; echo Slow ended' &&
2794 sem --id foo --semaphoretimeout 1 'echo Forced running after 1 sec' &&
2795 sem --id foo --semaphoretimeout -2 'echo Give up after 2 secs'
2796 sem --id foo --wait
2797 Output:
2799 Slow started
2801 parallel: Warning: Semaphore timed out. Stealing the semaphore.
2802 Forced running after 1 sec
2803 parallel: Warning: Semaphore timed out. Exiting.
2804 Slow ended
2805 Note how the 'Give up' was not run.
2807
2809 GNU parallel has some options to give short information about the
2810 configuration.
2811 --help will print a summary of the most important options:
2813 parallel --help
2815 Output:
2817 Usage:
2819 parallel [options] [command [arguments]] < list_of_arguments
2821 parallel [options] [command [arguments]] (::: arguments|:::: argfile(s))...
2822 cat ... | parallel --pipe [options] [command [arguments]]
2823 -j n Run n jobs in parallel
2825 -k Keep same order
2826 -X Multiple arguments with context replace
2827 --colsep regexp Split input on regexp for positional replacements
2828 {} {.} {/} {/.} {#} {%} {= perl code =} Replacement strings
2829 {3} {3.} {3/} {3/.} {=3 perl code =} Positional replacement strings
2830 With --plus: {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} =
2831 {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}
2832 -S sshlogin Example: foo@server.example.com
2834 --slf .. Use ~/.parallel/sshloginfile as the list of sshlogins
2835 --trc {}.bar Shorthand for --transfer --return {}.bar --cleanup
2836 --onall Run the given command with argument on all sshlogins
2837 --nonall Run the given command with no arguments on all sshlogins
2838 --pipe Split stdin (standard input) to multiple jobs.
2840 --recend str Record end separator for --pipe.
2841 --recstart str Record start separator for --pipe.
2842 See 'man parallel' for details
2844 Academic tradition requires you to cite works you base your article on.
2846 When using programs that use GNU Parallel to process data for publication
2847 please cite:
2848 O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
2850 ;login: The USENIX Magazine, February 2011:42-47.
2851 This helps funding further development; AND IT WON'T COST YOU A CENT.
2853 If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
2854 When asking for help, always report the full output of this:
2856 parallel --version
2858 Output:
2860 GNU parallel 20230122
2862 Copyright (C) 2007-2023 Ole Tange, http://ole.tange.dk and Free Software
2863 Foundation, Inc.
2864 License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>
2865 This is free software: you are free to change and redistribute it.
2866 GNU parallel comes with no warranty.
2867 Web site: https://www.gnu.org/software/parallel
2869 When using programs that use GNU Parallel to process data for publication
2871 please cite as described in 'parallel --citation'.
2872 In scripts --minversion can be used to ensure the user has at least
2874 this version:
2875 parallel --minversion 20130722 && \
2877 echo Your version is at least 20130722.
2878 Output:
2880 20160322
2882 Your version is at least 20130722.
2883 If you are using GNU parallel for research the BibTeX citation can be
2885 generated using --citation:
2886 parallel --citation
2888 Output:
2890 Academic tradition requires you to cite works you base your article on.
2892 When using programs that use GNU Parallel to process data for publication
2893 please cite:
2894 @article{Tange2011a,
2896 title = {GNU Parallel - The Command-Line Power Tool},
2897 author = {O. Tange},
2898 address = {Frederiksberg, Denmark},
2899 journal = {;login: The USENIX Magazine},
2900 month = {Feb},
2901 number = {1},
2902 volume = {36},
2903 url = {https://www.gnu.org/s/parallel},
2904 year = {2011},
2905 pages = {42-47},
2906 doi = {10.5281/zenodo.16303}
2907 }
2908 (Feel free to use \nocite{Tange2011a})
2910 This helps funding further development; AND IT WON'T COST YOU A CENT.
2912 If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
2913 If you send a copy of your published article to tange@gnu.org, it will be
2915 mentioned in the release notes of next version of GNU Parallel.
2916 With --max-line-length-allowed GNU parallel will report the maximal
2918 size of the command line:
2919 parallel --max-line-length-allowed
2921 Output (may vary on different systems):
2923 131071
2925 --number-of-cpus and --number-of-cores run system specific code to
2927 determine the number of CPUs and CPU cores on the system. On
2928 unsupported platforms they will return 1:
2929 parallel --number-of-cpus
2931 parallel --number-of-cores
2932 Output (may vary on different systems):
2934 4
2936 64
2937
2939 The defaults for GNU parallel can be changed systemwide by putting the
2940 command line options in /etc/parallel/config. They can be changed for a
2941 user by putting them in ~/.parallel/config.
2942 Profiles work the same way, but have to be referred to with --profile:
2944 echo '--nice 17' > ~/.parallel/nicetimeout
2946 echo '--timeout 300%' >> ~/.parallel/nicetimeout
2947 parallel --profile nicetimeout echo ::: A B C
2948 Output:
2950 A
2952 B
2953 C
2954 Profiles can be combined:
2956 echo '-vv --dry-run' > ~/.parallel/dryverbose
2958 parallel --profile dryverbose --profile nicetimeout echo ::: A B C
2959 Output:
2961 echo A
2963 echo B
2964 echo C
2965
2967 I hope you have learned something from this tutorial.
2968 If you like GNU parallel:
2970 • (Re-)walk through the tutorial if you have not done so in the past
2972 year (https://www.gnu.org/software/parallel/parallel_tutorial.html)
2973 • Give a demo at your local user group/your team/your colleagues
2975 • Post the intro videos and the tutorial on Reddit, Mastodon,
2977 Diaspora*, forums, blogs, Identi.ca, Google+, Twitter, Facebook,
2978 Linkedin, and mailing lists
2979 • Request or write a review for your favourite blog or magazine
2981 (especially if you do something cool with GNU parallel)
2982 • Invite me for your next conference
2984 If you use GNU parallel for research:
2986 • Please cite GNU parallel in you publications (use --citation)
2988 If GNU parallel saves you money:
2990 • (Have your company) donate to FSF or become a member
2992 https://my.fsf.org/donate/
2993 (C) 2013-2023 Ole Tange, GFDLv1.3+ (See LICENSES/GFDL-1.3-or-later.txt)
299520230722 2023-07-28 PARALLEL_TUTORIAL(7)