mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-11-22 05:57:54 +00:00
env_parallel.*sh: Parsing 'type' depends on $LANG. Set LANG=C.
--tee: No longer spawns cat, but uses redirection instead.
This commit is contained in:
Ole Tange
parent
b60a203bd8
commit
8b050b68d4
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@ -199,7 +199,7 @@ to:parallel@gnu.org, bug-parallel@gnu.org
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stable-bcc: Jesse Alama <jessealama@fastmail.fm>
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Subject: GNU Parallel 20180422 ('Trèbes') released <<[stable]>>
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Subject: GNU Parallel 20180422 ('Trèbes/Tiangong-1/Winnie Mandela/ASIM/Algeria') released <<[stable]>>
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GNU Parallel 20180422 ('Trèbes') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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@ -212,6 +212,13 @@ Quote of the month:
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New in this release:
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Launch at DIKU
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https://userinfo.surfsara.nl/documentation/running-many-serial-jobs-efficiently
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http://fliplinux.com/gnu-parallel-6.html
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https://www.youtube.com/watch?v=sHpTywpb4_4
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<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>
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@ -51,11 +51,11 @@ env_parallel() {
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}
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_names_of_FUNCTIONS() {
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# myfunc is a function
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type `_names_of_maybe_FUNCTIONS` |
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LANG=C type `_names_of_maybe_FUNCTIONS` |
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perl -ne '/^(\S+) is a function$/ and not $seen{$1}++ and print "$1\n"'
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}
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_bodies_of_FUNCTIONS() {
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type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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LANG=C type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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}
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_names_of_VARIABLES() {
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# This may screw up if variables contain \n and =
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@ -131,7 +131,7 @@ env_parallel() {
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# parallel is a tracked alias for /usr/local/bin/parallel (ksh)
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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@ -152,7 +152,7 @@ env_parallel() {
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# which is hashed (/usr/bin/which)
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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@ -51,11 +51,11 @@ env_parallel() {
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}
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_names_of_FUNCTIONS() {
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# myfunc is a function
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type `_names_of_maybe_FUNCTIONS` |
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LANG=C type `_names_of_maybe_FUNCTIONS` |
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perl -ne '/^(\S+) is a function$/ and not $seen{$1}++ and print "$1\n"'
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}
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_bodies_of_FUNCTIONS() {
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type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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LANC=C type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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}
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_names_of_VARIABLES() {
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# This may screw up if variables contain \n and =
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@ -131,7 +131,7 @@ env_parallel() {
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# parallel is a tracked alias for /usr/local/bin/parallel (ksh)
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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@ -111,7 +111,7 @@ env_parallel() {
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# parallel is a tracked alias for /usr/local/bin/parallel (ksh)
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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@ -51,11 +51,11 @@ env_parallel() {
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}
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_names_of_FUNCTIONS() {
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# myfunc is a function
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type `_names_of_maybe_FUNCTIONS` |
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LANG=C type `_names_of_maybe_FUNCTIONS` |
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perl -ne '/^(\S+) is a function$/ and not $seen{$1}++ and print "$1\n"'
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}
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_bodies_of_FUNCTIONS() {
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type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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LANG=C type "$@" | perl -ne '/^(\S+) is a function$/ or print'
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}
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_names_of_VARIABLES() {
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# This may screw up if variables contain \n and =
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@ -131,7 +131,7 @@ env_parallel() {
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# parallel is a tracked alias for /usr/local/bin/parallel (ksh)
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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@ -105,7 +105,7 @@ env_parallel() {
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# which is hashed (/usr/bin/which)
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# aliased to `alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde'
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# Return 0 if found, 1 otherwise
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type "$@" |
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LANG=C type "$@" |
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perl -pe '$exit += (s/ is an alias for .*// ||
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s/ is aliased to .*// ||
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s/ is a function// ||
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55
src/parallel
55
src/parallel
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@ -48,7 +48,6 @@ if($Global::max_number_of_args) {
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}
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my @command = @ARGV;
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my @input_source_fh;
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if($opt::pipepart) {
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if($opt::tee) {
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@ -226,10 +225,11 @@ sub pipepart_setup {
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# $Global::JobQueue
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if($opt::tee) {
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# Prepend each command with
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# cat file
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my $cat_string = "cat ".::shell_quote_scalar($opt::a[0]);
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# < file
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my $cat_string = "< ".::shell_quote_scalar($opt::a[0]);
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for(1..$Global::JobQueue->total_jobs()) {
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push @Global::cat_prepends, $cat_string;
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push @Global::cat_appends, $cat_string;
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push @Global::cat_prepends, "";
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}
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} else {
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if(not $opt::blocksize) {
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@ -286,15 +286,13 @@ sub pipe_tee_setup {
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open STDOUT, ">","/dev/null";
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exec "tee",@fifos;
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}
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# Make cats for each fifo
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# cat fifo1 | grep 1
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# cat fifo2 | grep 2
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# cat fifo3 | grep 3
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# cat fifo4 | grep 4
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# cat fifo5 | grep 5
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# For each fifo
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# (rm fifo1; grep 1) < fifo1
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# (rm fifo2; grep 2) < fifo2
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# (rm fifo3; grep 3) < fifo3
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# Remove the tmpfifo as soon as it is open
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# 'exec' saves a process
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@Global::cat_prepends = map { "(rm $_; exec cat) < $_" } @fifos;
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@Global::cat_prepends = map { "(rm $_;" } @fifos;
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@Global::cat_appends = map { ") < $_" } @fifos;
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}
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sub pipe_part_files {
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@ -407,7 +405,10 @@ sub find_split_positions {
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}
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}
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}
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push(@pos,$size);
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if($pos[$#pos] != $size) {
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# Last splitpoint was not at end of the file: add it
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push(@pos,$size);
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}
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close $fh;
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return @pos;
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}
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@ -440,7 +441,7 @@ sub cat_partial {
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}
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});
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return "<". shell_quote_scalar($file) .
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" perl -e '$script' @start_len";
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" perl -e '$script' @start_len |";
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}
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sub spreadstdin {
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@ -4097,8 +4098,8 @@ sub usage {
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"If you use programs that use GNU Parallel to process data for an article in a",
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"scientific publication, please cite:",
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"",
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" O. Tange (2011): GNU Parallel - The Command-Line Power Tool,",
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" ;login: The USENIX Magazine, February 2011:42-47.",
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" O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,",
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" DOI https://doi.org/10.5281/zenodo.1146014",
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"",
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"This helps funding further development; AND IT WON'T COST YOU A CENT.",
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"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
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@ -4125,12 +4126,15 @@ sub citation_notice {
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"If you use programs that use GNU Parallel to process data for an article in a",
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"scientific publication, please cite:",
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"",
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" O. Tange (2011): GNU Parallel - The Command-Line Power Tool,",
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" ;login: The USENIX Magazine, February 2011:42-47.",
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" O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,",
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" DOI https://doi.org/10.5281/zenodo.1146014",
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"",
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"This helps funding further development; AND IT WON'T COST YOU A CENT.",
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"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
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"",
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"More about funding GNU Parallel and the citation notice:",
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"https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice",
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"",
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"To silence this citation notice: run 'parallel --citation' once.",
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""
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);
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@ -4216,8 +4220,9 @@ sub citation {
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" author = {Tange, Ole},",
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" title = {GNU Parallel 2018},",
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" publisher = {Ole Tange},",
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" month = Apr,",
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" year = 2018,",
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" month = apr,",
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" ISBN = {9781387509881},",
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" doi = {10.5281/zenodo.1146014},",
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" url = {https://doi.org/10.5281/zenodo.1146014}",
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"}",
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@ -4227,6 +4232,9 @@ sub citation {
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"This helps funding further development; AND IT WON'T COST YOU A CENT.",
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"If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
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"",
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"More about funding GNU Parallel and the citation notice:",
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"https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice",
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"",
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"If you send a copy of your published article to tange\@gnu.org, it will be",
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"mentioned in the release notes of next version of GNU Parallel.",
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""
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@ -7765,11 +7773,12 @@ sub wrapped {
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# }' 0 0 0 11 |
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#
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# --pipepart --tee: prepend:
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# cat dash-a-file |
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# < dash-a-file
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#
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# --pipe --tee: prepend:
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# cat fifo |
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$command = (shift @Global::cat_prepends). " | ($command)";
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# --pipe --tee: wrap:
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# (rm fifo; ... ) < fifo
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$command = (shift @Global::cat_prepends). "($command)".
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(shift @Global::cat_appends);
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} elsif($opt::pipe) {
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# Wrap with EOF-detector to avoid starting $command if EOF.
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$command = empty_input_wrapper($command);
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@ -2485,7 +2485,7 @@ a bc " -> "a bc". This is the default if B<--colsep> is used.
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=item B<-u>
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Ungroup output. Output is printed as soon as possible and by passes
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Ungroup output. Output is printed as soon as possible and bypasses
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GNU B<parallel> internal processing. This may cause output from
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different commands to be mixed thus should only be used if you do not
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care about the output. Compare these:
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@ -2917,7 +2917,35 @@ for Blue Marble world map and create a 10240x20480 map.
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convert -append line{0..19}.jpg world.jpg
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=head1 EXAMPLE: Copy files as last modified date (ISO8601) with added random digits
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=head1 EXAMPLE: Download Apollo-11 images from NASA using jq
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Search NASA using their API to get JSON for images related to 'apollo
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11' and has 'moon landing' in the description.
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The search query returns JSON containing URLs to JSON containing
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collections of pictures. One of the pictures in each of these
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collection is I<large>.
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B<wget> is used to get the JSON for the search query. B<jq> is then
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used to extract the URLs of the collections. B<parallel> then calls
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B<wget> to get each collection, which is passed to B<jq> to extract
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the URLs of all images. B<grep> filters out the I<large> images, and
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B<parallel> finally uses B<wget> to fetch the images.
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base="https://images-api.nasa.gov/search"
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q="q=apollo 11"
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description="description=moon landing"
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media_type="media_type=image"
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wget -O - "$base?$q&$description&$media_type" |
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jq -r .collection.items[].href |
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parallel wget -O - |
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jq -r .[] |
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grep large |
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parallel wget
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=head1 EXAMPLE: Copy files as last modified date (ISO8601) with added
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random digits
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find . | parallel cp {} '../destdir/{= $a=int(10000*rand); $_=pQ($_);
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$_=`date -r "$_" +%FT%T"$a"`; chomp; =}'
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@ -3205,7 +3233,8 @@ significant. Compare the speed of these:
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If your program cannot take multiple arguments, then you can use GNU
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B<parallel> to spawn multiple GNU B<parallel>s:
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seq -w 0 999999 | parallel -j10 --pipe parallel -j0 touch pict{}.jpg
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seq -w 0 9999999 |
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parallel -j10 -q -I,, --pipe parallel -j0 touch pict{}.jpg
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If B<-j0> normally spawns 252 jobs, then the above will try to spawn
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2520 jobs. On a normal GNU/Linux system you can spawn 32000 jobs using
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@ -1294,8 +1294,9 @@ While you I<can> use multi-lined commands in GNU B<parallel>, to
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improve readibilty GNU B<parallel> discourages the use of multi-line
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commands. In most cases it can be written as a function:
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seq 1 3 | parallel --timeout 2 --joblog my.log 'sleep {}; echo {}; \
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echo finish {}'
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seq 1 3 |
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parallel --timeout 2 --joblog my.log 'sleep {}; echo {}; \
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echo finish {}'
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Could be written as:
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@ -1311,7 +1312,7 @@ The failed commands can be resumed with:
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seq 1 3 |
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parallel --resume-failed --joblog my.log 'sleep {}; echo {};\
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echo finish {}'
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echo finish {}'
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=back
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@ -5,11 +5,20 @@
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This tutorial shows off much of GNU B<parallel>'s functionality. The
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tutorial is meant to learn the options in and syntax of GNU
|
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B<parallel>. The tutorial is B<not> to show realistic examples from the
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real world. For realistic examples see B<man parallel> in the EXAMPLE
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section.
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real world.
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=head2 Reader's guide
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Start by watching the intro videos for a quick introduction:
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http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
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Then look at the B<EXAMPLE>s after the list of B<OPTIONS> in B<man
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parallel> (Use B<LESS=+/EXAMPLE\: man parallel>). That will give you
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an idea of what GNU B<parallel> is capable of.
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|
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Then spend a couple of hours walking through this tutorial (B<man
|
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parallel_tutorial>). Your command line will love you for it.
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Spend an hour walking through the tutorial. Your command line will
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love you for it.
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=head1 Prerequisites
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|
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@ -315,8 +315,8 @@ par_tcsh_man Academic tradition requires you to cite works you base your article
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par_tcsh_man If you use programs that use GNU Parallel to process data for an article in a
|
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par_tcsh_man scientific publication, please cite:
|
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par_tcsh_man
|
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par_tcsh_man O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
|
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par_tcsh_man ;login: The USENIX Magazine, February 2011:42-47.
|
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par_tcsh_man O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,
|
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par_tcsh_man DOI https://doi.org/10.5281/zenodo.1146014
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par_tcsh_man
|
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par_tcsh_man This helps funding further development; AND IT WON'T COST YOU A CENT.
|
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par_tcsh_man If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
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|
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@ -1019,8 +1019,8 @@ par_csh_man
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par_csh_man
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par_csh_man
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par_csh_man {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}
|
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par_csh_man ;login: The USENIX Magazine, February 2011:42-47.
|
||||
par_csh_man O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
|
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par_csh_man DOI https://doi.org/10.5281/zenodo.1146014
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par_csh_man O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,
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par_csh_man ### From man env_parallel
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par_csh_man --colsep regexp Split input on regexp for positional replacements
|
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par_csh_man --nonall Run the given command with no arguments on all sshlogins
|
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|
|
|
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|
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@ -4,12 +4,15 @@ Academic tradition requires you to cite works you base your article on.
|
|||
If you use programs that use GNU Parallel to process data for an article in a
|
||||
scientific publication, please cite:
|
||||
|
||||
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
|
||||
;login: The USENIX Magazine, February 2011:42-47.
|
||||
O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,
|
||||
DOI https://doi.org/10.5281/zenodo.1146014
|
||||
|
||||
This helps funding further development; AND IT WON'T COST YOU A CENT.
|
||||
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
||||
|
||||
More about funding GNU Parallel and the citation notice:
|
||||
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
|
||||
|
||||
To silence this citation notice: run 'parallel --citation' once.
|
||||
|
||||
echo a
|
||||
|
|
@ -24,12 +27,15 @@ Academic tradition requires you to cite works you base your article on.
|
|||
If you use programs that use GNU Parallel to process data for an article in a
|
||||
scientific publication, please cite:
|
||||
|
||||
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
|
||||
;login: The USENIX Magazine, February 2011:42-47.
|
||||
O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,
|
||||
DOI https://doi.org/10.5281/zenodo.1146014
|
||||
|
||||
This helps funding further development; AND IT WON'T COST YOU A CENT.
|
||||
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
||||
|
||||
More about funding GNU Parallel and the citation notice:
|
||||
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
|
||||
|
||||
To silence this citation notice: run 'parallel --citation' once.
|
||||
|
||||
10 files to edit
|
||||
|
|
@ -41,8 +47,9 @@ scientific publication, please cite:
|
|||
author = {Tange, Ole},
|
||||
title = {GNU Parallel 2018},
|
||||
publisher = {Ole Tange},
|
||||
month = Apr,
|
||||
year = 2018,
|
||||
month = apr,
|
||||
ISBN = {9781387509881},
|
||||
doi = {10.5281/zenodo.1146014},
|
||||
url = {https://doi.org/10.5281/zenodo.1146014}
|
||||
}
|
||||
|
|
@ -52,6 +59,9 @@ scientific publication, please cite:
|
|||
This helps funding further development; AND IT WON'T COST YOU A CENT.
|
||||
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
||||
|
||||
More about funding GNU Parallel and the citation notice:
|
||||
https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice
|
||||
|
||||
If you send a copy of your published article to tange@gnu.org, it will be
|
||||
mentioned in the release notes of next version of GNU Parallel.
|
||||
|
||||
|
|
|
|||
|
|
@ -75,11 +75,11 @@ parallel: Error: --pipepart is incompatible with --max-replace-args, --max-lines
|
|||
echo '### bug #42893: --block should not cause decimals in cat_partial'
|
||||
### bug #42893: --block should not cause decimals in cat_partial
|
||||
seq 100000 >/tmp/parallel-decimal; parallel --dry-run -kvv --pipepart --block 0.12345M -a /tmp/parallel-decimal true; rm /tmp/parallel-decimal
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 0 129450 | (true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 129450 129450 | (true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 258900 129450 | (true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 388350 129450 | (true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 517800 71095 | (true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 0 129450 |(true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 129450 129450 |(true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 258900 129450 |(true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 388350 129450 |(true)
|
||||
</tmp/parallel-decimal perl -e 'while(@ARGV){sysseek(STDIN,shift,0)||die;$left=shift;while($read=sysread(STDIN,$buf,$left>1048524?1048524:$left)){$left-=$read;syswrite(STDOUT,$buf);}}' 0 0 517800 71095 |(true)
|
||||
echo '### bug #42902: profiles containing arguments with space'
|
||||
### bug #42902: profiles containing arguments with space
|
||||
echo "--rpl 'FULLPATH chomp(\$_=\"/bin/bash=\".\`readlink -f \$_\`);' " > ~/.parallel/FULLPATH; parallel -JFULLPATH echo FULLPATH ::: $0
|
||||
|
|
|
|||
|
|
@ -171,8 +171,8 @@ Academic tradition requires you to cite works you base your article on.
|
|||
If you use programs that use GNU Parallel to process data for an article in a
|
||||
scientific publication, please cite:
|
||||
|
||||
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
|
||||
;login: The USENIX Magazine, February 2011:42-47.
|
||||
O. Tange (2018): GNU Parallel 2018, Apr 2018, ISBN 9781387509881,
|
||||
DOI https://doi.org/10.5281/zenodo.1146014
|
||||
|
||||
This helps funding further development; AND IT WON'T COST YOU A CENT.
|
||||
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
|
||||
|
|
|
|||
Loading…
Reference in a new issue