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Documentation update.
This commit is contained in:
Ole Tange
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@ -209,9 +209,9 @@ from:tange@gnu.org
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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 20191022 ('Driving IT') released <<[stable]>>
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Subject: GNU Parallel 20191122 ('Berlin/Morales') released <<[stable]>>
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GNU Parallel 20191022 ('Driving IT') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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GNU Parallel 20191122 ('') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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@ -221,30 +221,14 @@ See https://www.gnu.org/software/parallel/10-years-anniversary.html
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Quote of the month:
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I've said it before: The command line program GNU Parallel is a godsend.
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-- Jo Chr. Oterhals @oterhals@twitter
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New in this release:
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* --tee will use --output-error=warn-nopipe if supported by tee.
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* GNU Parallel was presented at Driving IT. Slides:
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* GNU Parallel will be presented at Driving IT 2019: https://ida.dk/arrangementer-og-kurser/konferencer/driving-it/tools
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https://blog.naderman.de/2019/11/14/restarting-supervisord-processes-in-parallel/
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* UMN Duluth: Job parallelization with task arrays and GNU parallel https://www.msi.umn.edu/tutorials/umn-duluth-job-parallelization-task-arrays-and-gnu-parallel
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* Genome updater uses GNU Parallel https://github.com/pirovc/genome_updater
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* Using GNU-Parallel for bioinformatics https://www.danielecook.com/using-gnu-parallel-for-bioinformatics/
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* Speeding up PostgreSQL ETL pipeline with the help of GODS https://cfengine.com/company/blog-detail/speeding-up-postgresql-etl-pipeline-with-the-help-of-gods/
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* Runing linux commands in parallel https://dev.to/voyeg3r/runing-linux-commands-in-parallel-4ff8
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* Research Computing University of Colorado Boulder contains an intro to GNU Parallel https://readthedocs.org/projects/curc/downloads/pdf/latest/
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* 如何使用Parallel在Shell中并行执行命令https://www.myfreax.com/gnu-parallel/
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* 如何测试 Amazon Elastic File System https://aws.amazon.com/cn/blogs/china/how-to-test-drive-amazon-elastic-file-system/
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* https://www.reddit.com/r/DataHoarder/comments/dsgmhc/parallel_archiving_techniques/
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* Bug fixes and man page updates.
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11
src/parallel
11
src/parallel
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@ -1193,7 +1193,7 @@ sub nindex($$) {
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# until one is empty and a new block is passed
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if(@robin_queue) {
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# Rotate queue once so new blocks get a fair chance
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# to be given to another block
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# to be given to another slot
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push @robin_queue, shift @robin_queue;
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} else {
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# Make a queue to spread the blocks evenly
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@ -1950,7 +1950,7 @@ sub parse_options(@) {
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# If you want GNU Parallel to be maintained in the future keep
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# this line.
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citation_notice();
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# Seriously: YOU will be harming free software by removing the
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# Seriously: *You* will be harming free software by removing the
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# notice. You make it harder to justify spending time developing
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# it. If you *do* remove the line, please email
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# hallofshame@tange.dk if you want to avoid being put in a hall of
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@ -8291,7 +8291,7 @@ sub non_blocking_write($) {
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if (!defined($rv) && $! == ::EAGAIN()) {
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# would block - but would have written
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$something_written = 0;
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# avoid triggering auto expanding block
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# avoid triggering auto expanding block size
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$Global::no_autoexpand_block ||= 1;
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} elsif ($self->{'block_pos'}+$rv != $self->{'block_length'}) {
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# incomplete write
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@ -9174,6 +9174,10 @@ sub remote_cleanup($) {
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}
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sub exitstatuswrapper(@) {
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# Input:
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# @shellcode = shell code to execute
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# Returns:
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# shell script that returns current status after executing @shellcode
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if($Global::cshell) {
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return ('set _EXIT_status=$status; ' .
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join(" ",@_).
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@ -9185,7 +9189,6 @@ sub exitstatuswrapper(@) {
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}
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}
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sub workdir($) {
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# Returns:
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# the workdir on a remote machine
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@ -2847,6 +2847,7 @@ Exit if the size (see the B<-s> option) is exceeded.
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=back
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=head1 EXAMPLE: Working as xargs -n1. Argument appending
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GNU B<parallel> can work similar to B<xargs -n1>.
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@ -3992,7 +3993,13 @@ then the obvious solution would be this, but it B<does not work>:
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It does not work because the command is dequoted by B<ssh> twice where
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as GNU B<parallel> only expects it to be dequoted once.
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So instead put this in B<~/.ssh/config>:
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You can use a bash function and have GNU B<parallel> quote the command:
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jumpssh() { ssh -A jumphost ssh $(parallel --shellquote ::: "$@"); }
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export -f jumpssh
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parallel --ssh jumpssh -S host1 echo ::: this works
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Or you can instead put this in B<~/.ssh/config>:
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Host host1 host2 host3
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ProxyCommand ssh jumphost.domain nc -w 1 %h 22
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@ -4224,6 +4231,25 @@ To run 100 processes simultaneously do:
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As there is not a I<command> the jobs will be evaluated by the shell.
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=head1 EXAMPLE: Call program with FASTA sequence
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FASTA files have the format:
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>Sequence name1
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sequence
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sequence continued
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>Sequence name2
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sequence
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sequence continued
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more sequence
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To call B<myprog> with the sequence as argument run:
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cat file.fasta |
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parallel --pipe -N1 --recstart '>' --rrs \
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'read a; echo Name: "$a"; myprog $(tr -d "\n")'
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=head1 EXAMPLE: Processing a big file using more CPUs
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To process a big file or some output you can use B<--pipe> to split up
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@ -5248,8 +5274,11 @@ A copy of the full license is included in the file as cc-by-sa.txt.
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=head1 DEPENDENCIES
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GNU B<parallel> uses Perl, and the Perl modules Getopt::Long,
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IPC::Open3, Symbol, IO::File, POSIX, and File::Temp. For remote usage
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it also uses rsync with ssh.
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IPC::Open3, Symbol, IO::File, POSIX, and File::Temp.
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For B<--csv> it uses the Perl module Text::CSV.
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For remote usage it uses B<rsync> with B<ssh>.
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=head1 SEE ALSO
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