GNU Parallel - News: GNU Parallel 20150622 ('Løkke') released

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GNU Parallel 20150622 ('Løkke') released

Item posted by Ole Tange <tange> on Mon 22 Jun 2015 07:28:38 PM UTC.

GNU Parallel 20150622 ('Løkke') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/

A performance chart has been made to compare the performance of different versions: http://www.gnu.org/software/parallel/boxplot-j2-3.0ghz-3000-1000.pdf The recent jump is due to every job being wrapped in a Perl-script doing setpgrp.

Haiku of the month:

Programs very slow.
Multiple can run at once.
Use GNU Parallel.
-- Ole Tange

New in this release:

--halt has been rewritten completely. You can now combine percentages with success or fail. See the man page.

Exit values 102..254 have been removed. 101 means more than 100 jobs failed.

Killing through --timeout, --memfree, or --halt is now done as a process group (whence the setpgrp wrapper).

--termseq determines which signals are sent when a job is killed.

An empty argument would previously cause no string to be inserted. This is now changed to '' being inserted, thus prepending a space to the output of: parallel echo {} b ::: ''

$PARALLEL_ENV can now be set to an environment prepending the command. Used in env_parallel as mentioned in the manpage.

--retry-failed will retry all failed jobs in a joblog. It will ignore any command given.

--ssh and $PARALLEL_SSH can be used to set the command used for ssh. The command is assumed to behave the same way as ssh.

--fifo now works in csh, too.

Q(...) can be used in {= =} to shell quote a string.

GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/06/05/016527.full.pdf

GNU Parallel was cited in: DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations http://www.mdpi.com/1420-3049/20/6/9977

GNU Parallel was cited in: Swedes Online: You Are More Tracked Than You Think http://www.diva-portal.org/smash/get/diva2:807623/FULLTEXT01.pdf

GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D scattering and resonance calculations http://arxiv.org/pdf/1505.07691.pdf

GNU Parallel was cited in: A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data http://link.springer.com/article/10.1186/s13742-015-0058-5

GNU Parallel was cited in: A composite genome approach to identify phylogenetically informative data from next-generation sequencing http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf

GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D scattering and resonance calculations http://arxiv.org/pdf/1505.07691.pdf

GNU Parallel is used in: taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/

GNU Parallel is used in: https://github.com/d2207197/local-mapreduce

GNU Parallel is used in: wiki-edit-news https://github.com/albert-decatur/wiki-edit-news

GNU Parallel is used in: A Fingerprint Identification System https://curve.carleton.ca/system/files/theses/28733.pdf

Job ad asking for GNU Parallel experience: http://searchjobs.intel.com/gdansk-pol/software-validation-engineer/63A06826DAF24797AB414DC146201C2E/job/

Using BLAT http://wangzhengyuan.blogspot.dk/2015/06/using-blat.html

Bug fixes and man page updates.

GNU Parallel - For people who live life in the parallel lane.

About GNU Parallel

GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job is can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU Parallel can then split the input and pipe it into commands in parallel.

If you use xargs and tee today you will find GNU Parallel very easy to use as GNU Parallel is written to have the same options as xargs. If you write loops in shell, you will find GNU Parallel may be able to replace most of the loops and make them run faster by running several jobs in parallel. GNU Parallel can even replace nested loops.

GNU Parallel makes sure output from the commands is the same output as you would get had you run the commands sequentially. This makes it possible to use output from GNU Parallel as input for other programs.

You can find more about GNU Parallel at: http://www.gnu.org/s/parallel/

You can install GNU Parallel in just 10 seconds with: (wget -O - pi.dk/3 || curl pi.dk/3/) | bash

Watch the intro video on http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

Walk through the tutorial (man parallel_tutorial). Your commandline will love you for it.

When using programs that use GNU Parallel to process data for publication please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47.

If you like GNU Parallel:

Give a demo at your local user group/team/colleagues
Post the intro videos on Reddit/Diaspora*/forums/blogs/ Identi.ca/Google /Twitter/Facebook/Linkedin/mailing lists
Get the merchandise https://www.gnu.org/s/parallel/merchandise.html
Request or write a review for your favourite blog or magazine
Request or build a package for your favourite distribution (if it is not already there)
Invite me for your next conference

If you use GNU Parallel for research:

Please cite GNU Parallel in you publications (use --bibtex)

If GNU Parallel saves you money:

(Have your company) donate to FSF https://my.fsf.org/donate/

About GNU SQL

GNU sql aims to give a simple, unified interface for accessing databases through all the different databases' command line clients. So far the focus has been on giving a common way to specify login information (protocol, username, password, hostname, and port number), size (database and table size), and running queries.

The database is addressed using a DBURL. If commands are left out you will get that database's interactive shell.

When using GNU SQL for a publication please cite:

O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.

About GNU Niceload

GNU niceload slows down a program when the computer load average (or other system activity) is above a certain limit. When the limit is reached the program will be suspended for some time. If the limit is a soft limit the program will be allowed to run for short amounts of time before being suspended again. If the limit is a hard limit the program will only be allowed to run when the system is below the limit.