GNU Parallel - News: GNU Parallel 20160722 ('Brexit') released

GNU Parallel 20160722 ('Brexit') released

Item posted by Ole Tange <tange> on Fri 22 Jul 2016 10:45:28 PM UTC.

GNU Parallel 20160722 ('Brexit') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/

Haiku of the month:

  Pipes are fast and good.
  Use them in your programs, too.
  Use GNU Parallel
    -- Ole Tange

New in this release:

• env_parallel is now ready for wider testing. It is still beta quality.

• env_parallel is heavily modified for all shells and testing has been increased.

• Selectively choosing what to export using --env now works for env_parallel (bash, csh, fish, ksh, pdksh, tcsh, zsh).

• --round-robin now gives more work to a job that processes faster instead of same amount to all jobs.

• --pipepart works on block devices on GNU/Linux.

• GNU Parallel was cited in: HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment http://www.bioone.org/doi/full/10.3732/apps.1600016

• GNU Parallel was cited in: StrAuto - Automation and Parallelization of STRUCTURE Analysis http://www.crypticlineage.net/download/strauto/strauto_doc.pdf

• GNU Parallel was cited in: Tools and techniques for computational reproducibility http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0135-4

• GNU Parallel was cited in: FlashPCA: fast sparse canonical correlation analysis of genomic data http://biorxiv.org/content/biorxiv/suppl/2016/04/06/047217.DC1/047217-1.pdf

• GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16

• GNU Parallel was cited in: Math Indexer and Searcher under the Hood: Fine-tuning Query Expansion and Unification Strategies http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings12/pdf/ntcir/MathIR/05-NTCIR12-MathIR-RuzickaM.pdf

• GNU Parallel was cited in: The Evolution and Fate of Super-Chandrasekhar Mass White Dwarf Merger Remnants http://arxiv.org/pdf/1606.02300.pdf

• GNU Parallel was cited in: Evaluation of Coastal Scatterometer Products https://mdc.coaps.fsu.edu/scatterometry/meeting/docs/2016/Thu_AM/coastal-poster.pdf

• GNU Parallel was used in: https://github.com/splitice/bulkdnsblcheck

• The iconv slurp misfeature http://www.openfusion.net/linux/iconv_slurp_misfeature

• แบบว่า CPU เหลือ https://veer66.wordpress.com/2016/06/15/gnu-parallel/

• 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 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 programs that use GNU Parallel for research:

• Please cite GNU Parallel in you publications (use --citation)

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.