GNU Parallel - News: GNU Parallel 20130822 ('Compostela') released

GNU Parallel 20130822 ('Compostela') released

Item posted by Ole Tange <tange> on Thu 22 Aug 2013 03:44:44 PM UTC.

GNU Parallel 20130822 ('Compostela') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/

It includes a big code reorganization making this release beta quality.

New in this release:

• A tutorial showing much of GNU Parallel's functionality. Spend an hour walking through the tutorial. Your commandline will love you for it. man parallel_tutorial                                                                                 

• --line-buffer will buffer output on line basis. --group keeps the output together for a whole job. --ungroup allows output to mixup with half a line coming from one job and half a line coming from another job. --line-buffer fits between these two; it prints a full line, but will allow for mixing lines of different jobs.

• --record-env records all variables and functions set. Useful to record the normal environment before using --env _.

• --env _ exports all functions and variables to the remote server except for the ones recorded.

• New signing key. Due to recommendations from NIST http://www.keylength.com/en/4/ the signing key was changed from 1024D/ID:FFFFFFF1 to 9888R/ID:88888888.

• Agalma: an automated phylogenomics workflow http://arxiv.org/pdf/1307.6432

• Job ad asking for GNU Parallel expertise http://seattle.craigslist.org/est/sof/4006079352.html

• Transient Beowulf Clustering with GNU Parallel and SSHfs http://www.reddit.com/r/linux/comments/1ka8mn/transient_beowulf_clustering_with_gnu_parallel/

• Aligning to unique regions http://davetang.org/muse/2013/07/22/aligning-to-unique-regions/

• Top 10 scripting tricks for basic bioinformatics http://students.washington.edu/bowmanjs/wordpress/?p=873

• Using GNU Parallel to speed up and simplify data analyzes http://www.sergeymarkov.com/blog/2013/07/using-gnu-parallel-to-speed-up-and-simplify-data-analyzes/

• Compression of files in parallel using GNU parallel http://codextechnicanum.blogspot.dk/2013/07/compression-of-files-in-parallel-using.html

• Using GNU Parallel to roll-your-own Map Reduce! http://www.rankfocus.com/?p=1

• Using GNU Parallel with Amazon media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf

• Some useful comments on GNU Parallel https://news.ycombinator.com/item?id=6209767

• Using GNU Parallel to count reads mapping to genes for multiple BAMs http://drduanehassane.com/blog/sequencing-resources

• TimeMachineっぽいバックアップスクリプト http://rio.tc/2013/07/timemachine-1.html

• GNU ParallelでAndroid NDKの全バージョンを一括ダウンロード http://qiita.com/mazgi/items/b10bf0ff3da2045d19ab

• Bug fixes and man page updates.

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 | sh

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 GNU Parallel for a publication please cite:

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

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.