GNU Parallel 20140722 ('MH17') released

[Ole Tange]

GNU Parallel 20140722 ('MH17') has been released. It is available for
download at: http://ftp.gnu.org/gnu/parallel/

This release contains a major change in central parts of the code and
should be considered beta quality. As always it passes the testsuite,
so most functionality clearly works.

Thanks to Malcolm Cook for the brilliant idea to use a general perl
expression as a replacement string.

Haiku of the month:

  Are you tired of
  inflexible replacements?
  Use Perl expressions.
         -- Ole Tange

New in this release:

* {= perl expression =} can be used as replacement string. The
expression should modify $_. E.g. {= s/\.gz$// =} to remove .gz from
the string. This makes replacement strings extremely flexible.

* Positional perl expressions (similar to {2}) are given as {=2 perl
expression=} where 2 is the position.

* One small backwards incompatability: {1}_{2} will replace {2} with
the empty string if there is only one argument. Previously {2} would
have been left untouched.

* Replacement strings can be defined using --rpl. E.g. parallel --rpl
'{.gz} s/\.gz$//' echo {.gz} ::: *.gz

* The parenthesis around {= perl expression =} can be changed with --parens.

* --tmux will direct the output to a tmux session instead of files.
Each running jobs will be in its own window.

* --halt 10% will stop spawning new jobs if 10% failed so far.

* GNU Parallel was cited in: bammds: A tool for assessing the ancestry
of low depth whole genome data using multidimensional scaling (MDS)
http://bioinformatics.oxfordjournals.org/content/early/2014/06/28/bioinformatics.btu410.abstract

* GNU Parallel was cited in: Molecular ferroelectric contributions to
anomalous hysteresis in hybrid perovskite solar cells
http://people.bath.ac.uk/aw558/publications/2014/arxiv_hysteresis_14.pdf

* GNU Parallel was cited in: Energy Sorghum-a genetic model for the
design of C4 grass bioenergy crops
http://jxb.oxfordjournals.org/content/early/2014/06/20/jxb.eru229.short

* GNU Parallel was cited in: Web-scale Content Reuse Detection
www.isi.edu/~johnh/PAPERS/Ardi14a.pdf

* Tell your friends to sign up for the Webcast at 2014-08-20 covering
GNU Parallel: Data Science at the Command Line
http://www.oreilly.com/pub/e/3115

* GNU Parallel all the things!
http://longwayaround.org.uk/notes/gnu-parallel-all-the-things/

* Shell command composition and dispatch
http://lukeluo.blogspot.dk/2014/07/linux-virtual-console6-shell-command.html

* Parallelising plink (or anything else) the easy way
http://chrisladroue.com/2012/03/parallelising-plink-or-anything-else-the-easy-way/

* Easy and cheap cluster building on AWS
https://grapeot.me/easy-and-cheap-cluster-building-on-aws.html

* Paralelizace běžných činností v konzoli pomocí GNU Parallel
http://www.abclinuxu.cz/clanky/paralelizace-beznych-cinnosti-v-konzoli-pomoci-gnu-parallel

* [原] Ubuntu 下使用 parallel 命令的注意事项
http://blog.ailms.me/2014/06/28/ubuntu-with-parallel.html

* 简单的并行, 可使用GNU parallel http://jerkwin.github.io/2014/06/10/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 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.


= 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.