GNU Parallel Bug Reports GNU Parallel 20150522 ('Nepal') released [stable]

[Ole Tange]

GNU Parallel 20150522 ('Nepal') has been released. It is available for
download at: http://ftp.gnu.org/gnu/parallel/

No new functionality was introduced so this is a good candidate for a
stable release.

Haiku of the month:

  Many jobs to run.
  Idle cores is not your thing.
  Use GNU Parallel.
      -- Ole Tange

New in this release:

* Security: The security issue for --sshlogin + --fifo/--cat has been
fixed. Thereby all issues with
http://lists.gnu.org/archive/html/parallel/2015-04/msg00045.html have
been fixed.

* Security: After further security analysis the issue fixed in
20150422 also fixed the problem for --tmux.

* GNU Parallel was cited in: CIDER: a pipeline for detecting waves of
coordinated transcriptional regulation in gene expression time-course
data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf

* GNU Parallel was cited in: Building Genomic Analysis Pipelines in a
Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics,
Metagenomics and RNA-seq
http://biorxiv.org/content/biorxiv/early/2015/05/05/018085.full.pdf

* GNU Parallel was cited in: Toward Enhanced Metadata Quality of
Large-Scale Digital Libraries: Estimating Volume Time Range
https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf

* GNU Parallel was cited in: Sequencing the cap-snatching repertoire
of H1N1 influenza provides insight into the mechanism of viral
transcription initiation
http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv333.full.pdf

* GNU Parallel was cited in: Genome assembly using Nanopore-guided
long and error-free DNA reads
http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf

* 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/2015/03/13/016527.full.pdf

* GNU Parallel was used (unfortunately with wrong citation) in:
Comparing the CarbonTracker and TM5-4DVar data assimilation systems
for CO2 surface flux inversions
http://www.atmos-chem-phys-discuss.net/15/8883/2015/acpd-15-8883-2015-discussion.html

* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method
https://bitbucket.org/srp33/gsoa

* A Quick and Neat :) Orchestrator using GNU Parallel
http://www.elsotanillo.net/2015/05/a-quick-and-neat-orchestrator-using-gnu-parallel/

* Execute commands on multiple computers using GNU Parallel (setting
up a cluster on the cheap)
https://spectraldifferences.wordpress.com/2015/04/26/execute-commands-on-multiple-computers-using-gnu-parallel-setting-up-a-cluster-on-the-cheap/

* Functions and GNU parallel for effective cluster load management
http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html

* Use parallel processing to save time importing databases
http://drupalsun.com/node/41854

* Run multiple ssh commands in parallel with GNU Parallel
http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html

* Importing huge databases faster
https://www.lullabot.com/blog/article/importing-huge-databases-faster

* Run multiple ssh commands in parallel with GNU Parallel
https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1

* Parallel? Gnu parallel! https://debian.pro/1834

* 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.