GNU Parallel 20150322 ('Hellwig') released

[Ole Tange]

GNU Parallel 20150322 ('Hellwig') has been released. It is available
for download at: http://ftp.gnu.org/gnu/parallel/

Haiku of the month:

  Stand up for your rights.
  VMware does not comply.
  Hellwig goes to court.

  (https://sfconservancy.org/linux-compliance/vmware-lawsuit-faq.html)

New in this release:

* --number-of-cores respects 'taskset' on GNU/Linux.

* --joblog --pipe gives the data send and received in the log.

* GNU Parallel was tested to support 100 GB sized records in --pipe. A
few bugs was fixed to support >2 GB records. It works, but is rather
slow.

* GNU Parallel was cited in: RIG: Recalibration and Interrelation of
genomic sequence data with the GATK
http://www.g3journal.org/content/early/2015/02/13/g3.115.017012.full.pdf+html

* GNU Parallel was cited in: MPI-blastn and NCBI-TaxCollector:
Improving metagenomic analysis with high performance classification
and wide taxonomic attachment
http://www.worldscientific.com/doi/abs/10.1142/S0219720014500139?af=R&;

* GNU Parallel was cited in: Recent evolution in Rattus norvegicus is
shaped by declining effective population size
http://biorxiv.org/content/biorxiv/early/2015/03/01/015818.full.pdf

* GNU Parallel was cited in: Evidence for DCO+ as a probe of
ionization in the warm disk surface
http://arxiv.org/pdf/1503.02659.pdf

* GNU Parallel was cited in: De novo assembly and annotation of the
Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from
raw genomic reads and comparative analysis with the yellow fever
mosquito (Aedes aegypti)
http://gbe.oxfordjournals.org/content/early/2015/03/11/gbe.evv050.full.pdf

* GNU Parallel was cited in: A General Approach to Network
Configuration Analysis
http://research.microsoft.com/en-us/um/people/ratul/papers/nsdi2015-batfish.pdf

* GNU Parallel was cited in: Scrimer: designing primers from
transcriptome data
http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12403/pdf

* GNU Parallel was cited in: Efficient Retrieval of Key Material for
Inspecting Potentially Malicious Traffic in the Cloud
http://sacko.uk/pdf/2015.1.pdf

* GNU Parallel will be presented at Strataconf: Poor Man's Parallel
Pipelines 
http://strataconf.com/big-data-conference-uk-2015/public/schedule/detail/40031

* GNU Parallel was used in:
https://github.com/alexbyrnes/FCC-Political-Ads_The-Code

* GNU Parallel was used in: https://github.com/martymac/fpart

* GNU Parallel was used in: https://github.com/hoytak/diabetic-retinopathy-code

* GNU Parallel was used in: https://github.com/mehmattski/HybSeqPipeline

* GNU Parallel was used in:
http://search.cpan.org/~ajpage/Bio-Roary-2.0.0/lib/Bio/Roary/JobRunner/Parallel.pm

* Using GNU Parallel on a Raspberry Pi cluster:
http://www.dcglug.org.uk/cluster-progress/

* An introduction to vector tiling and map reduce in postgis:
http://dimensionaledge.com/intro-vector-tiling-map-reduce-postgis/

* Running scripts in parallel with GNU Parallel:
http://code.jasonbhill.com/2015/03/

* Mahout: Parallelising the creation of DecisionTrees:
http://www.markhneedham.com/blog/2012/12/27/mahout-parallelising-the-creation-of-decisiontrees/

* High-Performance Scientific Computing: Running serial jobs in
parallel 
https://support.scinet.utoronto.ca/education/staticpublic/course178/serial.pdf

* Parallel cardinality on your laptop
https://highonscience.wordpress.com/2015/03/15/parallel-cardinality-on-your-laptop/

* Experiments about a better locate using grep
http://a3nm.net/blog/better_locate.html

* Homework with GNU Parallel:
https://support.scinet.utoronto.ca/education/staticpublic/course178content349.html

* Parallel - Jobs in Skripten parallelisieren:
https://slzm.de/blog/linux-tool-des-tages-parallel-jobs-in-skripten-parallelisieren/#more-612

* GNU Parallel, czyli 100% użycia procesora
http://matmatyk.blogspot.dk/2015/03/gnu-parallel-czyli-100-uzycia-procesora.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.