GNU Parallel Bug Reports GNU Parallel 20150122 (' (((:~{> Je Suis Charlie') released

[Ole Tange]

GNU Parallel 20150122 (' (((:~{> Je Suis Charlie') has been released.
It is available for download at: http://ftp.gnu.org/gnu/parallel/

Haiku of the month:

If not enough time:
Run jobs using Parallel.
Keeps CPUs warm.
  -- Ole Tange

New in this release:

* Remote jobs now send stderr (standard error) to stderr (standard
error) instead of stdout (standard output).

* Remote execution command is now packed using base64 encoded bzip2.
This means that big environments (app. 100 KB) can be transferred.
This change makes remote execution alpha quality.

* --semaphoretimeout now takes a negative value. This means give up if
the semaphore is not gotten within the timeout.

* --halt -1 and -2 now means halt if a job succeeds (so the opposite
of 1 and 2).

* --no-keep-order will reverse --keep-order.

* Bash's second fix of shellshock caused --env to break again when
exporting functions. This has been fixed again.

* A semibig refactoring of big functions. All non-trivial functions
are now less than 100 lines. The refactoring makes this release beta
quality.

* A description of the design decisions for GNU Parallel can be found
in 'man parallel_design'.

* A bug fix in replacement strings caused rewrite of the replacement
function. This makes use of replacement strings alpha quality.

* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for
the Histological Quantification of Whole Slide Images
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289

* GNU Parallel was cited in: Improving Energy and Performance with
Spintronics Caches in Multicore Systems
http://link.springer.com/chapter/10.1007/978-3-319-14313-2_24

* GNU Parallel was cited in: Parallel post-processing with MPI-Bash
http://dl.acm.org/citation.cfm?id=2691137

* GNU Parallel was cited in: Distinguishing cause from effect using
observational data: methods and benchmarks
http://arxiv-web3.library.cornell.edu/pdf/1412.3773.pdf

* GNU Parallel was cited in: Data Science at the Command Line
http://cdn.oreillystatic.com/oreilly/booksamplers/9781491947852_sampler.pdf

* GNU Parallel was cited in: Resolution of Genetic Map Expansion
Caused by Excess Heterozygosity in Plant Recombinant Inbred
Populations http://www.g3journal.org/content/4/10/1963.full.pdf

* GNU Parallel was cited in: Bayesian Inference of Protein Structure
from Chemical Shift Data https://peerj.com/preprints/692v1.pdf

* GNU Parallel was cited in: Clonal interference and Muller's ratchet
in spatial habitats http://iopscience.iop.org/1478-3975/11/5/056003

* GNU Parallel was cited in: Web-scale content reuse detection
ftp://info.isi.edu/isi-pubs/tr-692.pdf

* GNU Parallel was cited in: Computação Verde na Camada de Aplicação
https://linux.ime.usp.br/~tpaiva/mac0499/files/monografia.pdf

* GNU Parallel was cited in: Frameshift alignment: statistics and
post-genomic applications
http://bioinformatics.oxfordjournals.org/content/30/24/3575.full.pdf+html

* GNU Parallel was cited in: Towards Recommender Engineering Tools and
Experiments for Identifying Recommender Differences
http://elehack.net/research/thesis/mde-thesis.pdf

* GNU Parallel was cited in: Speaker Environment Classification Using
Rhythm Metrics in Levantine Arabic Dialect
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6923918

* GNU Parallel was cited in: A Formal Proof Of The Kepler Conjecture
http://arxiv.org/pdf/1501.02155.pdf

* GNU Parallel was cited in: Allocation Policy Analysis for Cache
Coherence Protocols for STT-MRAM-based caches
http://conservancy.umn.edu/bitstream/handle/11299/169362/Nandkar_umn_0130M_15551.pdf

* GNU Parallel was cited in: Using Trusted Platform Module for
securing virtual environment access in Cloud
http://dar.aucegypt.edu:8080/bitstream/handle/10526/4237/Using%20Trusted%20Platform%20Module%20for%20Securing%20Virtual%20Environment%20Access%20in%20Cloud.pdf

* GNU Parallel was cited in: Weakly Supervised Learning for
Compositional Sentiment Recognition
http://computerlinguist.org/static/downloads/ma-thesis/Master_Thesis-Michael_Haas-Weakly_Supervised_Learning_for_Compositional_Sentiment_Recognition.pdf

* GNU Parallel was cited in: Agility and Performance in Elastic
Distributed Storage http://dl.acm.org/citation.cfm?id=2668129

* GNU Parallel was used (unfortunately without citation) in: Large
Scale Author Name Disambiguation in Digital Libraries
http://semanticommunity.info/@api/deki/files/31523/P227_3546.pdf

* GNU Parallel is used in BEDOPS:
https://media.readthedocs.org/pdf/bedops/v2p5p0/bedops.pdf

* Job ad asking for GNU Parallel skills:
http://www.aplitrak.com/?adid=dXMzMTYxMjQuMzg0MTkuMTU1MEBtYW5wb3dlcmZveG5hLmFwbGl0cmFrLmNvbQ#sthash.kYCIhhty.KcoT6HnJ.dpbs

* GNU Parallel: Open Source For You (OSFY) magazine, October 2013
edition http://www.shakthimaan.com/posts/2014/11/27/gnu-parallel/news.html

* Multithreaded Encryption and Compression
http://www.krazyworks.com/multithreaded-encryption-and-compression/

* GNU Parallel on OSX and Linux
https://darknightelf.wordpress.com/2015/01/01/gnu-parallel-on-osx/

* How to build gnu parallel from source on Ubuntu PC?
http://blog.ovidiuparvu.com/build-gnu-parallel-source-ubuntu-pc/

* GNU parallel for openaddr-process-one
https://nelsonslog.wordpress.com/2015/01/09/gnu-parallel-for-openaddr-process-one/

* From SRA Project to FastQ http://danielecook.com/sra-project-fastq/

* Software Development Tooling
http://www.computer.org/csdl/mags/so/2014/06/mso2014060021.pdf

* コマンドを並列に実行するGNU parallelがとても便利
http://bicycle1885.hatenablog.com/entry/2014/08/10/143612

* 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.