GNU Parallel 20160522 ('TTIPleaks') released

[ole....@gmail.com]

GNU Parallel 20160522 ('TTIPleaks') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/

Haiku of the month:

Programs using net
only spare capacity
niceload dash dash net
-- Ole Tange

New in this release:

* niceload --net pauses the program if the internet connection is overloaded.

* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046

* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf

* GNU Parallel was cited in: Improving computation efficiency by parallel programming http://www.irbis-nbuv.gov.ua/cgi-bin/irbis_nbuv/cgiirbis_64.exe?C21COM=2&I21DBN=UJRN&P21DBN=UJRN&IMAGE_FILE_DOWNLOAD=1&Image_file_name=PDF/ape_2013_3_44.pdf

* GNU Parallel was cited in: A supernova feedback implementation for the astrophysical simulation software Arepo https://arxiv.org/abs/1604.06071

* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf

* GNU Parallel was cited in: Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections https://arxiv.org/abs/1512.06296

* GNU Parallel was cited in: Pacific People, Metabolic Disease and Evolutionary Processes: a mitochondrial DNA study https://otago.ourarchive.ac.nz/handle/10523/6340

* GNU Parallel was cited in: The effect of domain modeling on efficiency of planning: Lessons from the Nomystery domain http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7407131

* GNU Parallel was cited in: Oops, my tests broke the build: An analysis of Travis CI buildswith GitHub https://peerj.com/preprints/1984/

* GNU Parallel was cited in: Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution http://www.g3journal.org/content/5/5/719.full.pdf+html

* GNU Parallel was cited in: An Empirical Comparison of Neural Architectures for Reinforcement Learning in Partially Observable Environments http://biorxiv.org/content/biorxiv/early/2016/03/24/022707.full.pdf

* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/early/2016/04/11/048066.abstract

* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict Management in Requester-wins Hardware Transactional Memory http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072

* GNU Parallel was cited in: EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models http://www.sciencedirect.com/science/article/pii/S0022283616000310

* GNU Parallel was cited in: A new orthology assessment method for phylogenomic data: Unrooted Phylogenetic Orthology http://mbe.oxfordjournals.org/content/early/2016/04/06/molbev.msw069.short https://github.com/ballesterus/UPhO

* GNU Parallel was cited in: Distinctive Interest Point Selection for Efficient Near-duplicate Image Retrieval http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7459172

* GNU Parallel was cited in: The Evolution of C Programming Practices: A Study of the Unix Operating System 1973-2015 https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest thumbnail graphs I have ever seen scattered all over the text)

* GNU Parallel was cited in: StrAuto: Automation and Parallelization of STRUCTURE Analysis http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf

* GNU Parallel was cited in: Data processing pipeline for serial femtosecond crystallography at SACLA http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html

* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral Dynamics http://arxiv.org/pdf/1512.01460.pdf

* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf

* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1004381.PDF

* GNU Parallel was cited in: Genomic legacy of the African cheetah, Acinonyx jubatus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/pdf/13059_2015_Article_837.pdf

* GNU Parallel was cited in: Don't Forget to Lock the Back Door! A Characterization of IPv6 Network Security Policy http://benign-research-probe2.eecs.umich.edu/ndss16_ipv6_final.pdf

* GNU Parallel was cited in: Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0147221.PDF

* GNU Parallel was cited in: Stride Search: a general algorithm for storm detection in high-resolution climate data http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf

* GNU Parallel was cited in: How attention influences perceptual decision making: Single-trial EEG correlates of drift-diffusion model parameters http://www.cidlab.com/prints/nunez2016attention.pdf

* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads http://repository.upenn.edu/edissertations/1460/

* GNU Parallel was cited in: AT-GIS: Highly Parallel Spatial Query Processing with Associative Transducers http://lsds.doc.ic.ac.uk/sites/default/files/ATGIS-SIGMOD16.pdf

* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf

* GNU Parallel was cited in: Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life http://opus.bath.ac.uk/43955/

* GNU Parallel was cited in: Shannon: An Information-Optimal de NovoRNA-Seq Assembler http://biorxiv.org/content/biorxiv/early/2016/02/09/039230.full.pdf

* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter Estimation for Coastal Ocean Modeling https://repositories.lib.utexas.edu/handle/2152/32435

* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16

* GNU Parallel was cited in: Reference genotype and exome data from an Australian Aboriginal population for health-based research http://www.nature.com/articles/sdata201623

* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16

* GNU Parallel was cited in: Do aye-ayes echolocate? http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf

* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/biorxiv/early/2016/04/11/048066.full.pdf

* GNU Parallel was cited in: From genomes to phenotypes: Traitar, the microbial trait analyzer http://biorxiv.org/content/biorxiv/early/2016/03/12/043315.full.pdf

* GNU Parallel was mentioned in: Fast Playback Framework for Analysis of Ground-Based Doppler Radar Observations Using MapReduce Technology http://journals.ametsoc.org/doi/pdf/10.1175/JTECH-D-15-0118.1

* NCBI blast tutorial https://github.com/enormandeau/ncbi_blast_tutorial

* Distributed Preservation Made Simple https://blog.archive.org/2016/02/26/distributed-preservation-made-simple/

* Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.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 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.