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parallel/NEWS
Ole Tange 3d9baf9275 Released as 20170322 ('MyTag')
2017-03-21 23:31:46 +01:00

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20170322
* --rpl can now take arguments by adding '(regexp)' in the replacement
string.
* Vote for GNU Parallel's community ads on
http://meta.unix.stackexchange.com/a/4356/2972
http://meta.askubuntu.com/a/16750/22307
http://meta.serverfault.com/a/9040/45704
* GNU Parallel was cited in: shmlast: An improved implementation of
Conditional Reciprocal Best Hits with LAST and Python
https://joss.theoj.org/papers/3cde54de7dfbcada7c0fc04f569b36c7
* GNU Parallel was cited in: Prediction of relativistic electron flux
in the Earth’s outer radiation belt at geostationary orbit by
adaptive methods
https://link.springer.com/article/10.1134/S0016793217010108
* GNU Parallel was cited in: Proper experimental design requires
randomization/balancing of molecular ecology experiments
http://biorxiv.org/content/biorxiv/early/2017/02/17/109280.full.pdf
* GNU Parallel was cited in: Higher likelihood of multiple bit-flips
due to neutron-induced strikes on logic gates
https://arxiv.org/pdf/1612.08239.pdf
* GNU Parallel was cited in: A Monte Carlo Resampling Approach for the
Calculation of Hybrid Classical and Quantum Free Energies
http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.6b00506
* GNU Parallel was cited in: Learning string distance with smoothing
for OCR spelling correction
https://link.springer.com/article/10.1007/s11042-016-4185-5
* GNU Parallel was cited in: The Breakdown of String Perturbation
Theory for Many External Particles
https://arxiv.org/pdf/1611.08003.pdf
* GNU Parallel was cited in: Large-scale benchmarking reveals false
discoveries and count transformation sensitivity in 16S rRNA gene
amplicon data analysis methods used in microbiome studies
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0208-8
* GNU Parallel was cited in: Operations Research Applications in
Nuclear Energy
https://dspace.library.colostate.edu/bitstream/handle/11124/170687/Johnson_mines_0052E_11207.pdf?sequence=1&isAllowed=y
* GNU Parallel was cited in: Parallel Computing: GNU Parallel
http://www.blopig.com/blog/2017/02/parallel-computing-gnu-parallel/
* Stig Sandbeck Mathisen: Change All The Passwords (Again)
http://garf.us/2017/02/stig-sandbeck-mathisen-change-all-the-passwords-again/
* Trabalhando como Paralelismo no Bash usando o GNU Parallel
http://www.beyeler.com.br/2017/03/trabalhando-como-paralelismo-no-bash-usando-o-gnu-parallel/
* GNU parallel と SQL*Loader 組み合わせ実行例
https://blogs.oracle.com/LetTheSunShineIn/entry/gnu_parallel_%E3%81%A8_sql_loader
* Bug fixes and man page updates.
20170222
* env_parallel now supports /bin/sh, ash, dash.
* --tee will pipe all data to all jobs. Used with --pipe/--pipepart
and :::. Small example: seq 3333 | parallel --pipe --tee --tag 'grep
{} | wc -l' ::: {0..9}
* If --results {replstr} ends in /: save in dir. Otherwise save as
file. Example: parallel --results {} echo {} ::: a b c
* Vote for GNU Parallel's community ads on
http://meta.unix.stackexchange.com/a/4356/2972
http://meta.askubuntu.com/a/16750/22307
http://meta.serverfault.com/a/9040/45704
* GNU Parallel was cited in: Low-delay forwarding with multiple
candidates for VANETs using multi-criteria decision making
http://ieeexplore.ieee.org/document/7835961/
* GNU Parallel was cited in: An Integrated Simulator and Dataset that
Combines Grasping and Vision for Deep Learning
https://arxiv.org/pdf/1702.02103.pdf
* GNU Parallel was cited in: A Bayesian model selection approach for
identifying differentially expressed transcripts from RNA sequencing
data http://onlinelibrary.wiley.com/doi/10.1111/rssc.12213/full
* GNU Parallel was cited in: The impact of copy number variation on
gout, and the apple genome
https://ourarchive.otago.ac.nz/bitstream/handle/10523/7060/BoocockJames2016MSc.pdf?sequence=3
* GNU Parallel was cited in: Determination of crystal structures of
proteins of unknown identity using a marathon molecular replacement
procedure: structure of Stenotrophomonas maltophilia
phosphate-binding protein
https://www.researchgate.net/publication/308186413_Determination_of_crystal_structures_of_proteins_of_unknown_identity_using_a_marathon_molecular_replacement_procedure_Structure_of_Stenotrophomonas_maltophilia_phosphate-binding_protein
* GNU Parallel was cited in: Reaction rates for reaction-diffusion
kinetics on unstructured meshes
http://aip.scitation.org/doi/10.1063/1.4975167
* GNU Parallel was cited in: Modeling prediction error improves power
of transcriptome-wide association studies
http://biorxiv.org/content/biorxiv/early/2017/02/14/108316.full.pdf
* GNU Parallel was cited in: Proper experimental design requires
randomization/balancing of molecular ecology experiments
http://biorxiv.org/content/biorxiv/early/2017/02/17/109280.full.pdf
* GNU Parallel was cited in: Experiment-based thermal micromagnetic
simulations of the magnetization reversal for ns-range clocked
nanomagnetic logic
http://aip.scitation.org/doi/full/10.1063/1.4974021
* GNU Parallel was cited in: The University of Edinburgh’s systems
submission to the MT task at IWSLT
http://workshop2016.iwslt.org/downloads/IWSLT_2016_paper_27.pdf
* Fast-GBS uses GNU Parallel: https://bitbucket.org/jerlar73/fast-gbs
* Job: DevOps Engineer/Senior Systems Administrator in New York, New
York
http://rockefeller.jobs/new-york-ny/devops-engineersenior-systems-administrator/2DB3408EAC9E4617AD238550F31C7641/job/
* Training in GNU Parallel:
https://www.carc.unm.edu/education-outreach/workshops--training/
* Training in GNU Parallel:
http://www.hpc.lsu.edu/training/registration.php?topic=Parallel%20Serial%20Jobs%20Using%20GNU%20Parallel&date=February%2022,%202017&time=9:00%20AM%20-%2011:00%20AM&place=307%20Frey&deadline=2017-02-21%2016:30:00
* Batch Convert Images from PNG to JPEG
http://coreygoldberg.blogspot.dk/2017/02/batch-convert-images-from-png-to-jpeg.html
* Accelerating Oxford Nanopore Basecalling
http://fowlerlab.org/2017/01/26/accelerating-oxford-nanopore-basecalling/
* parallel и imagemagick в loop на bash
https://www.linux.org.ru/forum/development/13190247
* Bug fixes and man page updates.
20170206alpha
* --tee introduced.
20170122
* sql now uses a temporary credentials file for MySQL to avoid
warning.
* --sqlmaster and --sqlworker have been reworked.
* --sqlworker only reads from the DBURL: any command and any arguments
are ignored.
* --sqlmaster +DBURL will append different commands to the DBURL and
not erase the table.
* If --results contain a replacement string, no tree structure with
args will be generated.
* --fg --tmux or --fg --tmuxpane will connect to the tmux.
* GNU Parallel was cited in: Fast, Automated Indoor Light Detection,
Classification, and Measurement
https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-212.pdf
* GNU Parallel was cited in: Unbiased RNA Shotgun Metagenomics in
Social and Solitary Wild Bees Detects Associations with Eukaryote
Parasites and New Viruses
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168456
* GNU Parallel was cited in: Almost Event-Rate Independent Monitoring
of Metric Temporal Logic
http://people.inf.ethz.ch/trayteld/papers/tacas17-aerial/aerial.pdf
* 使用GNU parallel命令并行预处理数据: https://blog.razrlele.com/p/1843
* GNU Parallel as a queuing system:
http://puntoblogspot.blogspot.com/2017/01/gnu-parallel-as-queuing-system.html
* AWS re:Invent 2016: Deep Dive on Amazon Elastic File System (STG202)
slide 45
http://www.slideshare.net/AmazonWebServices/aws-reinvent-2016-deep-dive-on-amazon-elastic-file-system-stg202
and https://youtu.be/PlTuJx4VnGw?t=30m16s
* Bug fixes and man page updates.
20161222
* --results foo.csv will save output as a CSV-file. Can be directly
imported into R or LibreCalc.
* When using --pipepart a negative --block-size is not interpreted as
a block size but as the number of blocks each jobslot should have.
* --sqlmaster/--sqlandworker will append jobs to the DBURL if the
DBURL is prepended with +.
* GNU Parallel was cited in: A cloud-based workflow to quantify
transcript-expression levels in public cancer compendia
http://www.nature.com/articles/srep39259
* GNU Parallel was cited in: Learning string distance with smoothing
for OCR spelling correction
http://paperity.org/p/78557440/learning-string-distance-with-smoothing-for-ocr-spelling-correction
* GNU Parallel was cited in: Transient compute clustering with GNU
Parallel and sshfs
https://gist.github.com/Brainiarc7/24c966c8a001061ee86cc4bc05826bf4
* GNU Parallel was cited in: Determination of crystal structures of
proteins of unknown identity using a marathon molecular replacement
procedure: Structure of Stenotrophomonas maltophilia
phosphate-binding protein
https://www.researchgate.net/publication/308186413_Determination_of_crystal_structures_of_proteins_of_unknown_identity_using_a_marathon_molecular_replacement_procedure_Structure_of_Stenotrophomonas_maltophilia_phosphate-binding_protein
* GNU Parallel was cited in: The Outer Solar System Origins Survey:
I. Design and First-Quarter Discoveries
https://arxiv.org/pdf/1511.02895v2.pdf
* GNU Parallel was cited in: Large-scale benchmarking reveals false
discoveries and count transformation sensitivity in 16S rRNA gene
amplicon data analysis methods used in microbiome studies
http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0208-8
* GNU Parallel was cited in: Decomposing Images into Layers via
RGB-space Geometry
https://cs.gmu.edu/~ygingold/singleimage/Decomposing%20Images%20into%20Layers%20via%20RGB-space%20Geometry%20(Tan%20et%20al%202016%20TOG)%20small.pdf
* 4 Ways to Batch Convert Your PNG to JPG and Vice-Versa
http://www.tecmint.com/linux-image-conversion-tools/
* All's Fair in Love and Distributed Storage
http://cohesity.com/blog/alls-fair-love-distributed-storage/
* How can I use GNU Parallel to run a lot of commands in parallel
https://www.msi.umn.edu/support/faq/how-can-i-use-gnu-parallel-run-lot-commands-parallel
* 정해영의 블로그 - JEONG Haeyoung's blog
http://blog.genoglobe.com/2016/11/gnu-parallel.html
* 在Linux下将PNG和JPG批量互转的四种方法
http://os.51cto.com/art/201612/524182.htm
* Running in parallel http://tomkimpson.com/howto/gnuparallel/
* Taco Bell Parallel Programming
https://giorgos.sealabs.net/taco-bell-parallel-programming.html
* Bug fixes and man page updates.
20161122
* --record-env can now be used with env_parallel for bash, ksh, pdksh,
and zsh.
* GNU Parallel was cited in: An improved implementation of Conditional
Reciprocal Best Hits with LAST and Python
https://pypi.python.org/pypi/shmlast/1.0.3
* GNU Parallel was cited in: miRPathDB: a new dictionary on microRNAs
and target pathways
http://nar.oxfordjournals.org/content/early/2016/10/13/nar.gkw926.full
* GNU/Parallel – Run multiple commands simultaneously
https://vinusumi.wordpress.com/2016/11/08/gnuparallel-run-multiple-commands-simultaneously/
* Tutorial: Parallel web scraping with CasperJS and GNU Parallel
http://g-liu.com/blog/2016/10/tutorial-parallel-web-scraping-with-casperjs-and-gnu-parallel/
* Bug fixes and man page updates.
20161022
* First command no longer gets stdin as it causes unpredictable issues.
* GNU Parallel was cited in: Efficiently parallelized modeling of
tightly focused, large bandwidth laser pulses
https://arxiv.org/pdf/1609.08146v1.pdf
* How to crunch lots of geodata in parallel
http://blog.faraday.io/how-to-crunch-lots-of-geodata-in-parallel/
* GNU parallel is my new toaster
http://amedee.me/gnu-parallel-is-my-new-toaster/index.html
* Bug fixes and man page updates.
20160922
* parcat - cat files or fifos in parallel
* GNU Parallel was cited in: Velocity: A Netflow Based Optimized
Geo-IP Lookup Tool
https://mospace.umsystem.edu/xmlui/bitstream/handle/10355/50842/Thesis_2016_Pakhare.pdf?sequence=1&isAllowed=y
* GNU Parallel was cited in: Viral deep sequencing needs an adaptive
approach: IRMA, the iterative refinement meta-assembler
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011931/
* GNU Parallel is used in Gene Set Omic Analysis:
https://bitbucket.org/srp33/gsoa
* Using GNU Parallel and ImageMagick for Conversions
https://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
* Training in GNU Parallel
http://www.cism.ucl.ac.be/Services/Formations/parcomp.pdf
* Chown Ceph OSD data directory using GNU Parallel
http://blog.widodh.nl/2016/08/chown-ceph-osd-data-directory-using-gnu-parallel/
* FastGBS uses GNU Parallel https://bitbucket.org/jerlar73/fastgbs
* dDocent: A guide to ddRAD sequencing
https://ddocent.wordpress.com/ddocent-pipeline-user-guide/
* SOFTWARE GNU Parallel
http://msi-riss.readthedocs.io/en/latest/software/gnu-parallel.html
* Bug fixes and man page updates.
20160822
* --tmuxpane opens jobs in panes in tmux. Useful if you want to
monitor progress of less than 100 simultaneous jobs.
* --linebuffer now treats \r as line ending, too.
* Perl changes forces use of floats to be given with leading zero, so
0.1 and not .1
* --xapply renamed to --link.
* Support for pdksh will fade until someone packages it for Ubuntu 16.
* GNU Parallel was cited in: Exome sequencing of geographically
diverse barley landraces and wild relatives gives insights into
environmental adaptation
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3612.html?WT.feed_name=subjects_genetics#references
* GNU Parallel was cited in: Vision-Enhanced Lidar Odometry and
Mapping https://www.ri.cmu.edu/pub_files/2016/8/DLL-thesis.pdf
* Easy parallelization with GNU parallel
http://mpharrigan.com/2016/08/02/parallel.html
* Facebook V: Predicting Check Ins, Winner's Interview: 2nd Place,
Markus Kliegl
http://blog.kaggle.com/2016/08/02/facebook-v-predicting-check-ins-winners-interview-2nd-place-markus-kliegl/
* Parallel import
http://www.manitou-mail.org/blog/2016/07/parallel-import/
* Large file batch processing using NodeJs and GNU Parallel
http://www.zacorndorff.com/2016/07/27/large-file-batch-processing-using-nodejs-and-gnu-parallel/
* Bug fixes and man page updates.
20160722
* env_parallel is now ready for wider testing. It is still beta
quality.
* env_parallel is heavily modified for all shells and testing has been
increased.
* Selectively choosing what to export using --env now works for
env_parallel (bash, csh, fish, ksh, pdksh, tcsh, zsh).
* --round-robin now gives more work to a job that processes faster
instead of same amount to all jobs.
* --pipepart works on block devices on GNU/Linux.
* GNU Parallel was cited in: HybPiper: Extracting Coding Sequence and
Introns for Phylogenetics from High-Throughput Sequencing Reads
Using Target Enrichment
http://www.bioone.org/doi/full/10.3732/apps.1600016
* GNU Parallel was cited in: StrAuto - Automation and Parallelization
of STRUCTURE Analysis
http://www.crypticlineage.net/download/strauto/strauto_doc.pdf
* GNU Parallel was cited in: Tools and techniques for computational
reproducibility
http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0135-4
* GNU Parallel was cited in: FlashPCA: fast sparse canonical
correlation analysis of genomic data
http://biorxiv.org/content/biorxiv/suppl/2016/04/06/047217.DC1/047217-1.pdf
* 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: Math Indexer and Searcher under the Hood:
Fine-tuning Query Expansion and Unification Strategies
http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings12/pdf/ntcir/MathIR/05-NTCIR12-MathIR-RuzickaM.pdf
* GNU Parallel was cited in: The Evolution and Fate of
Super-Chandrasekhar Mass White Dwarf Merger Remnants
http://arxiv.org/pdf/1606.02300.pdf
* GNU Parallel was cited in: Evaluation of Coastal Scatterometer
Products
https://mdc.coaps.fsu.edu/scatterometry/meeting/docs/2016/Thu_AM/coastal-poster.pdf
* GNU Parallel was used in: https://github.com/splitice/bulkdnsblcheck
* The iconv slurp misfeature
http://www.openfusion.net/linux/iconv_slurp_misfeature
* แบบว่า CPU เหลือ https://veer66.wordpress.com/2016/06/15/gnu-parallel/
* Bug fixes and man page updates.
20160622
* $PATH can now be exported using --env PATH. Useful if GNU Parallel
is not in your path on remote machines.
* If --block is left out, --pipepart will use a block size that will
result in 10 jobs per jobslot.
* The cookie from 2016-01-04 was won by Morgan Rodgers on the
2016-06-06 after 5 months.
* Vote for GNU Parallel's community ad on
https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
* GNU Parallel was cited in: Genotypic Resistance Tests Sequences
Reveal the Role of Marginalized Populations in HIV-1 Transmission in
Switzerland http://www.nature.com/articles/srep27580
* GNU Parallel was cited in: A Deep-Learning Approach for Operation of
an Automated Realtime Flare Forecast
https://arxiv.org/pdf/1606.01587.pdf
* Unix parallel: Populating all the USB sticks
http://www.markhneedham.com/blog/2016/06/01/unix-parallel-populating-all-the-usb-sticks/
* GNU Parallel is a fantastic utility https://www.dray.be/parallel/
* Combining a large number of VCF files
https://gtamazian.com/2016/06/16/combining-a-large-number-of-vcf-files/
* Useful Scraping Techniques
http://blog.apps.npr.org/2016/06/17/scraping-tips.html
* Tools of the trade
http://onox.com.br/2015/05/tools-of-the-trade/#more-198
* Armslist scraper https://github.com/nprapps/armslist-scraper/
* Bug fixes and man page updates.
20160522
* 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.
20160422
* :::+ and ::::+ work like ::: and :::: but links this input source to
the previous input source in a --xapply fashion. Contrary to
--xapply values do not wrap: The shortest input source determines
the length.
* --line-buffer --keep-order now outputs continously from the oldest
job still running. This is more what you would expect than the
earlier behaviour where --keep-order had no effect with
--line-buffer.
* env_parallel supports tcsh, csh, pdksh. In fish it now supports
arrays. In csh/tcsh it now supports variables, aliases, and arrays
with no special chars. In pdksh it supports aliases, functions,
variables, and arrays.
* Function exporting on Mac OS X works around old Bash version.
* Better CPU detection on OpenIndiana.
* GNU Parallel was cited in: How Can We Measure the Similarity Between
Resumes of Selected Candidates for a Job?
https://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_resumes_of_selected_candidates_for_a_job
* GNU Parallel was cited in: Automatic Methods for Assisted
Recruitment
https://www.researchgate.net/publication/297738658_Automatic_Methods_for_Assisted_Recruitment
* GNU Parallel was cited in: Tools and techniques for computational
reproducibility
http://biorxiv.org/content/biorxiv/early/2016/03/17/022707.full.pdf
* GNU Parallel was cited in: Reinterpretation of ATLAS 8 TeV searches
for Natural SUSY with a R-Sneutrino LSP
http://arxiv.org/pdf/1603.06130.pdf
* GNU Parallel was cited in: An Operational Radiometric Landsat
Preprocessing Framework for Large-Area Time Series Applications
https://www.uni-trier.de/fileadmin/fb6/prof/FER/Publikationen/frantz_et_al_ieee-tgrs-2016-post-print.pdf
* A basic demo of how GNU Parallel can speed up execution of commands
https://www.youtube.com/watch?v=kl8LO2jcvMc
* Downloading a list of URLs
http://blog.gypsydave5.com/2016/02/04/xargs-and-curl/
* qbatch uses GNU Parallel: https://pypi.python.org/pypi/qbatch/1.0rc2
* FaceCrop uses GNU Parallel: https://github.com/EderSantana/FaceCrop
* Parallel Processing with Catmandu
https://librecatproject.wordpress.com/2016/04/20/parallel-processing-with-catmandu/
* GNU parallel 應用範例
http://staypython.blogspot.dk/2016/04/gnu-parallel.html
* Bug fixes and man page updates.
20160322
* env_parallel is a function that exports the environment (functions,
aliases, variables, and arrays) to GNU Parallel. Run 'man
env_parallel' for details.
* niceload --prg now searches for substrings if no process with the
name is found.
* GNU Parallel was cited in: Random Forest DBSCAN for USPTO Inventor
Name Disambiguation http://arxiv.org/pdf/1602.01792.pdf
* GNU Parallel was mentioned (with wrong citation) in: Dual Level
Parallel Computations for LargeScale High-Fidelity Database to
Design Aerospace Vehicles
http://www.nas.nasa.gov/assets/pdf/papers/Guruswamy_2013_DualLevelParallelComputations.pdf
* Using ‘Parallel’ in Unix
https://shearnrylan.wordpress.com/2016/02/22/using-parallel-in-unix/
* JPEG Squish uses (and co-distributes) GNU Parallel:
http://dantidswell.co.uk/jpeg-squish/
* Bug fixes and man page updates.
20160222
* Vote for new community on Superuser, Ask Ubuntu, Unix&Linux
http://meta.superuser.com/questions/11127/community-promotion-ads-2016/11225#11225
http://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
http://meta.unix.stackexchange.com/questions/3854/community-promotion-ads-2016/3893#3893
* Daily Quick Tip: parallel
https://medium.com/@jacaetevha/daily-quick-tip-parallel-8772435f6582
* Downloading a list of URLs
http://blog.gypsydave5.com/2016/02/04/xargs-and-curl/
* Using GNU Parallel and ImageMagick for Conversions
http://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
* Running bash commands in parallel
http://linuxcommando.blogspot.dk/2016/01/running-bash-commands-in-parallel.html
* parallel processing in PDAL
https://smathermather.wordpress.com/2016/01/28/parallel-processing-in-pdal/
* A Million Text Files And A Single Laptop
http://randyzwitch.com/gnu-parallel-medium-data/
* 「今日から使い切る」ための GNU Parallelによる並列処理入門
http://www.slideshare.net/koji_matsuda/gnu-parallel
* Bug fixes and man page updates.
20160122
* --sql DBURL uses DBURL as storage for jobs and output. It does not
run any jobs so it requires at least one --sqlworker. DBURL must
point to a table.
* --sqlworker DBURL gets jobs from DBURL and stores the result back to
DBURL.
* --sqlandworker is a shorthand for --sql and --sqlworker.
* --sqlworker requires the output of a single job to fit in memory.
* --results now also saves a file called 'seq' containing the sequence
number.
* If $PARALLEL_ENV is a file, then that file will be read into
$PARALLEL_ENV.
* man parallel_tutorial has been given an overhaul.
* --workdir now accepts replacementstrings.
* GNU Parallel was cited in: Possum - A Framework for
Three-Dimensional Reconstruction of Brain Images from Serial
Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
* GNU Parallel was cited in: A Genetic Algorithm for the selection of
structural MRI features for classification of Mild Cognitive
Impairment and Alzheimer's Disease
http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7359909&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7359909
* GNU Parallel was cited in: The Effect of Domain Modeling on
Performance of Planning Algorithms
http://isaim2016.cs.virginia.edu/papers/ISAIM2016_Bartak_Vodrazka.pdf
* Plotting time tables for jobs run by GNU Parallel
https://github.com/ziotom78/plot_joblog
* GNU Parallel was used in: Mission Impossible: you have 1 minute to
analyze the Ebola Genome https://www.biostars.org/p/119397
* GNU Parallel is used in LAST: http://last.cbrc.jp/
* Distributed Log Search Using GNU Parallel
http://codehate.com/blog/2015/12/01/distributed-log-search-using-gnu-parallel/
* Bug fixes and man page updates.
20151222
* --transfer is now an alias for --transferfile {}.
* --transferfile works like --transfer, but takes an argument like
--return. This makes it possible to combine transferring files
with multiple input sources: parallel -S server --tf {1} wc {2}
{1} ::: * ::: -l -w -c
* total_jobs() can now be used in {= =}: parallel echo job {#} of '{=
$_=total_jobs() =}' ::: {1..50}
* GNU Parallel was cited in: Evolution and Learning in Heterogeneous
Environments
http://research.gold.ac.uk/15078/1/COM_thesis_JonesD_2015.pdf
* GNU Parallel was cited in: Contrasting genetic architectures of
schizophrenia and other complex diseases using fast
variance-components analysis
http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html
* GNU Parallel was cited in: Efficient Retrieval of Key Material for
Inspecting Potentially Malicious Traffic in the Cloud
http://www.cs.bham.ac.uk/~bxb/Papres/2015.1.pdf
* GNU Parallel was cited in: Achieving Consistent Doppler Measurements
from SDO/HMI Vector Field Inversions
http://arxiv.org/pdf/1511.06500.pdf
* Flo uses GNU Parallel: https://github.com/wurmlab/flo
* 使用 GNU parallel 來平行運算
http://mutolisp.logdown.com/posts/316959-using-gnu-parallel-to-parallel-computing
* Bug fixes and man page updates.
20151122
* GNU Parallel packaged for CERN CentOS:
http://linuxsoft.cern.ch/cern/centos/7/cern/x86_64/repoview/parallel.html
* 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: Contrasting genetic architectures of
schizophrenia and other complex diseases using fast
variance-components analysis
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3431.html
* GNU Parallel was cited in: Named-Entity Chunking for Norwegian Text
using Support Vector Machines
http://ojs.bibsys.no/index.php/NIK/article/viewFile/248/211
* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics
Using Brownian Dynamics, Molecular Dynamics and Milestoning
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004381#pcbi.1004381.ref072
* GNU Parallel was cited in: A Detailed Characterization of Errors in
Logic Circuits due to Single-Event Transients
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=7302348&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7302348
* GNU Parallel was cited in: Arabic Speaker Emotion Classification
Using Rhythm Metrics and Neural Networks
http://www.eurasip.org/Proceedings/Eusipco/Eusipco2015/papers/1570104855.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: Decomposing Digital Paintings into Layers
via RGB-space Geometry http://arxiv.org/pdf/1509.03335.pdf
* GNU Parallel was cited in: Structure and evolutionary history of a
large family of NLR proteins in the zebrafish
http://www.biorxiv.org/content/biorxiv/early/2015/09/18/027151.full.pdf
* GNU Parallel was cited in: Evolution of movement strategies under
competitive interactions
http://digital.csic.es/bitstream/10261/115973/1/evolution_movement_strategies_Kiziridis.pdf
* Automating large numbers of tasks
https://rcc.uchicago.edu/docs/tutorials/kicp-tutorials/running-jobs.html
* Max out your IOPs with GNU Parallel
http://blog.bitratchet.com/2015/11/11/max-out-your-iops-with-gnu-parallel/
* Bug fixes and man page updates.
20151022
* --plus makes it possible to use {##} as a shorthand for
{= $_=$Global::JobQueue->total_jobs() =} which gives the the number
of jobs to run in total.
* {= $_=$Global::JobQueue->total_jobs() =} is incompatible with -X,
-m, and --xargs.
* GNU Parallel is now mostly compatible with lsh
(http://www.lysator.liu.se/~nisse/lsh/) and somewhat compatible with
autossh (http://www.harding.motd.ca/autossh/).
* --workdir ... now also works when run locally.
* GNU Parallel was cited in: There is no (75, 32, 10, 16) strongly
regular graph http://arxiv.org/pdf/1509.05933.pdf
* GNU Parallel was cited in: Roary: rapid large-scale prokaryote pan
genome analysis
http://bioinformatics.oxfordjournals.org/content/early/2015/08/05/bioinformatics.btv421.full.pdf+html
* GNU Parallel is used in TraitAR:
https://testpypi.python.org/pypi/traitar/0.1.4
* GNU Parallel is used in youtube-dl-parallel:
https://github.com/dlh/youtube-dl-parallel
* A parallel and fast way to download multiple files
http://onetipperday.blogspot.com/2015/10/a-parallel-and-fast-way-to-download.html
* Usar GNU Parallel para aumentar el rendimiento de tus scripts
http://adrianarroyocalle.github.io/blog/2015/10/20/usar-gnu-parallel/
* Bug fixes and man page updates.
20150922
* GNU Parallel was cited in: Flexible Modeling of Epidemics with an
Empirical Bayes Framework
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004382
* GNU Parallel was cited in: BL1: 2D Potts Model with a Twist
https://sucs.swan.ac.uk/~rjames93/Dissertation.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic
Platform Bridging the Gap between the Robust Validation of Docking
Protocols and Virtual Screening Simulations
http://www.mdpi.com/1420-3049/20/6/9977/pdf
* GNU Parallel was cited in: A Scalable Parallel Implementation of
Evolutionary Algorithms for Multi-Objective Optimization on GPUs
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7257074
* GNU Parallel was cited in: Tools and techniques for computational
reproducibility
http://biorxiv.org/content/biorxiv/early/2015/07/17/022707.full.pdf
* GNU Parallel was cited in: How Can We Measure the Similarity Between
Résumés of Selected Candidates for a Job?
http://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_rsums_of_selected_candidates_for_a_job
* GNU Parallel was cited in: Interplay of cell dynamics and epithelial
tension during morphogenesis of the Drosophila pupal wing
http://www.researchgate.net/profile/Raphael_Etournay/publication/279061859_Interplay_of_cell_dynamics_and_epithelial_tension_during_morphogenesis_of_the_Drosophila_pupal_wing/links/558a95ad08aeae8413bcceea.pdf
* Third-party selling GNU Parallel T-shirts
http://www.aliexpress.com/item/2015F-BSO-GNU-LOGO-GNU-PARALLEL-men-s-shirt-sleeve-visual-illusion-error/32464827966.html
* Joys of gnu parallel
http://scottolesen.com/index.php/2015/08/26/joys-of-gnu-parallel/
* Crop and resize images with bash and ImageMagick
https://www.simonholywell.com/post/2015/08/image-resize-crop-bash-imagemagick/
* Three Ways to Script Processes in Parallel
http://www.codeword.xyz/2015/09/02/three-ways-to-script-processes-in-parallel/
* What It Looks Like to Process 3.5 Million Books
http://blog.gdeltproject.org/what-it-looks-like-to-process-3-5-million-books/
* Bug fixes and man page updates.
20150822
* If $job->skip() is called in {= =} the job will not be run.
* @arg can now be used in {= =}: parallel echo '{= $arg[2] < 5 and
$_="j" =}' ::: 1 2 3 ::: 4 5 6
* Version of GNU Parallel that uses PostgreSQL as backend
https://github.com/stephen-fralich/parallel-sql/
* A composite genome approach to identify phylogenetically informative
data from next-generation sequencing
http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
* SpeedSeq: ultra-fast personal genome analysis and interpretation
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html
* GNU Parallel is used in elPrep: https://github.com/ExaScience/elprep
* Who actually reads the code?
http://www.fsf.org/blogs/community/who-actually-reads-the-code
* Introduction to GNU Parallel
http://erictleung.com/2015/08/06/intro-to-gnu-parallel/
* ¿Alguien se lee el código?
http://www.taringa.net/post/linux/18854759/Alguien-se-lee-el-codigo.html
* ¿Quién se lee el código fuente?
https://victorhckinthefreeworld.wordpress.com/2015/08/12/quien-se-lee-el-codigo-fuente/
* Distribution des traitements avec GNU Parallel
http://blog.inovia-conseil.fr/?p=226#4
* Эксперимент по проверке, читают ли код открытых проектов
http://www.opennet.ru/opennews/art.shtml?num=42718
* 多核心主機搭配 GNU parallel
http://blog.zeroplex.tw/2015/08/gnu-parallel.html
* Bug fixes and man page updates.
20150722
* If a record fits in a block, --block only reads upto the size of
--block. If not: --block reads a full --block more.
* Due to widely spread distributions still using --tollef even after a
year of being retired following a year of being obsolete, --tollef
now gives an error unless used with --gnu.
* --nice now uses a perl wrapper instead of the nice command.
* Cookie 2013-08-18 was won by Mark Maimone, 1 year and 11 months
after release.
* A parser for GNU Parallel --joblog files:
https://github.com/harryjubb/joblog
* GNU Parallel was cited in: Dynamical formation & scattering of
hierarchical triples: Cross sections, Kozai-Lidov oscillations, and
collisions http://arxiv.org/pdf/1507.03593.pdf
* GNU Parallel was cited in: A Fast Compiler for NetKAT
http://arxiv.org/pdf/1506.06378.pdf
* GNU Parallel was cited in: Flexible Modeling of Epidemics with an
Empirical Bayes Framework
http://www.stat.cmu.edu/~ryantibs/papers/empbayes.pdf
* GNU Parallel was cited in: Decomposing Time-Lapse Paintings into
Layers
http://cs.gmu.edu/~ygingold/timemap/Decomposing%20Time-Lapse%20Paintings%20into%20Layers%20(Tan%20et%20al%202015%20SIGGRAPH)%20600dpi.pdf
* GNU Parallel was used in: Somatic mutation calling from the matched
tumor-normal exome-sequencing
http://fafner.meb.ki.se/biostatwiki/somac/
* Parallel Processing from the Command Line
https://www.perpetual-beta.org/weblog/parallel-processing-from-the-command-line.html
* Using GNU Parallel to speed up network operations
http://vielmetti.typepad.com/vacuum/2015/06/using-gnu-parallel-to-speed-up-network-operations.html
* Crawl faster with "parallel" - but how fast?
http://andreas-wpv.blogspot.com/2015/07/crawl-faster-with-parallel-but-how-fast.html
* Simultaneously benchmark many URLs with ApacheBench and GNU parallel
https://www.simonholywell.com/post/2015/06/parallel-benchmark-many-urls-with-apachebench/
* Bug fixes and man page updates.
20150622
* --halt has been rewritten completely. You can now combine
percentages with success or fail. See the man page.
* Exit values 102..254 have been removed. 101 means more than 100 jobs
failed.
* Killing through --timeout, --memfree, or --halt is now done as a
process group.
* --termseq determines which signals are sent when a job is killed.
* An empty argument would previously cause no string to be
inserted. This is now changed to '' being inserted, thus prepending
a space to the output of: parallel echo {} b ::: ''
* $PARALLEL_ENV can now be set to an environment prepending the
command. Used in env_parallel as mentioned in the manpage.
* --retry-failed will retry all failed jobs in a joblog. It will
ignore any command given.
* --ssh and $PARALLEL_SSH can be used to set the command used for
ssh. The command is assumed to behave the same way as ssh.
* --fifo now works in csh, too.
* Q(...) can be used in {= =} to shell quote a string.
* 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/2015/06/05/016527.full.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic
Platform Bridging the Gap between the Robust Validation of Docking
Protocols and Virtual Screening Simulations
http://www.mdpi.com/1420-3049/20/6/9977
* GNU Parallel was cited in: Swedes Online: You Are More Tracked Than
You Think
http://www.diva-portal.org/smash/get/diva2:807623/FULLTEXT01.pdf
* GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D
scattering and resonance calculations
http://arxiv.org/pdf/1505.07691.pdf
* GNU Parallel was cited in: A quantitative assessment of the Hadoop
framework for analyzing massively parallel DNA sequencing data
http://link.springer.com/article/10.1186/s13742-015-0058-5
* GNU Parallel was cited in: A composite genome approach to identify
phylogenetically informative data from next-generation sequencing
http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
* GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D
scattering and resonance calculations
http://arxiv.org/pdf/1505.07691.pdf
* GNU Parallel is used in: taxator-tk
http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/
* GNU Parallel is used in: https://github.com/d2207197/local-mapreduce
* GNU Parallel is used in: wiki-edit-news https://github.com/albert-decatur/wiki-edit-news
* GNU Parallel is used in: A Fingerprint Identification System
https://curve.carleton.ca/system/files/theses/28733.pdf
* Job ad asking for GNU Parallel experience:
http://searchjobs.intel.com/gdansk-pol/software-validation-engineer/63A06826DAF24797AB414DC146201C2E/job/
* Using BLAT http://wangzhengyuan.blogspot.dk/2015/06/using-blat.html
* Bug fixes and man page updates.
20150522
* 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.
20150422
New in this release:
* Security fix. An attacker on the local system could make you
overwrite one of your own files with a single byte. The problem
exist when you use --compress or --tmux or --pipe or --cat or
--fifo. The attacker must figure out the randomly chosen file name
and create a symlink within a time window of 15 ms.
* --shuf will generate all jobs, and shuffle them before running
them. This is useful to get a quick preview of the results before
running the full batch.
* GNU Parallel now has a DOI: https://dx.doi.org/10.5281/zenodo.16303
* GNU Parallel was cited in: Scaling Machine Learning for Target
Prediction in Drug Discovery using Apache Spark
https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf
* GNU Parallel was cited in: Bayesian inference of protein structure
from chemical shift data https://peerj.com/articles/861/
* 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: 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 cited in: Experimental study on the Wind Farm
Substation Cable Installation Problem
http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
* GNU Parallel was used in: landsat-gifworks
https://github.com/KAPPS-/landsat-gifworks
* GNU Parallel was used in: https://github.com/exascience/elprep
* GNU Parallel was used in:
http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
* GNU Parallel was used in:
http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
* GNU Parallel was used in: Rapid haploid SNP calling
https://github.com/tseemann/snippy
* Pictures and Metadata
http://www.ozzy.no/2015/02/05/pictures-and-metadata/
* Task automation with bash and parallel
https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
* How To: Speed Up File Transfers in Linux using RSync with GNU
Parallel
http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html
* Mirroring a Git Repository
https://avacariu.me/articles/mirroring-a-git-repository.html
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles
https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
* GNU Parallel (Sebuah Uji Coba)
http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
* 你见过的最牛逼的命令行程序是什么？
http://www.zhihu.com/question/29257300
* Bug fixes and man page updates.
20150322
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.
20150222
* --tmux has gotten a major overhaul.
* GNU Parallel was cited in: RaftLib: A C++ Template Library for High
Performance Stream Parallel Processing
http://www.cs.wustl.edu/~lip/pubs/pmam15_jbeard.pdf
* GNU Parallel was cited in: Quantifying properties of hot and dense
QCD matter through systematic model-to-data comparison
http://arxiv.org/pdf/1502.00339.pdf
* GNU Parallel was cited in: Towards Collaborative Exploration and
Analysis of Big Data from Mars: A Noachis Terra Case Study
http://link.springer.com/chapter/10.1007/978-3-319-13865-7_25
* 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 used (unfortunately with wrong citation) in:
Performance and Scaling Comparison Study of RDBMS and NoSQL
(MongoDB)
http://ijact.in/wp-content/uploads/2014/11/COMPUSOFT-311-1270-1275.pdf
* GNU Parallel was used (unfortunately without citation) in: Parallel
Implementation of Big Data Pre-Processing Algorithms for Sentiment
Analysis of Social Networking Data
http://www.researchmathsci.org/IJFMAart/ijfma-v6n2-7.pdf
* GNU Parallel was used (unfortunately without citation) in: SpeedSeq:
Ultra-fast personal genome analysis and interpretation
http://biorxiv.org/content/biorxiv/early/2014/12/05/012179.full.pdf
* Zip Folders with GNU Parallel
http://fazky.github.io/posts/Linux/2015-01-07-GNU-Parallel.html
* Using GNU Parallel with Freesurfer
http://programminginadarkroom.blogspot.dk/2015/02/using-gnu-parallel-with-freesurfer.html
* GNU Parallel is used in Velociraptor: https://github.com/ericwhyne/Velociraptor
* Marcus Beach GNU Parallel http://marcusbeach.co/gnu-parallel/
* Bug fixes and man page updates.
20150122
* 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 Mullerʼs 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.
20141122
* Remote systems can be divided into hostgroups (e.g. web and db) by
prepending '@groupname/' to the sshlogin. Multiple groups can be
given by separating groups with '+'. E.g. @web/www1 @web+db/www2
@db/mariadb
* Remote execution can be restricted to servers that are part of one
or more groups by '@groupname' as an sshlogin. Multiple groups can
be given by separating groups with '+'. E.g. -S @web or -S @db+web
* With --hostgroup you can restrict arguments to certain hostgroups by
appending '@groupname' to the argument. Multiple groups can be
given by separating groups with '+'. E.g. my_web_arg@web
db-or-web-arg@db+web db-only-arg@db Thanks to Michel Courtine for
developing a prototype for this.
* GNU Parallel was cited in: HTSeq-Hadoop: Extending HTSeq for
Massively Parallel Sequencing Data Analysis using Hadoop
http://essenceofescience.se/wp-content/uploads/2014/11/Siretskiy.pdf
* 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#close
* GNU Parallel was cited in: Exploring a multiprocessor design space
to analyze the impact of using STT-RAM in the memory hierarchy
http://conservancy.umn.edu/bitstream/handle/11299/167286/Borse_umn_0130M_15431.pdf
* Command-Line OCR with Tesseract on Mac OS X
https://ryanfb.github.io/etc/2014/11/13/command_line_ocr_on_mac_os_x.html
* Bug fixes and man page updates.
20141022
* --env was changed to deal with Bash's new way of exporting a function.
* GNU Parallel was cited in: Exclusion of cosmic rays in
protoplanetary disks. II. Chemical gradients and observational
signatures http://iopscience.iop.org/0004-637X/794/2/123/article
* GNU Parallel was cited in: Application of Machine Learning to
Algorithm Selection for TSP
http://www.dbai.tuwien.ac.at/staff/musliu/art_ictai_cam.pdf
* GNU Parallel was cited in: Performance Models for LTE-Advanced
Random Access
http://repository.asu.edu/attachments/137242/content/Tyagi_asu_0010E_14116.pdf
* GNU Parallel was used (unfortunately without citation) in: De Novo
Insertions and Deletions of Predominantly Paternal Origin Are
Associated with Autism Spectrum Disorder
http://www.cell.com/cms/attachment/2019079667/2039310868/mmc1.pdf
* GNU Parallel was determined 'popular' by Statistical Analysis of
Popular Open Source Software Projects and Their Communities
http://andiwre.itmaranatha.org/prosiding/ICITEE2014/PaperAndiWRE-ICITEE2014.pdf
* GNU Parallel is demonstrated in: Data Science at the Command Line:
Facing the Future with Time-Tested Tools
* GNU Parallel was covered in a talk at Sydney Perl Mongers group
http://www.openfusion.net/talks/pwp/#24
* GNU Parallel and how to get started with it
http://www.jduck.net/blog/2014/09/30/gnu-paralell/
* Behat/Selenium/Parallel
http://jaffamonkey.com/behat-selenium-parallel/
* Comparing Golang, Scala, Elixir and Ruby for ETL
http://www.dimroc.com/2014/09/29/etl-language-showdown/
* Parallelizing Batch Jobs for Fun and Profit
http://mikeseidle.com/tech/programming/2013/03/parallelizing-batch-jobs
* Assemble a list of which of these hosts are up or down
http://opsfun.wordpress.com/2014/03/31/gnu-parallel/
* Running commands on many nodes simultaneously
http://opsfun.wordpress.com/2014/03/31/19/
* Ubuntu 13.04でGNU ParallelをGNUモードで動かす
http://qiita.com/YusukeSuzuki@github/items/7b96b5876bf980f21e85
* Bug fixes and man page updates.
20140922
* If the file give as --sshloginfile is changed it will be re-read
when a job finishes though at most once per second. This makes it
possible to add and remove hosts while running.
* Brutha uses GNU Parallel https://pypi.python.org/pypi/brutha/1.0.2
* OCRmyPDF uses GNU Parallel https://github.com/fritz-hh/OCRmyPDF/
* GNU Parallel was presented at Balti and Bioinformatics "On-Air"
http://youtu.be/UtXlr19xTh8?t=2h5m0s
* Pleiades Plus uses GNU Parallel
https://github.com/ryanfb/pleiades-plus
* Imagemagick and GNU Parallel
http://deepdish.io/2014/09/15/gnu-parallel/
* GNU Parallel (Sebuah Uji Coba)
http://pr4ka5a.wordpress.com/2014/09/04/gnu-parallel-sebuah-uji-coba/
* GNU Parallel: 并行执行Linux命令
http://blog.csdn.net/xzz_hust/article/details/39183837
20140822
* GNU Parallel now uses the same shell it was started from as the
command shell for local jobs. So if GNU Parallel is started from
tcsh it will use tcsh as its shell even if the login $SHELL is
different. For remote jobs the login $SHELL will be used.
* The whole current environment in bash can be copied by using a shell
wrapper function (Search manual for env_parallel).
* --plus adds the replacement strings {+/} {+.} {+..} {+...} {..}
{...} {/..} {/...}. The idea being that '+foo' matches the opposite
of 'foo' and {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..}
= {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...}
* GNU Parallel now deals correctly with the combination
rsync-3.1.X-client and rsync-2.5.7-server
* GNU Parallel was cited in: A Web Service for Scholarly Big Data
Information Extraction
http://patshih.ist.psu.edu/publications/Williams-CiteSeerExtractor-ICWS14.pdf
* Comparison of the speed of different GNU Parallel versions:
http://lists.gnu.org/archive/html/parallel/2014-08/msg00030.html
* GNU Parallel was covered in the webcast 2014-08-20: Data Science at
the Command Line http://www.oreilly.com/pub/e/3115
* Distributed processing with GNU parallel
http://kazjote.eu/2014/08/11/distributed-processing-with-gnu-parallel
* A Peek into GNU Parallel
http://blog.dataweave.in/post/94238943763/a-peek-into-gnu-parallel
* Сборка GNU parallel для CentOS/RHEL
http://www.stableit.ru/2014/07/gnu-parallel-centosrhel.html
* Bug fixes and man page updates.
20140722
* {= 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 incompatibility: {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.
20140622
* --shebang and --shebang-wrap now works on FreeBSD.
* --pipepart works with --header, --regexp, --cat and --fifo.
* ./configure --disable-documentation will not build documentation.
* {%} works as job slot.
* GNU Parallel was cited in: Energy Efficient, High-speed
Communication in WSNs
https://gupea.ub.gu.se/bitstream/2077/35801/1/gupea_2077_35801_1.pdf
* GNU Parallel was cited in: Ferroelectric contributions to anomalous
hysteresis in hybrid perovskite solar cells
http://arxiv.org/pdf/1405.5810.pdf
* Processes Paralleling to Speed up Computing and Tasks Execution in
Linux
http://kukuruku.co/hub/nix/processes-paralleling-to-speed-up-computing-and-tasks-execution-in-linux
* Moving / Copying lots of s3 files quickly using gnu parallel
http://blog.aclarke.eu/moving-copying-lots-of-s3-files-quickly-using-gnu-parallel/
* Speeding up grep log queries with GNU Parallel
http://www.tripwire.com/state-of-security/incident-detection/speeding-grep-queries-gnu-parallel/
* Ubuntu - Gnu parallel - It's awesome
http://kasunweranga.blogspot.dk/2014/06/ubuntu-gnu-parallel-its-awesome.html
* Export quicklooks with vector overlay using TuiView
http://spectraldifferences.wordpress.com/2014/03/08/export-quicklooks-with-vector-overlay-using-tuiview/
* GNU Parallel指南 http://my.oschina.net/enyo/blog/271612
* GNU parallelで違和感 http://jarp.does.notwork.org/diary/201405c.html#201405301
* Bug fixes and man page updates.
20140522
* Use --semaphoretimeout to ignore the semaphore lock after a while.
* {%} introduced as job slot replacement string. It has known bugs.
* --slotreplace changes slot replacement string.
* GNU Parallel officially in Solaris 11.2beta
https://blogs.oracle.com/alanc/entry/solaris_11_2_changes_to
* GNU Parallel was cited in: A Comparison of Antenna Placement
Algorithms http://abhinavjauhri.com/publications/eap.pdf
* Using GNU Parallel on a PBS cluster (nice use of --shebang-wrap)
https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing
* BioLite uses GNU Parallel: https://bitbucket.org/caseywdunn/biolite
* Isitdown uses GNU Parallel: http://www.isi.edu/~calvin/isitdown.md
* Convert FLAC to MP3 with GNU parallel
http://www.blogobramje.nl/posts/Convert_FLAC_to_MP3_with_GNU_parallel/
* JD Edwards Business Function Documentation
http://www.azertech.net/content/jd-edwards-business-function-documentation
* Tools of the trade http://blog.eikeland.se/2014/05/01/tools-of-the-trade/
* How I start a bioinformatics project
http://nickloman.github.io/2014/05/14/how-i-start-a-bioinformatics-project/
* No:The-Me GNU Parallel http://adityalaghate.in/gnu-parallel.html
* Bug fixes and man page updates.
20140422
* --pipepart is a highly efficient alternative to --pipe if the input
is a real file and not a pipe.
* If using --cat or --fifo with --pipe the {} in the command will be
replaced with the name of a physical file and a fifo respectively
containing the block from --pipe. Useful for commands that cannot
read from standard input (stdin).
* --controlmaster has gotten an overhaul and is no longer
experimental.
* --env is now copied when determining CPUs on remote system. Useful
for copying $PATH if parallel is not in the normal path.
* --results now chops the argument if the argument is longer than the
allowed path length.
* Build now survives if pod2* are not installed.
* The git repository now contains tags of releases.
* GNU Parallel was cited in: Proactive System for Digital Forensic
Investigation
http://dspace.library.uvic.ca:8080/bitstream/handle/1828/5237/Alharbi_Soltan_PhD_2014.pdf
* GNU Parallel was cited in: Beyond MAP estimation with the
track-oriented multiple hypothesis tracker
http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=6766651&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6766651
* GNU Parallel was cited in: Prokka: rapid prokaryotic genome
annotation
http://bioinformatics.oxfordjournals.org/content/early/2014/03/18/bioinformatics.btu153.short
* GNU Parallel was used (unfortunately with improper citation) in:
Perspectives in magnetic resonance: NMR in the post-FFT era
http://www.sciencedirect.com/science/article/pii/S1090780713003054
* GNU Parallel is used in https://github.com/cc2qe/speedseq
* Batch XML validation at the command line.
http://horothesia.blogspot.dk/2014/04/batch-xml-validation-at-command-line.html
* freebayes-parallel uses GNU Parallel
https://github.com/ekg/freebayes/commit/31ee997984cebe8a196381c3de57e618e34a2281
* Org-mode with Parallel Babel http://draketo.de/english/emacs/parallel-babel#sec-2
* Speeding Up Grep Log Queries with GNU Parallel
http://www.cybersecurity.io/speeding-grep-queries-gnu-parallel/
* How to run tbss_2_reg in parallel
http://tadpolebrainimaging.blogspot.dk/2014/03/how-to-run-tbss2reg-in-parallel.html
* GNU parallel example: blastn https://asciinema.org/a/8775
* Iterative DNS Brute Forcing
http://www.room362.com/blog/2014/02/19/iterative-dns-brute-forcing/
* Ejecutando comandos en paralelo
http://jesusmercado.com/guias/ejecutando-comandos-en-paralelo/
* Ejecutando en paralelo en bash (ejemplo con rsync)
http://eithel-inside.blogspot.dk/2014/04/ejecutando-en-paralelo-en-bash-ejemplo.html
* Bug fixes and man page updates.
20140322
* Offical package for Alpine Linux now exists:
http://alpinelinux.org/apk/main/x86/parallel
* GNU Parallel was cited in: Estimating uncertainties in statistics
computed from direct numerical simulation
http://dx.doi.org/10.1063/1.4866813
* GNU Parallel was cited in: Vehicle routing problems with time
windows and multiple service workers: a systematic comparison
between ACO and GRASP
http://link.springer.com/article/10.1007/s10100-014-0341-z
* GNU Parallel, quick and easy
http://www.reganmian.net/blog/2014/03/09/gnu-parallel-quick-and-easy/
* Using Multiple CPU Cores With Command Line Tools
http://prateekvjoshi.com/2014/03/07/using-multiple-cpu-cores-with-command-line-tools/
* Batch convert mp3 CBR to VBR
http://blogs.zercle.com/bouroo/2013/03/batch-convert-mp3-cbr-to-vbr/
* Running Behat in parallel with Selenium grid
http://zalas.eu/running-behat-in-parallel-with-selenium-grid/
* Git-Mirror per cronjob aktuell halten
https://www.schtobia.de/2013/git-mirror-per-cronjob-aktuell-halten/
* Пишем многопоточный скрипт на bash
http://dafter.ru/duf/howto/130.html
* 如何利用多核CPU来加速你的Linux命令
http://www.chinadmd.com/file/xpcr6wpctzwtuu3ivwiaatcs_1.html
* Bug fixes and man page updates.
20140222
* --tollef has been retired.
* --compress has be redesigned due to bugs.
* Format of --eta and --joblog has changed slightly.
* GNU Parallel was cited in: Speaker Verification and Keyword Spotting
Systems for Forensic Applications
http://lantana.tenet.res.in/website_files/thesis/Phd/srikanth.pdf
* GNU Parallel was cited in: Scaleable Code Clone Detection
http://scg.unibe.ch/archive/phd/schwarz-phd.pdf
* GNU Parallel was cited in: Clone Detection that scales
http://scg.unibe.ch/archive/masters/Vogt14a.pdf
* GNU Parallel was cited in: Scalable Positional Analysis for Studying
Evolution of Nodes in Networks
http://arxiv-web3.library.cornell.edu/pdf/1402.3797
* GNU Parallel was cited in: Aggregate Characterization of User
Behavior in Twitter and Analysis of the Retweet Graph
http://arxiv.org/pdf/1402.2671v1
* GNU Parallel was used (unfortunately without citation) in: Causal
Network Models for Predicting Compound Targets and Driving Pathways
in Cancer
http://jbx.sagepub.com/content/early/2014/02/10/1087057114522690.full
* GNU Parallel was used (unfortunately without citation) in:
Performance and Energy Efficiency of Common Compression /
Decompression Utilities
http://www.researchgate.net/publication/243962643_Performance_and_Energy_Efficiency_of_Common_CompressionDecompression_Utilities_An_Experimental_Study_in_Mobile_and_Workstation_Computer_Platforms/file/3deec51d1dbc0474f9.pdf
* GNU Parallel was used (unfortunately without citation) in: SpringFS:
Bridging Agility and Performance in Elastic Distributed Storage
http://www.istc-cc.cmu.edu/publications/papers/2014/SpringFS-FAST14.pdf
* GNU Parallel was recommended (without citation) in: Redesigning the
Specificity of Protein-DNA Interactions with Rosetta
http://link.springer.com/protocol/10.1007/978-1-62703-968-0_17
* GNU Parallel is co-distributed with RepeatExplorer
http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
* Convert MP3 to a scrolling spectrum waterfall plot video
http://jdesbonnet.blogspot.dk/2014/02/convert-mp3-to-scrolling-spectrum.html
* PHP wrapper class for the GNU Parallel tool
https://github.com/geopal-solutions/gnu-parallel-wrapper/tree/master
* Exploratory Data Analysis http://www.slideshare.net/thinrhino/gnunify
* Copias de archivos con rsync y parallel
http://linuxmanr4.com/2014/02/20/copias-de-archivos-con-rsync-y-parallel
* Single-Thread-Programme auf Multicore-Rechnern parallelisieren
http://www.adlerweb.info/blog/2014/02/08/linux-single-thread-programme-auf-multicore-rechnern-parallelisieren
* Распараллеливаем процессы для ускорения вычислений и выполнения
заданий в Linux http://savepearlharbor.com/?p=210480
* Bug fixes and man page updates.
20140122
* GNU Parallel was cited in: On the likelihood of multiple bit upsets
in logic circuits
http://arxiv-web3.library.cornell.edu/pdf/1401.1003
* HaploClique uses GNU Parallel
https://github.com/armintoepfer/haploclique
* Scraping NSScreencast
https://blog.nicolai86.eu/posts/2014-01-12/scraping-nsscreencast/
* 30 Cool Open Source Software I Discovered in 2013
http://www.cyberciti.biz/open-source/30-cool-best-open-source-softwares-of-2013/
* [Unix] 13. The power of doing things in Parallel
http://leetaey.tistory.com/384
* Parallel the execution of a job that read from stdin
http://www.linuxask.com/questions/parallel-the-execution-of-a-job-that-read-from-stdin
* Mon Make à moi (6:38-11:50)
http://videos.rennes.inria.fr/ReNaBI-GO2013/indexPierreLindenbaum.html
* Shell-Abarbeitung beschleunigen: Wie Sie mit parallelen Prozesse
effizienter in der Shell arbeiten
https://www.hosteurope.ch/blog/shell-abarbeitung-beschleunigen-wie-sie-mit-parallelen-prozesse-effizienter-in-der-shell-arbeiten/
* Summary of GNU Parallel tutorial
http://hacktracking.blogspot.dk/2014/01/gnu-parallel-tutorial.html
* Bug fixes and man page updates.
20131222
* GNU Parallel now has a motto: For people who live life in the
parallel lane.
* Detect if the buffer dir $TMPDIR runs out of space. This changes a
central piece of code, making this release alpha quality.
* --keep-order --(n)onall will sort according to the sshlogin.
* Detect the number of CPUs on DEC Tru64.
* GNU sql: --list-tables for sqlite3.
* GNU Parallel was cited in: Variational Message-Passing: Extension to
Continuous Variables and Applications in Multi-Target Tracking
http://www.ics.uci.edu/~ajfrank/pubs/thesis.pdf
* GNU Parallel was cited in: Genome Assembly: Scaffolding Guided by
Related Genomes
https://www.duo.uio.no/handle/10852/37431
* GNU Parallel was cited in: Metagenomic analysis of Mariana Trench
sediment samples
http://repositorio.ul.pt/handle/10451/9436
* GNU Parallel was cited in: Diacritization, automatic segmentation
and labeling for Levantine Arabic speech
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6642556
* GNU Parallel was cited in: Investigation of emotion classification
using speech rhythm metrics
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6642591
* GNU Parallel was cited in: A Rhythm-Based Analysis of Arabic Native
and Non-Native Speaking Styles
http://www.ijsps.com/uploadfile/2013/1128/20131128014413279.pdf
* GNU Parallel was cited in: Evolutionary optimization of wetlands
design
http://dl.acm.org/citation.cfm?id=2480400
* GNU Parallel was cited (unfortunately with wrong citation) in:
RDBMS vs NoSQL: Performance and Scaling Comparison
http://www.epcc.ed.ac.uk/sites/default/files/Dissertations/2012-2013/RDBMS%20vs%20NoSQL%20-%20Performance%20and%20Scaling%20Comparison.pdf
* GNU Parallel was used (without proper citation) in: Comprehensive
Analysis Pipeline for Discovery of Human Genetic Variation
http://www.google.com/patents/US20130311106
* Encrypt and decrypt in parallel with GPG
http://blog.tkassembled.com/412/encrypt-and-decrypt-in-parallel-with-gpg/
* Using GNU Parallel to create a SVM classifier
http://ivanyu.me/blog/2013/12/01/parallel/
* Parallel xz compression
http://anthon.home.xs4all.nl/rants/2013/parallel_xz/
* Got CPUs to burn? Put 'em to work with GNU parallel
http://baoilleach.blogspot.dk/2013/11/got-cpus-to-burn-put-em-to-work-with.html
* Parallel rsync
http://pastebin.com/JmnB9ffq
* Gnu Parallel for fun and profit
https://gist.github.com/celoyd/f7eb55ad69c9b33fd8c3
* Parallelization of Exploitation
http://rantsideasstuff.com/parallelization-of-exploitation/
* Running assemblies in parallel
https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html
* Procesando la contabilidad del PP
http://www.neorazorx.com/2013/07/procesando-la-contabilidad-del-pp.html
* Mon make à moi (French)
http://www.slideshare.net/lindenb/mon-make-moi-tout-sauf-galaxy
* Bug fixes and man page updates.
20131122
* A citation notice is printed on stderr only if stderr is a terminal,
the user has not specified --no-notice and the user has not run
--bibtex once. This makes the release alpha quality.
* --compress will compress temporary files. If the output is big and
very compressible this will take up less disk space in $TMPDIR and
possibly be faster due to less disk I/O.
* --compress-program comtrols which program to use for compressing
temporary files.
* --bar show progress as a progress bar compatible with zenity.
* --resume can now be used with --result: Jobs already run will be
skipped.
* --transfer and --basefile support paths relative to the --workdir by
inserting /./ into the path.
* GNU Parallel was cited in: 'fastphylo: Fast tools for phylogenetics'
http://www.biomedcentral.com/1471-2105/14/334/abstract
* Using GNU parallel
http://davetang.org/muse/2013/11/18/using-gnu-parallel/
* Techlux - GNU - Parallel (German)
https://techlux.de/blog/2013/11/07/gnu-parallel/
* awk, sed, bzip2, grep, wc на всех ядрах
http://vk.com/page-30666517_45528467
* 如何利用多核CPU來加速你的Linux命令 — awk, sed, bzip2, grep, wc等
http://www.hksilicon.com/kb/articles/290543/CPULinuxawk-sed-bzip2-grep-wc
* GNU Parallel (Japanese)
http://jarp.does.notwork.org/diary/201311b.html#20131117
* Bug fixes and man page updates.
20131022
* --transfer files with /./ in the path will copy the files relative
to the --workdir.
* The maximal command length is now cached in a file halfing the
startup time.
* GNU Parallel was cited in: Investigating speaker gender using rhythm
metrics in Arabic dialects
http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6602389
* GNU Parallel was cited in: Tiedon erist ̈minen ja visualisointi a
lastensuojelun asiakaskertomuksista
https://tampub.uta.fi/handle/10024/84978
* Some Additional Useful Bioinformatics Software
http://nix-bio.blogspot.dk/2013/10/additional-software-for-bioinformatics.html
* GNU Parallel Example Screen Cast (bil to Geotiff conversion)
http://www.youtube.com/watch?v=PpF27eC7Mys
* Using GNU Parallel to roll-your-own Map Reduce!
http://www.rankfocus.com/hello-world/
* Use multiple CPU Cores with your Linux commands
http://www.rankfocus.com/use-cpu-cores-linux-commands/
* Using GNU Parallel at HPC @ Uni.lu
https://hpc.uni.lu/users/use_cases/
* Scaling up with parallelization
https://www.msi.umn.edu/sites/default/files/AdvPython_1.pdf
* How to teach yourself to be a technical tester
http://infiniteundo.com/post/62421363463/qa-toc
* Faster Rasters For All
http://2013.foss4g.org/conf/programme/presentations/52/
* Optimizing translated file downloads
http://www.smartling.com/blog/2013/05/20/optimizing-translated-file-downloads/
* EMC NetWorker parallel saveset cloning with nsrclone and GNU parallel
http://www.beebotech.com.au/2013/10/emc-networker-parallel-saveset-cloning-with-nsrclone-and-gnu-parallel/
* Best Practices for Amazon EMR
http://media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf
* Computing checksums for backup
https://identi.ca/evan/note/6yf1GzAARtyBhj__xzMvAg
* Un exemplu de utilizare a programului GNU parallel
http://vundicind.blogspot.dk/2013/10/exemplu-utilizare-gnu-parallel.html
* 平行化你的工作
http://www.slideshare.net/drakeguan/part1-23705978
* なんか気持ちよかです Gnu Parallel
http://a3-lab.jpn.org/note/%E3%81%AA%E3%82%93%E3%81%8B%E6%B0%97%E6%8C%81%E3%81%A1%E3%82%88%E3%81%8B%E3%81%A7%E3%81%99-gnu-parallel
* Bug fixes and man page updates.
20130922
* PDF-files of documentation is now included.
* Cloning at warp speed 100 VMs in 1 minute using one command line
http://www.beebotech.com.au/tag/command-line/
* Calcul Quebec's introduction to GNU Parallel
https://wiki.calculquebec.ca/w/GNU_parallel
* Brincando com o GNU parallel
http://blog.tadeucruz.com/2013/09/brincando-com-o-gnu-parallel/
* GNU Parallelで並列処理を行う
http://qiita.com/PENGUINANA_/items/af27a833e835fe17f09b
* Bug fixes and man page updates.
20130822
* A tutorial showing much of GNU Parallel's functionality. Spend an
hour walking through the tutorial. Your commandline will love you
for it. man parallel_tutorial
* --line-buffer will buffer output on line basis. --group keeps the
output together for a whole job. --ungroup allows output to mixup
with half a line coming from one job and half a line coming from
another job. --line-buffer fits between these two; it prints a full
line, but will allow for mixing lines of different jobs.
* --record-env records all variables and functions set. Useful to
record the normal environment before using --env _.
* --env _ exports all functions and variables to the remote server
except for the ones recorded.
* New signing key. Due to recommendations from NIST
http://www.keylength.com/en/4/ the signing key was changed from
1024D/ID:FFFFFFF1 to 9888R/ID:88888888.
* Agalma: an automated phylogenomics workflow
http://arxiv.org/pdf/1307.6432
* Job ad asking for GNU Parallel expertise
http://seattle.craigslist.org/est/sof/4006079352.html
* Transient Beowulf Clustering with GNU Parallel and SSHfs
http://www.reddit.com/r/linux/comments/1ka8mn/transient_beowulf_clustering_with_gnu_parallel/
* Aligning to unique regions
http://davetang.org/muse/2013/07/22/aligning-to-unique-regions/
* Top 10 scripting tricks for basic bioinformatics
http://students.washington.edu/bowmanjs/wordpress/?p=873
* Using GNU Parallel to speed up and simplify data analyzes
http://www.sergeymarkov.com/blog/2013/07/using-gnu-parallel-to-speed-up-and-simplify-data-analyzes/
* Compression of files in parallel using GNU parallel
http://codextechnicanum.blogspot.dk/2013/07/compression-of-files-in-parallel-using.html
* Using GNU Parallel to roll-your-own Map Reduce!
http://www.rankfocus.com/?p=1
* Using GNU Parallel with Amazon
media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf
* Some useful comments on GNU Parallel
https://news.ycombinator.com/item?id=6209767
* Using GNU Parallel to count reads mapping to genes for multiple BAMs
http://drduanehassane.com/blog/sequencing-resources
* TimeMachineっぽいバックアップスクリプト
http://rio.tc/2013/07/timemachine-1.html
* GNU ParallelでAndroid NDKの全バージョンを一括ダウンロード
http://qiita.com/mazgi/items/b10bf0ff3da2045d19ab
* Bug fixes and man page updates.
20130722
* --round-robin with --pipe will write all blocks to already running
jobs.
* --env can now transfer Bash function for remote execution. That is
pretty cool!
* GNU Parallel was used (unfortunately with improper citation) in:
Understanding the Impact of E-Commerce Software on the Adoption of Structured Data on the Web
http://link.springer.com/chapter/10.1007/978-3-642-38366-3_9#page-1
* GNU Parallel was used (unfortunately with improper citation) in:
CWI at TREC 2012, KBA track and Session Track
http://trec.nist.gov/pubs/trec21/papers/CWI.kba.session.final.pdf
* Mitigation of Adverse Effects Caused by Shock Wave Boundary Layer
Interactions through Optimal Wall Shaping.
http://arc.aiaa.org/doi/abs/10.2514/6.2013-2653
* Using GNU parallel to convert images.
http://www.brunokim.com.br/blog/?p=18
* A quick way to parallelize.
http://timotheepoisot.fr/2013/07/08/parallel/
* GNU Parallel 20130522 ('Rana Plaza') 发布，并行作业执行.
http://www.open-open.com/news/view/371301
* Quite a few bug fixes and man page updates.
20130622
* --xapply now recycles arguments if an input source has more
arguments than others.
* The sleep time between jobs is now both increased and decreased
exponentially.
* 10 seconds installation check the signature using GnuPG if GnuPG is
installed.
* Developer job asking for GNU Parallel expertise.
http://careers.stackoverflow.com/jobs/35562/developer-big-data-geo-and-web-climate-central
* A small utility program to run youtube-dl in parallel.
https://github.com/dlh/youtube-dl-parallel
* Parallelizing Freesurfer:
http://blog.cogneurostats.com/?p=148
* Bug fixes and man page updates.
20130522
* --ctrlc is now default if --pipe is not used; thus making it
possible to kill remotely started jobs simply by pressing Ctrl-C.
* --timeout 200% now means kill jobs that take more than twice the
time of the median run time of a job.
* Jobs are now distributed round robin when having mulitiple
--sshlogin instead of filling up one --sshlogin at a time.
* niceload: darwin version of --io --mem --swap. Thanks to Anders F
Björklund.
* Bug fixes and man page updates.
20130422
* 10 seconds installation: wget -O - pi.dk/3 | sh
* HPUX CPU/core detection. Thanks to Javier Tarradas.
* CPU detection for HURD, IRIX, SCO OpenServer and (old) HPUX.
* --ctrlc will send SIGINT to tasks running on remote computers and
thus killing them.
* --load now uses 'ps' to see immediately see the number of running
processes instead of 'uptime' thus making --load react much faster.
* Testing on Centos 3.9 and FreeBSD 7 revealed a lot of compability
bugs. Some of these required quite extensive changes making this
release beta quality.
* --retries works with --onall.
* The new --load computation now works on FreeBSD 7.
* --nice works under tcsh.
* GNU Parallel is officially supported in NetBSD.
http://ftp.netbsd.org/pub/pkgsrc/current/pkgsrc/parallel/parallel/README.html
* GNU Parallel is accepted for openSUSE.
http://software.opensuse.org/package/gnu_parallel
* GNU Parallel can be installed under Microsoft Windows (CygWin).
http://blogs.msdn.com/b/hpctrekker/archive/2013/03/30/preparing-and-uploading-datasets-for-hdinsight.aspx
* Excuses for not installing GNU Parallel.
http://oletange.blogspot.dk/2013/04/why-not-install-gnu-parallel.html
* Job advert that requires GNU Parallel competence.
http://versium.com/about/careers/
* Parallelizing Batch Jobs for Fun and Profit.
http://mikeseidle.com/tech/programming/2013/03/parallelizing-batch-jobs
* Processing Transcription Start Sites(TSS) for the entire Mouse genome.
http://qbrc.swmed.edu/2013/03/gnu-parallel-speeding-up-unix-commands-and-scripts/
* GNU parallel is used throughout Scrimer.
http://scrimer.readthedocs.org/en/latest/
* GNU Parallel helped making public documents searchable.
http://danpalmer.me/blog/articles/2013-04-06-unlocking-hillsborough.html
* Identifying big movie files (German).
http://blackappsolutions.wordpress.com/2013/03/23/wenn-der-plattenplatz-knapp-wird-filme-identifizieren-die-viel-platz-belegen/
* Bug fixes and man page updates.
20130222
* --resume works with --pipe.
* --resume-failed will go through --joblog, redo the failed jobs and
then continue like --resume.
* Negative positional arguments count from the end: {-1} means the
last argument, {-2} the second to last.
* NetBSD CPU detection.
* --blocksize increases exponentially if it smaller than a full
record.
* Processing n-line records (--pipe -L n) is now much faster.
* --tollef is obsoleted after discussion on the mailing list.
* GNU Parallel is the highest rated tool on:
http://www.biostars.org/show/tools/?sort=votes&since=all%20time
* GNU Parallel was loved during FSFE's #ilovefs campaign.
http://fsfe.org/news/2013/news-20130212-01.en.html
* Using GNU Parallel with s3cmd (Japanese).
http://blog.suz-lab.com/2013/02/s3cmd-gnu-paralells3.html
* Intro to GNU Parallel (Chinese).
http://guiquanz.github.com/2013/02/12/gnu-parallel-intro/
* Bug fixes and man page updates.
20130122
* --sshdelay Delay starting next ssh by secs seconds. GNU parallel
will pause secs seconds after starting each ssh. secs can be less
than 1 seconds.
* Official OpenBSD port:
http://ftp.openbsd.org/ports/sysutils/parallel/
* Official DragonFlyBSD package:
http://www.mirrorservice.org/sites/ftp.dragonflybsd.org/packages/amd64/DragonFly-3.0.0/stable/parallel/
* Post about niceload in Hungarian:
http://commandline.blog.hu/2013/01/02/niceload
* 自炊スキャンデータをKobo Gloに最適化
http://interstadial.wordpress.com/2013/01/20/
* GNU parallel+ssh で複数のリモートホストに複数のコマンドを実行させる
http://oshiire.to/archives/1686
* Bug fixes and man page updates.
20121222
* --shebang-wrap makes is possible to parallelize scripts by putting
parallel in the shebang line (the first #! line in scripts).
* --delay puts in a delay after starting each job. Useful to avoid
raceconditions and thundering herd problems.
* --results now uses / as separator instead of TAB and thus creates
subdirs. Thanks to Drew Frank.
* parallel: OpenBSD CPU detection. Thanks to Michał Markowski.
* niceload --sensor allows for negative numbers to signify a lower
number means the limit is lower.
* niceload --prg suspend a named program that is already running.
* niceload multiple --pid suspend process ids that are already running.
* Convertir des images avec find et imagemagick
http://roger.b.over-blog.com/article-convertir-des-images-avec-find-et-imagemagick-113416637.html
* Bug fixes and man page updates.
20121122
* niceload --sensor makes it possible to use a program to control if a
program should be suspended.
* GNU Parallel was part of the justification for Nordic Free Software
Award 2012
https://fsfe.org/news/2012/news-20121112-01.html
* Dateien schneller packen und konvertieren mit GNU parallel
http://www.linux-community.de/Archiv/Tipp-der-Woche/Dateien-schneller-packen-und-konvertieren-mit-GNU-parallel
* Processing images from Lunar Reconnaissance Orbiter Narrow Angle
Camera http://lunokhod.org/?p=774
* GNU Parallel is used in types2: Type and Hapax Accumulation Curves
http://www.cs.helsinki.fi/u/josuomel/types2/
* GNU Parallel used in: A Hybrid Factor Analysis and Probabilistic
PCA-based system for Dictionary Learning and Encoding for Robust
Speaker Recognition
http://www.superlectures.com/odyssey2012/lecture.php?id=8&lang=en
http://www.cse.iitm.ac.in/~mrsri/ppca.pdf
* Mapreduce avec parallel, cat et une redirection
http://datacratic.com/site/blog/mapreduce-avec-parallel-cat-et-une-redirection
* GNU Parallel for Large Batches of Small Jobs
https://support.scinet.utoronto.ca/wiki/images/7/7b/Tech-talk-gnu-parallel.pdf
* GNU Parallel used in black belt tip (8:50-10:12)
https://aws.amazon.com/apac/awspodcast/episode20/
* Bug fixes and man page updates.
20121022
* --results structures output files so they can be imported using
Pandas (http://pandas.pydata.org/). Useful when doing simulations to
select output from some arguments.
* Use --env to transfer environment variables through ssh to remote
machines.
* GNU Parallel is accepted for Ubuntu Quantal.
http://packages.ubuntu.com/quantal/parallel
* GNU Parallel was requested for OpenSUSE (go vote!)
https://features.opensuse.org/314461
* Kneth's Korner: Map/Reduce and GNU Parallel
http://kenneth.geisshirt.dk/2012/10/mapreduce-and-gnu-parallel.html
* Blog post in Japanese by Siguniang.
https://siguniang.wordpress.com/2012/09/09/notes-on-gnu-parallel-the-command-line-power-tool/
(Siguniang mentions the logo is called 'The Cafe Wall Illusion')
http://www.michaelbach.de/ot/ang_cafewall/index.html
* GNU Parallel, where have you been all my life?
http://ssdigit.nothingisreal.com/2012/09/gnu-parallel-where-have-you-been-all-my.html
* Reference-free ddRADseq analysis tools uses GNU Parallel.
https://github.com/brantp/rtd#readme
* When bash just isn’t quick enough.
https://soimasysadmin.wordpress.com/2012/08/15/gnu-parallel-when-bash-just-isnt-quick-enough/
* Using GNU Parallel to Package Multiple Jobs in a Single PBS Job.
http://www.nas.nasa.gov/hecc/support/kb/Using-GNU-Parallel-to-Package-Multiple-Jobs-in-a-Single-PBS-Job_303.html
* GNU Parallel Notes.
http://xed.ch/help/parallel.html
* Bug fixes and man page updates.
20120822
* Due to a bugfix the main flow has changed. Making this release beta
quality.
* Parallel Proxy Scraper & Checker Tool
https://www.youtube.com/watch?v=iXCeR_XsP6o
* Bug fixes and man page updates.
20120722
* GNU Parallel was presented at Chiang Mai Bar Camp
http://barcampchiangmai.org/
See write up here:
http://www.cnx-software.com/2012/07/02/use-gnu-parallel-to-speed-up-script-execution-on-multiple-cores-andor-machines/
* I don't always max out all my CPUs, but when I do, I do it with GNU
Parallel.
http://memegenerator.net/instance/22638454
* Bug fixes and man page updates.
20120622
* '-L n --pipe' will use records of n lines. This is useful when
processing data that have fixed records with a fixed number of
lines (e.g. fastq).
* --filter-hosts will remove down hosts. For each remote host: check
that login through ssh works. If not: do not use this host.
Currently you can not put --filter-hosts in a profile, $PARALLEL,
/etc/parallel/config or similar. This is because GNU Parallel uses
GNU Parallel to compute this, so you will get an infinite loop. This
will likely be fixed in a later release.
* --pipe now uses fork() instead of busy wait. The performance should
be better on computers with >10 cores while remaining the same on
computers with few cores.
* GNU Parallel will be represented at Chiang Mai Bar Camp.
http://barcampchiangmai.org/
* Indexing Big Data on Amazon AWS: The Screencast
(Check out his T-shirt at 18:40-21:00).
http://www.opensourceconnections.com/2012/06/06/indexing-big-data-on-amazon-aws-screencast/
* biotoolbox uses GNU Parallel.
https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper
* Spiceweasel uses GNU Parallel.
https://github.com/mattray/spiceweasel
* GNU Parallel part of The Administrators Challenge.
http://challenge.twistedrack.com/questions/qs3.php
* Finding Oldest Firefox Code using GNU Parallel.
http://gregoryszorc.com/blog/2012/06/18/finding-oldest-firefox-code/
* Bug fixes (quite a few for remote job running) and man page updates.
20120522
* Timings in --joblog now with milliseconds.
* Thesis using GNU Parallel (correctly cited; hooray!).
http://scholarworks.sjsu.edu/etd_projects/222/
* Package for AIX.
http://www.perzl.org/aix/index.php?n=Main.Parallel
* Prokka uses GNU Parallel.
http://bioinformatics.net.au/prokka-manual.html
* GNU Parallel was presented at MUUG.
http://muug.mb.ca/blog/meetings/2012/05/09/may-8th-2012-rtfm-gnu-parallel1/
* Blog post: Manipulating many or large files with GNU parallel.
http://compbiously.blogspot.com/2012/05/manipulating-many-or-large-files-with.html
* Blog post: Running commands in parallel using bash.
http://blog.michaelboman.org/2012/04/running-commands-in-parallel-using-bash.html
* Blog post: Efficient log processing.
http://www.francoismaillet.com/blog/?p=399
* Blog post about GNU Parallel and Amazon EC2.
http://blog.kevinformatics.com/post/4970574713/interested-in-your-experience-using-gnu-parallel-in
* Blog post in Hungarian.
http://commandline.blog.hu/2012/05/03/gnu_parallel
* Popularity of GNU Parallel in Debian explodes.
http://qa.debian.org/popcon-graph.php?packages=parallel
* Bug fixes and man page updates.
20120422
* A race condition bug caused restructuring of a central piece of the
code. Thus this release of GNU Parallel should be considered beta
quality.
* sql --dbsize will now list sizes of all databases if given no
database.
* GNU Parallel is now in Debian Unstable.
apt-get install parallel
* Article: Computational and experimental analyses of
retrotransposon-associated minisatellite DNAs in the soybean genome.
http://www.biomedcentral.com/content/supplementary/1471-2105-13-s2-s13-s1.pdf
* Blog post: GNU parallel - the best thing since sliced bread.
https://arrayal.wordpress.com/2012/03/27/gnu-parallel-the-best-thing-since-sliced-bread/
* Blog post: GNU Parallel makes everything faster.
http://compbiously.blogspot.com/2012/03/gnu-parallel-makes-everything-faster.html
* Blog post (German): Howto: GNU parallel.
http://d24m.de/2012/04/05/howto-gnu-parallel/
* Blog post: Running in Parallel
http://interactivity.ifactory.com/2012/04/running-in-parallel/
* 20000 watched the first intro video.
http://pi.dk/1
* The first 5 have received their GNU Parallel merchandise
https://www.gnu.org/software/parallel/merchandise.html
* Bug fixes and man page updates.
20120322
* Parallel Process Database Dumps.
http://blog.mattoates.co.uk/2012/02/parallel-process-database-dumps.html
* Using GNU Parallel to process images from Mars.
http://lunokhod.org/?p=468
* Using GNU Parallel with bzgrep.
http://filip.rembialkowski.net/did-you-know-gnu-parallel/
* Bug fixes and man page updates.
20120222
* --workdir . will use the current working dir. If the current working
dir is beneath your home dir, the value . is treated as the relative
path to your home dir. This means that if your home dir is different
on remote computers (e.g. if your login is different) the relative
path will still be relative to your home dir.
* A texinfo file is now generated from the POD file using pod2texi.
* The bioinformatics article "Fast large-scale clustering of protein
structures using Gauss integrals" mentions GNU Parallel. They forgot
to add the reference. Please remember --bibtex if you use GNU
Parallel in an article.
http://bioinformatics.oxfordjournals.org/content/28/4/510.short
* The first supporter received his merchandise. Did you order yours?
https://www.gnu.org/software/parallel/merchandise.html
* How to use GNU Parallel with samtools.
http://zvfak.blogspot.com/2012/02/samtools-in-parallel.html
* How to use GNU Parallel for vacuuming PostgreSQL tables.
http://blog.timmattison.com/archives/2012/01/24/mini-hack-parallel-vacuuming-in-postgresql/
* Converting e-books with Calibre and GNU Parallel.
http://www.linkhal.de/blog/2012/01/converting-massive-e-book-collections-with-calibre-and-gnu-parrallel/
* Using GNU Parallel for tailing logfiles from multiple servers.
http://silviud.blogspot.com/2012/02/shell-parallel-processing.html
* Bug fixes and man page updates.
20120122
* --header : uses the first input line as column names and you can
then use {colname} as a replacement string in the command. This also
works with multiple :::'s.
* --header <regexp> matches a header as a regular expression and
repeats the header for each block with --pipe.
* --resume resumes from the last unfinished job. Useful if you stop
GNU Parallel and restart it later with the same arguments.
* niceload now propagates exit status correctly.
* Show your support for GNU Parallel. For a limited time you can get a
GNU Parallel T-shirt+mug+pen+100 postcards at 20 EUR. See
https://www.gnu.org/software/parallel/merchandise.html
* Options -g -B -T -U -W -Y are retired as warned 6 months ago.
* GNU Parallel referenced in article on Holographic Grid Cloud. Thanks
to Stefano Gallozzi. http://arxiv.org/pdf/1112.6128
* Article in IEEE Software on GNU Parallel. Thanks to Diomidis
Spinellis. http://www.spinellis.gr/blog/20110911/
* An article on Narwhal which uses GNU Parallel. They forgot to add
the reference. Please remember --bibtex if you use GNU Parallel in
an article.
http://bioinformatics.oxfordjournals.org/content/early/2011/11/08/bioinformatics.btr613.full.pdf
* Blog post on using GNU Parallel to speed up BLAST queries:
http://blog.mckuhn.de/2012/01/embarrassingly-parallel-blast-search.html
* Video showing Wake-on-LAN with GNU Parallel.
https://www.youtube.com/watch?v=0mB-yIyKFLQ
* Using GNU Parallel with Solr.
http://sujitpal.blogspot.com/2011/12/solr-report-generation-with-python.html
* First job ad including GNU Parallel:
http://seeker.dice.com/jobsearch/servlet/JobSearch?op=101&dockey=xml/7/6/76f858de083a094f74b1a5d3ba53ffc5@endecaindex
* Bug fixes and man page updates.
20111222
* --timeout will now kill grandchildren.
* Interview in Hacker Public Radio.
http://hackerpublicradio.org/eps.php?id=0860
* Blog post in Chinese.
http://blog.sina.com.cn/s/blog_3f7652740100y0ju.html
* Bug fixes and man page updates.
20111122
* GNU Parallel package for Fedora.
https://admin.fedoraproject.org/pkgdb/acls/name/parallel
* Using GNU Parallel with Mozilla cross referencing.
https://blog.mozilla.com/it/2011/11/15/mxr-improvements/
* Neat flash presentation of GNU Parallel.
http://prezi.com/0nq74b2elgtx/about-gnu-parallel/
* How to create tar files of dirs in parallel.
https://joneslee85.wordpress.com/2011/11/22/shell-tips-how-to-recursively-archive-many-folders/
* Article in Admin Network&Security by Ben Martin.
http://www.admin-magazine.com/HPC/Articles/GNU-Parallel
* Blog post in Polish.
http://blog.tiger.com.pl/2011/01/05/gnu-parallel/
* Blog post on using GNU Parallel of Mac OS X.
http://www.0xcb0.com/2011/10/19/running-parallel-bash-tasks-on-os-x/
* Blog post in English about using zip with GNU Parallel.
http://nuclear-imaging.info/site_content/2011/05/11/gnu-parallel/
* Blog post in English by researcher.
http://zandyware.wordpress.com/2011/10/15/gnu-parallell-make-best-use-of-your-multicore-computer/
* Blog entry in Chinese.
http://blog.csdn.net/tossense/article/details/6889026
* Blog entry in Japanese on managing many servers.
http://hiroakis.com/blog/2011/11/13/gnu-parallel/
* GNU Parallel is now part of ppbs.
http://physiology.med.cornell.edu/faculty/mason/lab/ppbs/introduction/introduction.html
* How to use GNU Parallel with MCX.
http://mcx.sourceforge.net/cgi-bin/index.cgi?MMC/Doc/MMCCluster
* Bug fixes and man page updates.
20111022
* --tag prepends lines with the argument(s). If used with --(n)onall
the line will be prepended with the sshlogin instead.
* --shellquote does not run the command but quotes it using \'s.
Useful for making quoted composed commands.
* --profile can now be repeated merging multiple profiles.
* --bibtex now gives the BibTeX entry.
Thanks to Aleksandr Levchuk for testing.
* Makefile for simple .deb package.
cd packager/debian; make
* sql: --list-databases lists the databases.
* GNU Parallel officially in Fedora 16
http://www.spinics.net/lists/fedora-package-announce/msg67130.html
* Blog post on recompression FLAC audio.
http://blog.oxplot.com/2011/08/reflac-flac-cleanser.html
* The most complex use of ::: I have seen so far.
http://agentzlerich.blogspot.com/2011/09/following-up-on-previous-failures-ive.html
* Example of using GNU Parallel with sudo.
http://loopkid.net/articles/2011/10/07/recursive-chmod-and-chown-on-files
* Use wget and gnu parallel to download mp3s at rocket speed.
http://sdbrain.posterous.com/use-wget-and-gnu-parallel-to-download-mp3s-at
* First CV referring to GNU Parallel.
http://www.peopleperhour.com/freelancers/stephen_/internet_researcher_and_protocol_develop/140602
* Cartwright labs usage of GNU Parallel.
http://cartwrightlab.wikispaces.com/The+Most+Bang+for+Your+Buck
* Bug fixes and man page updates.
20110822
* --timeout implemented so that slow commands can be killed
* CPU detection improved for Mac OSX. Thanks to Wayne E. Seguin.
* Example of a parallel webcrawler in the man page.
* Backup up PostgreSQL with GNU Parallel. Thanks to Stephane Wirtel.
http://wirtel.be/2011/07/15/rsync_parallel/
* Blog post in Japanese.
http://dminor11th.blogspot.com/2011/08/gnu-parallel.html
* Blog post about optimizing JPEGs. Thanks to Thomas Jost.
http://schnouki.net/2011/07/22/optimizing-jpeg-pictures/
* Bug fixes and man page updates.
20110722
* niceload: --hard will suspend a program if a limit is reached - as
opposed to just slowing the program down.
* niceload: --soft will slow the program down - as opposed to
suspending the program completely.
* niceload: --run-io will slow down a program if disk io goes above a
certain limit.
* niceload: --run-load will slow down a program if loadaverage goes
above a certain limit.
* niceload: --run-mem will slow down a program if free memory goes
below a certain limit.
* niceload: --run-noswap will slow down a program if the computer is
swapping.
* niceload: --start-io, --start-load, --start-mem, --start-noswap will
defer starting a program until the system is below the limit.
* --io, --load, --mem, and --noswap sets both --run-* and --start-*.
* niceload got a major rewrite and is now object oriented.
* GNU Parallel was presented at Nordic Perl Workshop 2011.
http://conferences.yapceurope.org/npw2011/talk/3416
* Blog post about zcat and GNU Parallel. Thanks to Dr. John.
http://drjohnstechtalk.com/blog/2011/06/gnu-parallel-really-helps-with-zcat/
* 2 blog posts in Japanese. Thanks to Negima.
http://d.hatena.ne.jp/negima1976/20110607/1307412660
http://d.hatena.ne.jp/negima1976/20110628/1309252494
* Blog post for bioinformatics. Thanks to Chris Miller.
http://chrisamiller.com/science/2010/05/26/use-parallel-for-easy-multi-processor-execution/
* Bug fixes and man page updates.
20110622
* --onall will run all the jobs on all the computers. This is useful
for systemadinistrators having multiple servers.
* --nonall runs like --onall but reads no arguments from stdin
(standard input), so is possible to do:
parallel --nonall -S computer1,computer2 uptime
* Context replace now works with multiple input sources:
parallel -X echo {1}-{2} ::: 1 2 3 ::: a b c
* --noswap do not start a job on a server that is swapping.
* Article: Parallel processing without Hadoop!
http://www.solutionhacker.com/parallel-processing-without-hadoop/
* Article in Linux Magazine (Spanish). Thanks to Ben Martin.
http://www.linux-magazine.es/issue/67/
* First blog post in Korean. Thanks to 민병국.
http://blog.daum.net/_blog/BlogTypeView.do?blogid=02RQ3&articleno=13380895&admin=#
* Blog post in Japanese. Thanks to Naoya Nakazawa.
http://www.sssg.org/blogs/naoya/archives/2003
* Blog post in English. Thanks to Dagon.
http://hekate.homeip.net/2011/05/29/
* Bug fixes and man page updates.
20110522
* Multiple ::: can be put on the command line and will be treated
similar to contents from multiple -a's.
* ::: and :::: can now be mixed on the command line. Use {1} .. {n} to
refer to inputs from the different input sources.
* --xapply is now needed to get xapply's behaviour of reading one line
from each of the input sources.
* Multiple input sources will cause all combinations of arguments from
the sources to be generated. E.g. 'parallel echo {1}+{2} ::: 1 2 :::
a b c' will print 1+a 1+b 1+c 2+a 2+b 2+c. This can often replace
nested loops.
* Implemented {//} for the input line with the basename removed (dirname).
* New video showing the new ::: and :::: input sources.
http://tinyogg.com/watch/iOdhU/ http://www.youtube.com/watch?v=fOX1EyHkQwc
* GNU Parallel now has a logo.
http://www.gnu.org/software/parallel/logo.png
* Article about GNU SQL in USENIX Magazine ;login: (print)
http://www.usenix.org/publications/login/2011-04/
* Using GNU Parallel with EC2. Thanks to Kevin Wu.
http://blog.kevinformatics.com/post/4970574713/interested-in-your-experience-using-gnu-parallel-in
* Review with idea for {..} and {...} in Japanese. Thanks to ichii386.
http://d.hatena.ne.jp/ichii386/20110426
* Upgrade GNU Parallel using Macports. Thanks to Phil Hollenback.
http://www.hollenback.net/index.php/MacportsParallel
* Robert from Echo One discusses using processes instead of threads:
http://rrees.wordpress.com/2011/04/25/many-cores-many-threads/
* How to run GNU Parallel on a SLURM cluster. Thanks to Kevin Stock.
http://www.kevinstock.org/2011/04/using-the-ri-cluster/
* Short article about using GNU Parallel with lame:
http://loopkid.net/articles/2011/04/30/accelerate-lame-mp3-conversion
* Using GNU Parallel to run tail -f in Japanese. Thanks to Clouder.
http://blog.clouder.jp/archives/001140.html
* BBC Research & Development uses GNU Parallel:
http://www.bbc.co.uk/blogs/researchanddevelopment/2010/11/prototyping-weeknotes-41-26112.shtml
* Short article about using GNU Parallel on RHEL. Thanks to Rishi Deshpande.
http://nuclear-imaging.info/site_content/2011/05/11/gnu-parallel/
* Using GNU Parallel for FLAC->MP3 conversion. Thanks to Derek Marcotte.
http://derek.chezmarcotte.ca/?p=286
* Bug fixes and man page updates.
20110422
* {#} now works as an alias for $PARALLEL_PID.
* --eta now estimates way more accurately.
* CPU detection code for AIX thanks to Christian Netrwal.
* --joblog contains exitcode.
* Thanks to Ævar Arnfjörð Bjarmason for reading my code.
* GNU Parallel was presented at:
- LUGA, Augsburg, 2011-03-26, http://www.luga.de/Aktionen/LIT-2011/Programm
- OSAA.dk, Aarhus, 2011-04-12
* Blog entry in Japanese. Thanks to Riywo.
http://blog.riywo.com/2011/04/19/022802
* Example of how to use GNU Parallel on PBS clusters. Thanks to Andrew
J Dolgert: http://web0.tc.cornell.edu/wiki/index.php?title=Gnu_Parallel
* First example of using GNU Parallel in Hebrew. Thanks to omry.
http://nd.gd/jk
* Intro video got past 10000 hits.
http://www.youtube.com/watch?v=OpaiGYxkSuQ
* Bug fixes and man page updates.
20110322
* --tollef to be switch compatible with Tollef's parallel. This will
cause -l to mean --load, and the argument separator will be --
instead of :::
* --gnu will force GNU Parallel to behave like GNU Parallel even if
--tollef is set.
* Site wide config file: /etc/parallel/config
This should solve the issue with some packagers renaming GNU
Parallel to gparallel to avoid the naming conflict.
By putting --tollef in the site wide config file you can deinstall
Tollef's parallel and install GNU Parallel instead without any
change for users or scripts. This is useful for packagers that
currently rename GNU Parallel or simply do not distribute GNU
Parallel because the command name conflicts with Tollef's parallel.
* -L 0 -n 0, and -N 0 implemented. They will read one argument,
but insert 0 arguments on the command line. Useful if you just want
to run the same command with the same arguments a number of times.
* GNU Parallel is now in Fink. Thanks to Jesse Alama.
http://pdb.finkproject.org/pdb/package.php/parallel
* Opscode Cookbook for Chef. Thanks to Joshua Timberman.
https://github.com/opscode/cookbooks/tree/master/gnu_parallel
* Man page examples translated into Japanese. Thanks to Koshigoe.
http://w.koshigoe.jp/study/?%5Bsystem%5D+GNU+parallel+%BB%C8%CD%D1%CE%E3#l13
* GNU Parallel will be presented at:
- LUGA, Augsburg, 2011-03-26, http://www.luga.de/Aktionen/LIT-2011/Programm
- OSAA.dk, Aarhus, 2011-04-12
* Video of presentation from FSCONS 2010-11-07. The presenter was
_really_ hoarse that day (Something to do with loads of alcohol the
night before). http://vimeo.com/20838834
* Review with examples in German. Thanks to M. Nieberg.
http://kenntwas.de/2011/linux/gnu-parallel/
* A review of the --pipe option in German. Thanks to Mathias Huber.
http://www.linux-magazin.de/NEWS/GNU-Parallel-20110205-stueckelt-Daten
* A small example of grepping maillogs. Thanks to François Maillet.
http://www.francoismaillet.com/blog/?p=399
* Using GNU Parallel instead of xargs. Thanks to James Cuff.
http://blog.jcuff.net/2011/02/on-train-ride-in.html
* Using GNU Parallel from 0install (German). Thanks to AdaMin.
http://forum.ubuntuusers.de/topic/gnu-parallel-mit-zero-install-kurzinfo-kein-wi/
* Bug fixes and man page updates.
20110205
* --pipe splits piped data into blocks. Each block is piped to a
program for processing. The piping and the programs will be run in
parallel. Useful if the data you want to process is data for a
program and not arguments.
* --blocksize sets the blocksize in bytes for --pipe. The blocksize is
approximate. It can deviate as much as the size of one record.
Default is 1M.
* --recstart sets the string matching the start of a
record. Default is "".
* --recend sets the string matching the end of a
record. Default is '\n'. To specify none use --recend "".
If both --recstart and --recend are set, the end of a record must be
followed immediately by a start of a record. This is useful if
either recend or recstart can occur in the middle of a record.
* --remove-rec-sep removes the string matched by --recstart and
--recend.
* --regexp will make GNU Parallel treat --recstart and --recend as
regular expressions.
* --output-as-files will put the output of the programs into files and
instead of giving the output GNU Parallel will output the name of
these files.
* -N if used with --pipe sets the number of records to read.
* New video showing --pipe at
http://www.youtube.com/watch?v=1ntxT-47VPA
* GNU Parallel was presented at FOSDEM.
* Article in USENIX Magazine ;login: (print)
http://www.usenix.org/publications/login/2011-02/
* GNU Parallel is now on ohloh.net. Thanks to Wim Muskee.
https://www.ohloh.net/p/gnu-parallel
* Advanced recursive example. Thanks to Ruarí Ødegaard.
http://my.opera.com/ruario/blog/2011/01/24/editing-debian-packages-more-fun-with-gnu
* Small example on using GNU Parallel through 0install (German).
http://forum.ubuntuusers.de/topic/gnu-parallel-mit-zero-install-kurzinfo-kein-wi/
* Bug fixes and man page updates.
20110122
* --joblog makes a simple log of completed jobs.
* -X now spreads arguments between job slots when reaching last
argument. Use -j1 to avoid this.
* People on the email list have voted -j+0 to be the new default
instead of -j9.
* First review in Polish. Thanks to Patryk Krawaczyński.
http://nfsec.pl/root/2458
* Review in Spanish (in print).
https://www.linux-magazine.es/issue/67/moreinfo.html
* Review in English. Thanks to Brian Gough.
http://blogs.fsfe.org/bjg/2011/01/gnu-parallel-a-map-operator-for-the-command-line/
* Review in French. Thanks to Denis Dordoigne.
http://linuxfr.org/2010/12/29/27715.html
* Review in Spanish.
http://gufete.net/index.php?entry=entry110116-200022
* Article with advanced recursive example. Thanks to Ruarí Ødegaard
http://my.opera.com/ruario/blog/2011/01/18/fun-with-gnu-parallel
* Use case for memcache.
http://www.dctrwatson.com/2010/12/how-to-dump-memcache-keyvalue-pairs-fast/
* Bug fixes and man page updates.
20101222
* GNU niceload is now part of GNU Parallel. GNU niceload slows down a
program if the load average is above a certain limit.
* Implemented --tmpdir to buffer standard output and standard error in
a different place.
* Implemented --load to wait until the load is below a limit before
starting another job on that computer.
* Implemented --nice set the niceness of jobs running both locally and
remotely.
* Implemented --dry-run to print the job without running it.
* Implemented --tty as the old default of assigning a tty to the first
job causes problems.
* Review with focus on clusters. Thanks to Taylor Gillespie
http://www.unixpronews.com/unixpronews-49-20101019GNUParallelSpeedUpProcessingWithMulticoresClusters.html
* Review with focus on protein similarity.
http://kevinformatics.tumblr.com/post/2142473893/cluster-like-computing-using-gnu-parallel
* Review in Spanish.
http://gr3p.com/2010/12/gnu-parallel-acelera-tus-scripts-en-linux
* Quite a few bug fixes and man page updates.
20101202
* Implemented {/} for the input line with the path removed (basename).
* Implemented {/.} for the input line with extension and path removed
(basename).
* Output from --progress is now sent to standard error instead of
standard output.
* --eta was broken and counted down from 0. Now fixed.
* Standard output and standard error are flushed after every job so if
standard output does not end with a newline it will still be grouped
with the rest of standard output.
* --command, -c, --file, and -f are now removed as options. They were
never used in practice.
* GetOptionsFromArray rewritten to work with old Perl libraries.
* The file COPYING now contains the GNU General Public License 3
* Major rewrite to make the code more object oriented and easier to
maintain in the future.
20101113
* Using -j myfile the number of jobs can be changed while GNU Parallel
is running simply by changing the content of myfile.
* Implemented --profile to use different .parallel/config for
different situations.
* Ugly newlines in $PARALLEL and .parallel/config are no longer
needed. Instead you have to use \ in front of special shell
characters.
* --workdir puts the files transferred to remote machines in a
specified directory.
* $PARALLEL_PID is set to the process id of GNU Parallel.
* $PARALLEL_SEQ is set to the sequence number of the job.
* -v now only shows the command to run. Use -v -v to show the
ssh/rsync wrapping.
* Slow spawning error is now only a warning.
* If stdin is a tty and input is read from stdin you now get a
warning.
* GNU sql: \n and \x0a in arguments is replaced with newline.
* Patch for Debian package and spelling mistakes. Thanks to Rogério
Brito <rbrito at ime dot usp dot br>
* Mac OS X Homebrew package. Thanks to Jonathan Palardy <jonathan dot
palardy at gmail dot com>
* FreeBSD port. Thanks to Chris Howey <howeyc at gmail dot com>
* Pardus package. Thanks to Fethican Coşkuner
<fethicanc at gmail dot com>
* First review in Chinese. Thanks to 曾義峰:
http://antbsd.twbbs.org/~ant/wordpress/?p=2876
* First review in print:
http://www.linux-magazine.com/Issues/2010 Nov 2010
* First review in Spanish:
http://www.muylinux.com/2010/10/18/gnu-parallel-computacion-paralela-a-golpe-de-comando
* First review in Dutch thanks to Koen Vervloesem <koen at vervloesem
dot eu>:
http://techworld.nl/technologie/33493/gebruik-al-je-processorkernen-met-gnu-parallel.html
* Blog review thanks to R. Tyler Croy <tyler at monkeypox dot org>:
http://unethicalblogger.com/posts/2010/11/gnuparallel_changed_my_life
* 5000 views of the intro video:
http://www.youtube.com/watch?v=OpaiGYxkSuQ
* As usual a bunch of bugfixes and more usage examples in the man
page.
* GNU Parallel was presented at FSCONS 2010-11-07:
http://www.fscons.org/fs/gnu-parallel Hopefully the
video will be online soon.
20100922
* See GNU Parallel live at FSCONS 2010-11-07:
http://www.fscons.org/fs/gnu-parallel
* Untested Debian and xUbuntu packages available through OpenSUSE
build service:
https://build.opensuse.org/package/show?package=parallel&project=home%3Atange
* Using --retries a job will be retried on another computer if it
fails. This is useful if some jobs fail for no apparent reason (such
as network failure).
* BSD xargs -o (open /dev/tty) is now default for the job running in
foreground. Useful for interactive commands like:
ls | parallel -Xuj1 vi
* GNU sql now supports SQLite.
* Renamed .dburl.aliases to .sql/aliases and /etc/sql/aliases.
* GNU sql now support --list-tables
* Alias for DBURL can contain '?query' part with %-quoting.
20100906
* Using --shebang GNU Parallel can be used as the parser for a script.
E.g: #!/usr/bin/parallel --shebang traceroute (followed by lines of
hosts)
* First community generated bugfixes
* Alt Linux package of GNU Parallel. Thanks to Michael Shigorin <mike
at altlinux dot org>
* Sunfreeware package of GNU Parallel. Thanks to Steven M. Christensen
<sunfreeware at gmail.com>
* Untested CentOS, Fedora, Mandriva, RedHat, and SUSE packages
available through OpenSUSE build service:
https://build.opensuse.org/package/show?package=parallel&project=home%3Atange
* Review of GNU Parallel. Thanks to Andrew McFague amcfague at wgen dot net
http://www.andrew-mcfague.com/linux/utilities-linux/
commands-every-serious-nix-user-should-know/#parallel
* First 1000 views of the intro video
* sql - a small script to access sql bases from the command line which
is a handy companion to parallel --colsep
20100822
* Counting semaphore functionality: start a job in the background. If
N jobs are already running, wait for one to complete. Examples:
sem 'sleep 2; echo foo'; sem 'sleep 1; echo bar'; sem --wait
sem -j2 'sleep 2; echo foo'; sem -j2 'sleep 1; echo bar'; sem --wait
* With --colsep a table can be used as input. Example:
cat tab_sep_table | parallel --colsep '\t' echo col1 {1} col2 {2}
* --trim can remove white space around arguments.
* --sshloginfile '..' means use ~/.parallel/sshloginfile
* Zero install package. Thanks to Tim Cuthbertson <tim3d dot junk at
gmail dot com>
* OpenSUSE package. Thanks to Markus Ammer <mkmm at gmx-topmail dot
de>
* NixOS package. Thanks to Ludovic Courtès <ludo at gnu dot org>
* Web review http://oentend.blogspot.com/2010/08/gnu-parallel.html
Thanks to Pavel Nuzhdin <pnzhdin at gmail dot com>
* Web review http://psung.blogspot.com/2010/08/gnu-parallel.html
Thanks to Phil Sung <psung at alum dot mit dot edu>
20100722
* Arguments can now be given on the command line. Example:
parallel bzip2 ::: *.txt
* xapply like functionality. Example:
parallel diff {1} {2} :::: filelist1 filelist2
parallel diff {1} {2} ">"{1.}-{2.}.diff :::: filelist1 filelist2
* Arch Linux package. Thanks to Peter Simons <simons at cryp dot to>
* Mandriva package. Thanks to Sandro Cazzaniga <kharec at mandriva dot
org>
* -L -l -n -s now implies -X unless -m is set
20100620
* New video showing the new options.
http://www.youtube.com/watch?v=OpaiGYxkSuQ or at
http://tinyogg.com/watch/TORaR/ and http://tinyogg.com/watch/hfxKj/
* 100% options complete with xargs. All options for xargs can now be
used in GNU Parallel - even the more exotic.
* --basefile for transferring basedata. When running jobs on remote
computers --basefile will transfer files before the first jobs is
run. It can be used to transfer data that remains the same for each
job such as scripts or lookup tables.
* --progress shows progress. To see how many jobs is running on each
server use --progress. It can be turned on even after GNU Parallel
is started.
* --eta shows estimated time left in seconds.
* --halt-on-error stops if an error occurs. GNU Parallel will default
to run all jobs - even if some of them fail. With --halt-on-error
GNU Parallel can ignore errors, wait for the currently running jobs
to finish, or stop immediately when an error occurs.
20100601
* GNU Parallel now has support for running jobs on remote machines
* Intro video http://www.youtube.com/watch?v=LlXDtd_pRaY
http://openvideo.dailymotion.com/video/xdmqwz_gnu-parallel-script-processing-and_tech
20100424
* GNU Parallel is now official GNU software
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