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parallel: limit buffering to 1..2 (stdout..stderr).

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testsuite: Compatibility fix with perl-5.14.
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Ole Tange 2016-05-22 22:43:53 +02:00
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171
NEWS
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@ -1,90 +1,173 @@
20160522 20160522
* niceload --net pauses the program if the internet connection is overloaded. * 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 * 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 * 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 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 * 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 * 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/ * 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 * Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.html
@ -232,7 +315,7 @@
* --workdir now accepts replacementstrings. * --workdir now accepts replacementstrings.
* GNU Parallel was cited in: Possum - A Framework for * GNU Parallel was cited in: Possum - A Framework for
Three-Dimensional Reconstruction of Brain Images rfom Serial Three-Dimensional Reconstruction of Brain Images from Serial
Sections http://link.springer.com/article/10.1007/s12021-015-9286-1 Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
* GNU Parallel was cited in: A Genetic Algorithm for the selection of * GNU Parallel was cited in: A Genetic Algorithm for the selection of

2
doc/boxplot-runtime
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@ -49,7 +49,7 @@ measure() {
pdf("/tmp/boxplot.pdf"); pdf("/tmp/boxplot.pdf");
par(cex.axis=0.5); par(cex.axis=0.5);
boxplot(JobRuntime/$INNER*1000~Command,data=jl,las=2,outline=F, boxplot(JobRuntime/$INNER*1000~Command,data=jl,las=2,outline=F,
ylab="milliseconds/job",main="GNU Parallel performance\n$OUTER trials each running $INNER"); ylab="milliseconds/job",main="GNU Parallel performance of different versions\n$OUTER trials each running $INNER jobs");
_ _
cp /tmp/boxplot.pdf $HOME/tmp/boxplot-j$CORES-${MHZ}MHz-$OUTER-${INNER}v$VERSION.pdf cp /tmp/boxplot.pdf $HOME/tmp/boxplot-j$CORES-${MHZ}MHz-$OUTER-${INNER}v$VERSION.pdf
evince /tmp/boxplot.pdf evince /tmp/boxplot.pdf

100
doc/release_new_version
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@ -219,26 +219,24 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>, Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
Jesse Alama <jesse.alama@gmail.com> Jesse Alama <jesse.alama@gmail.com>
Subject: GNU Parallel 20160522 ('ttipleaks') released <<[stable]>> Subject: GNU Parallel 20160622 ('brexit') released <<[stable]>>
GNU Parallel 20160522 ('ttipleaks') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/ GNU Parallel 20160622 ('brexit') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
<<No new functionality was introduced so this is a good candidate for a stable release.>> <<No new functionality was introduced so this is a good candidate for a stable release.>>
Haiku of the month: Haiku of the month:
Programs using net <<>>
only spare capacity
niceload dash dash net
-- Ole Tange -- Ole Tange
New in this release: New in this release:
* niceload --net pauses the program if the internet connection is overloaded. * <<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046 * <<Possibly http://link.springer.com/article/10.1007/s12021-015-9290-5>>
* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf * <<Possibly http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_14>>
* << kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>> * << kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>>
@ -260,88 +258,6 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
* <<link No citation: Next-generation TCP for ns-3 simulator http://www.sciencedirect.com/science/article/pii/S1569190X15300939>> * <<link No citation: Next-generation TCP for ns-3 simulator http://www.sciencedirect.com/science/article/pii/S1569190X15300939>>
* 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. * Bug fixes and man page updates.
GNU Parallel - For people who live life in the parallel lane. GNU Parallel - For people who live life in the parallel lane.
@ -376,9 +292,9 @@ If you like GNU Parallel:
* Request or build a package for your favourite distribution (if it is not already there) * Request or build a package for your favourite distribution (if it is not already there)
* Invite me for your next conference * Invite me for your next conference
If you use GNU Parallel for research: If you use programs that use GNU Parallel for research:
* Please cite GNU Parallel in you publications (use --bibtex) * Please cite GNU Parallel in you publications (use --citation)
If GNU Parallel saves you money: If GNU Parallel saves you money:

2
src/niceload
View file

@ -24,7 +24,7 @@
use strict; use strict;
use Getopt::Long; use Getopt::Long;
$Global::progname="niceload"; $Global::progname="niceload";
$Global::version = 20160522; $Global::version = 20160523;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

12
src/niceload.pod
View file

@ -32,9 +32,9 @@ run 1 second, suspend (3.00-1.00) seconds, run 1 second, suspend
=over 9 =over 9
=item B<-B> (alpha testing) =item B<-B> (beta testing)
=item B<--battery> (alpha testing) =item B<--battery> (beta testing)
Suspend if the system is running on battery. Shorthand for: -l -1 --sensor 'cat /sys/class/power_supply/BAT0/status /proc/acpi/battery/BAT0/state 2>/dev/null |grep -i -q discharging; echo $?' Suspend if the system is running on battery. Shorthand for: -l -1 --sensor 'cat /sys/class/power_supply/BAT0/status /proc/acpi/battery/BAT0/state 2>/dev/null |grep -i -q discharging; echo $?'
@ -102,12 +102,12 @@ B<--noswap> is over limit if the system is swapping both in and out.
B<--noswap> will set both B<--start-noswap> and B<run-noswap>. B<--noswap> will set both B<--start-noswap> and B<run-noswap>.
=item B<--net> (alpha testing) =item B<--net> (beta testing)
Shorthand for B<--nethops 3>. Shorthand for B<--nethops 3>.
=item B<--nethops> I<h> (alpha testing) =item B<--nethops> I<h> (beta testing)
Network nice. Pause if the internet connection is overloaded. Network nice. Pause if the internet connection is overloaded.
@ -140,9 +140,9 @@ Process ID of process to suspend. You can specify multiple process IDs
with multiple B<-p> I<PID>. with multiple B<-p> I<PID>.
=item B<--prg> I<program> (alpha testing) =item B<--prg> I<program> (beta testing)
=item B<--program> I<program> (alpha testing) =item B<--program> I<program> (beta testing)
Name of running program to suspend. You can specify multiple programs Name of running program to suspend. You can specify multiple programs
with multiple B<--prg> I<program>. If no processes with the name with multiple B<--prg> I<program>. If no processes with the name

11
src/parallel
View file

@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20160522; $Global::version = 20160523;
$Global::progname = 'parallel'; $Global::progname = 'parallel';
$Global::infinity = 2**31; $Global::infinity = 2**31;
$Global::debug = 0; $Global::debug = 0;
@ -1953,9 +1953,12 @@ sub save_stdin_stdout_stderr {
# $Global::original_stdin # $Global::original_stdin
# Returns: N/A # Returns: N/A
# Find file descriptors that are already opened (by the shell) # TODO Disabled until we have an open3 that will take n filehandles
for my $fdno (1..61) { # for my $fdno (1..61) {
# /dev/fd/62 and above are used by bash for <(cmd) # # /dev/fd/62 and above are used by bash for <(cmd)
# # Find file descriptors that are already opened (by the shell)
# Only focus on stdout+stderr for now
for my $fdno (1..2) {
my $fh; my $fh;
# 2-argument-open is used to be compatible with old perl 5.8.0 # 2-argument-open is used to be compatible with old perl 5.8.0
# bug #43570: Perl 5.8.0 creates 61 files # bug #43570: Perl 5.8.0 creates 61 files

10
src/parallel.pod
View file

@ -285,7 +285,7 @@ positional replacement strings see B<{>I<n>B<}>.
See also: B<{=perl expression=}> B<{>I<n>B<}>. See also: B<{=perl expression=}> B<{>I<n>B<}>.
=item B<:::> I<arguments> (beta testing) =item B<:::> I<arguments>
Use arguments from the command line as input source instead of stdin Use arguments from the command line as input source instead of stdin
(standard input). Unlike other options for GNU B<parallel> B<:::> is (standard input). Unlike other options for GNU B<parallel> B<:::> is
@ -326,7 +326,7 @@ B<:::> and B<::::> can be mixed. So these are equivalent:
::: 1 2 3 ::: 1 2 3
=item B<:::+> I<arguments> (beta testing) =item B<:::+> I<arguments>
Like B<:::> but linked like B<--xapply> to the previous input source. Like B<:::> but linked like B<--xapply> to the previous input source.
@ -338,7 +338,7 @@ Example:
parallel echo ::: a b c :::+ 1 2 3 ::: X Y :::+ 11 22 parallel echo ::: a b c :::+ 1 2 3 ::: X Y :::+ 11 22
=item B<::::> I<argfiles> (beta testing) =item B<::::> I<argfiles>
Another way to write B<-a> I<argfile1> B<-a> I<argfile2> ... Another way to write B<-a> I<argfile1> B<-a> I<argfile2> ...
@ -347,7 +347,7 @@ B<:::> and B<::::> can be mixed.
See B<-a>, B<:::> and B<--xapply>. See B<-a>, B<:::> and B<--xapply>.
=item B<::::+> I<argfiles> (beta testing) =item B<::::+> I<argfiles>
Like B<::::+> but linked like B<--xapply> to the previous input source. Like B<::::+> but linked like B<--xapply> to the previous input source.
@ -611,7 +611,7 @@ If I<eof-str> is omitted, there is no end of file string. If neither
B<-E> nor B<-e> is used, no end of file string is used. B<-E> nor B<-e> is used, no end of file string is used.
=item B<--env> I<var> (beta testing) =item B<--env> I<var>
Copy environment variable I<var>. This will copy I<var> to the Copy environment variable I<var>. This will copy I<var> to the
environment that the command is run in. This is especially useful for environment that the command is run in. This is especially useful for

2
src/sql
View file

@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err); exit ($err);
sub parse_options { sub parse_options {
$Global::version = 20160522; $Global::version = 20160523;
$Global::progname = 'sql'; $Global::progname = 'sql';
# This must be done first as this may exec myself # This must be done first as this may exec myself

4
testsuite/tests-to-run/parallel-local-mem.sh
View file

@ -6,6 +6,7 @@ mkdir -p $TMPDIR
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -vj1 -k --joblog /tmp/jl-`basename $0` -L1 cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -vj1 -k --joblog /tmp/jl-`basename $0` -L1
echo '### bug #44358: 2 GB records cause problems for -N' echo '### bug #44358: 2 GB records cause problems for -N'
echo '5 GB version: Eats 12.5 GB' echo '5 GB version: Eats 12.5 GB'
PATH=input-files/perl-v5.14.2:$PATH;
(yes "`seq 3000`" | head -c 5000000000; echo FOO; (yes "`seq 3000`" | head -c 5000000000; echo FOO;
yes "`seq 3000`" | head -c 3000000000; echo FOO; yes "`seq 3000`" | head -c 3000000000; echo FOO;
yes "`seq 3000`" | head -c 1000000000;) | yes "`seq 3000`" | head -c 1000000000;) |
@ -13,6 +14,7 @@ echo '5 GB version: Eats 12.5 GB'
`which parallel` --pipe --recend FOO -N2 --block 1g -k LANG=c wc -c `which parallel` --pipe --recend FOO -N2 --block 1g -k LANG=c wc -c
echo '2 GB version: eats 10 GB' echo '2 GB version: eats 10 GB'
PATH=input-files/perl-v5.14.2:$PATH;
(yes "`seq 3000`" | head -c 2300M; echo FOO; (yes "`seq 3000`" | head -c 2300M; echo FOO;
yes "`seq 3000`" | head -c 2300M; echo FOO; yes "`seq 3000`" | head -c 2300M; echo FOO;
yes "`seq 3000`" | head -c 1000M;) | yes "`seq 3000`" | head -c 1000M;) |
@ -34,9 +36,11 @@ echo 'Eats 4 GB'
perl -e '$buf=("x"x(2**31))."x"; substr($buf,0,2**31+1)=""; print ((length $buf)."\n")' perl -e '$buf=("x"x(2**31))."x"; substr($buf,0,2**31+1)=""; print ((length $buf)."\n")'
echo 'Eats 4.7 GB' echo 'Eats 4.7 GB'
PATH=input-files/perl-v5.14.2:$PATH;
(yes "`seq 3000`" | head -c 2300M; echo ged) | (yes "`seq 3000`" | head -c 2300M; echo ged) |
PERL5LIB=input-files/perl-v5.14.2/lib input-files/perl-v5.14.2/perl `which parallel` -k --block 2G --pipe --recend ged md5sum PERL5LIB=input-files/perl-v5.14.2/lib input-files/perl-v5.14.2/perl `which parallel` -k --block 2G --pipe --recend ged md5sum
echo 'Eats 4.7 GB' echo 'Eats 4.7 GB'
PATH=input-files/perl-v5.14.2:$PATH;
(yes "`seq 3000`" | head -c 2300M; echo ged) | (yes "`seq 3000`" | head -c 2300M; echo ged) |
PERL5LIB=input-files/perl-v5.14.2/lib input-files/perl-v5.14.2/perl `which parallel` -k --block 2G --pipe --recend ged cat | wc -c PERL5LIB=input-files/perl-v5.14.2/lib input-files/perl-v5.14.2/perl `which parallel` -k --block 2G --pipe --recend ged cat | wc -c