mirror of
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parallel: limit buffering to 1..2 (stdout..stderr).
testsuite: Compatibility fix with perl-5.14.
This commit is contained in:
Ole Tange
parent
8b96f84864
commit
618220910a
171
NEWS
171
NEWS
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@ -1,90 +1,173 @@
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20160522
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* niceload --net pauses the program if the internet connection is overloaded.
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* niceload --net pauses the program if the internet connection is
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overloaded.
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* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
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* Vote for GNU Parallel's community ad on
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https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
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* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
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* Updated speed comparison between versions
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https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
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* 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
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* GNU Parallel was cited in: Improving computation efficiency by
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parallel programming
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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
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* GNU Parallel was cited in: A supernova feedback implementation for the astrophysical simulation software Arepo https://arxiv.org/abs/1604.06071
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* GNU Parallel was cited in: A supernova feedback implementation for
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the astrophysical simulation software Arepo
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https://arxiv.org/abs/1604.06071
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|
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* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf
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* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and
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resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf
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|
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* 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
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* GNU Parallel was cited in: Host-pathogen co-evolution and the
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emergence of broadly neutralizing antibodies in chronic infections
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https://arxiv.org/abs/1512.06296
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* GNU Parallel was cited in: Pacific People, Metabolic Disease and Evolutionary Processes: a mitochondrial DNA study https://otago.ourarchive.ac.nz/handle/10523/6340
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* GNU Parallel was cited in: Pacific People, Metabolic Disease and
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Evolutionary Processes: a mitochondrial DNA study
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https://otago.ourarchive.ac.nz/handle/10523/6340
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* 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
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* GNU Parallel was cited in: The effect of domain modeling on
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efficiency of planning: Lessons from the Nomystery domain
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http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7407131
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* GNU Parallel was cited in: Oops, my tests broke the build: An analysis of Travis CI buildswith GitHub https://peerj.com/preprints/1984/
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* GNU Parallel was cited in: Oops, my tests broke the build: An
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analysis of Travis CI buildswith GitHub
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https://peerj.com/preprints/1984/
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* 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
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* GNU Parallel was cited in: Drosophila Muller F Elements Maintain a
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Distinct Set of Genomic Properties Over 40 Million Years of
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Evolution http://www.g3journal.org/content/5/5/719.full.pdf+html
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* 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
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* GNU Parallel was cited in: An Empirical Comparison of Neural
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Architectures for Reinforcement Learning in Partially Observable
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Environments
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http://biorxiv.org/content/biorxiv/early/2016/03/24/022707.full.pdf
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* 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
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* GNU Parallel was cited in: Functional enrichments of disease
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variants across thousands of independent loci in eight diseases
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http://biorxiv.org/content/early/2016/04/11/048066.abstract
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* 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
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* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict
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Management in Requester-wins Hardware Transactional Memory
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http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072
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* 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
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* GNU Parallel was cited in: EASE-MM: Sequence-Based Prediction of
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Mutation-Induced Stability Changes with Feature-Based Multiple
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Models
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http://www.sciencedirect.com/science/article/pii/S0022283616000310
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* 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
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* GNU Parallel was cited in: A new orthology assessment method for
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phylogenomic data: Unrooted Phylogenetic Orthology
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http://mbe.oxfordjournals.org/content/early/2016/04/06/molbev.msw069.short
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https://github.com/ballesterus/UPhO
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* 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
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* GNU Parallel was cited in: Distinctive Interest Point Selection for
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Efficient Near-duplicate Image Retrieval
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http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7459172
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* 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)
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* GNU Parallel was cited in: The Evolution of C Programming Practices:
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A Study of the Unix Operating System 1973–2015
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https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest
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thumbnail graphs I have ever seen scattered all over the text)
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* GNU Parallel was cited in: StrAuto: Automation and Parallelization of STRUCTURE Analysis http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
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* GNU Parallel was cited in: StrAuto: Automation and Parallelization
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of STRUCTURE Analysis
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http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
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* 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
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* GNU Parallel was cited in: Data processing pipeline for serial
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femtosecond crystallography at SACLA
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http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html
|
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* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral Dynamics http://arxiv.org/pdf/1512.01460.pdf
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* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral
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Dynamics http://arxiv.org/pdf/1512.01460.pdf
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* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf
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* GNU Parallel was cited in: The Outer Solar System Origins Survey:
|
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I. Design and First-Quarter Discoveries
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http://arxiv.org/pdf/1511.02895.pdf
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* 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
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* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics
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Using Brownian Dynamics, Molecular Dynamics and Milestoning
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||||
http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1004381.PDF
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|
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* 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
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* GNU Parallel was cited in: Genomic legacy of the African cheetah,
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Acinonyx jubatus
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/pdf/13059_2015_Article_837.pdf
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|
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* 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
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* GNU Parallel was cited in: Don’t Forget to Lock the Back Door! A
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Characterization of IPv6 Network Security Policy
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http://benign-research-probe2.eecs.umich.edu/ndss16_ipv6_final.pdf
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|
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* 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
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* GNU Parallel was cited in: Comprehensive Annotation of the
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Parastagonospora nodorum Reference Genome Using Next-Generation
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Genomics, Transcriptomics and Proteogenomics
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http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0147221.PDF
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* 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
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* GNU Parallel was cited in: Stride Search: a general algorithm for
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storm detection in high-resolution climate data
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http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
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* 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
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* GNU Parallel was cited in: How attention influences perceptual
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decision making: Single-trial EEG correlates of drift-diffusion
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model parameters http://www.cidlab.com/prints/nunez2016attention.pdf
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* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads http://repository.upenn.edu/edissertations/1460/
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* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis
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Using High-Throughput Sequencing Reads
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http://repository.upenn.edu/edissertations/1460/
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* 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
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* GNU Parallel was cited in: AT-GIS: Highly Parallel Spatial Query
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Processing with Associative Transducers
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http://lsds.doc.ic.ac.uk/sites/default/files/ATGIS-SIGMOD16.pdf
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* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
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* GNU Parallel was cited in: PVAIR: Partial Variable Assignment
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InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
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* 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/
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* GNU Parallel was cited in: Comparative Cladistics: Fossils,
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Morphological Data Partitions and Lost Branches in the Fossil Tree
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of Life http://opus.bath.ac.uk/43955/
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* 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
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* GNU Parallel was cited in: Shannon: An Information-Optimal de
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NovoRNA-Seq Assembler
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http://biorxiv.org/content/biorxiv/early/2016/02/09/039230.full.pdf
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* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter Estimation for Coastal Ocean Modeling https://repositories.lib.utexas.edu/handle/2152/32435
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* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter
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Estimation for Coastal Ocean Modeling
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https://repositories.lib.utexas.edu/handle/2152/32435
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* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
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* GNU Parallel was cited in: Computational Design of DNA-Binding
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Proteins
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http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
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* 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
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* GNU Parallel was cited in: Reference genotype and exome data from an
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Australian Aboriginal population for health-based research
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http://www.nature.com/articles/sdata201623
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* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
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* GNU Parallel was cited in: Computational Design of DNA-Binding
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Proteins
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http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
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* GNU Parallel was cited in: Do aye-ayes echolocate? http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
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* GNU Parallel was cited in: Do aye-ayes echolocate?
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http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
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* 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
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* GNU Parallel was cited in: Functional enrichments of disease
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variants across thousands of independent loci in eight diseases
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http://biorxiv.org/content/biorxiv/early/2016/04/11/048066.full.pdf
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* 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
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* GNU Parallel was cited in: From genomes to phenotypes: Traitar, the
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microbial trait analyzer
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http://biorxiv.org/content/biorxiv/early/2016/03/12/043315.full.pdf
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* 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
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* GNU Parallel was mentioned in: Fast Playback Framework for Analysis
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of Ground-Based Doppler Radar Observations Using MapReduce
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Technology
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http://journals.ametsoc.org/doi/pdf/10.1175/JTECH-D-15-0118.1
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* NCBI blast tutorial https://github.com/enormandeau/ncbi_blast_tutorial
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* NCBI blast tutorial
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https://github.com/enormandeau/ncbi_blast_tutorial
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* Distributed Preservation Made Simple https://blog.archive.org/2016/02/26/distributed-preservation-made-simple/
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* Distributed Preservation Made Simple
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https://blog.archive.org/2016/02/26/distributed-preservation-made-simple/
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* Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.html
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@ -232,7 +315,7 @@
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* --workdir now accepts replacementstrings.
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* GNU Parallel was cited in: Possum - A Framework for
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Three-Dimensional Reconstruction of Brain Images rfom Serial
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Three-Dimensional Reconstruction of Brain Images from Serial
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Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
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* GNU Parallel was cited in: A Genetic Algorithm for the selection of
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@ -49,7 +49,7 @@ measure() {
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pdf("/tmp/boxplot.pdf");
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par(cex.axis=0.5);
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boxplot(JobRuntime/$INNER*1000~Command,data=jl,las=2,outline=F,
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ylab="milliseconds/job",main="GNU Parallel performance\n$OUTER trials each running $INNER");
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ylab="milliseconds/job",main="GNU Parallel performance of different versions\n$OUTER trials each running $INNER jobs");
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_
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cp /tmp/boxplot.pdf $HOME/tmp/boxplot-j$CORES-${MHZ}MHz-$OUTER-${INNER}v$VERSION.pdf
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evince /tmp/boxplot.pdf
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@ -219,26 +219,24 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
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Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
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Jesse Alama <jesse.alama@gmail.com>
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Subject: GNU Parallel 20160522 ('ttipleaks') released <<[stable]>>
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Subject: GNU Parallel 20160622 ('brexit') released <<[stable]>>
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GNU Parallel 20160522 ('ttipleaks') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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GNU Parallel 20160622 ('brexit') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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Haiku of the month:
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Programs using net
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only spare capacity
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niceload dash dash net
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<<>>
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-- Ole Tange
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New in this release:
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* niceload --net pauses the program if the internet connection is overloaded.
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* <<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
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* 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>>
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* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
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* <<Possibly http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_14>>
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* << 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>>
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@ -260,88 +258,6 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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* <<link No citation: Next-generation TCP for ns-3 simulator http://www.sciencedirect.com/science/article/pii/S1569190X15300939>>
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* 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
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|
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* GNU Parallel was cited in: A supernova feedback implementation for the astrophysical simulation software Arepo https://arxiv.org/abs/1604.06071
|
||||
|
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* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf
|
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|
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* 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
|
||||
|
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* GNU Parallel was cited in: Pacific People, Metabolic Disease and Evolutionary Processes: a mitochondrial DNA study https://otago.ourarchive.ac.nz/handle/10523/6340
|
||||
|
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* 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
|
||||
|
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* 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
|
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|
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* 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
|
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|
||||
* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict Management in Requester-wins Hardware Transactional Memory http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072
|
||||
|
||||
* GNU Parallel was cited in: EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models http://www.sciencedirect.com/science/article/pii/S0022283616000310
|
||||
|
||||
* GNU Parallel was cited in: A new orthology assessment method for phylogenomic data: Unrooted Phylogenetic Orthology http://mbe.oxfordjournals.org/content/early/2016/04/06/molbev.msw069.short https://github.com/ballesterus/UPhO
|
||||
|
||||
* GNU Parallel was cited in: Distinctive Interest Point Selection for Efficient Near-duplicate Image Retrieval http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7459172
|
||||
|
||||
* GNU Parallel was cited in: The Evolution of C Programming Practices: A Study of the Unix Operating System 1973–2015 https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest thumbnail graphs I have ever seen scattered all over the text)
|
||||
|
||||
* GNU Parallel was cited in: StrAuto: Automation and Parallelization of STRUCTURE Analysis http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
|
||||
|
||||
* GNU Parallel was cited in: Data processing pipeline for serial femtosecond crystallography at SACLA http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html
|
||||
|
||||
* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral Dynamics http://arxiv.org/pdf/1512.01460.pdf
|
||||
|
||||
* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf
|
||||
|
||||
* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1004381.PDF
|
||||
|
||||
* GNU Parallel was cited in: Genomic legacy of the African cheetah, Acinonyx jubatus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/pdf/13059_2015_Article_837.pdf
|
||||
|
||||
* GNU Parallel was cited in: Don’t Forget to Lock the Back Door! A Characterization of IPv6 Network Security Policy http://benign-research-probe2.eecs.umich.edu/ndss16_ipv6_final.pdf
|
||||
|
||||
* GNU Parallel was cited in: Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0147221.PDF
|
||||
|
||||
* GNU Parallel was cited in: Stride Search: a general algorithm for storm detection in high-resolution climate data http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
|
||||
|
||||
* GNU Parallel was cited in: How attention influences perceptual decision making: Single-trial EEG correlates of drift-diffusion model parameters http://www.cidlab.com/prints/nunez2016attention.pdf
|
||||
|
||||
* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads http://repository.upenn.edu/edissertations/1460/
|
||||
|
||||
* GNU Parallel was cited in: AT-GIS: Highly Parallel Spatial Query Processing with Associative Transducers http://lsds.doc.ic.ac.uk/sites/default/files/ATGIS-SIGMOD16.pdf
|
||||
|
||||
* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
|
||||
|
||||
* GNU Parallel was cited in: Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life http://opus.bath.ac.uk/43955/
|
||||
|
||||
* GNU Parallel was cited in: Shannon: An Information-Optimal de NovoRNA-Seq Assembler http://biorxiv.org/content/biorxiv/early/2016/02/09/039230.full.pdf
|
||||
|
||||
* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter Estimation for Coastal Ocean Modeling https://repositories.lib.utexas.edu/handle/2152/32435
|
||||
|
||||
* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
|
||||
|
||||
* GNU Parallel was cited in: Reference genotype and exome data from an Australian Aboriginal population for health-based research http://www.nature.com/articles/sdata201623
|
||||
|
||||
* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
|
||||
|
||||
* GNU Parallel was cited in: Do aye-ayes echolocate? http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
|
||||
|
||||
* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/biorxiv/early/2016/04/11/048066.full.pdf
|
||||
|
||||
* GNU Parallel was cited in: From genomes to phenotypes: Traitar, the microbial trait analyzer http://biorxiv.org/content/biorxiv/early/2016/03/12/043315.full.pdf
|
||||
|
||||
* GNU Parallel was mentioned in: Fast Playback Framework for Analysis of Ground-Based Doppler Radar Observations Using MapReduce Technology http://journals.ametsoc.org/doi/pdf/10.1175/JTECH-D-15-0118.1
|
||||
|
||||
* NCBI blast tutorial https://github.com/enormandeau/ncbi_blast_tutorial
|
||||
|
||||
* Distributed Preservation Made Simple https://blog.archive.org/2016/02/26/distributed-preservation-made-simple/
|
||||
|
||||
* Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.html
|
||||
|
||||
* Bug fixes and man page updates.
|
||||
|
||||
GNU Parallel - For people who live life in the parallel lane.
|
||||
|
|
@ -376,9 +292,9 @@ If you like GNU Parallel:
|
|||
* Request or build a package for your favourite distribution (if it is not already there)
|
||||
* Invite me for your next conference
|
||||
|
||||
If you use GNU Parallel for research:
|
||||
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:
|
||||
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@
|
|||
use strict;
|
||||
use Getopt::Long;
|
||||
$Global::progname="niceload";
|
||||
$Global::version = 20160522;
|
||||
$Global::version = 20160523;
|
||||
Getopt::Long::Configure("bundling","require_order");
|
||||
get_options_from_array(\@ARGV) || die_usage();
|
||||
if($opt::version) {
|
||||
|
|
|
|||
|
|
@ -32,9 +32,9 @@ run 1 second, suspend (3.00-1.00) seconds, run 1 second, suspend
|
|||
|
||||
=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 $?'
|
||||
|
||||
|
|
@ -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>.
|
||||
|
||||
|
||||
=item B<--net> (alpha testing)
|
||||
=item B<--net> (beta testing)
|
||||
|
||||
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.
|
||||
|
||||
|
|
@ -140,9 +140,9 @@ Process ID of process to suspend. You can specify multiple process IDs
|
|||
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
|
||||
with multiple B<--prg> I<program>. If no processes with the name
|
||||
|
|
|
|||
25
src/parallel
25
src/parallel
|
|
@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations {
|
|||
|
||||
sub init_globals {
|
||||
# Defaults:
|
||||
$Global::version = 20160522;
|
||||
$Global::version = 20160523;
|
||||
$Global::progname = 'parallel';
|
||||
$Global::infinity = 2**31;
|
||||
$Global::debug = 0;
|
||||
|
|
@ -1952,16 +1952,19 @@ sub save_stdin_stdout_stderr {
|
|||
# $Global::original_stderr
|
||||
# $Global::original_stdin
|
||||
# Returns: N/A
|
||||
|
||||
# Find file descriptors that are already opened (by the shell)
|
||||
for my $fdno (1..61) {
|
||||
# /dev/fd/62 and above are used by bash for <(cmd)
|
||||
my $fh;
|
||||
# 2-argument-open is used to be compatible with old perl 5.8.0
|
||||
# bug #43570: Perl 5.8.0 creates 61 files
|
||||
if(open($fh,">&=$fdno")) {
|
||||
$Global::fd{$fdno}=$fh;
|
||||
}
|
||||
|
||||
# TODO Disabled until we have an open3 that will take n filehandles
|
||||
# for my $fdno (1..61) {
|
||||
# # /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 $fh;
|
||||
# 2-argument-open is used to be compatible with old perl 5.8.0
|
||||
# bug #43570: Perl 5.8.0 creates 61 files
|
||||
if(open($fh,">&=$fdno")) {
|
||||
$Global::fd{$fdno}=$fh;
|
||||
}
|
||||
}
|
||||
open $Global::original_stderr, ">&", "STDERR" or
|
||||
::die_bug("Can't dup STDERR: $!");
|
||||
|
|
|
|||
|
|
@ -285,7 +285,7 @@ positional replacement strings see 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
|
||||
(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
|
||||
|
||||
|
||||
=item B<:::+> I<arguments> (beta testing)
|
||||
=item B<:::+> I<arguments>
|
||||
|
||||
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
|
||||
|
||||
|
||||
=item B<::::> I<argfiles> (beta testing)
|
||||
=item B<::::> I<argfiles>
|
||||
|
||||
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>.
|
||||
|
||||
|
||||
=item B<::::+> I<argfiles> (beta testing)
|
||||
=item B<::::+> I<argfiles>
|
||||
|
||||
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.
|
||||
|
||||
|
||||
=item B<--env> I<var> (beta testing)
|
||||
=item B<--env> I<var>
|
||||
|
||||
Copy environment variable I<var>. This will copy I<var> to the
|
||||
environment that the command is run in. This is especially useful for
|
||||
|
|
|
|||
2
src/sql
2
src/sql
|
|
@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
|
|||
exit ($err);
|
||||
|
||||
sub parse_options {
|
||||
$Global::version = 20160522;
|
||||
$Global::version = 20160523;
|
||||
$Global::progname = 'sql';
|
||||
|
||||
# This must be done first as this may exec myself
|
||||
|
|
|
|||
|
|
@ -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 $0` -L1
|
||||
echo '### bug #44358: 2 GB records cause problems for -N'
|
||||
echo '5 GB version: Eats 12.5 GB'
|
||||
PATH=input-files/perl-v5.14.2:$PATH;
|
||||
(yes "`seq 3000`" | head -c 5000000000; echo FOO;
|
||||
yes "`seq 3000`" | head -c 3000000000; echo FOO;
|
||||
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
|
||||
|
||||
echo '2 GB version: eats 10 GB'
|
||||
PATH=input-files/perl-v5.14.2:$PATH;
|
||||
(yes "`seq 3000`" | head -c 2300M; echo FOO;
|
||||
yes "`seq 3000`" | head -c 2300M; echo FOO;
|
||||
yes "`seq 3000`" | head -c 1000M;) |
|
||||
|
|
@ -34,9 +36,11 @@ echo 'Eats 4 GB'
|
|||
perl -e '$buf=("x"x(2**31))."x"; substr($buf,0,2**31+1)=""; print ((length $buf)."\n")'
|
||||
|
||||
echo 'Eats 4.7 GB'
|
||||
PATH=input-files/perl-v5.14.2:$PATH;
|
||||
(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
|
||||
echo 'Eats 4.7 GB'
|
||||
PATH=input-files/perl-v5.14.2:$PATH;
|
||||
(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
|
||||
|
||||
|
|
|
|||
Loading…
Reference in a new issue