From 8b96f8486481e660a252127aa7401087aae9b478 Mon Sep 17 00:00:00 2001 From: Ole Tange Date: Sun, 22 May 2016 14:21:46 +0200 Subject: [PATCH] Released as 20160522 ('TTIPleaks') --- NEWS | 93 +++++++++++++++++++ README | 12 +-- configure | 20 ++-- configure.ac | 2 +- .../obs/home:tange/parallel/parallel.spec | 2 +- src/niceload | 2 +- src/parallel | 2 +- src/sql | 2 +- 8 files changed, 114 insertions(+), 21 deletions(-) diff --git a/NEWS b/NEWS index d816a07d..e2a32803 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,96 @@ +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 diff --git a/README b/README index 9d6a4e28..a39beb53 100644 --- a/README +++ b/README @@ -40,9 +40,9 @@ document. Full installation of GNU Parallel is as simple as: - wget http://ftpmirror.gnu.org/parallel/parallel-20160422.tar.bz2 - bzip2 -dc parallel-20160422.tar.bz2 | tar xvf - - cd parallel-20160422 + wget http://ftpmirror.gnu.org/parallel/parallel-20160522.tar.bz2 + bzip2 -dc parallel-20160522.tar.bz2 | tar xvf - + cd parallel-20160522 ./configure && make && sudo make install @@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as: If you are not root you can add ~/bin to your path and install in ~/bin and ~/share: - wget http://ftpmirror.gnu.org/parallel/parallel-20160422.tar.bz2 - bzip2 -dc parallel-20160422.tar.bz2 | tar xvf - - cd parallel-20160422 + wget http://ftpmirror.gnu.org/parallel/parallel-20160522.tar.bz2 + bzip2 -dc parallel-20160522.tar.bz2 | tar xvf - + cd parallel-20160522 ./configure --prefix=$HOME && make && make install Or if your system lacks 'make' you can simply copy src/parallel diff --git a/configure b/configure index 5bd47cab..2d233253 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for parallel 20160422. +# Generated by GNU Autoconf 2.69 for parallel 20160522. # # Report bugs to . # @@ -579,8 +579,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='parallel' PACKAGE_TARNAME='parallel' -PACKAGE_VERSION='20160422' -PACKAGE_STRING='parallel 20160422' +PACKAGE_VERSION='20160522' +PACKAGE_STRING='parallel 20160522' PACKAGE_BUGREPORT='bug-parallel@gnu.org' PACKAGE_URL='' @@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures parallel 20160422 to adapt to many kinds of systems. +\`configure' configures parallel 20160522 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1269,7 +1269,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of parallel 20160422:";; + short | recursive ) echo "Configuration of parallel 20160522:";; esac cat <<\_ACEOF @@ -1345,7 +1345,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -parallel configure 20160422 +parallel configure 20160522 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by parallel $as_me 20160422, which was +It was created by parallel $as_me 20160522, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2225,7 +2225,7 @@ fi # Define the identity of the package. PACKAGE='parallel' - VERSION='20160422' + VERSION='20160522' cat >>confdefs.h <<_ACEOF @@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by parallel $as_me 20160422, which was +This file was extended by parallel $as_me 20160522, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -2929,7 +2929,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -parallel config.status 20160422 +parallel config.status 20160522 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/configure.ac b/configure.ac index 836ae513..b4ed294a 100644 --- a/configure.ac +++ b/configure.ac @@ -1,4 +1,4 @@ -AC_INIT([parallel], [20160422], [bug-parallel@gnu.org]) +AC_INIT([parallel], [20160522], [bug-parallel@gnu.org]) AM_INIT_AUTOMAKE([-Wall -Werror foreign]) AC_CONFIG_HEADERS([config.h]) AC_CONFIG_FILES([ diff --git a/packager/obs/home:tange/parallel/parallel.spec b/packager/obs/home:tange/parallel/parallel.spec index 78ee049e..d1f1367f 100644 --- a/packager/obs/home:tange/parallel/parallel.spec +++ b/packager/obs/home:tange/parallel/parallel.spec @@ -1,6 +1,6 @@ Summary: Shell tool for executing jobs in parallel Name: parallel -Version: 20160422 +Version: 20160522 Release: 1.1 License: GPL Group: Productivity/File utilities diff --git a/src/niceload b/src/niceload index aee1878e..233fa2bc 100755 --- a/src/niceload +++ b/src/niceload @@ -24,7 +24,7 @@ use strict; use Getopt::Long; $Global::progname="niceload"; -$Global::version = 20160423; +$Global::version = 20160522; Getopt::Long::Configure("bundling","require_order"); get_options_from_array(\@ARGV) || die_usage(); if($opt::version) { diff --git a/src/parallel b/src/parallel index 4ced9efe..37d31548 100755 --- a/src/parallel +++ b/src/parallel @@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations { sub init_globals { # Defaults: - $Global::version = 20160423; + $Global::version = 20160522; $Global::progname = 'parallel'; $Global::infinity = 2**31; $Global::debug = 0; diff --git a/src/sql b/src/sql index 128394e7..8842da84 100755 --- a/src/sql +++ b/src/sql @@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile; exit ($err); sub parse_options { - $Global::version = 20160423; + $Global::version = 20160522; $Global::progname = 'sql'; # This must be done first as this may exec myself