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parallel: Transfer functions through csh if PARALLEL_SHELL is set to bash.
This commit is contained in:
Ole Tange
parent
e4738dfb97
commit
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@ -219,9 +219,9 @@ 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 20160422 ('PanamaPapers') released <<[stable]>>
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Subject: GNU Parallel 20160522 ('ttipleaks') released <<[stable]>>
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GNU Parallel 20160422 ('PanamaPapers') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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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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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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@ -232,6 +232,8 @@ Haiku of the month:
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New in this release:
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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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* << 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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* <<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345
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@ -248,37 +250,49 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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* <<Citation needed: Introspecting for RSA Key Material to Assist Intrusion Detection http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7331177&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7331177>>
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* :::+ and ::::+ work like ::: and :::: but links this input source to the previous input source in a --xapply fashion. Contrary to --xapply values do not wrap: The shortest input source determines the length.
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* GNU Parallel was cited in: Structure and evolutionary history of a large family of NLR proteins in the zebrafish http://rsob.royalsocietypublishing.org/content/royopenbio/6/4/160009.full.pdf
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* --line-buffer --keep-order now outputs continously from the oldest job still running. This is more what you would expect than the earlier behaviour where --keep-order had no effect with --line-buffer.
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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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* env_parallel supports tcsh, csh, pdksh. In fish it now supports arrays. In csh/tcsh it now supports variables, aliases, and arrays with no special chars. In pdksh it supports aliases, functions, variables, and arrays.
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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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* Function exporting on Mac OS X works around old Bash version.
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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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* Better CPU detection on OpenIndiana.
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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: How Can We Measure the Similarity Between Resumes of Selected Candidates for a Job? https://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_resumes_of_selected_candidates_for_a_job
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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: Automatic Methods for Assisted Recruitment https://www.researchgate.net/publication/297738658_Automatic_Methods_for_Assisted_Recruitment
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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: Tools and techniques for computational reproducibility http://biorxiv.org/content/biorxiv/early/2016/03/17/022707.full.pdf
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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: Reinterpretation of ATLAS 8 TeV searches for Natural SUSY with a R-Sneutrino LSP http://arxiv.org/pdf/1603.06130.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: An Operational Radiometric Landsat Preprocessing Framework for Large-Area Time Series Applications https://www.uni-trier.de/fileadmin/fb6/prof/FER/Publikationen/frantz_et_al_ieee-tgrs-2016-post-print.pdf
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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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* A basic demo of how GNU Parallel can speed up execution of commands https://www.youtube.com/watch?v=kl8LO2jcvMc
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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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* Downloading a list of URLs http://blog.gypsydave5.com/2016/02/04/xargs-and-curl/
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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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* qbatch uses GNU Parallel: https://pypi.python.org/pypi/qbatch/1.0rc2
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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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* FaceCrop uses GNU Parallel: https://github.com/EderSantana/FaceCrop
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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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* Parallel Processing with Catmandu https://librecatproject.wordpress.com/2016/04/20/parallel-processing-with-catmandu/
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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 應用範例 http://staypython.blogspot.dk/2016/04/gnu-parallel.html
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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: 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: 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 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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* NCBI blast tutorial 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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* Parallel Jobs in Luigi http://rjbaxley.com/posts/2016/03/13/parallel_jobs_in_luigi.html
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* Bug fixes and man page updates.
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@ -1,8 +1,8 @@
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#!/bin/csh
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# This file must be sourced in csh:
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# This file must be sourced in tcsh:
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#
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# source `which env_parallel.csh`
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# source `which env_parallel.tcsh`
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#
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# after which 'env_parallel' works
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#
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@ -60,8 +60,6 @@ else
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# Quoted: s/\\047/\\047\\042\\047\\042\\047/g\;
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# Remove () from second column
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# s/^(\S+)(\s+)\((.*)\)/\1\2\3/
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# \047 => '
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# s/^(\S+)(\s+)\((.*)\)/\1\2\3/;
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# Quoted: s/\^\(\\S+\)\(\\s+\)\\\(\(.\*\)\\\)/\\1\\2\\3/\;
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20160422;
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$Global::version = 20160423;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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@ -346,9 +346,9 @@ sub die_bug {
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sub usleep {
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# Sleep this many milliseconds.
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my $secs = shift;
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::debug("Sleeping ",$secs," millisecs\n");
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select(undef, undef, undef, $secs/1000);
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my $ms = shift;
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::debug("Sleeping ",$ms," millisecs\n");
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select(undef, undef, undef, $ms/1000);
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}
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10
src/parallel
10
src/parallel
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@ -764,7 +764,7 @@ sub options_hash {
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"sqlmaster=s" => \$opt::sqlmaster,
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"sqlworker=s" => \$opt::sqlworker,
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"sqlandworker=s" => \$opt::sqlandworker,
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"joblog=s" => \$opt::joblog,
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"joblog|jl=s" => \$opt::joblog,
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"results|result|res=s" => \$opt::results,
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"resume" => \$opt::resume,
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"resume-failed|resumefailed" => \$opt::resume_failed,
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@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations {
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sub init_globals {
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# Defaults:
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$Global::version = 20160422;
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$Global::version = 20160423;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -7112,13 +7112,13 @@ sub sshlogin_wrap {
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my $bashfuncset;
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if(@bashfunc) {
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# Functions are not supported for all shells
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if($Global::shell !~ m:/(bash|rbash|zsh|rzsh|dash|ksh):) {
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if($Global::shell !~ m:(bash|rbash|zsh|rzsh|dash|ksh):) {
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::warning("Shell functions may not be supported in $Global::shell.");
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}
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$bashfuncset =
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'@bash_functions=qw('."@bash_functions".");".
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::spacefree(1,q{
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if($ENV{"SHELL"}=~/csh/) {
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::spacefree(1,'$shell="'.($ENV{'PARALLEL_SHELL'} || '$ENV{SHELL}').'";'.q{
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if($shell=~/csh/) {
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print STDERR "CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset @bash_functions\n";
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exec "false";
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}
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@ -285,7 +285,7 @@ positional replacement strings see B<{>I<n>B<}>.
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See also: B<{=perl expression=}> B<{>I<n>B<}>.
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=item B<:::> I<arguments> (alpha testing)
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=item B<:::> I<arguments> (beta testing)
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Use arguments from the command line as input source instead of stdin
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(standard input). Unlike other options for GNU B<parallel> B<:::> is
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@ -326,7 +326,7 @@ B<:::> and B<::::> can be mixed. So these are equivalent:
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::: 1 2 3
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=item B<:::+> I<arguments> (alpha testing)
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=item B<:::+> I<arguments> (beta testing)
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Like B<:::> but linked like B<--xapply> to the previous input source.
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@ -338,7 +338,7 @@ Example:
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parallel echo ::: a b c :::+ 1 2 3 ::: X Y :::+ 11 22
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=item B<::::> I<argfiles> (alpha testing)
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=item B<::::> I<argfiles> (beta testing)
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Another way to write B<-a> I<argfile1> B<-a> I<argfile2> ...
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@ -347,7 +347,7 @@ B<:::> and B<::::> can be mixed.
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See B<-a>, B<:::> and B<--xapply>.
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=item B<::::+> I<argfiles> (alpha testing)
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=item B<::::+> I<argfiles> (beta testing)
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Like B<::::+> but linked like B<--xapply> to the previous input source.
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@ -611,7 +611,7 @@ If I<eof-str> is omitted, there is no end of file string. If neither
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B<-E> nor B<-e> is used, no end of file string is used.
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=item B<--env> I<var> (alpha testing)
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=item B<--env> I<var> (beta testing)
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Copy environment variable I<var>. This will copy I<var> to the
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environment that the command is run in. This is especially useful for
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2
src/sql
2
src/sql
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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
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exit ($err);
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sub parse_options {
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$Global::version = 20160422;
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$Global::version = 20160423;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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@ -77,4 +77,10 @@ echo '### bug #45907: --header : + --return {header}'
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echo "### bug #47608: parallel --nonall -S lo 'echo ::: ' blocks"
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parallel --nonall -S lo 'echo ::: '
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echo '### exported function to csh but with PARALLEL_SHELL=bash'
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doit() { echo "$1"; };
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export -f doit;
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stdout parallel --env doit -S csh@lo doit ::: not_OK;
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PARALLEL_SHELL=bash parallel --env doit -S csh@lo doit ::: OK
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EOF
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@ -62,7 +62,6 @@ bash -c 'echo bug \#43358: shellshock breaks exporting functions using --env _;
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bug #43358: shellshock breaks exporting functions using --env _
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Non-shellshock-hardened to non-shellshock-hardened
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Function non-shellshock-hardened
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parallel: Warning: Shell functions may not be supported in bash.
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bash -c 'echo bug \#43358: shellshock breaks exporting functions using --env _; echo Non-shellshock-hardened to shellshock-hardened; funky() { echo Function $1; }; export -f funky; parallel --env funky -S parallel@192.168.1.72 funky ::: shellshock-hardened'
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bug #43358: shellshock breaks exporting functions using --env _
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Non-shellshock-hardened to shellshock-hardened
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### bug #47608: parallel --nonall -S lo 'echo ::: ' blocks
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parallel --nonall -S lo 'echo ::: '
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:::
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echo '### exported function to csh but with PARALLEL_SHELL=bash'
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### exported function to csh but with PARALLEL_SHELL=bash
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doit() { echo "$1"; }; export -f doit; stdout parallel --env doit -S csh@lo doit ::: not_OK; PARALLEL_SHELL=bash parallel --env doit -S csh@lo doit ::: OK
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CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset doit
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OK
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