mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-11-22 14:07:55 +00:00
parallel: Transfer functions through csh if PARALLEL_SHELL is set to bash.
This commit is contained in:
Ole Tange
parent
e4738dfb97
commit
f8d1474943
|
|
@ -219,9 +219,9 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
|
|||
Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
|
||||
Jesse Alama <jesse.alama@gmail.com>
|
||||
|
||||
Subject: GNU Parallel 20160422 ('PanamaPapers') released <<[stable]>>
|
||||
Subject: GNU Parallel 20160522 ('ttipleaks') released <<[stable]>>
|
||||
|
||||
GNU Parallel 20160422 ('PanamaPapers') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
|
||||
GNU Parallel 20160522 ('ttipleaks') <<[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.>>
|
||||
|
||||
|
|
@ -232,6 +232,8 @@ Haiku of the month:
|
|||
|
||||
New in this release:
|
||||
|
||||
* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
|
||||
|
||||
* << 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>>
|
||||
|
||||
* <<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
|
||||
|
|
@ -248,37 +250,49 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
|
|||
|
||||
* <<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>>
|
||||
|
||||
* :::+ 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.
|
||||
* 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
|
||||
|
||||
* --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.
|
||||
* 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
|
||||
|
||||
* 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.
|
||||
* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral Dynamics http://arxiv.org/pdf/1512.01460.pdf
|
||||
|
||||
* Function exporting on Mac OS X works around old Bash version.
|
||||
* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf
|
||||
|
||||
* Better CPU detection on OpenIndiana.
|
||||
* 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: How Can We Measure the Similarity Between Resumes of Selected Candidates for a Job? https://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_resumes_of_selected_candidates_for_a_job
|
||||
* GNU Parallel was cited in: 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: Automatic Methods for Assisted Recruitment https://www.researchgate.net/publication/297738658_Automatic_Methods_for_Assisted_Recruitment
|
||||
* 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: Tools and techniques for computational reproducibility http://biorxiv.org/content/biorxiv/early/2016/03/17/022707.full.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: Reinterpretation of ATLAS 8 TeV searches for Natural SUSY with a R-Sneutrino LSP http://arxiv.org/pdf/1603.06130.pdf
|
||||
* GNU Parallel was cited in: 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: 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
|
||||
* 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
|
||||
|
||||
* A basic demo of how GNU Parallel can speed up execution of commands https://www.youtube.com/watch?v=kl8LO2jcvMc
|
||||
* 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
|
||||
|
||||
* Downloading a list of URLs http://blog.gypsydave5.com/2016/02/04/xargs-and-curl/
|
||||
* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
|
||||
|
||||
* qbatch uses GNU Parallel: https://pypi.python.org/pypi/qbatch/1.0rc2
|
||||
* 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
|
||||
|
||||
* FaceCrop uses GNU Parallel: https://github.com/EderSantana/FaceCrop
|
||||
* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
|
||||
|
||||
* Parallel Processing with Catmandu https://librecatproject.wordpress.com/2016/04/20/parallel-processing-with-catmandu/
|
||||
* 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 應用範例 http://staypython.blogspot.dk/2016/04/gnu-parallel.html
|
||||
* 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.
|
||||
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
#!/bin/csh
|
||||
|
||||
# This file must be sourced in csh:
|
||||
# This file must be sourced in tcsh:
|
||||
#
|
||||
# source `which env_parallel.csh`
|
||||
# source `which env_parallel.tcsh`
|
||||
#
|
||||
# after which 'env_parallel' works
|
||||
#
|
||||
|
|
@ -60,8 +60,6 @@ else
|
|||
# Quoted: s/\\047/\\047\\042\\047\\042\\047/g\;
|
||||
|
||||
# Remove () from second column
|
||||
# s/^(\S+)(\s+)\((.*)\)/\1\2\3/
|
||||
# \047 => '
|
||||
# s/^(\S+)(\s+)\((.*)\)/\1\2\3/;
|
||||
# Quoted: s/\^\(\\S+\)\(\\s+\)\\\(\(.\*\)\\\)/\\1\\2\\3/\;
|
||||
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@
|
|||
use strict;
|
||||
use Getopt::Long;
|
||||
$Global::progname="niceload";
|
||||
$Global::version = 20160422;
|
||||
$Global::version = 20160423;
|
||||
Getopt::Long::Configure("bundling","require_order");
|
||||
get_options_from_array(\@ARGV) || die_usage();
|
||||
if($opt::version) {
|
||||
|
|
@ -346,9 +346,9 @@ sub die_bug {
|
|||
|
||||
sub usleep {
|
||||
# Sleep this many milliseconds.
|
||||
my $secs = shift;
|
||||
::debug("Sleeping ",$secs," millisecs\n");
|
||||
select(undef, undef, undef, $secs/1000);
|
||||
my $ms = shift;
|
||||
::debug("Sleeping ",$ms," millisecs\n");
|
||||
select(undef, undef, undef, $ms/1000);
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
10
src/parallel
10
src/parallel
|
|
@ -764,7 +764,7 @@ sub options_hash {
|
|||
"sqlmaster=s" => \$opt::sqlmaster,
|
||||
"sqlworker=s" => \$opt::sqlworker,
|
||||
"sqlandworker=s" => \$opt::sqlandworker,
|
||||
"joblog=s" => \$opt::joblog,
|
||||
"joblog|jl=s" => \$opt::joblog,
|
||||
"results|result|res=s" => \$opt::results,
|
||||
"resume" => \$opt::resume,
|
||||
"resume-failed|resumefailed" => \$opt::resume_failed,
|
||||
|
|
@ -1183,7 +1183,7 @@ sub check_invalid_option_combinations {
|
|||
|
||||
sub init_globals {
|
||||
# Defaults:
|
||||
$Global::version = 20160422;
|
||||
$Global::version = 20160423;
|
||||
$Global::progname = 'parallel';
|
||||
$Global::infinity = 2**31;
|
||||
$Global::debug = 0;
|
||||
|
|
@ -7112,13 +7112,13 @@ sub sshlogin_wrap {
|
|||
my $bashfuncset;
|
||||
if(@bashfunc) {
|
||||
# Functions are not supported for all shells
|
||||
if($Global::shell !~ m:/(bash|rbash|zsh|rzsh|dash|ksh):) {
|
||||
if($Global::shell !~ m:(bash|rbash|zsh|rzsh|dash|ksh):) {
|
||||
::warning("Shell functions may not be supported in $Global::shell.");
|
||||
}
|
||||
$bashfuncset =
|
||||
'@bash_functions=qw('."@bash_functions".");".
|
||||
::spacefree(1,q{
|
||||
if($ENV{"SHELL"}=~/csh/) {
|
||||
::spacefree(1,'$shell="'.($ENV{'PARALLEL_SHELL'} || '$ENV{SHELL}').'";'.q{
|
||||
if($shell=~/csh/) {
|
||||
print STDERR "CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset @bash_functions\n";
|
||||
exec "false";
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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> (alpha testing)
|
||||
=item B<:::> I<arguments> (beta testing)
|
||||
|
||||
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> (alpha testing)
|
||||
=item B<:::+> I<arguments> (beta testing)
|
||||
|
||||
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> (alpha testing)
|
||||
=item B<::::> I<argfiles> (beta testing)
|
||||
|
||||
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> (alpha testing)
|
||||
=item B<::::+> I<argfiles> (beta testing)
|
||||
|
||||
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> (alpha testing)
|
||||
=item B<--env> I<var> (beta testing)
|
||||
|
||||
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 = 20160422;
|
||||
$Global::version = 20160423;
|
||||
$Global::progname = 'sql';
|
||||
|
||||
# This must be done first as this may exec myself
|
||||
|
|
|
|||
|
|
@ -77,4 +77,10 @@ echo '### bug #45907: --header : + --return {header}'
|
|||
echo "### bug #47608: parallel --nonall -S lo 'echo ::: ' blocks"
|
||||
parallel --nonall -S lo 'echo ::: '
|
||||
|
||||
echo '### exported function to csh but with PARALLEL_SHELL=bash'
|
||||
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
|
||||
|
||||
EOF
|
||||
|
|
|
|||
|
|
@ -62,7 +62,6 @@ bash -c 'echo bug \#43358: shellshock breaks exporting functions using --env _;
|
|||
bug #43358: shellshock breaks exporting functions using --env _
|
||||
Non-shellshock-hardened to non-shellshock-hardened
|
||||
Function non-shellshock-hardened
|
||||
parallel: Warning: Shell functions may not be supported in bash.
|
||||
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'
|
||||
bug #43358: shellshock breaks exporting functions using --env _
|
||||
Non-shellshock-hardened to shellshock-hardened
|
||||
|
|
|
|||
|
|
@ -117,3 +117,8 @@ echo "### bug #47608: parallel --nonall -S lo 'echo ::: ' blocks"
|
|||
### bug #47608: parallel --nonall -S lo 'echo ::: ' blocks
|
||||
parallel --nonall -S lo 'echo ::: '
|
||||
:::
|
||||
echo '### exported function to csh but with PARALLEL_SHELL=bash'
|
||||
### exported function to csh but with PARALLEL_SHELL=bash
|
||||
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
|
||||
CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset doit
|
||||
OK
|
||||
|
|
|
|||
Loading…
Reference in a new issue