mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-11-26 07:57:58 +00:00
Merge security fix into stable.
This commit is contained in:
Ole Tange
commit
09fccc68fc
1
CITATION
1
CITATION
|
|
@ -11,6 +11,7 @@ When using programs that use GNU Parallel to process data for publication please
|
|||
url = {http://www.gnu.org/s/parallel},
|
||||
year = {2011},
|
||||
pages = {42-47}
|
||||
doi = {10.5281/zenodo.16303}
|
||||
}
|
||||
|
||||
(Feel free to use \nocite{Tange2011a})
|
||||
|
|
|
|||
64
NEWS
64
NEWS
|
|
@ -2,45 +2,73 @@
|
|||
|
||||
New in this release:
|
||||
|
||||
* Security fix. An attacker on the local system could make you overwrite one of your own files with a single byte. The problem exist when you use --compress or --tmux or --pipe or --cat or --fifo. The attacker must figure out the randomly chosen file name and create a symlink within a time window of 15 ms.
|
||||
* Security fix. An attacker on the local system could make you
|
||||
overwrite one of your own files with a single byte. The problem
|
||||
exist when you use --compress or --tmux or --pipe or --cat or
|
||||
--fifo. The attacker must figure out the randomly chosen file name
|
||||
and create a symlink within a time window of 15 ms.
|
||||
|
||||
* --shuf will generate all jobs, and shuffle them before running them. This is useful to get a quick preview of the results before running the full batch.
|
||||
* --shuf will generate all jobs, and shuffle them before running
|
||||
them. This is useful to get a quick preview of the results before
|
||||
running the full batch.
|
||||
|
||||
* GNU Parallel now has a DOI: https://dx.doi.org/10.5281/zenodo.16303
|
||||
|
||||
* GNU Parallel was cited in: Scaling Machine Learning for Target Prediction in Drug Discovery using Apache Spark https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf
|
||||
* GNU Parallel was cited in: Scaling Machine Learning for Target
|
||||
Prediction in Drug Discovery using Apache Spark
|
||||
https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf
|
||||
|
||||
* GNU Parallel was cited in: Bayesian inference of protein structure from chemical shift data https://peerj.com/articles/861/
|
||||
* GNU Parallel was cited in: Bayesian inference of protein structure
|
||||
from chemical shift data https://peerj.com/articles/861/
|
||||
|
||||
* GNU Parallel was cited in: Toward Enhanced Metadata Quality of Large-Scale Digital Libraries: Estimating Volume Time Range https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
|
||||
* GNU Parallel was cited in: Toward Enhanced Metadata Quality of
|
||||
Large-Scale Digital Libraries: Estimating Volume Time Range
|
||||
https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
|
||||
|
||||
* GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
|
||||
* GNU Parallel was cited in: Contrasting regional architectures of
|
||||
schizophrenia and other complex diseases using fast variance
|
||||
components analysis
|
||||
http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
|
||||
|
||||
* GNU Parallel was cited in: Experimental study on the Wind Farm Substation Cable Installation Problem http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
|
||||
* GNU Parallel was cited in: Experimental study on the Wind Farm
|
||||
Substation Cable Installation Problem
|
||||
http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
|
||||
|
||||
* GNU Parallel was used in: landsat-gifworks https://github.com/KAPPS-/landsat-gifworks
|
||||
* GNU Parallel was used in: landsat-gifworks
|
||||
https://github.com/KAPPS-/landsat-gifworks
|
||||
|
||||
* GNU Parallel was used in: https://github.com/exascience/elprep
|
||||
|
||||
* GNU Parallel was used in: http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
|
||||
* GNU Parallel was used in:
|
||||
http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
|
||||
|
||||
* GNU Parallel was used in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
|
||||
* GNU Parallel was used in:
|
||||
http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
|
||||
|
||||
* GNU Parallel was used in: Rapid haploid SNP calling https://github.com/tseemann/snippy
|
||||
* GNU Parallel was used in: Rapid haploid SNP calling
|
||||
https://github.com/tseemann/snippy
|
||||
|
||||
* Pictures and Metadata http://www.ozzy.no/2015/02/05/pictures-and-metadata/
|
||||
* Pictures and Metadata
|
||||
http://www.ozzy.no/2015/02/05/pictures-and-metadata/
|
||||
|
||||
* Task automation with bash and parallel https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
|
||||
* Task automation with bash and parallel
|
||||
https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
|
||||
|
||||
* How To: Speed Up File Transfers in Linux using RSync with GNU Parallel http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html
|
||||
* How To: Speed Up File Transfers in Linux using RSync with GNU
|
||||
Parallel
|
||||
http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html
|
||||
|
||||
* Mirroring a Git Repository https://avacariu.me/articles/mirroring-a-git-repository.html
|
||||
* Mirroring a Git Repository
|
||||
https://avacariu.me/articles/mirroring-a-git-repository.html
|
||||
|
||||
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
|
||||
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles
|
||||
https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
|
||||
|
||||
* GNU Parallel (Sebuah Uji Coba) http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
|
||||
* GNU Parallel (Sebuah Uji Coba)
|
||||
http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
|
||||
|
||||
* 你见过的最牛逼的命令行程序是什么？ http://www.zhihu.com/question/29257300
|
||||
* 你见过的最牛逼的命令行程序是什么？
|
||||
http://www.zhihu.com/question/29257300
|
||||
|
||||
* Bug fixes and man page updates.
|
||||
|
||||
|
|
|
|||
|
|
@ -58,6 +58,7 @@ pushd
|
|||
== Upload ==
|
||||
|
||||
export YYYYMMDD=`yyyymmdd`
|
||||
eval `gpg-agent --daemon`
|
||||
make upload
|
||||
|
||||
# Only needed for alpha:
|
||||
|
|
@ -141,8 +142,7 @@ YYYYMMDD=`yyyymmdd`
|
|||
TAG=MyTag
|
||||
echo "Released as $YYYYMMDD ('$TAG')."
|
||||
|
||||
git commit -a
|
||||
|
||||
git commit -a -m "Released as $YYYYMMDD ('$TAG')"
|
||||
git tag -s -m "Released as $YYYYMMDD ('$TAG')" $TAG
|
||||
git tag -s -m "Released as $YYYYMMDD ('$TAG')" $YYYYMMDD
|
||||
|
||||
|
|
@ -209,66 +209,43 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
|
|||
Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
|
||||
Jesse Alama <jesse.alama@gmail.com>
|
||||
|
||||
Subject: GNU Parallel 20150422 ('Germanwings') released
|
||||
Subject: GNU Parallel 20150522 ('Nepal') released
|
||||
|
||||
GNU Parallel 20150422 ('Germanwings') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
|
||||
GNU Parallel 20150522 ('Nepal') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
|
||||
|
||||
Haiku of the month:
|
||||
|
||||
SSH set up?
|
||||
Instant cluster needed now?
|
||||
Many jobs to run.
|
||||
Idle cores is not your thing.
|
||||
Use GNU Parallel.
|
||||
-- Ole Tange
|
||||
|
||||
New in this release:
|
||||
|
||||
* Security fix. An attacker on the local system could make you overwrite one of your own files with a single byte. The problem exist when you use --compress or --tmux or --pipe or --cat or --fifo. The attacker must figure out the randomly chosen file name and create a symlink within a time window of 15 ms.
|
||||
|
||||
* GNU Parallel now has a DOI: https://dx.doi.org/10.5281/zenodo.16303
|
||||
|
||||
* GNU Parallel was cited in: Scaling Machine Learning for Target Prediction in Drug Discovery using Apache Spark https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf
|
||||
|
||||
* GNU Parallel was cited in: Bayesian inference of protein structure from chemical shift data https://peerj.com/articles/861/
|
||||
|
||||
* GNU Parallel was cited in: Toward Enhanced Metadata Quality of Large-Scale Digital Libraries: Estimating Volume Time Range https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
|
||||
|
||||
* GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
|
||||
|
||||
* GNU Parallel was cited in: Experimental study on the Wind Farm Substation Cable Installation Problem http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
|
||||
|
||||
* <<afventer - rykket >> Comparing the CarbonTracker and TM5-4DVar data assimilation systems for CO2 surface flux inversions http://www.atmos-chem-phys-discuss.net/15/8883/2015/acpd-15-8883-2015-discussion.html
|
||||
|
||||
* <<afventer opdatering>> CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf
|
||||
|
||||
|
||||
* <<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
|
||||
|
||||
taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
|
||||
|
||||
* << afventer svar fra Rachel >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
|
||||
|
||||
* GNU Parallel was used in: landsat-gifworks https://github.com/KAPPS-/landsat-gifworks
|
||||
* GNU Parallel was cited in: Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv333.full.pdf
|
||||
|
||||
* GNU Parallel was used in: https://github.com/exascience/elprep
|
||||
* GNU Parallel was cited in: Genome assemblyusing Nanopore-guided long and error-free DNA reads http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
|
||||
|
||||
* GNU Parallel was used in: http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/
|
||||
* GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
|
||||
|
||||
* GNU Parallel was used in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm
|
||||
* <<kontakt>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
|
||||
|
||||
* GNU Parallel was used in: Rapid haploid SNP calling https://github.com/tseemann/snippy
|
||||
* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method https://bitbucket.org/srp33/gsoa
|
||||
|
||||
* Pictures and Metadata http://www.ozzy.no/2015/02/05/pictures-and-metadata/
|
||||
* Execute commands on multiple computers using GNU Parallel (setting up a cluster on the cheap) https://spectraldifferences.wordpress.com/2015/04/26/execute-commands-on-multiple-computers-using-gnu-parallel-setting-up-a-cluster-on-the-cheap/
|
||||
|
||||
* Task automation with bash and parallel https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/
|
||||
|
||||
* How To: Speed Up File Transfers in Linux using RSync with GNU Parallel http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html
|
||||
|
||||
* Mirroring a Git Repository https://avacariu.me/articles/mirroring-a-git-repository.html
|
||||
|
||||
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
|
||||
|
||||
* GNU Parallel (Sebuah Uji Coba) http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
|
||||
|
||||
* 你见过的最牛逼的命令行程序是什么？ http://www.zhihu.com/question/29257300
|
||||
* Functions and GNU parallel for effective cluster load management http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
|
||||
|
||||
* Bug fixes and man page updates.
|
||||
|
||||
|
|
|
|||
|
|
@ -725,7 +725,6 @@ sub options_hash {
|
|||
"use-cpus-instead-of-cores" => \$opt::use_cpus_instead_of_cores,
|
||||
"shellquote|shell_quote|shell-quote" => \$opt::shellquote,
|
||||
"nice=i" => \$opt::nice,
|
||||
"timeout=s" => \$opt::timeout,
|
||||
"tag" => \$opt::tag,
|
||||
"tagstring|tag-string=s" => \$opt::tagstring,
|
||||
"onall" => \$opt::onall,
|
||||
|
|
@ -751,9 +750,7 @@ sub options_hash {
|
|||
"compress" => \$opt::compress,
|
||||
"tty" => \$opt::tty,
|
||||
"T" => \$opt::retired,
|
||||
"halt-on-error|halt=s" => \$opt::halt,
|
||||
"H=i" => \$opt::retired,
|
||||
"retries=i" => \$opt::retries,
|
||||
"dry-run|dryrun" => \$opt::dryrun,
|
||||
"progress" => \$opt::progress,
|
||||
"eta" => \$opt::eta,
|
||||
|
|
@ -779,7 +776,11 @@ sub options_hash {
|
|||
"xapply" => \$opt::xapply,
|
||||
"bibtex" => \$opt::bibtex,
|
||||
"wc|willcite|will-cite|nn|nonotice|no-notice" => \$opt::willcite,
|
||||
# Termination and retries
|
||||
"halt-on-error|halt=s" => \$opt::halt,
|
||||
"memfree=s" => \$opt::memfree,
|
||||
"retries=i" => \$opt::retries,
|
||||
"timeout=s" => \$opt::timeout,
|
||||
# xargs-compatibility - implemented, man, testsuite
|
||||
"max-procs|P=s" => \$opt::jobs,
|
||||
"delimiter|d=s" => \$opt::d,
|
||||
|
|
@ -1053,7 +1054,7 @@ sub parse_options {
|
|||
|
||||
sub init_globals {
|
||||
# Defaults:
|
||||
$Global::version = 20150422;
|
||||
$Global::version = 20150424;
|
||||
$Global::progname = 'parallel';
|
||||
$Global::infinity = 2**31;
|
||||
$Global::debug = 0;
|
||||
|
|
|
|||
|
|
@ -488,7 +488,7 @@ I<regexp> is a Perl Regular Expression:
|
|||
http://perldoc.perl.org/perlre.html
|
||||
|
||||
|
||||
=item B<--compress> (beta testing)
|
||||
=item B<--compress>
|
||||
|
||||
Compress temporary files. If the output is big and very compressible
|
||||
this will take up less disk space in $TMPDIR and possibly be faster
|
||||
|
|
@ -499,9 +499,9 @@ B<plzip>, B<bzip2>, B<lzma>, B<lzip>, B<xz> in that order, and use the
|
|||
first available.
|
||||
|
||||
|
||||
=item B<--compress-program> I<prg> (beta testing)
|
||||
=item B<--compress-program> I<prg>
|
||||
|
||||
=item B<--decompress-program> I<prg> (beta testing)
|
||||
=item B<--decompress-program> I<prg>
|
||||
|
||||
Use I<prg> for (de)compressing temporary files. It is assumed that I<prg
|
||||
-dc> will decompress stdin (standard input) to stdout (standard
|
||||
|
|
@ -514,9 +514,9 @@ If receiving SIGNING, GNU B<parallel> will send SIGINT to tasks
|
|||
running on remote computers thus killing them.
|
||||
|
||||
|
||||
=item B<--delimiter> I<delim> (beta testing)
|
||||
=item B<--delimiter> I<delim>
|
||||
|
||||
=item B<-d> I<delim> (beta testing)
|
||||
=item B<-d> I<delim>
|
||||
|
||||
Input items are terminated by I<delim>. Quotes and backslash are not
|
||||
special; every character in the input is taken literally. Disables
|
||||
|
|
@ -568,7 +568,7 @@ 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
|
||||
|
|
@ -782,7 +782,7 @@ specified, and for B<-I>{} otherwise. This option is deprecated;
|
|||
use B<-I> instead.
|
||||
|
||||
|
||||
=item B<--joblog> I<logfile> (beta testing)
|
||||
=item B<--joblog> I<logfile>
|
||||
|
||||
Logfile for executed jobs. Save a list of the executed jobs to
|
||||
I<logfile> in the following TAB separated format: sequence number,
|
||||
|
|
@ -1039,9 +1039,9 @@ of each job is saved in a file and the filename is then printed.
|
|||
|
||||
See also: B<--results>
|
||||
|
||||
=item B<--pipe> (beta testing)
|
||||
=item B<--pipe>
|
||||
|
||||
=item B<--spreadstdin> (beta testing)
|
||||
=item B<--spreadstdin>
|
||||
|
||||
Spread input to jobs on stdin (standard input). Read a block of data
|
||||
from stdin (standard input) and give one block of data as input to one
|
||||
|
|
@ -1068,7 +1068,7 @@ B<--files> is often used with B<--pipe>.
|
|||
See also: B<--recstart>, B<--recend>, B<--fifo>, B<--cat>, B<--pipepart>.
|
||||
|
||||
|
||||
=item B<--pipepart> (alpha testing)
|
||||
=item B<--pipepart> (beta testing)
|
||||
|
||||
Pipe parts of a physical file. B<--pipepart> works similar to
|
||||
B<--pipe>, but is much faster. It has a few limitations:
|
||||
|
|
@ -1162,13 +1162,13 @@ exit (used by GNU B<parallel> itself to determine the line length
|
|||
on remote computers).
|
||||
|
||||
|
||||
=item B<--number-of-cpus> (beta testing)
|
||||
=item B<--number-of-cpus>
|
||||
|
||||
Print the number of physical CPUs and exit (used by GNU B<parallel>
|
||||
itself to determine the number of physical CPUs on remote computers).
|
||||
|
||||
|
||||
=item B<--number-of-cores> (beta testing)
|
||||
=item B<--number-of-cores>
|
||||
|
||||
Print the number of CPU cores and exit (used by GNU B<parallel> itself
|
||||
to determine the number of CPU cores on remote computers).
|
||||
|
|
@ -1180,7 +1180,7 @@ Overrides an earlier B<--keep-order> (e.g. if set in
|
|||
B<~/.parallel/config>).
|
||||
|
||||
|
||||
=item B<--nice> I<niceness> (beta testing)
|
||||
=item B<--nice> I<niceness>
|
||||
|
||||
Run the command at this niceness. For simple commands you can just add
|
||||
B<nice> in front of the command. But if the command consists of more
|
||||
|
|
@ -1441,7 +1441,7 @@ B<--keep-order> will not work with B<--round-robin> as it is
|
|||
impossible to track which input block corresponds to which output.
|
||||
|
||||
|
||||
=item B<--rpl> 'I<tag> I<perl expression>' (beta testing)
|
||||
=item B<--rpl> 'I<tag> I<perl expression>'
|
||||
|
||||
Use I<tag> as a replacement string for I<perl expression>. This makes
|
||||
it possible to define your own replacement strings. GNU B<parallel>'s
|
||||
|
|
@ -1616,7 +1616,7 @@ Does not run the command but quotes it. Useful for making quoted
|
|||
composed commands for GNU B<parallel>.
|
||||
|
||||
|
||||
=item B<--shuf> (alpha testing)
|
||||
=item B<--shuf> (beta testing)
|
||||
|
||||
Shuffle jobs. When having multiple input sources it is hard to
|
||||
randomize jobs. --shuf will generate all jobs, and shuffle them before
|
||||
|
|
@ -1781,7 +1781,7 @@ the lines will be prepended with the sshlogin instead.
|
|||
B<--tag> is ignored when using B<-u>.
|
||||
|
||||
|
||||
=item B<--tagstring> I<str> (beta testing)
|
||||
=item B<--tagstring> I<str>
|
||||
|
||||
Tag lines with a string. Each output line will be prepended with
|
||||
I<str> and TAB (\t). I<str> can contain replacement strings such as
|
||||
|
|
@ -1798,7 +1798,7 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
|
|||
setting $TMPDIR.
|
||||
|
||||
|
||||
=item B<--tmux> (beta testing)
|
||||
=item B<--tmux>
|
||||
|
||||
Use B<tmux> for output. Start a B<tmux> session and run each job in a
|
||||
window in that session. No other output will be produced.
|
||||
|
|
|
|||
Loading…
Reference in a new issue