mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-12-22 20:57:53 +00:00
Released as 20150622 ('Løkke')
This commit is contained in:
Ole Tange
parent
210e9db387
commit
2ea31ecb17
144
NEWS
144
NEWS
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@ -1,38 +1,148 @@
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20150622
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* --halt has been rewritten completely. You can now combine
|
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percentages with success or fail. See the man page.
|
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|
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* Exit values 102..254 have been removed. 101 means more than 100 jobs
|
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failed.
|
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|
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* Killing through --timeout, --memfree, or --halt is now done as a
|
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process group.
|
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|
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* --termseq determines which signals are sent when a job is killed.
|
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|
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* An empty argument would previously cause no string to be
|
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inserted. This is now changed to '' being inserted, thus prepending
|
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a space to the output of: parallel echo {} b ::: ''
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* $PARALLEL_ENV can now be set to an environment prepending the
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command. Used in env_parallel as mentioned in the manpage.
|
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|
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* --retry-failed will retry all failed jobs in a joblog. It will
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ignore any command given.
|
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|
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* --ssh and $PARALLEL_SSH can be used to set the command used for
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ssh. The command is assumed to behave the same way as ssh.
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* --fifo now works in csh, too.
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* Q(...) can be used in {= =} to shell quote a string.
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* GNU Parallel was cited in: Contrasting regional architectures of
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schizophrenia and other complex diseases using fast variance
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components analysis
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http://biorxiv.org/content/biorxiv/early/2015/06/05/016527.full.pdf
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* GNU Parallel was cited in: DockBench: An Integrated Informatic
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Platform Bridging the Gap between the Robust Validation of Docking
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Protocols and Virtual Screening Simulations
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http://www.mdpi.com/1420-3049/20/6/9977
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* GNU Parallel was cited in: Swedes Online: You Are More Tracked Than
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You Think
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http://www.diva-portal.org/smash/get/diva2:807623/FULLTEXT01.pdf
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* GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D
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scattering and resonance calculations
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http://arxiv.org/pdf/1505.07691.pdf
|
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|
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* GNU Parallel was cited in: A quantitative assessment of the Hadoop
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framework for analyzing massively parallel DNA sequencing data
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http://link.springer.com/article/10.1186/s13742-015-0058-5
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* GNU Parallel was cited in: A composite genome approach to identify
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phylogenetically informative data from next-generation sequencing
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http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
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|
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* GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D
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scattering and resonance calculations
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http://arxiv.org/pdf/1505.07691.pdf
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|
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* GNU Parallel is used in: taxator-tk
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http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/
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* GNU Parallel is used in: https://github.com/d2207197/local-mapreduce
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|
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* GNU Parallel is used in: wiki-edit-news https://github.com/albert-decatur/wiki-edit-news
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|
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* GNU Parallel is used in: A Fingerprint Identification System
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https://curve.carleton.ca/system/files/theses/28733.pdf
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|
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* Job ad asking for GNU Parallel experience:
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http://searchjobs.intel.com/gdansk-pol/software-validation-engineer/63A06826DAF24797AB414DC146201C2E/job/
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|
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* Using BLAT http://wangzhengyuan.blogspot.dk/2015/06/using-blat.html
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* Bug fixes and man page updates.
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|
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20150522
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* Security: The security issue for --sshlogin + --fifo/--cat has been fixed. Thereby all issues with http://lists.gnu.org/archive/html/parallel/2015-04/msg00045.html have been fixed.
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* Security: The security issue for --sshlogin + --fifo/--cat has been
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fixed. Thereby all issues with
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http://lists.gnu.org/archive/html/parallel/2015-04/msg00045.html
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have been fixed.
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* Security: After further security analysis the issue fixed in 20150422 also fixed the problem for --tmux.
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* Security: After further security analysis the issue fixed in
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20150422 also fixed the problem for --tmux.
|
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* GNU Parallel was cited in: 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
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* GNU Parallel was cited in: CIDER: a pipeline for detecting waves of
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coordinated transcriptional regulation in gene expression
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time-course data
|
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http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf
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* GNU Parallel was cited in: Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq http://biorxiv.org/content/biorxiv/early/2015/05/05/018085.full.pdf
|
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* GNU Parallel was cited in: Building Genomic Analysis Pipelines in a
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Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics,
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Metagenomics and RNA-seq
|
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http://biorxiv.org/content/biorxiv/early/2015/05/05/018085.full.pdf
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* 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
|
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* GNU Parallel was cited in: Toward Enhanced Metadata Quality of
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Large-Scale Digital Libraries: Estimating Volume Time Range
|
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https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
|
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* 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
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* GNU Parallel was cited in: Sequencing the cap-snatching repertoire
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of H1N1 influenza provides insight into the mechanism of viral
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transcription initiation
|
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http://nar.oxfordjournals.org/content/early/2015/04/20/nar.gkv333.full.pdf
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* GNU Parallel was cited in: Genome assembly using Nanopore-guided long and error-free DNA reads http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
|
||||
* GNU Parallel was cited in: Genome assembly using Nanopore-guided
|
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long and error-free DNA reads
|
||||
http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.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
|
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schizophrenia and other complex diseases using fast variance
|
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components analysis
|
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http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
|
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|
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* GNU Parallel was used (unfortunately with wrong citation) in: 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
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* GNU Parallel was used (unfortunately with wrong citation) in:
|
||||
Comparing the CarbonTracker and TM5-4DVar data assimilation systems
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for CO2 surface flux inversions
|
||||
http://www.atmos-chem-phys-discuss.net/15/8883/2015/acpd-15-8883-2015-discussion.html
|
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* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method https://bitbucket.org/srp33/gsoa
|
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* GNU Parallel was used in: Gene Set Omic Analysis (GSOA) method
|
||||
https://bitbucket.org/srp33/gsoa
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|
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* A Quick and Neat :) Orchestrator using GNU Parallel http://www.elsotanillo.net/2015/05/a-quick-and-neat-orchestrator-using-gnu-parallel/
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* A Quick and Neat :) Orchestrator using GNU Parallel
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http://www.elsotanillo.net/2015/05/a-quick-and-neat-orchestrator-using-gnu-parallel/
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|
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* 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/
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* Execute commands on multiple computers using GNU Parallel (setting
|
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up a cluster on the cheap)
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||||
https://spectraldifferences.wordpress.com/2015/04/26/execute-commands-on-multiple-computers-using-gnu-parallel-setting-up-a-cluster-on-the-cheap/
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|
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* Functions and GNU parallel for effective cluster load management http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
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* Functions and GNU parallel for effective cluster load management
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http://genomespot.blogspot.dk/2015/04/functions-and-gnu-parallel-for.html
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|
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* Use parallel processing to save time importing databases http://drupalsun.com/node/41854
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* Use parallel processing to save time importing databases
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http://drupalsun.com/node/41854
|
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|
||||
* Run multiple ssh commands in parallel with GNU Parallel http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html
|
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* Run multiple ssh commands in parallel with GNU Parallel
|
||||
http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html
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|
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* Importing huge databases faster https://www.lullabot.com/blog/article/importing-huge-databases-faster
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* Importing huge databases faster
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https://www.lullabot.com/blog/article/importing-huge-databases-faster
|
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|
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* Run multiple ssh commands in parallel with GNU Parallel https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1
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* Run multiple ssh commands in parallel with GNU Parallel
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https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1
|
||||
|
||||
* Parallel? Gnu parallel! https://debian.pro/1834
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12
README
12
README
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|
@ -40,9 +40,9 @@ document.
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|||
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||||
Full installation of GNU Parallel is as simple as:
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||||
wget http://ftpmirror.gnu.org/parallel/parallel-20150607.tar.bz2
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bzip2 -dc parallel-20150607.tar.bz2 | tar xvf -
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cd parallel-20150607
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wget http://ftpmirror.gnu.org/parallel/parallel-20150622.tar.bz2
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bzip2 -dc parallel-20150622.tar.bz2 | tar xvf -
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cd parallel-20150622
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./configure && make && sudo make install
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|
@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
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|||
If you are not root you can add ~/bin to your path and install in
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~/bin and ~/share:
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|
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wget http://ftpmirror.gnu.org/parallel/parallel-20150607.tar.bz2
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||||
bzip2 -dc parallel-20150607.tar.bz2 | tar xvf -
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cd parallel-20150607
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||||
wget http://ftpmirror.gnu.org/parallel/parallel-20150622.tar.bz2
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||||
bzip2 -dc parallel-20150622.tar.bz2 | tar xvf -
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||||
cd parallel-20150622
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./configure --prefix=$HOME && make && make install
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|
||||
Or if your system lacks 'make' you can simply copy src/parallel
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|
|
|
|||
20
configure
vendored
20
configure
vendored
|
|
@ -1,6 +1,6 @@
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|||
#! /bin/sh
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# Guess values for system-dependent variables and create Makefiles.
|
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# Generated by GNU Autoconf 2.69 for parallel 20150607.
|
||||
# Generated by GNU Autoconf 2.69 for parallel 20150622.
|
||||
#
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# Report bugs to <bug-parallel@gnu.org>.
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#
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|
@ -579,8 +579,8 @@ MAKEFLAGS=
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|||
# Identity of this package.
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||||
PACKAGE_NAME='parallel'
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PACKAGE_TARNAME='parallel'
|
||||
PACKAGE_VERSION='20150607'
|
||||
PACKAGE_STRING='parallel 20150607'
|
||||
PACKAGE_VERSION='20150622'
|
||||
PACKAGE_STRING='parallel 20150622'
|
||||
PACKAGE_BUGREPORT='bug-parallel@gnu.org'
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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
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\`configure' configures parallel 20150607 to adapt to many kinds of systems.
|
||||
\`configure' configures parallel 20150622 to adapt to many kinds of systems.
|
||||
|
||||
Usage: $0 [OPTION]... [VAR=VALUE]...
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|
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|
|
@ -1269,7 +1269,7 @@ fi
|
|||
|
||||
if test -n "$ac_init_help"; then
|
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case $ac_init_help in
|
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short | recursive ) echo "Configuration of parallel 20150607:";;
|
||||
short | recursive ) echo "Configuration of parallel 20150622:";;
|
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esac
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cat <<\_ACEOF
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|
|
@ -1345,7 +1345,7 @@ fi
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test -n "$ac_init_help" && exit $ac_status
|
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if $ac_init_version; then
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cat <<\_ACEOF
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parallel configure 20150607
|
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parallel configure 20150622
|
||||
generated by GNU Autoconf 2.69
|
||||
|
||||
Copyright (C) 2012 Free Software Foundation, Inc.
|
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|
|
@ -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 20150607, which was
|
||||
It was created by parallel $as_me 20150622, which was
|
||||
generated by GNU Autoconf 2.69. Invocation command line was
|
||||
|
||||
$ $0 $@
|
||||
|
|
@ -2225,7 +2225,7 @@ fi
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|
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# Define the identity of the package.
|
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PACKAGE='parallel'
|
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VERSION='20150607'
|
||||
VERSION='20150622'
|
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|
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|
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cat >>confdefs.h <<_ACEOF
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|
@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
|
|||
# report actual input values of CONFIG_FILES etc. instead of their
|
||||
# values after options handling.
|
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ac_log="
|
||||
This file was extended by parallel $as_me 20150607, which was
|
||||
This file was extended by parallel $as_me 20150622, which was
|
||||
generated by GNU Autoconf 2.69. Invocation command line was
|
||||
|
||||
CONFIG_FILES = $CONFIG_FILES
|
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|
|
@ -2929,7 +2929,7 @@ _ACEOF
|
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cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
|
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ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
|
||||
ac_cs_version="\\
|
||||
parallel config.status 20150607
|
||||
parallel config.status 20150622
|
||||
configured by $0, generated by GNU Autoconf 2.69,
|
||||
with options \\"\$ac_cs_config\\"
|
||||
|
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|
|
|
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|
|
@ -1,4 +1,4 @@
|
|||
AC_INIT([parallel], [20150607], [bug-parallel@gnu.org])
|
||||
AC_INIT([parallel], [20150622], [bug-parallel@gnu.org])
|
||||
AM_INIT_AUTOMAKE([-Wall -Werror foreign])
|
||||
AC_CONFIG_HEADERS([config.h])
|
||||
AC_CONFIG_FILES([
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|
|
|
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|
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@ -4,7 +4,7 @@
|
|||
|
||||
Check that documentation is updated (compare to web):
|
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|
||||
Fixet for 20150522
|
||||
Fixet for 20150622
|
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git diff last-release-commit
|
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Unmodified beta since last version => production
|
||||
Unmodified alpha since last version => beta
|
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@ -213,6 +213,8 @@ Subject: GNU Parallel 20150622 ('Løkke') released
|
|||
|
||||
GNU Parallel 20150622 ('Løkke') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
|
||||
|
||||
A performance chart has been made to compare the performance of different versions: http://www.gnu.org/software/parallel/boxplot-j2-3.0ghz-3000-1000.pdf The recent jump is due to every job being wrapped in a Perl-script doing setpgrp.
|
||||
|
||||
Haiku of the month:
|
||||
|
||||
Programs very slow.
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|
|
@ -222,12 +224,16 @@ Haiku of the month:
|
|||
|
||||
New in this release:
|
||||
|
||||
* An empty argument would previously cause no string to be inserted. This is now changed to '' being inserted, thus prepending a space to the output of: parallel echo {} b ::: ''
|
||||
|
||||
* --halt has been rewritten completely. You can now combine percentages with success or fail. See the man page.
|
||||
|
||||
* Exit values 102..254 have been removed. 101 means more than 100 jobs failed.
|
||||
|
||||
* Killing through --timeout, --memfree, or --halt is now done as a process group (whence the setpgrp wrapper).
|
||||
|
||||
* --termseq determines which signals are sent when a job is killed.
|
||||
|
||||
* An empty argument would previously cause no string to be inserted. This is now changed to '' being inserted, thus prepending a space to the output of: parallel echo {} b ::: ''
|
||||
|
||||
* $PARALLEL_ENV can now be set to an environment prepending the command. Used in env_parallel as mentioned in the manpage.
|
||||
|
||||
* --retry-failed will retry all failed jobs in a joblog. It will ignore any command given.
|
||||
|
|
@ -236,7 +242,7 @@ New in this release:
|
|||
|
||||
* --fifo now works in csh, too.
|
||||
|
||||
* Killing through --timeout, --memfree, or --halt is now done as a process group.
|
||||
* Q(...) can be used in {= =} to shell quote a string.
|
||||
|
||||
* 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/2015/06/05/016527.full.pdf
|
||||
|
||||
|
|
@ -256,12 +262,12 @@ New in this release:
|
|||
|
||||
* <<Afventer updateret publisering>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487
|
||||
|
||||
* <<kontaktet 2015-05-09>> 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
|
||||
|
||||
* taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
|
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* <<kontaktet 2015-06-22>> 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
|
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|
||||
* << Update forventet juni Rachel har lige svaret >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
|
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|
||||
* GNU Parallel is used in: taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/
|
||||
|
||||
* GNU Parallel is used in: https://github.com/d2207197/local-mapreduce
|
||||
|
||||
* GNU Parallel is used in: wiki-edit-news https://github.com/albert-decatur/wiki-edit-news
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
Summary: Shell tool for executing jobs in parallel
|
||||
Name: parallel
|
||||
Version: 20150522
|
||||
Version: 20150622
|
||||
Release: 1
|
||||
License: GPL
|
||||
Group: Productivity/File utilities
|
||||
|
|
|
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|
|
@ -24,7 +24,7 @@
|
|||
use strict;
|
||||
use Getopt::Long;
|
||||
$Global::progname="niceload";
|
||||
$Global::version = 20150607;
|
||||
$Global::version = 20150622;
|
||||
Getopt::Long::Configure("bundling","require_order");
|
||||
get_options_from_array(\@ARGV) || die_usage();
|
||||
if($opt::version) {
|
||||
|
|
|
|||
|
|
@ -1079,7 +1079,7 @@ sub parse_options {
|
|||
|
||||
sub init_globals {
|
||||
# Defaults:
|
||||
$Global::version = 20150620;
|
||||
$Global::version = 20150622;
|
||||
$Global::progname = 'parallel';
|
||||
$Global::infinity = 2**31;
|
||||
$Global::debug = 0;
|
||||
|
|
@ -6429,6 +6429,7 @@ sub wrapped {
|
|||
if($ENV{'PARALLEL_ENV'}) {
|
||||
# If $PARALLEL_ENV set, put that in front of the command
|
||||
# Used for importing functions for fish
|
||||
# Map \001 to \n to make it easer to quote \n in $PARALLEL_ENV
|
||||
$ENV{'PARALLEL_ENV'} =~ s/\001/\n/g;
|
||||
$command = $ENV{'PARALLEL_ENV'}."\n".$command;
|
||||
}
|
||||
|
|
@ -7074,8 +7075,9 @@ sub start {
|
|||
local (*OUT,*ERR);
|
||||
open OUT, '>&', $stdout_fh or ::die_bug("Can't dup STDOUT: $!");
|
||||
open ERR, '>&', $stderr_fh or ::die_bug("Can't dup STDERR: $!");
|
||||
$pid = ::open3("<&IN", ">&OUT", ">&ERR",
|
||||
"exec $Global::shell -c ".::shell_quote_scalar_default($command)) ||
|
||||
$pid = ::open3("<&IN", ">&OUT", ">&ERR",
|
||||
"exec $Global::shell -c ".
|
||||
::shell_quote_scalar_default($command)) ||
|
||||
::die_bug("open3-/dev/tty");
|
||||
$Global::tty_taken = $pid;
|
||||
close $devtty_fh;
|
||||
|
|
|
|||
|
|
@ -306,7 +306,8 @@ Replace with calculated I<perl expression>. B<$_> will contain the
|
|||
same as B<{}>. After evaluating I<perl expression> B<$_> will be used
|
||||
as the value. It is recommended to only change $_ but you have full
|
||||
access to all of GNU B<parallel>'s internal functions and data
|
||||
structures.
|
||||
structures. You can use the function B<Q(>I<string>B<)> to shell quote
|
||||
a string.
|
||||
|
||||
The B<{=>I<perl expression>B<=}> must be given as a single string.
|
||||
|
||||
|
|
@ -501,7 +502,7 @@ I<size> defaults to 1M.
|
|||
See B<--pipe> and B<--pipepart> for use of this.
|
||||
|
||||
|
||||
=item B<--cat>
|
||||
=item B<--cat> (alpha testing)
|
||||
|
||||
Create a temporary file with content. Normally B<--pipe>/B<--pipepart>
|
||||
will give data to the program on stdin (standard input). With B<--cat>
|
||||
|
|
@ -694,7 +695,7 @@ Implies B<--semaphore>.
|
|||
See also B<--bg>, B<man sem>.
|
||||
|
||||
|
||||
=item B<--fifo>
|
||||
=item B<--fifo> (alpha testing)
|
||||
|
||||
Create a temporary fifo with content. Normally B<--pipe> and
|
||||
B<--pipepart> will give data to the program on stdin (standard
|
||||
|
|
@ -1735,7 +1736,7 @@ 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
|
||||
|
|
@ -1919,8 +1920,8 @@ B<--tagstring> is ignored when using B<-u>, B<--onall>, and B<--nonall>.
|
|||
=item B<--termseq> I<sequence> (alpha testing)
|
||||
|
||||
Termination sequence. When a job is killed due to B<--timeout>,
|
||||
B<--memfree>, or abnormal termination of GNU B<parallel>, I<sequence>
|
||||
determines how the job is killed. The default is:
|
||||
B<--memfree>, B<--halt>, or abnormal termination of GNU B<parallel>,
|
||||
I<sequence> determines how the job is killed. The default is:
|
||||
|
||||
TERM,200,TERM,100,TERM,50,KILL,25
|
||||
|
||||
|
|
|
|||
Loading…
Reference in a new issue