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Cleanup for next release.
This commit is contained in:
Ole Tange
parent
1eafde239f
commit
585a29c062
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@ -4,7 +4,7 @@
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Check that documentation is updated (compare to web):
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Fixet for 20150122
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Fixet for 20150422
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git diff last-release-commit
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Unmodified beta since last version => production
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Unmodified alpha since last version => beta
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@ -208,75 +208,21 @@ 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 20150322 ('Hellwig') released
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Subject: GNU Parallel 20150422 ('') released
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GNU Parallel 20150322 ('Hellwig') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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GNU Parallel 20150422 ('') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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Haiku of the month:
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Stand up for your rights.
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VMware does not comply.
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Hellwig goes to court.
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(https://sfconservancy.org/linux-compliance/vmware-lawsuit-faq.html)
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<<>>
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New in this release:
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* --number-of-cores respects 'taskset' on GNU/Linux.
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* <<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
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* --joblog --pipe gives the data send and received in the log.
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* <<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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* GNU Parallel was tested to support 100 GB sized records in --pipe. A few bugs was fixed to support >2 GB records. It works, but is rather slow.
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* GNU Parallel was cited in: RIG: Recalibration and Interrelation of genomic sequence data with the GATK http://www.g3journal.org/content/early/2015/02/13/g3.115.017012.full.pdf+html
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* GNU Parallel was cited in: MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment http://www.worldscientific.com/doi/abs/10.1142/S0219720014500139?af=R&
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* GNU Parallel was cited in: Recent evolution in Rattus norvegicus is shaped by declining effective population size http://biorxiv.org/content/biorxiv/early/2015/03/01/015818.full.pdf
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* GNU Parallel was cited in: Evidence for DCO+ as a probe of ionization in the warm disk surface http://arxiv.org/pdf/1503.02659.pdf
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* GNU Parallel was cited in: De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti) http://gbe.oxfordjournals.org/content/early/2015/03/11/gbe.evv050.full.pdf
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* GNU Parallel was cited in: A General Approach to Network Configuration Analysis http://research.microsoft.com/en-us/um/people/ratul/papers/nsdi2015-batfish.pdf
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* GNU Parallel was cited in: Scrimer: designing primers from transcriptome data http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12403/pdf
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* GNU Parallel was cited in: Efficient Retrieval of Key Material for Inspecting Potentially Malicious Traffic in the Cloud http://sacko.uk/pdf/2015.1.pdf
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* GNU Parallel will be presented at Strataconf: Poor Man's Parallel Pipelines http://strataconf.com/big-data-conference-uk-2015/public/schedule/detail/40031
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* GNU Parallel was used in: https://github.com/alexbyrnes/FCC-Political-Ads_The-Code
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* GNU Parallel was used in: https://github.com/martymac/fpart
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* GNU Parallel was used in: https://github.com/hoytak/diabetic-retinopathy-code
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* GNU Parallel was used in: https://github.com/mehmattski/HybSeqPipeline
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* GNU Parallel was used in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.0/lib/Bio/Roary/JobRunner/Parallel.pm
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* Using GNU Parallel on a Raspberry Pi cluster: http://www.dcglug.org.uk/cluster-progress/
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* An introduction to vector tiling and map reduce in postgis: http://dimensionaledge.com/intro-vector-tiling-map-reduce-postgis/
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* Running scripts in parallel with GNU Parallel: http://code.jasonbhill.com/2015/03/
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* Mahout: Parallelising the creation of DecisionTrees: http://www.markhneedham.com/blog/2012/12/27/mahout-parallelising-the-creation-of-decisiontrees/
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* High-Performance Scientific Computing: Running serial jobs in parallel https://support.scinet.utoronto.ca/education/staticpublic/course178/serial.pdf
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* Parallel cardinality on your laptop https://highonscience.wordpress.com/2015/03/15/parallel-cardinality-on-your-laptop/
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* Experiments about a better locate using grep http://a3nm.net/blog/better_locate.html
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* Homework with GNU Parallel: https://support.scinet.utoronto.ca/education/staticpublic/course178content349.html
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* Parallel - Jobs in Skripten parallelisieren: https://slzm.de/blog/linux-tool-des-tages-parallel-jobs-in-skripten-parallelisieren/#more-612
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* GNU Parallel, czyli 100% użycia procesora http://matmatyk.blogspot.dk/2015/03/gnu-parallel-czyli-100-uzycia-procesora.html
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* Bug fixes and man page updates.
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taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
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GNU Parallel - For people who live life in the parallel lane.
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14
src/parallel
14
src/parallel
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@ -1052,7 +1052,7 @@ sub parse_options {
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sub init_globals {
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# Defaults:
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$Global::version = 20150322;
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$Global::version = 20150323;
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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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@ -3524,6 +3524,7 @@ sub tmpfile {
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# N/A
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if(not $disk_full_fh) {
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($disk_full_fh, $name) = ::tmpfile(SUFFIX => ".df");
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# Separate unlink due to NFS dealing badly with File::Temp
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unlink $name;
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$b8193 = "x"x8193;
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}
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@ -3787,14 +3788,7 @@ sub memfree {
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# Returns:
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# $memfree in bytes
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my $self = shift;
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if(not $self->{'memfree'}) {
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$self->memfree_recompute();
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}
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# if(time - $self->{'last_memfree'} >= 1) {
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# More than 10 seconds old: Recompute
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$self->{'last_memfree'} = time;
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$self->memfree_recompute();
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# }
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$self->memfree_recompute();
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return (not defined $self->{'memfree'} or $self->{'memfree'})
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}
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@ -5640,7 +5634,7 @@ sub max_file_name_length {
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rmdir($testdir."/".$dir);
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$len *= 16;
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$dir = "x"x$len;
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} while (mkdir $testdir."/".$dir);
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} while ($len < $upper and mkdir $testdir."/".$dir);
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# Then search for the actual max length between $len/16 and $len
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my $min = $len/16;
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my $max = $len;
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@ -488,7 +488,7 @@ I<regexp> is a Perl Regular Expression:
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http://perldoc.perl.org/perlre.html
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=item B<--compress> (alpha testing)
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=item B<--compress> (beta testing)
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Compress temporary files. If the output is big and very compressible
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this will take up less disk space in $TMPDIR and possibly be faster
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@ -499,9 +499,9 @@ B<plzip>, B<bzip2>, B<lzma>, B<lzip>, B<xz> in that order, and use the
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first available.
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=item B<--compress-program> I<prg> (alpha testing)
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=item B<--compress-program> I<prg> (beta testing)
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=item B<--decompress-program> I<prg> (alpha testing)
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=item B<--decompress-program> I<prg> (beta testing)
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Use I<prg> for (de)compressing temporary files. It is assumed that I<prg
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-dc> will decompress stdin (standard input) to stdout (standard
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@ -514,9 +514,9 @@ If receiving SIGNING, GNU B<parallel> will send SIGINT to tasks
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running on remote computers thus killing them.
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=item B<--delimiter> I<delim> (alpha testing)
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=item B<--delimiter> I<delim> (beta testing)
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=item B<-d> I<delim> (alpha testing)
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=item B<-d> I<delim> (beta testing)
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Input items are terminated by I<delim>. Quotes and backslash are not
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special; every character in the input is taken literally. Disables
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@ -780,7 +780,7 @@ specified, and for B<-I>{} otherwise. This option is deprecated;
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use B<-I> instead.
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=item B<--joblog> I<logfile> (alpha testing)
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=item B<--joblog> I<logfile> (beta testing)
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Logfile for executed jobs. Save a list of the executed jobs to
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I<logfile> in the following TAB separated format: sequence number,
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@ -1037,9 +1037,9 @@ of each job is saved in a file and the filename is then printed.
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See also: B<--results>
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=item B<--pipe> (alpha testing)
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=item B<--pipe> (beta testing)
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=item B<--spreadstdin> (alpha testing)
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=item B<--spreadstdin> (beta testing)
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Spread input to jobs on stdin (standard input). Read a block of data
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from stdin (standard input) and give one block of data as input to one
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@ -1160,13 +1160,13 @@ exit (used by GNU B<parallel> itself to determine the line length
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on remote computers).
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=item B<--number-of-cpus> (alpha testing)
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=item B<--number-of-cpus> (beta testing)
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Print the number of physical CPUs and exit (used by GNU B<parallel>
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itself to determine the number of physical CPUs on remote computers).
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=item B<--number-of-cores> (alpha testing)
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=item B<--number-of-cores> (beta testing)
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Print the number of CPU cores and exit (used by GNU B<parallel> itself
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to determine the number of CPU cores on remote computers).
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@ -1178,7 +1178,7 @@ Overrides an earlier B<--keep-order> (e.g. if set in
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B<~/.parallel/config>).
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=item B<--nice> I<niceness> (alpha testing)
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=item B<--nice> I<niceness> (beta testing)
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Run the command at this niceness. For simple commands you can just add
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B<nice> in front of the command. But if the command consists of more
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@ -1387,7 +1387,7 @@ useful if some jobs fail for no apparent reason (such as network
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failure).
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=item B<--return> I<filename> (beta testing)
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=item B<--return> I<filename>
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Transfer files from remote computers. B<--return> is used with
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B<--sshlogin> when the arguments are files on the remote computers. When
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@ -1435,7 +1435,7 @@ B<--keep-order> will not work with B<--round-robin> as it is
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impossible to track which input block corresponds to which output.
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=item B<--rpl> 'I<tag> I<perl expression>' (alpha testing)
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=item B<--rpl> 'I<tag> I<perl expression>' (beta testing)
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Use I<tag> as a replacement string for I<perl expression>. This makes
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it possible to define your own replacement strings. GNU B<parallel>'s
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@ -1763,7 +1763,7 @@ the lines will be prepended with the sshlogin instead.
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B<--tag> is ignored when using B<-u>.
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=item B<--tagstring> I<str> (alpha testing)
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=item B<--tagstring> I<str> (beta testing)
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Tag lines with a string. Each output line will be prepended with
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I<str> and TAB (\t). I<str> can contain replacement strings such as
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@ -1780,7 +1780,7 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
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setting $TMPDIR.
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=item B<--tmux> (alpha testing)
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=item B<--tmux> (beta testing)
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Use B<tmux> for output. Start a B<tmux> session and run each job in a
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window in that session. No other output will be produced.
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