Builds on OBS.

NEWS

@@ -1,3 +1,102 @@
+20150322
+
+New in this release:
+
+* --number-of-cores respects 'taskset' on GNU/Linux.
+
+* --joblog --pipe gives the data send and received in the log.
+
+* 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.
+
+* 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
+
+* 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&
+
+* 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
+
+* 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
+
+* 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
+
+* 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
+
+* GNU Parallel was cited in: Scrimer: designing primers from
+  transcriptome data
+  http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12403/pdf
+
+* 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
+
+* GNU Parallel will be presented at Strataconf: Poor Man's Parallel
+  Pipelines
+  http://strataconf.com/big-data-conference-uk-2015/public/schedule/detail/40031
+
+* GNU Parallel was used in:
+  https://github.com/alexbyrnes/FCC-Political-Ads_The-Code
+
+* GNU Parallel was used in: https://github.com/martymac/fpart
+
+* GNU Parallel was used in:
+  https://github.com/hoytak/diabetic-retinopathy-code
+
+* GNU Parallel was used in:
+  https://github.com/mehmattski/HybSeqPipeline
+
+* GNU Parallel was used in:
+  http://search.cpan.org/~ajpage/Bio-Roary-2.0.0/lib/Bio/Roary/JobRunner/Parallel.pm
+
+* Using GNU Parallel on a Raspberry Pi cluster:
+  http://www.dcglug.org.uk/cluster-progress/
+
+* An introduction to vector tiling and map reduce in postgis:
+  http://dimensionaledge.com/intro-vector-tiling-map-reduce-postgis/
+
+* Running scripts in parallel with GNU Parallel:
+  http://code.jasonbhill.com/2015/03/
+
+* Mahout: Parallelising the creation of DecisionTrees:
+  http://www.markhneedham.com/blog/2012/12/27/mahout-parallelising-the-creation-of-decisiontrees/
+
+* High-Performance Scientific Computing: Running serial jobs in
+  parallel
+  https://support.scinet.utoronto.ca/education/staticpublic/course178/serial.pdf
+
+* Parallel cardinality on your laptop
+  https://highonscience.wordpress.com/2015/03/15/parallel-cardinality-on-your-laptop/
+
+* Experiments about a better locate using grep
+  http://a3nm.net/blog/better_locate.html
+
+* Homework with GNU Parallel:
+  https://support.scinet.utoronto.ca/education/staticpublic/course178content349.html
+
+* Parallel - Jobs in Skripten parallelisieren:
+  https://slzm.de/blog/linux-tool-des-tages-parallel-jobs-in-skripten-parallelisieren/#more-612
+
+* GNU Parallel, czyli 100% użycia procesora
+  http://matmatyk.blogspot.dk/2015/03/gnu-parallel-czyli-100-uzycia-procesora.html
+
+* Bug fixes and man page updates.
+
+
 20150222
 
 * --tmux has gotten a major overhaul.

README

@@ -40,9 +40,9 @@ document.
 
 Full installation of GNU Parallel is as simple as:
 
-    wget http://ftpmirror.gnu.org/parallel/parallel-20150222.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20150322.tar.bz2
-    bzip2 -dc parallel-20150222.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20150322.tar.bz2 | tar xvf -
-    cd parallel-20150222
+    cd parallel-20150322
     ./configure && make && make install
 
 
@@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
 If you are not root you can add ~/bin to your path and install in
 ~/bin and ~/share:
 
-    wget http://ftpmirror.gnu.org/parallel/parallel-20150222.tar.bz2
+    wget http://ftpmirror.gnu.org/parallel/parallel-20150322.tar.bz2
-    bzip2 -dc parallel-20150222.tar.bz2 | tar xvf -
+    bzip2 -dc parallel-20150322.tar.bz2 | tar xvf -
-    cd parallel-20150222
+    cd parallel-20150322
     ./configure --prefix=$HOME && make && make install
 
 Or if your system lacks 'make' you can simply copy src/parallel

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for parallel 20150222.
+# Generated by GNU Autoconf 2.69 for parallel 20150322.
 #
 # Report bugs to <bug-parallel@gnu.org>.
 #
@@ -579,8 +579,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='parallel'
 PACKAGE_TARNAME='parallel'
-PACKAGE_VERSION='20150222'
+PACKAGE_VERSION='20150322'
-PACKAGE_STRING='parallel 20150222'
+PACKAGE_STRING='parallel 20150322'
 PACKAGE_BUGREPORT='bug-parallel@gnu.org'
 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
-\`configure' configures parallel 20150222 to adapt to many kinds of systems.
+\`configure' configures parallel 20150322 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1269,7 +1269,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of parallel 20150222:";;
+     short | recursive ) echo "Configuration of parallel 20150322:";;
    esac
   cat <<\_ACEOF
 
@@ -1345,7 +1345,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-parallel configure 20150222
+parallel configure 20150322
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -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 20150222, which was
+It was created by parallel $as_me 20150322, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2225,7 +2225,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='parallel'
- VERSION='20150222'
+ VERSION='20150322'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -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.
 ac_log="
-This file was extended by parallel $as_me 20150222, which was
+This file was extended by parallel $as_me 20150322, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2929,7 +2929,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-parallel config.status 20150222
+parallel config.status 20150322
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20150222], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20150322], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

doc/release_new_version

@@ -244,13 +244,6 @@ New in this release:
 
 * 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
 
-
-* <<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)
-
 * GNU Parallel will be presented at Strataconf: Poor Man's Parallel Pipelines http://strataconf.com/big-data-conference-uk-2015/public/schedule/detail/40031
 
 * GNU Parallel was used in: https://github.com/alexbyrnes/FCC-Political-Ads_The-Code

packager/obs/home:tange/parallel/parallel.spec

@@ -1,6 +1,6 @@
 Summary:	Shell tool for executing jobs in parallel
 Name: 		parallel
-Version: 	20150222
+Version: 	20150322
 Release: 	1
 License: 	GPL
 Group: 		Productivity/File utilities

src/niceload

@@ -24,7 +24,7 @@
 use strict;
 use Getopt::Long;
 $Global::progname="niceload";
-$Global::version = 20150222;
+$Global::version = 20150322;
 Getopt::Long::Configure("bundling","require_order");
 get_options_from_array(\@ARGV) || die_usage();
 if($opt::version) {

src/parallel

@@ -1052,7 +1052,7 @@ sub parse_options {
 
 sub init_globals {
     # Defaults:
-    $Global::version = 20150311;
+    $Global::version = 20150322;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;
@@ -6021,7 +6021,7 @@ sub wrapped {
 		    ::shell_quote_scalar($command);
 	    } else {
 		# Remote systems use $SHELL
-		$command = '\nice'. " -n". $opt::nice. 
+		$command = '\nice'. " -n". $opt::nice.
 		    ' $SHELL -c '.
 		    ::shell_quote_scalar($command);
 	    }

src/parallel.pod

@@ -488,7 +488,7 @@ I<regexp> is a Perl Regular Expression:
 http://perldoc.perl.org/perlre.html
 
 
-=item B<--compress>
+=item B<--compress> (alpha testing)
 
 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>
+=item B<--compress-program> I<prg> (alpha testing)
 
-=item B<--decompress-program> I<prg>
+=item B<--decompress-program> I<prg> (alpha testing)
 
 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>
+=item B<--delimiter> I<delim> (alpha testing)
 
-=item B<-d> I<delim>
+=item B<-d> I<delim> (alpha testing)
 
 Input items are terminated by I<delim>.  Quotes and backslash are not
 special; every character in the input is taken literally.  Disables
@@ -780,7 +780,7 @@ specified, and for B<-I>{} otherwise.  This option is deprecated;
 use B<-I> instead.
 
 
-=item B<--joblog> I<logfile>
+=item B<--joblog> I<logfile> (alpha testing)
 
 Logfile for executed jobs. Save a list of the executed jobs to
 I<logfile> in the following TAB separated format: sequence number,
@@ -788,6 +788,9 @@ sshlogin, start time as seconds since epoch, run time in seconds,
 bytes in files transferred, bytes in files returned, exit status,
 signal, and command run.
 
+For B<--pipe> bytes transferred and bytes returned are number of input
+and output of bytes.
+
 To convert the times into ISO-8601 strict do:
 
   perl -a -F"\t" -ne \
@@ -1034,9 +1037,9 @@ of each job is saved in a file and the filename is then printed.
 
 See also: B<--results>
 
-=item B<--pipe>
+=item B<--pipe> (alpha testing)
 
-=item B<--spreadstdin>
+=item B<--spreadstdin> (alpha testing)
 
 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
@@ -1157,13 +1160,13 @@ exit (used by GNU B<parallel> itself to determine the line length
 on remote computers).
 
 
-=item B<--number-of-cpus>
+=item B<--number-of-cpus> (alpha testing)
 
 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>
+=item B<--number-of-cores> (alpha testing)
 
 Print the number of CPU cores and exit (used by GNU B<parallel> itself
 to determine the number of CPU cores on remote computers).
@@ -1175,7 +1178,7 @@ Overrides an earlier B<--keep-order> (e.g. if set in
 B<~/.parallel/config>).
 
 
-=item B<--nice> I<niceness>
+=item B<--nice> I<niceness> (alpha testing)
 
 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
@@ -1432,7 +1435,7 @@ 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>'
+=item B<--rpl> 'I<tag> I<perl expression>' (alpha testing)
 
 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
@@ -1760,7 +1763,7 @@ 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> (alpha testing)
 
 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
@@ -1777,7 +1780,7 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
 setting $TMPDIR.
 
 
-=item B<--tmux> (beta testing)
+=item B<--tmux> (alpha testing)
 
 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.

src/sql

@@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20150222;
+    $Global::version = 20150322;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself