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Ole Tange
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99
NEWS
99
NEWS
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@ -1,3 +1,102 @@
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20150322
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New in this release:
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* --number-of-cores respects 'taskset' on GNU/Linux.
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* --joblog --pipe gives the data send and received in the log.
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* GNU Parallel was tested to support 100 GB sized records in --pipe. A
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few bugs was fixed to support >2 GB records. It works, but is rather
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slow.
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* GNU Parallel was cited in: RIG: Recalibration and Interrelation of
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genomic sequence data with the GATK
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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:
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Improving metagenomic analysis with high performance classification
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and wide taxonomic attachment
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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
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shaped by declining effective population size
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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
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ionization in the warm disk surface
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http://arxiv.org/pdf/1503.02659.pdf
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* GNU Parallel was cited in: De novo assembly and annotation of the
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Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE
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from raw genomic reads and comparative analysis with the yellow
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fever mosquito (Aedes aegypti)
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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
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Configuration Analysis
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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
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transcriptome data
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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
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Inspecting Potentially Malicious Traffic in the Cloud
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http://sacko.uk/pdf/2015.1.pdf
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* GNU Parallel will be presented at Strataconf: Poor Man's Parallel
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Pipelines
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http://strataconf.com/big-data-conference-uk-2015/public/schedule/detail/40031
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* GNU Parallel was used in:
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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:
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https://github.com/hoytak/diabetic-retinopathy-code
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* GNU Parallel was used in:
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https://github.com/mehmattski/HybSeqPipeline
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* GNU Parallel was used in:
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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:
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http://www.dcglug.org.uk/cluster-progress/
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* An introduction to vector tiling and map reduce in postgis:
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http://dimensionaledge.com/intro-vector-tiling-map-reduce-postgis/
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* Running scripts in parallel with GNU Parallel:
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http://code.jasonbhill.com/2015/03/
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* Mahout: Parallelising the creation of DecisionTrees:
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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
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parallel
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https://support.scinet.utoronto.ca/education/staticpublic/course178/serial.pdf
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* Parallel cardinality on your laptop
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https://highonscience.wordpress.com/2015/03/15/parallel-cardinality-on-your-laptop/
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* Experiments about a better locate using grep
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http://a3nm.net/blog/better_locate.html
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* Homework with GNU Parallel:
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https://support.scinet.utoronto.ca/education/staticpublic/course178content349.html
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* Parallel - Jobs in Skripten parallelisieren:
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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
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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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20150222
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* --tmux has gotten a major overhaul.
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12
README
12
README
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@ -40,9 +40,9 @@ document.
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Full installation of GNU Parallel is as simple as:
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wget http://ftpmirror.gnu.org/parallel/parallel-20150222.tar.bz2
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bzip2 -dc parallel-20150222.tar.bz2 | tar xvf -
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cd parallel-20150222
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wget http://ftpmirror.gnu.org/parallel/parallel-20150322.tar.bz2
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bzip2 -dc parallel-20150322.tar.bz2 | tar xvf -
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cd parallel-20150322
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./configure && make && 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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wget http://ftpmirror.gnu.org/parallel/parallel-20150222.tar.bz2
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bzip2 -dc parallel-20150222.tar.bz2 | tar xvf -
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cd parallel-20150222
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wget http://ftpmirror.gnu.org/parallel/parallel-20150322.tar.bz2
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bzip2 -dc parallel-20150322.tar.bz2 | tar xvf -
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cd parallel-20150322
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./configure --prefix=$HOME && make && make install
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Or if your system lacks 'make' you can simply copy src/parallel
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20
configure
vendored
20
configure
vendored
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@ -1,6 +1,6 @@
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#! /bin/sh
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# Guess values for system-dependent variables and create Makefiles.
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# Generated by GNU Autoconf 2.69 for parallel 20150222.
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# Generated by GNU Autoconf 2.69 for parallel 20150322.
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#
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# Report bugs to <bug-parallel@gnu.org>.
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#
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@ -579,8 +579,8 @@ MAKEFLAGS=
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# Identity of this package.
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PACKAGE_NAME='parallel'
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PACKAGE_TARNAME='parallel'
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PACKAGE_VERSION='20150222'
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PACKAGE_STRING='parallel 20150222'
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PACKAGE_VERSION='20150322'
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PACKAGE_STRING='parallel 20150322'
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PACKAGE_BUGREPORT='bug-parallel@gnu.org'
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PACKAGE_URL=''
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@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then
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# Omit some internal or obsolete options to make the list less imposing.
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# This message is too long to be a string in the A/UX 3.1 sh.
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cat <<_ACEOF
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\`configure' configures parallel 20150222 to adapt to many kinds of systems.
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\`configure' configures parallel 20150322 to adapt to many kinds of systems.
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Usage: $0 [OPTION]... [VAR=VALUE]...
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@ -1269,7 +1269,7 @@ fi
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if test -n "$ac_init_help"; then
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case $ac_init_help in
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short | recursive ) echo "Configuration of parallel 20150222:";;
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short | recursive ) echo "Configuration of parallel 20150322:";;
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esac
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cat <<\_ACEOF
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@ -1345,7 +1345,7 @@ fi
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test -n "$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 20150222
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parallel configure 20150322
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generated by GNU Autoconf 2.69
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Copyright (C) 2012 Free Software Foundation, Inc.
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@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
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This file contains any messages produced by compilers while
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running configure, to aid debugging if configure makes a mistake.
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It was created by parallel $as_me 20150222, which was
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It was created by parallel $as_me 20150322, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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$ $0 $@
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@ -2225,7 +2225,7 @@ fi
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# Define the identity of the package.
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PACKAGE='parallel'
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VERSION='20150222'
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VERSION='20150322'
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cat >>confdefs.h <<_ACEOF
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@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
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# report actual input values of CONFIG_FILES etc. instead of their
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# values after options handling.
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ac_log="
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This file was extended by parallel $as_me 20150222, which was
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This file was extended by parallel $as_me 20150322, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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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'`"
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ac_cs_version="\\
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parallel config.status 20150222
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parallel config.status 20150322
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configured by $0, generated by GNU Autoconf 2.69,
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with options \\"\$ac_cs_config\\"
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@ -1,4 +1,4 @@
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AC_INIT([parallel], [20150222], [bug-parallel@gnu.org])
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AC_INIT([parallel], [20150322], [bug-parallel@gnu.org])
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AM_INIT_AUTOMAKE([-Wall -Werror foreign])
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AC_CONFIG_HEADERS([config.h])
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AC_CONFIG_FILES([
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@ -244,13 +244,6 @@ New in this release:
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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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* <<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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* <<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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taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
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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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@ -1,6 +1,6 @@
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Summary: Shell tool for executing jobs in parallel
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Name: parallel
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Version: 20150222
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Version: 20150322
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Release: 1
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License: GPL
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Group: Productivity/File utilities
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20150222;
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$Global::version = 20150322;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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@ -1052,7 +1052,7 @@ sub parse_options {
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sub init_globals {
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# Defaults:
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$Global::version = 20150311;
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$Global::version = 20150322;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -6021,7 +6021,7 @@ sub wrapped {
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::shell_quote_scalar($command);
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} else {
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# Remote systems use $SHELL
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$command = '\nice'. " -n". $opt::nice.
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$command = '\nice'. " -n". $opt::nice.
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' $SHELL -c '.
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::shell_quote_scalar($command);
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}
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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>
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=item B<--compress> (alpha 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>
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=item B<--compress-program> I<prg> (alpha testing)
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=item B<--decompress-program> I<prg>
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=item B<--decompress-program> I<prg> (alpha 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>
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=item B<--delimiter> I<delim> (alpha testing)
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=item B<-d> I<delim>
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=item B<-d> I<delim> (alpha 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>
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=item B<--joblog> I<logfile> (alpha 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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@ -788,6 +788,9 @@ sshlogin, start time as seconds since epoch, run time in seconds,
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bytes in files transferred, bytes in files returned, exit status,
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signal, and command run.
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For B<--pipe> bytes transferred and bytes returned are number of input
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and output of bytes.
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To convert the times into ISO-8601 strict do:
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perl -a -F"\t" -ne \
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@ -1034,9 +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>
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=item B<--pipe> (alpha testing)
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=item B<--spreadstdin>
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=item B<--spreadstdin> (alpha 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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@ -1157,13 +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>
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=item B<--number-of-cpus> (alpha 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>
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=item B<--number-of-cores> (alpha 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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@ -1175,7 +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>
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=item B<--nice> I<niceness> (alpha 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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@ -1432,7 +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>'
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=item B<--rpl> 'I<tag> I<perl expression>' (alpha 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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@ -1760,7 +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> (beta testing)
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=item B<--tagstring> I<str> (alpha 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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@ -1777,7 +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> (beta testing)
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=item B<--tmux> (alpha testing)
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|
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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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|
|
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