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make 1 # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: parallel-20141022/COPYING0000644000175000017500000010451311537752476014207 0ustar rbritorbrito GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. 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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. 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Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . parallel-20141022/install-sh0000755000175000017500000003325512422006253015137 0ustar rbritorbrito#!/bin/sh # install - install a program, script, or datafile scriptversion=2011-11-20.07; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # 'make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. nl=' ' IFS=" "" $nl" # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit=${DOITPROG-} if test -z "$doit"; then doit_exec=exec else doit_exec=$doit fi # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_glob='?' initialize_posix_glob=' test "$posix_glob" != "?" || { if (set -f) 2>/dev/null; then posix_glob= else posix_glob=: fi } ' posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false no_target_directory= usage="\ Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE or: $0 [OPTION]... SRCFILES... DIRECTORY or: $0 [OPTION]... -t DIRECTORY SRCFILES... or: $0 [OPTION]... -d DIRECTORIES... In the 1st form, copy SRCFILE to DSTFILE. In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. In the 4th, create DIRECTORIES. Options: --help display this help and exit. --version display version info and exit. -c (ignored) -C install only if different (preserve the last data modification time) -d create directories instead of installing files. -g GROUP $chgrpprog installed files to GROUP. -m MODE $chmodprog installed files to MODE. -o USER $chownprog installed files to USER. -s $stripprog installed files. -t DIRECTORY install into DIRECTORY. -T report an error if DSTFILE is a directory. Environment variables override the default commands: CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG " while test $# -ne 0; do case $1 in -c) ;; -C) copy_on_change=true;; -d) dir_arg=true;; -g) chgrpcmd="$chgrpprog $2" shift;; --help) echo "$usage"; exit $?;; -m) mode=$2 case $mode in *' '* | *' '* | *' '* | *'*'* | *'?'* | *'['*) echo "$0: invalid mode: $mode" >&2 exit 1;; esac shift;; -o) chowncmd="$chownprog $2" shift;; -s) stripcmd=$stripprog;; -t) dst_arg=$2 # Protect names problematic for 'test' and other utilities. case $dst_arg in -* | [=\(\)!]) dst_arg=./$dst_arg;; esac shift;; -T) no_target_directory=true;; --version) echo "$0 $scriptversion"; exit $?;; --) shift break;; -*) echo "$0: invalid option: $1" >&2 exit 1;; *) break;; esac shift done if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then # When -d is used, all remaining arguments are directories to create. # When -t is used, the destination is already specified. # Otherwise, the last argument is the destination. 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We just wanted to have am__tar # and am__untar set. test -n "${am_cv_prog_tar_$1}" && break # tar/untar a dummy directory, and stop if the command works. rm -rf conftest.dir mkdir conftest.dir echo GrepMe > conftest.dir/file AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) rm -rf conftest.dir if test -s conftest.tar; then AM_RUN_LOG([$am__untar /dev/null 2>&1 && break fi done rm -rf conftest.dir AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) AC_MSG_RESULT([$am_cv_prog_tar_$1])]) AC_SUBST([am__tar]) AC_SUBST([am__untar]) ]) # _AM_PROG_TAR parallel-20141022/CITATION0000644000175000017500000000111612410302244014253 0ustar rbritorbritoWhen using programs that use GNU Parallel to process data for publication please cite: @article{Tange2011a, title = {GNU Parallel - The Command-Line Power Tool}, author = {O. Tange}, address = {Frederiksberg, Denmark}, journal = {;login: The USENIX Magazine}, month = {Feb}, number = {1}, volume = {36}, url = {http://www.gnu.org/s/parallel}, year = {2011}, pages = {42-47} } (Feel free to use \nocite{Tange2011a}) Or: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. This helps funding further development. parallel-20141022/config.h.in0000644000175000017500000000116112422006252015144 0ustar rbritorbrito/* config.h.in. Generated from configure.ac by autoheader. */ /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Version number of package */ #undef VERSION parallel-20141022/README0000644000175000017500000000604212422006235014005 0ustar rbritorbrito GNU Parallel README Please send problems and feedback to bug-parallel@gnu.org. = Presentation of GNU Parallel = GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job is can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU Parallel can then split the input and pipe it into commands in parallel. If you use xargs and tee today you will find GNU Parallel very easy to use as GNU Parallel is written to have the same options as xargs. If you write loops in shell, you will find GNU Parallel may be able to replace most of the loops and make them run faster by running several jobs in parallel. GNU Parallel makes sure output from the commands is the same output as you would get had you run the commands sequentially. This makes it possible to use output from GNU Parallel as input for other programs. = 10 seconds installation = The 10 seconds installation will try do to a full installation; if that fails, a personal installation; if that fails, a minimal installation. (wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash This will literally install faster than reading the rest of this document. = Full installation = Full installation of GNU Parallel is as simple as: wget http://ftpmirror.gnu.org/parallel/parallel-20141022.tar.bz2 bzip2 -dc parallel-20141022.tar.bz2 | tar xvf - cd parallel-20141022 ./configure && make && make install = Personal installation = 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-20141022.tar.bz2 bzip2 -dc parallel-20141022.tar.bz2 | tar xvf - cd parallel-20141022 ./configure --prefix=$HOME && make && make install Or if your system lacks 'make' you can simply copy src/parallel src/sem src/niceload src/sql to a dir in your path. = Minimal installation = If you just need parallel and do not have 'make' installed (maybe the system is old or Microsoft Windows): wget http://git.savannah.gnu.org/cgit/parallel.git/plain/src/parallel chmod 755 parallel cp parallel sem mv parallel sem dir-in-your-$PATH/bin/ = Test the installation = After this you should be able to do: parallel -j0 ping -nc 3 ::: foss.org.my gnu.org freenetproject.org This will send 3 ping packets to 3 different hosts in parallel and print the output when they complete. Watch the intro video for a quick introduction: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1 Walk through the tutorial (man parallel_tutorial). You command line will love you for it. When using programs that use GNU Parallel to process data for publication please cite: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. = New versions = New versions will be released at: ftp://ftp.gnu.org/gnu/parallel/ parallel-20141022/NEWS0000644000175000017500000020346012422006446013633 0ustar rbritorbrito20141022 * --env was changed to deal with Bash's new way of exporting a function. * GNU Parallel was cited in: Exclusion of cosmic rays in protoplanetary disks. II. Chemical gradients and observational signatures http://iopscience.iop.org/0004-637X/794/2/123/article * GNU Parallel was cited in: Application of Machine Learning to Algorithm Selection for TSP http://www.dbai.tuwien.ac.at/staff/musliu/art_ictai_cam.pdf * GNU Parallel was cited in: Performance Models for LTE-Advanced Random Access http://repository.asu.edu/attachments/137242/content/Tyagi_asu_0010E_14116.pdf * GNU Parallel was used (unfortunately without citation) in: De Novo Insertions and Deletions of Predominantly Paternal Origin Are Associated with Autism Spectrum Disorder http://www.cell.com/cms/attachment/2019079667/2039310868/mmc1.pdf * GNU Parallel was determined 'popular' by Statistical Analysis of Popular Open Source Software Projects and Their Communities http://andiwre.itmaranatha.org/prosiding/ICITEE2014/PaperAndiWRE-ICITEE2014.pdf * GNU Parallel is demonstrated in: Data Science at the Command Line: Facing the Future with Time-Tested Tools * GNU Parallel was covered in a talk at Sydney Perl Mongers group http://www.openfusion.net/talks/pwp/#24 * GNU Parallel and how to get started with it http://www.jduck.net/blog/2014/09/30/gnu-paralell/ * Behat/Selenium/Parallel http://jaffamonkey.com/behat-selenium-parallel/ * Comparing Golang, Scala, Elixir and Ruby for ETL http://www.dimroc.com/2014/09/29/etl-language-showdown/ * Parallelizing Batch Jobs for Fun and Profit http://mikeseidle.com/tech/programming/2013/03/parallelizing-batch-jobs * Assemble a list of which of these hosts are up or down http://opsfun.wordpress.com/2014/03/31/gnu-parallel/ * Running commands on many nodes simultaneously http://opsfun.wordpress.com/2014/03/31/19/ * Ubuntu 13.04でGNU ParallelをGNUモードで動かす http://qiita.com/YusukeSuzuki@github/items/7b96b5876bf980f21e85 * Bug fixes and man page updates. 20140922 * If the file give as --sshloginfile is changed it will be re-read when a job finishes though at most once per second. This makes it possible to add and remove hosts while running. * Brutha uses GNU Parallel https://pypi.python.org/pypi/brutha/1.0.2 * OCRmyPDF uses GNU Parallel https://github.com/fritz-hh/OCRmyPDF/ * GNU Parallel was presented at Balti and Bioinformatics "On-Air" http://youtu.be/UtXlr19xTh8?t=2h5m0s * Pleiades Plus uses GNU Parallel https://github.com/ryanfb/pleiades-plus * Imagemagick and GNU Parallel http://deepdish.io/2014/09/15/gnu-parallel/ * GNU Parallel (Sebuah Uji Coba) http://pr4ka5a.wordpress.com/2014/09/04/gnu-parallel-sebuah-uji-coba/ * GNU Parallel: 并行执行Linux命令 http://blog.csdn.net/xzz_hust/article/details/39183837 20140822 * GNU Parallel now uses the same shell it was started from as the command shell for local jobs. So if GNU Parallel is started from tcsh it will use tcsh as its shell even if the login $SHELL is different. For remote jobs the login $SHELL will be used. * The whole current environment in bash can be copied by using a shell wrapper function (Search manual for env_parallel). * --plus adds the replacement strings {+/} {+.} {+..} {+...} {..} {...} {/..} {/...}. The idea being that '+foo' matches the opposite of 'foo' and {} = {+/}/{/} = {.}.{+.} = {+/}/{/.}.{+.} = {..}.{+..} = {+/}/{/..}.{+..} = {...}.{+...} = {+/}/{/...}.{+...} * GNU Parallel now deals correctly with the combination rsync-3.1.X-client and rsync-2.5.7-server * GNU Parallel was cited in: A Web Service for Scholarly Big Data Information Extraction http://patshih.ist.psu.edu/publications/Williams-CiteSeerExtractor-ICWS14.pdf * Comparison of the speed of different GNU Parallel versions: http://lists.gnu.org/archive/html/parallel/2014-08/msg00030.html * GNU Parallel was covered in the webcast 2014-08-20: Data Science at the Command Line http://www.oreilly.com/pub/e/3115 * Distributed processing with GNU parallel http://kazjote.eu/2014/08/11/distributed-processing-with-gnu-parallel * A Peek into GNU Parallel http://blog.dataweave.in/post/94238943763/a-peek-into-gnu-parallel * Сборка GNU parallel для CentOS/RHEL http://www.stableit.ru/2014/07/gnu-parallel-centosrhel.html * Bug fixes and man page updates. 20140722 * {= perl expression =} can be used as replacement string. The expression should modify $_. E.g. {= s/\.gz$// =} to remove .gz from the string. This makes replacement strings extremely flexible. * Positional perl expressions (similar to {2}) are given as {=2 perl expression=} where 2 is the position. * One small backwards incompatibility: {1}_{2} will replace {2} with the empty string if there is only one argument. Previously {2} would have been left untouched. * Replacement strings can be defined using --rpl. E.g. parallel --rpl '{.gz} s/\.gz$//' echo {.gz} ::: *.gz * The parenthesis around {= perl expression =} can be changed with --parens. * --tmux will direct the output to a tmux session instead of files. Each running jobs will be in its own window. * --halt 10% will stop spawning new jobs if 10% failed so far. * GNU Parallel was cited in: bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS) http://bioinformatics.oxfordjournals.org/content/early/2014/06/28/bioinformatics.btu410.abstract * GNU Parallel was cited in: Molecular ferroelectric contributions to anomalous hysteresis in hybrid perovskite solar cells http://people.bath.ac.uk/aw558/publications/2014/arxiv_hysteresis_14.pdf * GNU Parallel was cited in: Energy Sorghum-a genetic model for the design of C4 grass bioenergy crops http://jxb.oxfordjournals.org/content/early/2014/06/20/jxb.eru229.short * GNU Parallel was cited in: Web-scale Content Reuse Detection www.isi.edu/~johnh/PAPERS/Ardi14a.pdf * Tell your friends to sign up for the Webcast at 2014-08-20 covering GNU Parallel: Data Science at the Command Line http://www.oreilly.com/pub/e/3115 * GNU Parallel all the things! http://longwayaround.org.uk/notes/gnu-parallel-all-the-things/ * Shell command composition and dispatch http://lukeluo.blogspot.dk/2014/07/linux-virtual-console6-shell-command.html * Parallelising plink (or anything else) the easy way http://chrisladroue.com/2012/03/parallelising-plink-or-anything-else-the-easy-way/ * Easy and cheap cluster building on AWS https://grapeot.me/easy-and-cheap-cluster-building-on-aws.html * Paralelizace běžných činností v konzoli pomocí GNU Parallel http://www.abclinuxu.cz/clanky/paralelizace-beznych-cinnosti-v-konzoli-pomoci-gnu-parallel * [原] Ubuntu 下使用 parallel 命令的注意事项 http://blog.ailms.me/2014/06/28/ubuntu-with-parallel.html * 简单的并行, 可使用GNU parallel http://jerkwin.github.io/2014/06/10/GNU-parallel/ * Bug fixes and man page updates. 20140622 * --shebang and --shebang-wrap now works on FreeBSD. * --pipepart works with --header, --regexp, --cat and --fifo. * ./configure --disable-documentation will not build documentation. * {%} works as job slot. * GNU Parallel was cited in: Energy Efficient, High-speed Communication in WSNs https://gupea.ub.gu.se/bitstream/2077/35801/1/gupea_2077_35801_1.pdf * GNU Parallel was cited in: Ferroelectric contributions to anomalous hysteresis in hybrid perovskite solar cells http://arxiv.org/pdf/1405.5810.pdf * Processes Paralleling to Speed up Computing and Tasks Execution in Linux http://kukuruku.co/hub/nix/processes-paralleling-to-speed-up-computing-and-tasks-execution-in-linux * Moving / Copying lots of s3 files quickly using gnu parallel http://blog.aclarke.eu/moving-copying-lots-of-s3-files-quickly-using-gnu-parallel/ * Speeding up grep log queries with GNU Parallel http://www.tripwire.com/state-of-security/incident-detection/speeding-grep-queries-gnu-parallel/ * Ubuntu - Gnu parallel - It's awesome http://kasunweranga.blogspot.dk/2014/06/ubuntu-gnu-parallel-its-awesome.html * Export quicklooks with vector overlay using TuiView http://spectraldifferences.wordpress.com/2014/03/08/export-quicklooks-with-vector-overlay-using-tuiview/ * GNU Parallel指南 http://my.oschina.net/enyo/blog/271612 * GNU parallelで違和感 http://jarp.does.notwork.org/diary/201405c.html#201405301 * Bug fixes and man page updates. 20140522 * Use --semaphoretimeout to ignore the semaphore lock after a while. * {%} introduced as job slot replacement string. It has known bugs. * --slotreplace changes slot replacement string. * GNU Parallel officially in Solaris 11.2beta https://blogs.oracle.com/alanc/entry/solaris_11_2_changes_to * GNU Parallel was cited in: A Comparison of Antenna Placement Algorithms http://abhinavjauhri.com/publications/eap.pdf * Using GNU Parallel on a PBS cluster (nice use of --shebang-wrap) https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing * BioLite uses GNU Parallel: https://bitbucket.org/caseywdunn/biolite * Isitdown uses GNU Parallel: http://www.isi.edu/~calvin/isitdown.md * Convert FLAC to MP3 with GNU parallel http://www.blogobramje.nl/posts/Convert_FLAC_to_MP3_with_GNU_parallel/ * JD Edwards Business Function Documentation http://www.azertech.net/content/jd-edwards-business-function-documentation * Tools of the trade http://blog.eikeland.se/2014/05/01/tools-of-the-trade/ * How I start a bioinformatics project http://nickloman.github.io/2014/05/14/how-i-start-a-bioinformatics-project/ * No:The-Me GNU Parallel http://adityalaghate.in/gnu-parallel.html * Bug fixes and man page updates. 20140422 * --pipepart is a highly efficient alternative to --pipe if the input is a real file and not a pipe. * If using --cat or --fifo with --pipe the {} in the command will be replaced with the name of a physical file and a fifo respectively containing the block from --pipe. Useful for commands that cannot read from standard input (stdin). * --controlmaster has gotten an overhaul and is no longer experimental. * --env is now copied when determining CPUs on remote system. Useful for copying $PATH if parallel is not in the normal path. * --results now chops the argument if the argument is longer than the allowed path length. * Build now survives if pod2* are not installed. * The git repository now contains tags of releases. * GNU Parallel was cited in: Proactive System for Digital Forensic Investigation http://dspace.library.uvic.ca:8080/bitstream/handle/1828/5237/Alharbi_Soltan_PhD_2014.pdf * GNU Parallel was cited in: Beyond MAP estimation with the track-oriented multiple hypothesis tracker http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=6766651&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6766651 * GNU Parallel was cited in: Prokka: rapid prokaryotic genome annotation http://bioinformatics.oxfordjournals.org/content/early/2014/03/18/bioinformatics.btu153.short * GNU Parallel was used (unfortunately with improper citation) in: Perspectives in magnetic resonance: NMR in the post-FFT era http://www.sciencedirect.com/science/article/pii/S1090780713003054 * GNU Parallel is used in https://github.com/cc2qe/speedseq * Batch XML validation at the command line. http://horothesia.blogspot.dk/2014/04/batch-xml-validation-at-command-line.html * freebayes-parallel uses GNU Parallel https://github.com/ekg/freebayes/commit/31ee997984cebe8a196381c3de57e618e34a2281 * Org-mode with Parallel Babel http://draketo.de/english/emacs/parallel-babel#sec-2 * Speeding Up Grep Log Queries with GNU Parallel http://www.cybersecurity.io/speeding-grep-queries-gnu-parallel/ * How to run tbss_2_reg in parallel http://tadpolebrainimaging.blogspot.dk/2014/03/how-to-run-tbss2reg-in-parallel.html * GNU parallel example: blastn https://asciinema.org/a/8775 * Iterative DNS Brute Forcing http://www.room362.com/blog/2014/02/19/iterative-dns-brute-forcing/ * Ejecutando comandos en paralelo http://jesusmercado.com/guias/ejecutando-comandos-en-paralelo/ * Ejecutando en paralelo en bash (ejemplo con rsync) http://eithel-inside.blogspot.dk/2014/04/ejecutando-en-paralelo-en-bash-ejemplo.html * Bug fixes and man page updates. 20140322 * Offical package for Alpine Linux now exists: http://alpinelinux.org/apk/main/x86/parallel * GNU Parallel was cited in: Estimating uncertainties in statistics computed from direct numerical simulation http://dx.doi.org/10.1063/1.4866813 * GNU Parallel was cited in: Vehicle routing problems with time windows and multiple service workers: a systematic comparison between ACO and GRASP http://link.springer.com/article/10.1007/s10100-014-0341-z * GNU Parallel, quick and easy http://www.reganmian.net/blog/2014/03/09/gnu-parallel-quick-and-easy/ * Using Multiple CPU Cores With Command Line Tools http://prateekvjoshi.com/2014/03/07/using-multiple-cpu-cores-with-command-line-tools/ * Batch convert mp3 CBR to VBR http://blogs.zercle.com/bouroo/2013/03/batch-convert-mp3-cbr-to-vbr/ * Running Behat in parallel with Selenium grid http://zalas.eu/running-behat-in-parallel-with-selenium-grid/ * Git-Mirror per cronjob aktuell halten https://www.schtobia.de/2013/git-mirror-per-cronjob-aktuell-halten/ * Пишем многопоточный скрипт на bash http://dafter.ru/duf/howto/130.html * 如何利用多核CPU来加速你的Linux命令 http://www.chinadmd.com/file/xpcr6wpctzwtuu3ivwiaatcs_1.html * Bug fixes and man page updates. 20140222 * --tollef has been retired. * --compress has be redesigned due to bugs. * Format of --eta and --joblog has changed slightly. * GNU Parallel was cited in: Speaker Verification and Keyword Spotting Systems for Forensic Applications http://lantana.tenet.res.in/website_files/thesis/Phd/srikanth.pdf * GNU Parallel was cited in: Scaleable Code Clone Detection http://scg.unibe.ch/archive/phd/schwarz-phd.pdf * GNU Parallel was cited in: Clone Detection that scales http://scg.unibe.ch/archive/masters/Vogt14a.pdf * GNU Parallel was cited in: Scalable Positional Analysis for Studying Evolution of Nodes in Networks http://arxiv-web3.library.cornell.edu/pdf/1402.3797 * GNU Parallel was cited in: Aggregate Characterization of User Behavior in Twitter and Analysis of the Retweet Graph http://arxiv.org/pdf/1402.2671v1 * GNU Parallel was used (unfortunately without citation) in: Causal Network Models for Predicting Compound Targets and Driving Pathways in Cancer http://jbx.sagepub.com/content/early/2014/02/10/1087057114522690.full * GNU Parallel was used (unfortunately without citation) in: Performance and Energy Efficiency of Common Compression / Decompression Utilities http://www.researchgate.net/publication/243962643_Performance_and_Energy_Efficiency_of_Common_CompressionDecompression_Utilities_An_Experimental_Study_in_Mobile_and_Workstation_Computer_Platforms/file/3deec51d1dbc0474f9.pdf * GNU Parallel was used (unfortunately without citation) in: SpringFS: Bridging Agility and Performance in Elastic Distributed Storage http://www.istc-cc.cmu.edu/publications/papers/2014/SpringFS-FAST14.pdf * GNU Parallel was recommended (without citation) in: Redesigning the Specificity of Protein-DNA Interactions with Rosetta http://link.springer.com/protocol/10.1007/978-1-62703-968-0_17 * GNU Parallel is co-distributed with RepeatExplorer http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt * Convert MP3 to a scrolling spectrum waterfall plot video http://jdesbonnet.blogspot.dk/2014/02/convert-mp3-to-scrolling-spectrum.html * PHP wrapper class for the GNU Parallel tool https://github.com/geopal-solutions/gnu-parallel-wrapper/tree/master * Exploratory Data Analysis http://www.slideshare.net/thinrhino/gnunify * Copias de archivos con rsync y parallel http://linuxmanr4.com/2014/02/20/copias-de-archivos-con-rsync-y-parallel * Single-Thread-Programme auf Multicore-Rechnern parallelisieren http://www.adlerweb.info/blog/2014/02/08/linux-single-thread-programme-auf-multicore-rechnern-parallelisieren * Распараллеливаем процессы для ускорения вычислений и выполнения заданий в Linux http://savepearlharbor.com/?p=210480 * Bug fixes and man page updates. 20140122 * GNU Parallel was cited in: On the likelihood of multiple bit upsets in logic circuits http://arxiv-web3.library.cornell.edu/pdf/1401.1003 * HaploClique uses GNU Parallel https://github.com/armintoepfer/haploclique * Scraping NSScreencast https://blog.nicolai86.eu/posts/2014-01-12/scraping-nsscreencast/ * 30 Cool Open Source Software I Discovered in 2013 http://www.cyberciti.biz/open-source/30-cool-best-open-source-softwares-of-2013/ * [Unix] 13. The power of doing things in Parallel http://leetaey.tistory.com/384 * Parallel the execution of a job that read from stdin http://www.linuxask.com/questions/parallel-the-execution-of-a-job-that-read-from-stdin * Mon Make à moi (6:38-11:50) http://videos.rennes.inria.fr/ReNaBI-GO2013/indexPierreLindenbaum.html * Shell-Abarbeitung beschleunigen: Wie Sie mit parallelen Prozesse effizienter in der Shell arbeiten https://www.hosteurope.ch/blog/shell-abarbeitung-beschleunigen-wie-sie-mit-parallelen-prozesse-effizienter-in-der-shell-arbeiten/ * Summary of GNU Parallel tutorial http://hacktracking.blogspot.dk/2014/01/gnu-parallel-tutorial.html * Bug fixes and man page updates. 20131222 * GNU Parallel now has a motto: For people who live life in the parallel lane. * Detect if the buffer dir $TMPDIR runs out of space. This changes a central piece of code, making this release alpha quality. * --keep-order --(n)onall will sort according to the sshlogin. * Detect the number of CPUs on DEC Tru64. * GNU sql: --list-tables for sqlite3. * GNU Parallel was cited in: Variational Message-Passing: Extension to Continuous Variables and Applications in Multi-Target Tracking http://www.ics.uci.edu/~ajfrank/pubs/thesis.pdf * GNU Parallel was cited in: Genome Assembly: Scaffolding Guided by Related Genomes https://www.duo.uio.no/handle/10852/37431 * GNU Parallel was cited in: Metagenomic analysis of Mariana Trench sediment samples http://repositorio.ul.pt/handle/10451/9436 * GNU Parallel was cited in: Diacritization, automatic segmentation and labeling for Levantine Arabic speech http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6642556 * GNU Parallel was cited in: Investigation of emotion classification using speech rhythm metrics http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6642591 * GNU Parallel was cited in: A Rhythm-Based Analysis of Arabic Native and Non-Native Speaking Styles http://www.ijsps.com/uploadfile/2013/1128/20131128014413279.pdf * GNU Parallel was cited in: Evolutionary optimization of wetlands design http://dl.acm.org/citation.cfm?id=2480400 * GNU Parallel was cited (unfortunately with wrong citation) in: RDBMS vs NoSQL: Performance and Scaling Comparison http://www.epcc.ed.ac.uk/sites/default/files/Dissertations/2012-2013/RDBMS%20vs%20NoSQL%20-%20Performance%20and%20Scaling%20Comparison.pdf * GNU Parallel was used (without proper citation) in: Comprehensive Analysis Pipeline for Discovery of Human Genetic Variation http://www.google.com/patents/US20130311106 * Encrypt and decrypt in parallel with GPG http://blog.tkassembled.com/412/encrypt-and-decrypt-in-parallel-with-gpg/ * Using GNU Parallel to create a SVM classifier http://ivanyu.me/blog/2013/12/01/parallel/ * Parallel xz compression http://anthon.home.xs4all.nl/rants/2013/parallel_xz/ * Got CPUs to burn? Put 'em to work with GNU parallel http://baoilleach.blogspot.dk/2013/11/got-cpus-to-burn-put-em-to-work-with.html * Parallel rsync http://pastebin.com/JmnB9ffq * Gnu Parallel for fun and profit https://gist.github.com/celoyd/f7eb55ad69c9b33fd8c3 * Parallelization of Exploitation http://rantsideasstuff.com/parallelization-of-exploitation/ * Running assemblies in parallel https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html * Procesando la contabilidad del PP http://www.neorazorx.com/2013/07/procesando-la-contabilidad-del-pp.html * Mon make à moi (French) http://www.slideshare.net/lindenb/mon-make-moi-tout-sauf-galaxy * Bug fixes and man page updates. 20131122 * A citation notice is printed on stderr only if stderr is a terminal, the user has not specified --no-notice and the user has not run --bibtex once. This makes the release alpha quality. * --compress will compress temporary files. If the output is big and very compressible this will take up less disk space in $TMPDIR and possibly be faster due to less disk I/O. * --compress-program comtrols which program to use for compressing temporary files. * --bar show progress as a progress bar compatible with zenity. * --resume can now be used with --result: Jobs already run will be skipped. * --transfer and --basefile support paths relative to the --workdir by inserting /./ into the path. * GNU Parallel was cited in: 'fastphylo: Fast tools for phylogenetics' http://www.biomedcentral.com/1471-2105/14/334/abstract * Using GNU parallel http://davetang.org/muse/2013/11/18/using-gnu-parallel/ * Techlux - GNU - Parallel (German) https://techlux.de/blog/2013/11/07/gnu-parallel/ * awk, sed, bzip2, grep, wc на всех ядрах http://vk.com/page-30666517_45528467 * 如何利用多核CPU來加速你的Linux命令 — awk, sed, bzip2, grep, wc等 http://www.hksilicon.com/kb/articles/290543/CPULinuxawk-sed-bzip2-grep-wc * GNU Parallel (Japanese) http://jarp.does.notwork.org/diary/201311b.html#20131117 * Bug fixes and man page updates. 20131022 * --transfer files with /./ in the path will copy the files relative to the --workdir. * The maximal command length is now cached in a file halfing the startup time. * GNU Parallel was cited in: Investigating speaker gender using rhythm metrics in Arabic dialects http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6602389 * GNU Parallel was cited in: Tiedon erist ̈minen ja visualisointi a lastensuojelun asiakaskertomuksista https://tampub.uta.fi/handle/10024/84978 * Some Additional Useful Bioinformatics Software http://nix-bio.blogspot.dk/2013/10/additional-software-for-bioinformatics.html * GNU Parallel Example Screen Cast (bil to Geotiff conversion) http://www.youtube.com/watch?v=PpF27eC7Mys * Using GNU Parallel to roll-your-own Map Reduce! http://www.rankfocus.com/hello-world/ * Use multiple CPU Cores with your Linux commands http://www.rankfocus.com/use-cpu-cores-linux-commands/ * Using GNU Parallel at HPC @ Uni.lu https://hpc.uni.lu/users/use_cases/ * Scaling up with parallelization https://www.msi.umn.edu/sites/default/files/AdvPython_1.pdf * How to teach yourself to be a technical tester http://infiniteundo.com/post/62421363463/qa-toc * Faster Rasters For All http://2013.foss4g.org/conf/programme/presentations/52/ * Optimizing translated file downloads http://www.smartling.com/blog/2013/05/20/optimizing-translated-file-downloads/ * EMC NetWorker parallel saveset cloning with nsrclone and GNU parallel http://www.beebotech.com.au/2013/10/emc-networker-parallel-saveset-cloning-with-nsrclone-and-gnu-parallel/ * Best Practices for Amazon EMR http://media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf * Computing checksums for backup https://identi.ca/evan/note/6yf1GzAARtyBhj__xzMvAg * Un exemplu de utilizare a programului GNU parallel http://vundicind.blogspot.dk/2013/10/exemplu-utilizare-gnu-parallel.html * 平行化你的工作 http://www.slideshare.net/drakeguan/part1-23705978 * なんか気持ちよかです Gnu Parallel http://a3-lab.jpn.org/note/%E3%81%AA%E3%82%93%E3%81%8B%E6%B0%97%E6%8C%81%E3%81%A1%E3%82%88%E3%81%8B%E3%81%A7%E3%81%99-gnu-parallel * Bug fixes and man page updates. 20130922 * PDF-files of documentation is now included. * Cloning at warp speed 100 VMs in 1 minute using one command line http://www.beebotech.com.au/tag/command-line/ * Calcul Quebec's introduction to GNU Parallel https://wiki.calculquebec.ca/w/GNU_parallel * Brincando com o GNU parallel http://blog.tadeucruz.com/2013/09/brincando-com-o-gnu-parallel/ * GNU Parallelで並列処理を行う http://qiita.com/PENGUINANA_/items/af27a833e835fe17f09b * Bug fixes and man page updates. 20130822 * A tutorial showing much of GNU Parallel's functionality. Spend an hour walking through the tutorial. Your commandline will love you for it. man parallel_tutorial * --line-buffer will buffer output on line basis. --group keeps the output together for a whole job. --ungroup allows output to mixup with half a line coming from one job and half a line coming from another job. --line-buffer fits between these two; it prints a full line, but will allow for mixing lines of different jobs. * --record-env records all variables and functions set. Useful to record the normal environment before using --env _. * --env _ exports all functions and variables to the remote server except for the ones recorded. * New signing key. Due to recommendations from NIST http://www.keylength.com/en/4/ the signing key was changed from 1024D/ID:FFFFFFF1 to 9888R/ID:88888888. * Agalma: an automated phylogenomics workflow http://arxiv.org/pdf/1307.6432 * Job ad asking for GNU Parallel expertise http://seattle.craigslist.org/est/sof/4006079352.html * Transient Beowulf Clustering with GNU Parallel and SSHfs http://www.reddit.com/r/linux/comments/1ka8mn/transient_beowulf_clustering_with_gnu_parallel/ * Aligning to unique regions http://davetang.org/muse/2013/07/22/aligning-to-unique-regions/ * Top 10 scripting tricks for basic bioinformatics http://students.washington.edu/bowmanjs/wordpress/?p=873 * Using GNU Parallel to speed up and simplify data analyzes http://www.sergeymarkov.com/blog/2013/07/using-gnu-parallel-to-speed-up-and-simplify-data-analyzes/ * Compression of files in parallel using GNU parallel http://codextechnicanum.blogspot.dk/2013/07/compression-of-files-in-parallel-using.html * Using GNU Parallel to roll-your-own Map Reduce! http://www.rankfocus.com/?p=1 * Using GNU Parallel with Amazon media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf * Some useful comments on GNU Parallel https://news.ycombinator.com/item?id=6209767 * Using GNU Parallel to count reads mapping to genes for multiple BAMs http://drduanehassane.com/blog/sequencing-resources * TimeMachineっぽいバックアップスクリプト http://rio.tc/2013/07/timemachine-1.html * GNU ParallelでAndroid NDKの全バージョンを一括ダウンロード http://qiita.com/mazgi/items/b10bf0ff3da2045d19ab * Bug fixes and man page updates. 20130722 * --round-robin with --pipe will write all blocks to already running jobs. * --env can now transfer Bash function for remote execution. That is pretty cool! * GNU Parallel was used (unfortunately with improper citation) in: Understanding the Impact of E-Commerce Software on the Adoption of Structured Data on the Web http://link.springer.com/chapter/10.1007/978-3-642-38366-3_9#page-1 * GNU Parallel was used (unfortunately with improper citation) in: CWI at TREC 2012, KBA track and Session Track http://trec.nist.gov/pubs/trec21/papers/CWI.kba.session.final.pdf * Mitigation of Adverse Effects Caused by Shock Wave Boundary Layer Interactions through Optimal Wall Shaping. http://arc.aiaa.org/doi/abs/10.2514/6.2013-2653 * Using GNU parallel to convert images. http://www.brunokim.com.br/blog/?p=18 * A quick way to parallelize. http://timotheepoisot.fr/2013/07/08/parallel/ * GNU Parallel 20130522 ('Rana Plaza') 发布，并行作业执行. http://www.open-open.com/news/view/371301 * Quite a few bug fixes and man page updates. 20130622 * --xapply now recycles arguments if an input source has more arguments than others. * The sleep time between jobs is now both increased and decreased exponentially. * 10 seconds installation check the signature using GnuPG if GnuPG is installed. * Developer job asking for GNU Parallel expertise. http://careers.stackoverflow.com/jobs/35562/developer-big-data-geo-and-web-climate-central * A small utility program to run youtube-dl in parallel. https://github.com/dlh/youtube-dl-parallel * Parallelizing Freesurfer: http://blog.cogneurostats.com/?p=148 * Bug fixes and man page updates. 20130522 * --ctrlc is now default if --pipe is not used; thus making it possible to kill remotely started jobs simply by pressing Ctrl-C. * --timeout 200% now means kill jobs that take more than twice the time of the median run time of a job. * Jobs are now distributed round robin when having mulitiple --sshlogin instead of filling up one --sshlogin at a time. * niceload: darwin version of --io --mem --swap. Thanks to Anders F Björklund. * Bug fixes and man page updates. 20130422 * 10 seconds installation: wget -O - pi.dk/3 | sh * HPUX CPU/core detection. Thanks to Javier Tarradas. * CPU detection for HURD, IRIX, SCO OpenServer and (old) HPUX. * --ctrlc will send SIGINT to tasks running on remote computers and thus killing them. * --load now uses 'ps' to see immediately see the number of running processes instead of 'uptime' thus making --load react much faster. * Testing on Centos 3.9 and FreeBSD 7 revealed a lot of compability bugs. Some of these required quite extensive changes making this release beta quality. * --retries works with --onall. * The new --load computation now works on FreeBSD 7. * --nice works under tcsh. * GNU Parallel is officially supported in NetBSD. http://ftp.netbsd.org/pub/pkgsrc/current/pkgsrc/parallel/parallel/README.html * GNU Parallel is accepted for openSUSE. http://software.opensuse.org/package/gnu_parallel * GNU Parallel can be installed under Microsoft Windows (CygWin). http://blogs.msdn.com/b/hpctrekker/archive/2013/03/30/preparing-and-uploading-datasets-for-hdinsight.aspx * Excuses for not installing GNU Parallel. http://oletange.blogspot.dk/2013/04/why-not-install-gnu-parallel.html * Job advert that requires GNU Parallel competence. http://versium.com/about/careers/ * Parallelizing Batch Jobs for Fun and Profit. http://mikeseidle.com/tech/programming/2013/03/parallelizing-batch-jobs * Processing Transcription Start Sites(TSS) for the entire Mouse genome. http://qbrc.swmed.edu/2013/03/gnu-parallel-speeding-up-unix-commands-and-scripts/ * GNU parallel is used throughout Scrimer. http://scrimer.readthedocs.org/en/latest/ * GNU Parallel helped making public documents searchable. http://danpalmer.me/blog/articles/2013-04-06-unlocking-hillsborough.html * Identifying big movie files (German). http://blackappsolutions.wordpress.com/2013/03/23/wenn-der-plattenplatz-knapp-wird-filme-identifizieren-die-viel-platz-belegen/ * Bug fixes and man page updates. 20130222 * --resume works with --pipe. * --resume-failed will go through --joblog, redo the failed jobs and then continue like --resume. * Negative positional arguments count from the end: {-1} means the last argument, {-2} the second to last. * NetBSD CPU detection. * --blocksize increases exponentially if it smaller than a full record. * Processing n-line records (--pipe -L n) is now much faster. * --tollef is obsoleted after discussion on the mailing list. * GNU Parallel is the highest rated tool on: http://www.biostars.org/show/tools/?sort=votes&since=all%20time * GNU Parallel was loved during FSFE's #ilovefs campaign. http://fsfe.org/news/2013/news-20130212-01.en.html * Using GNU Parallel with s3cmd (Japanese). http://blog.suz-lab.com/2013/02/s3cmd-gnu-paralells3.html * Intro to GNU Parallel (Chinese). http://guiquanz.github.com/2013/02/12/gnu-parallel-intro/ * Bug fixes and man page updates. 20130122 * --sshdelay Delay starting next ssh by secs seconds. GNU parallel will pause secs seconds after starting each ssh. secs can be less than 1 seconds. * Official OpenBSD port: http://ftp.openbsd.org/ports/sysutils/parallel/ * Official DragonFlyBSD package: http://www.mirrorservice.org/sites/ftp.dragonflybsd.org/packages/amd64/DragonFly-3.0.0/stable/parallel/ * Post about niceload in Hungarian: http://commandline.blog.hu/2013/01/02/niceload * 自炊スキャンデータをKobo Gloに最適化 http://interstadial.wordpress.com/2013/01/20/ * GNU parallel+ssh で複数のリモートホストに複数のコマンドを実行させる http://oshiire.to/archives/1686 * Bug fixes and man page updates. 20121222 * --shebang-wrap makes is possible to parallelize scripts by putting parallel in the shebang line (the first #! line in scripts). * --delay puts in a delay after starting each job. Useful to avoid raceconditions and thundering herd problems. * --results now uses / as separator instead of TAB and thus creates subdirs. Thanks to Drew Frank. * parallel: OpenBSD CPU detection. Thanks to Michał Markowski. * niceload --sensor allows for negative numbers to signify a lower number means the limit is lower. * niceload --prg suspend a named program that is already running. * niceload multiple --pid suspend process ids that are already running. * Convertir des images avec find et imagemagick http://roger.b.over-blog.com/article-convertir-des-images-avec-find-et-imagemagick-113416637.html * Bug fixes and man page updates. 20121122 * niceload --sensor makes it possible to use a program to control if a program should be suspended. * GNU Parallel was part of the justification for Nordic Free Software Award 2012 https://fsfe.org/news/2012/news-20121112-01.html * Dateien schneller packen und konvertieren mit GNU parallel http://www.linux-community.de/Archiv/Tipp-der-Woche/Dateien-schneller-packen-und-konvertieren-mit-GNU-parallel * Processing images from Lunar Reconnaissance Orbiter Narrow Angle Camera http://lunokhod.org/?p=774 * GNU Parallel is used in types2: Type and Hapax Accumulation Curves http://www.cs.helsinki.fi/u/josuomel/types2/ * GNU Parallel used in: A Hybrid Factor Analysis and Probabilistic PCA-based system for Dictionary Learning and Encoding for Robust Speaker Recognition http://www.superlectures.com/odyssey2012/lecture.php?id=8&lang=en http://www.cse.iitm.ac.in/~mrsri/ppca.pdf * Mapreduce avec parallel, cat et une redirection http://datacratic.com/site/blog/mapreduce-avec-parallel-cat-et-une-redirection * GNU Parallel for Large Batches of Small Jobs https://support.scinet.utoronto.ca/wiki/images/7/7b/Tech-talk-gnu-parallel.pdf * GNU Parallel used in black belt tip (8:50-10:12) https://aws.amazon.com/apac/awspodcast/episode20/ * Bug fixes and man page updates. 20121022 * --results structures output files so they can be imported using Pandas (http://pandas.pydata.org/). Useful when doing simulations to select output from some arguments. * Use --env to transfer environment variables through ssh to remote machines. * GNU Parallel is accepted for Ubuntu Quantal. http://packages.ubuntu.com/quantal/parallel * GNU Parallel was requested for OpenSUSE (go vote!) https://features.opensuse.org/314461 * Kneth's Korner: Map/Reduce and GNU Parallel http://kenneth.geisshirt.dk/2012/10/mapreduce-and-gnu-parallel.html * Blog post in Japanese by Siguniang. https://siguniang.wordpress.com/2012/09/09/notes-on-gnu-parallel-the-command-line-power-tool/ (Siguniang mentions the logo is called 'The Cafe Wall Illusion') http://www.michaelbach.de/ot/ang_cafewall/index.html * GNU Parallel, where have you been all my life? http://ssdigit.nothingisreal.com/2012/09/gnu-parallel-where-have-you-been-all-my.html * Reference-free ddRADseq analysis tools uses GNU Parallel. https://github.com/brantp/rtd#readme * When bash just isn’t quick enough. https://soimasysadmin.wordpress.com/2012/08/15/gnu-parallel-when-bash-just-isnt-quick-enough/ * Using GNU Parallel to Package Multiple Jobs in a Single PBS Job. http://www.nas.nasa.gov/hecc/support/kb/Using-GNU-Parallel-to-Package-Multiple-Jobs-in-a-Single-PBS-Job_303.html * GNU Parallel Notes. http://xed.ch/help/parallel.html * Bug fixes and man page updates. 20120822 * Due to a bugfix the main flow has changed. Making this release beta quality. * Parallel Proxy Scraper & Checker Tool https://www.youtube.com/watch?v=iXCeR_XsP6o * Bug fixes and man page updates. 20120722 * GNU Parallel was presented at Chiang Mai Bar Camp http://barcampchiangmai.org/ See write up here: http://www.cnx-software.com/2012/07/02/use-gnu-parallel-to-speed-up-script-execution-on-multiple-cores-andor-machines/ * I don't always max out all my CPUs, but when I do, I do it with GNU Parallel. http://memegenerator.net/instance/22638454 * Bug fixes and man page updates. 20120622 * '-L n --pipe' will use records of n lines. This is useful when processing data that have fixed records with a fixed number of lines (e.g. fastq). * --filter-hosts will remove down hosts. For each remote host: check that login through ssh works. If not: do not use this host. Currently you can not put --filter-hosts in a profile, $PARALLEL, /etc/parallel/config or similar. This is because GNU Parallel uses GNU Parallel to compute this, so you will get an infinite loop. This will likely be fixed in a later release. * --pipe now uses fork() instead of busy wait. The performance should be better on computers with >10 cores while remaining the same on computers with few cores. * GNU Parallel will be represented at Chiang Mai Bar Camp. http://barcampchiangmai.org/ * Indexing Big Data on Amazon AWS: The Screencast (Check out his T-shirt at 18:40-21:00). http://www.opensourceconnections.com/2012/06/06/indexing-big-data-on-amazon-aws-screencast/ * biotoolbox uses GNU Parallel. https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper * Spiceweasel uses GNU Parallel. https://github.com/mattray/spiceweasel * GNU Parallel part of The Administrators Challenge. http://challenge.twistedrack.com/questions/qs3.php * Finding Oldest Firefox Code using GNU Parallel. http://gregoryszorc.com/blog/2012/06/18/finding-oldest-firefox-code/ * Bug fixes (quite a few for remote job running) and man page updates. 20120522 * Timings in --joblog now with milliseconds. * Thesis using GNU Parallel (correctly cited; hooray!). http://scholarworks.sjsu.edu/etd_projects/222/ * Package for AIX. http://www.perzl.org/aix/index.php?n=Main.Parallel * Prokka uses GNU Parallel. http://bioinformatics.net.au/prokka-manual.html * GNU Parallel was presented at MUUG. http://muug.mb.ca/blog/meetings/2012/05/09/may-8th-2012-rtfm-gnu-parallel1/ * Blog post: Manipulating many or large files with GNU parallel. http://compbiously.blogspot.com/2012/05/manipulating-many-or-large-files-with.html * Blog post: Running commands in parallel using bash. http://blog.michaelboman.org/2012/04/running-commands-in-parallel-using-bash.html * Blog post: Efficient log processing. http://www.francoismaillet.com/blog/?p=399 * Blog post about GNU Parallel and Amazon EC2. http://blog.kevinformatics.com/post/4970574713/interested-in-your-experience-using-gnu-parallel-in * Blog post in Hungarian. http://commandline.blog.hu/2012/05/03/gnu_parallel * Popularity of GNU Parallel in Debian explodes. http://qa.debian.org/popcon-graph.php?packages=parallel * Bug fixes and man page updates. 20120422 * A race condition bug caused restructuring of a central piece of the code. Thus this release of GNU Parallel should be considered beta quality. * sql --dbsize will now list sizes of all databases if given no database. * GNU Parallel is now in Debian Unstable. apt-get install parallel * Article: Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome. http://www.biomedcentral.com/content/supplementary/1471-2105-13-s2-s13-s1.pdf * Blog post: GNU parallel - the best thing since sliced bread. https://arrayal.wordpress.com/2012/03/27/gnu-parallel-the-best-thing-since-sliced-bread/ * Blog post: GNU Parallel makes everything faster. http://compbiously.blogspot.com/2012/03/gnu-parallel-makes-everything-faster.html * Blog post (German): Howto: GNU parallel. http://d24m.de/2012/04/05/howto-gnu-parallel/ * Blog post: Running in Parallel http://interactivity.ifactory.com/2012/04/running-in-parallel/ * 20000 watched the first intro video. http://pi.dk/1 * The first 5 have received their GNU Parallel merchandise https://www.gnu.org/software/parallel/merchandise.html * Bug fixes and man page updates. 20120322 * Parallel Process Database Dumps. http://blog.mattoates.co.uk/2012/02/parallel-process-database-dumps.html * Using GNU Parallel to process images from Mars. http://lunokhod.org/?p=468 * Using GNU Parallel with bzgrep. http://filip.rembialkowski.net/did-you-know-gnu-parallel/ * Bug fixes and man page updates. 20120222 * --workdir . will use the current working dir. If the current working dir is beneath your home dir, the value . is treated as the relative path to your home dir. This means that if your home dir is different on remote computers (e.g. if your login is different) the relative path will still be relative to your home dir. * A texinfo file is now generated from the POD file using pod2texi. * The bioinformatics article "Fast large-scale clustering of protein structures using Gauss integrals" mentions GNU Parallel. They forgot to add the reference. Please remember --bibtex if you use GNU Parallel in an article. http://bioinformatics.oxfordjournals.org/content/28/4/510.short * The first supporter received his merchandise. Did you order yours? https://www.gnu.org/software/parallel/merchandise.html * How to use GNU Parallel with samtools. http://zvfak.blogspot.com/2012/02/samtools-in-parallel.html * How to use GNU Parallel for vacuuming PostgreSQL tables. http://blog.timmattison.com/archives/2012/01/24/mini-hack-parallel-vacuuming-in-postgresql/ * Converting e-books with Calibre and GNU Parallel. http://www.linkhal.de/blog/2012/01/converting-massive-e-book-collections-with-calibre-and-gnu-parrallel/ * Using GNU Parallel for tailing logfiles from multiple servers. http://silviud.blogspot.com/2012/02/shell-parallel-processing.html * Bug fixes and man page updates. 20120122 * --header : uses the first input line as column names and you can then use {colname} as a replacement string in the command. This also works with multiple :::'s. * --header matches a header as a regular expression and repeats the header for each block with --pipe. * --resume resumes from the last unfinished job. Useful if you stop GNU Parallel and restart it later with the same arguments. * niceload now propagates exit status correctly. * Show your support for GNU Parallel. For a limited time you can get a GNU Parallel T-shirt+mug+pen+100 postcards at 20 EUR. See https://www.gnu.org/software/parallel/merchandise.html * Options -g -B -T -U -W -Y are retired as warned 6 months ago. * GNU Parallel referenced in article on Holographic Grid Cloud. Thanks to Stefano Gallozzi. http://arxiv.org/pdf/1112.6128 * Article in IEEE Software on GNU Parallel. Thanks to Diomidis Spinellis. http://www.spinellis.gr/blog/20110911/ * An article on Narwhal which uses GNU Parallel. They forgot to add the reference. Please remember --bibtex if you use GNU Parallel in an article. http://bioinformatics.oxfordjournals.org/content/early/2011/11/08/bioinformatics.btr613.full.pdf * Blog post on using GNU Parallel to speed up BLAST queries: http://blog.mckuhn.de/2012/01/embarrassingly-parallel-blast-search.html * Video showing Wake-on-LAN with GNU Parallel. https://www.youtube.com/watch?v=0mB-yIyKFLQ * Using GNU Parallel with Solr. http://sujitpal.blogspot.com/2011/12/solr-report-generation-with-python.html * First job ad including GNU Parallel: http://seeker.dice.com/jobsearch/servlet/JobSearch?op=101&dockey=xml/7/6/76f858de083a094f74b1a5d3ba53ffc5@endecaindex * Bug fixes and man page updates. 20111222 * --timeout will now kill grandchildren. * Interview in Hacker Public Radio. http://hackerpublicradio.org/eps.php?id=0860 * Blog post in Chinese. http://blog.sina.com.cn/s/blog_3f7652740100y0ju.html * Bug fixes and man page updates. 20111122 * GNU Parallel package for Fedora. https://admin.fedoraproject.org/pkgdb/acls/name/parallel * Using GNU Parallel with Mozilla cross referencing. https://blog.mozilla.com/it/2011/11/15/mxr-improvements/ * Neat flash presentation of GNU Parallel. http://prezi.com/0nq74b2elgtx/about-gnu-parallel/ * How to create tar files of dirs in parallel. https://joneslee85.wordpress.com/2011/11/22/shell-tips-how-to-recursively-archive-many-folders/ * Article in Admin Network&Security by Ben Martin. http://www.admin-magazine.com/HPC/Articles/GNU-Parallel * Blog post in Polish. http://blog.tiger.com.pl/2011/01/05/gnu-parallel/ * Blog post on using GNU Parallel of Mac OS X. http://www.0xcb0.com/2011/10/19/running-parallel-bash-tasks-on-os-x/ * Blog post in English about using zip with GNU Parallel. http://nuclear-imaging.info/site_content/2011/05/11/gnu-parallel/ * Blog post in English by researcher. http://zandyware.wordpress.com/2011/10/15/gnu-parallell-make-best-use-of-your-multicore-computer/ * Blog entry in Chinese. http://blog.csdn.net/tossense/article/details/6889026 * Blog entry in Japanese on managing many servers. http://hiroakis.com/blog/2011/11/13/gnu-parallel/ * GNU Parallel is now part of ppbs. http://physiology.med.cornell.edu/faculty/mason/lab/ppbs/introduction/introduction.html * How to use GNU Parallel with MCX. http://mcx.sourceforge.net/cgi-bin/index.cgi?MMC/Doc/MMCCluster * Bug fixes and man page updates. 20111022 * --tag prepends lines with the argument(s). If used with --(n)onall the line will be prepended with the sshlogin instead. * --shellquote does not run the command but quotes it using \'s. Useful for making quoted composed commands. * --profile can now be repeated merging multiple profiles. * --bibtex now gives the BibTeX entry. Thanks to Aleksandr Levchuk for testing. * Makefile for simple .deb package. cd packager/debian; make * sql: --list-databases lists the databases. * GNU Parallel officially in Fedora 16 http://www.spinics.net/lists/fedora-package-announce/msg67130.html * Blog post on recompression FLAC audio. http://blog.oxplot.com/2011/08/reflac-flac-cleanser.html * The most complex use of ::: I have seen so far. http://agentzlerich.blogspot.com/2011/09/following-up-on-previous-failures-ive.html * Example of using GNU Parallel with sudo. http://loopkid.net/articles/2011/10/07/recursive-chmod-and-chown-on-files * Use wget and gnu parallel to download mp3s at rocket speed. http://sdbrain.posterous.com/use-wget-and-gnu-parallel-to-download-mp3s-at * First CV referring to GNU Parallel. http://www.peopleperhour.com/freelancers/stephen_/internet_researcher_and_protocol_develop/140602 * Cartwright labs usage of GNU Parallel. http://cartwrightlab.wikispaces.com/The+Most+Bang+for+Your+Buck * Bug fixes and man page updates. 20110822 * --timeout implemented so that slow commands can be killed * CPU detection improved for Mac OSX. Thanks to Wayne E. Seguin. * Example of a parallel webcrawler in the man page. * Backup up PostgreSQL with GNU Parallel. Thanks to Stephane Wirtel. http://wirtel.be/2011/07/15/rsync_parallel/ * Blog post in Japanese. http://dminor11th.blogspot.com/2011/08/gnu-parallel.html * Blog post about optimizing JPEGs. Thanks to Thomas Jost. http://schnouki.net/2011/07/22/optimizing-jpeg-pictures/ * Bug fixes and man page updates. 20110722 * niceload: --hard will suspend a program if a limit is reached - as opposed to just slowing the program down. * niceload: --soft will slow the program down - as opposed to suspending the program completely. * niceload: --run-io will slow down a program if disk io goes above a certain limit. * niceload: --run-load will slow down a program if loadaverage goes above a certain limit. * niceload: --run-mem will slow down a program if free memory goes below a certain limit. * niceload: --run-noswap will slow down a program if the computer is swapping. * niceload: --start-io, --start-load, --start-mem, --start-noswap will defer starting a program until the system is below the limit. * --io, --load, --mem, and --noswap sets both --run-* and --start-*. * niceload got a major rewrite and is now object oriented. * GNU Parallel was presented at Nordic Perl Workshop 2011. http://conferences.yapceurope.org/npw2011/talk/3416 * Blog post about zcat and GNU Parallel. Thanks to Dr. John. http://drjohnstechtalk.com/blog/2011/06/gnu-parallel-really-helps-with-zcat/ * 2 blog posts in Japanese. Thanks to Negima. http://d.hatena.ne.jp/negima1976/20110607/1307412660 http://d.hatena.ne.jp/negima1976/20110628/1309252494 * Blog post for bioinformatics. Thanks to Chris Miller. http://chrisamiller.com/science/2010/05/26/use-parallel-for-easy-multi-processor-execution/ * Bug fixes and man page updates. 20110622 * --onall will run all the jobs on all the computers. This is useful for systemadinistrators having multiple servers. * --nonall runs like --onall but reads no arguments from stdin (standard input), so is possible to do: parallel --nonall -S computer1,computer2 uptime * Context replace now works with multiple input sources: parallel -X echo {1}-{2} ::: 1 2 3 ::: a b c * --noswap do not start a job on a server that is swapping. * Article: Parallel processing without Hadoop! http://www.solutionhacker.com/parallel-processing-without-hadoop/ * Article in Linux Magazine (Spanish). Thanks to Ben Martin. http://www.linux-magazine.es/issue/67/ * First blog post in Korean. Thanks to 민병국. http://blog.daum.net/_blog/BlogTypeView.do?blogid=02RQ3&articleno=13380895&admin=# * Blog post in Japanese. Thanks to Naoya Nakazawa. http://www.sssg.org/blogs/naoya/archives/2003 * Blog post in English. Thanks to Dagon. http://hekate.homeip.net/2011/05/29/ * Bug fixes and man page updates. 20110522 * Multiple ::: can be put on the command line and will be treated similar to contents from multiple -a's. * ::: and :::: can now be mixed on the command line. Use {1} .. {n} to refer to inputs from the different input sources. * --xapply is now needed to get xapply's behaviour of reading one line from each of the input sources. * Multiple input sources will cause all combinations of arguments from the sources to be generated. E.g. 'parallel echo {1}+{2} ::: 1 2 ::: a b c' will print 1+a 1+b 1+c 2+a 2+b 2+c. This can often replace nested loops. * Implemented {//} for the input line with the basename removed (dirname). * New video showing the new ::: and :::: input sources. http://tinyogg.com/watch/iOdhU/ http://www.youtube.com/watch?v=fOX1EyHkQwc * GNU Parallel now has a logo. http://www.gnu.org/software/parallel/logo.png * Article about GNU SQL in USENIX Magazine ;login: (print) http://www.usenix.org/publications/login/2011-04/ * Using GNU Parallel with EC2. Thanks to Kevin Wu. http://blog.kevinformatics.com/post/4970574713/interested-in-your-experience-using-gnu-parallel-in * Review with idea for {..} and {...} in Japanese. Thanks to ichii386. http://d.hatena.ne.jp/ichii386/20110426 * Upgrade GNU Parallel using Macports. Thanks to Phil Hollenback. http://www.hollenback.net/index.php/MacportsParallel * Robert from Echo One discusses using processes instead of threads: http://rrees.wordpress.com/2011/04/25/many-cores-many-threads/ * How to run GNU Parallel on a SLURM cluster. Thanks to Kevin Stock. http://www.kevinstock.org/2011/04/using-the-ri-cluster/ * Short article about using GNU Parallel with lame: http://loopkid.net/articles/2011/04/30/accelerate-lame-mp3-conversion * Using GNU Parallel to run tail -f in Japanese. Thanks to Clouder. http://blog.clouder.jp/archives/001140.html * BBC Research & Development uses GNU Parallel: http://www.bbc.co.uk/blogs/researchanddevelopment/2010/11/prototyping-weeknotes-41-26112.shtml * Short article about using GNU Parallel on RHEL. Thanks to Rishi Deshpande. http://nuclear-imaging.info/site_content/2011/05/11/gnu-parallel/ * Using GNU Parallel for FLAC->MP3 conversion. Thanks to Derek Marcotte. http://derek.chezmarcotte.ca/?p=286 * Bug fixes and man page updates. 20110422 * {#} now works as an alias for $PARALLEL_PID. * --eta now estimates way more accurately. * CPU detection code for AIX thanks to Christian Netrwal. * --joblog contains exitcode. * Thanks to Ævar Arnfjörð Bjarmason for reading my code. * GNU Parallel was presented at: - LUGA, Augsburg, 2011-03-26, http://www.luga.de/Aktionen/LIT-2011/Programm - OSAA.dk, Aarhus, 2011-04-12 * Blog entry in Japanese. Thanks to Riywo. http://blog.riywo.com/2011/04/19/022802 * Example of how to use GNU Parallel on PBS clusters. Thanks to Andrew J Dolgert: http://web0.tc.cornell.edu/wiki/index.php?title=Gnu_Parallel * First example of using GNU Parallel in Hebrew. Thanks to omry. http://nd.gd/jk * Intro video got past 10000 hits. http://www.youtube.com/watch?v=OpaiGYxkSuQ * Bug fixes and man page updates. 20110322 * --tollef to be switch compatible with Tollef's parallel. This will cause -l to mean --load, and the argument separator will be -- instead of ::: * --gnu will force GNU Parallel to behave like GNU Parallel even if --tollef is set. * Site wide config file: /etc/parallel/config This should solve the issue with some packagers renaming GNU Parallel to gparallel to avoid the naming conflict. By putting --tollef in the site wide config file you can deinstall Tollef's parallel and install GNU Parallel instead without any change for users or scripts. This is useful for packagers that currently rename GNU Parallel or simply do not distribute GNU Parallel because the command name conflicts with Tollef's parallel. * -L 0 -n 0, and -N 0 implemented. They will read one argument, but insert 0 arguments on the command line. Useful if you just want to run the same command with the same arguments a number of times. * GNU Parallel is now in Fink. Thanks to Jesse Alama. http://pdb.finkproject.org/pdb/package.php/parallel * Opscode Cookbook for Chef. Thanks to Joshua Timberman. https://github.com/opscode/cookbooks/tree/master/gnu_parallel * Man page examples translated into Japanese. Thanks to Koshigoe. http://w.koshigoe.jp/study/?%5Bsystem%5D+GNU+parallel+%BB%C8%CD%D1%CE%E3#l13 * GNU Parallel will be presented at: - LUGA, Augsburg, 2011-03-26, http://www.luga.de/Aktionen/LIT-2011/Programm - OSAA.dk, Aarhus, 2011-04-12 * Video of presentation from FSCONS 2010-11-07. The presenter was _really_ hoarse that day (Something to do with loads of alcohol the night before). http://vimeo.com/20838834 * Review with examples in German. Thanks to M. Nieberg. http://kenntwas.de/2011/linux/gnu-parallel/ * A review of the --pipe option in German. Thanks to Mathias Huber. http://www.linux-magazin.de/NEWS/GNU-Parallel-20110205-stueckelt-Daten * A small example of grepping maillogs. Thanks to François Maillet. http://www.francoismaillet.com/blog/?p=399 * Using GNU Parallel instead of xargs. Thanks to James Cuff. http://blog.jcuff.net/2011/02/on-train-ride-in.html * Using GNU Parallel from 0install (German). Thanks to AdaMin. http://forum.ubuntuusers.de/topic/gnu-parallel-mit-zero-install-kurzinfo-kein-wi/ * Bug fixes and man page updates. 20110205 * --pipe splits piped data into blocks. Each block is piped to a program for processing. The piping and the programs will be run in parallel. Useful if the data you want to process is data for a program and not arguments. * --blocksize sets the blocksize in bytes for --pipe. The blocksize is approximate. It can deviate as much as the size of one record. Default is 1M. * --recstart sets the string matching the start of a record. Default is "". * --recend sets the string matching the end of a record. Default is '\n'. To specify none use --recend "". If both --recstart and --recend are set, the end of a record must be followed immediately by a start of a record. This is useful if either recend or recstart can occur in the middle of a record. * --remove-rec-sep removes the string matched by --recstart and --recend. * --regexp will make GNU Parallel treat --recstart and --recend as regular expressions. * --output-as-files will put the output of the programs into files and instead of giving the output GNU Parallel will output the name of these files. * -N if used with --pipe sets the number of records to read. * New video showing --pipe at http://www.youtube.com/watch?v=1ntxT-47VPA * GNU Parallel was presented at FOSDEM. * Article in USENIX Magazine ;login: (print) http://www.usenix.org/publications/login/2011-02/ * GNU Parallel is now on ohloh.net. Thanks to Wim Muskee. https://www.ohloh.net/p/gnu-parallel * Advanced recursive example. Thanks to Ruarí Ødegaard. http://my.opera.com/ruario/blog/2011/01/24/editing-debian-packages-more-fun-with-gnu * Small example on using GNU Parallel through 0install (German). http://forum.ubuntuusers.de/topic/gnu-parallel-mit-zero-install-kurzinfo-kein-wi/ * Bug fixes and man page updates. 20110122 * --joblog makes a simple log of completed jobs. * -X now spreads arguments between job slots when reaching last argument. Use -j1 to avoid this. * People on the email list have voted -j+0 to be the new default instead of -j9. * First review in Polish. Thanks to Patryk Krawaczyński. http://nfsec.pl/root/2458 * Review in Spanish (in print). https://www.linux-magazine.es/issue/67/moreinfo.html * Review in English. Thanks to Brian Gough. http://blogs.fsfe.org/bjg/2011/01/gnu-parallel-a-map-operator-for-the-command-line/ * Review in French. Thanks to Denis Dordoigne. http://linuxfr.org/2010/12/29/27715.html * Review in Spanish. http://gufete.net/index.php?entry=entry110116-200022 * Article with advanced recursive example. Thanks to Ruarí Ødegaard http://my.opera.com/ruario/blog/2011/01/18/fun-with-gnu-parallel * Use case for memcache. http://www.dctrwatson.com/2010/12/how-to-dump-memcache-keyvalue-pairs-fast/ * Bug fixes and man page updates. 20101222 * GNU niceload is now part of GNU Parallel. GNU niceload slows down a program if the load average is above a certain limit. * Implemented --tmpdir to buffer standard output and standard error in a different place. * Implemented --load to wait until the load is below a limit before starting another job on that computer. * Implemented --nice set the niceness of jobs running both locally and remotely. * Implemented --dry-run to print the job without running it. * Implemented --tty as the old default of assigning a tty to the first job causes problems. * Review with focus on clusters. Thanks to Taylor Gillespie http://www.unixpronews.com/unixpronews-49-20101019GNUParallelSpeedUpProcessingWithMulticoresClusters.html * Review with focus on protein similarity. http://kevinformatics.tumblr.com/post/2142473893/cluster-like-computing-using-gnu-parallel * Review in Spanish. http://gr3p.com/2010/12/gnu-parallel-acelera-tus-scripts-en-linux * Quite a few bug fixes and man page updates. 20101202 * Implemented {/} for the input line with the path removed (basename). * Implemented {/.} for the input line with extension and path removed (basename). * Output from --progress is now sent to standard error instead of standard output. * --eta was broken and counted down from 0. Now fixed. * Standard output and standard error are flushed after every job so if standard output does not end with a newline it will still be grouped with the rest of standard output. * --command, -c, --file, and -f are now removed as options. They were never used in practice. * GetOptionsFromArray rewritten to work with old Perl libraries. * The file COPYING now contains the GNU General Public License 3 * Major rewrite to make the code more object oriented and easier to maintain in the future. 20101113 * Using -j myfile the number of jobs can be changed while GNU Parallel is running simply by changing the content of myfile. * Implemented --profile to use different .parallel/config for different situations. * Ugly newlines in $PARALLEL and .parallel/config are no longer needed. Instead you have to use \ in front of special shell characters. * --workdir puts the files transferred to remote machines in a specified directory. * $PARALLEL_PID is set to the process id of GNU Parallel. * $PARALLEL_SEQ is set to the sequence number of the job. * -v now only shows the command to run. Use -v -v to show the ssh/rsync wrapping. * Slow spawning error is now only a warning. * If stdin is a tty and input is read from stdin you now get a warning. * GNU sql: \n and \x0a in arguments is replaced with newline. * Patch for Debian package and spelling mistakes. Thanks to Rogério Brito * Mac OS X Homebrew package. Thanks to Jonathan Palardy * FreeBSD port. Thanks to Chris Howey * Pardus package. Thanks to Fethican Coşkuner * First review in Chinese. Thanks to 曾義峰: http://antbsd.twbbs.org/~ant/wordpress/?p=2876 * First review in print: http://www.linux-magazine.com/Issues/2010 Nov 2010 * First review in Spanish: http://www.muylinux.com/2010/10/18/gnu-parallel-computacion-paralela-a-golpe-de-comando * First review in Dutch thanks to Koen Vervloesem : http://techworld.nl/technologie/33493/gebruik-al-je-processorkernen-met-gnu-parallel.html * Blog review thanks to R. Tyler Croy : http://unethicalblogger.com/posts/2010/11/gnuparallel_changed_my_life * 5000 views of the intro video: http://www.youtube.com/watch?v=OpaiGYxkSuQ * As usual a bunch of bugfixes and more usage examples in the man page. * GNU Parallel was presented at FSCONS 2010-11-07: http://www.fscons.org/fs/gnu-parallel Hopefully the video will be online soon. 20100922 * See GNU Parallel live at FSCONS 2010-11-07: http://www.fscons.org/fs/gnu-parallel * Untested Debian and xUbuntu packages available through OpenSUSE build service: https://build.opensuse.org/package/show?package=parallel&project=home%3Atange * Using --retries a job will be retried on another computer if it fails. This is useful if some jobs fail for no apparent reason (such as network failure). * BSD xargs -o (open /dev/tty) is now default for the job running in foreground. Useful for interactive commands like: ls | parallel -Xuj1 vi * GNU sql now supports SQLite. * Renamed .dburl.aliases to .sql/aliases and /etc/sql/aliases. * GNU sql now support --list-tables * Alias for DBURL can contain '?query' part with %-quoting. 20100906 * Using --shebang GNU Parallel can be used as the parser for a script. E.g: #!/usr/bin/parallel --shebang traceroute (followed by lines of hosts) * First community generated bugfixes * Alt Linux package of GNU Parallel. Thanks to Michael Shigorin * Sunfreeware package of GNU Parallel. Thanks to Steven M. Christensen * Untested CentOS, Fedora, Mandriva, RedHat, and SUSE packages available through OpenSUSE build service: https://build.opensuse.org/package/show?package=parallel&project=home%3Atange * Review of GNU Parallel. Thanks to Andrew McFague amcfague at wgen dot net http://www.andrew-mcfague.com/linux/utilities-linux/ commands-every-serious-nix-user-should-know/#parallel * First 1000 views of the intro video * sql - a small script to access sql bases from the command line which is a handy companion to parallel --colsep 20100822 * Counting semaphore functionality: start a job in the background. If N jobs are already running, wait for one to complete. Examples: sem 'sleep 2; echo foo'; sem 'sleep 1; echo bar'; sem --wait sem -j2 'sleep 2; echo foo'; sem -j2 'sleep 1; echo bar'; sem --wait * With --colsep a table can be used as input. Example: cat tab_sep_table | parallel --colsep '\t' echo col1 {1} col2 {2} * --trim can remove white space around arguments. * --sshloginfile '..' means use ~/.parallel/sshloginfile * Zero install package. Thanks to Tim Cuthbertson * OpenSUSE package. Thanks to Markus Ammer * NixOS package. Thanks to Ludovic Courtès * Web review http://oentend.blogspot.com/2010/08/gnu-parallel.html Thanks to Pavel Nuzhdin * Web review http://psung.blogspot.com/2010/08/gnu-parallel.html Thanks to Phil Sung 20100722 * Arguments can now be given on the command line. Example: parallel bzip2 ::: *.txt * xapply like functionality. Example: parallel diff {1} {2} :::: filelist1 filelist2 parallel diff {1} {2} ">"{1.}-{2.}.diff :::: filelist1 filelist2 * Arch Linux package. Thanks to Peter Simons * Mandriva package. Thanks to Sandro Cazzaniga * -L -l -n -s now implies -X unless -m is set 20100620 * New video showing the new options. http://www.youtube.com/watch?v=OpaiGYxkSuQ or at http://tinyogg.com/watch/TORaR/ and http://tinyogg.com/watch/hfxKj/ * 100% options complete with xargs. All options for xargs can now be used in GNU Parallel - even the more exotic. * --basefile for transferring basedata. When running jobs on remote computers --basefile will transfer files before the first jobs is run. It can be used to transfer data that remains the same for each job such as scripts or lookup tables. * --progress shows progress. To see how many jobs is running on each server use --progress. It can be turned on even after GNU Parallel is started. * --eta shows estimated time left in seconds. * --halt-on-error stops if an error occurs. GNU Parallel will default to run all jobs - even if some of them fail. With --halt-on-error GNU Parallel can ignore errors, wait for the currently running jobs to finish, or stop immediately when an error occurs. 20100601 * GNU Parallel now has support for running jobs on remote machines * Intro video http://www.youtube.com/watch?v=LlXDtd_pRaY http://openvideo.dailymotion.com/video/xdmqwz_gnu-parallel-script-processing-and_tech 20100424 * GNU Parallel is now official GNU software parallel-20141022/configure.ac0000644000175000017500000000067212422006235015416 0ustar rbritorbritoAC_INIT([parallel], [20141022], [bug-parallel@gnu.org]) AM_INIT_AUTOMAKE([-Wall -Werror foreign]) AC_CONFIG_HEADERS([config.h]) AC_CONFIG_FILES([ Makefile src/Makefile ]) AC_ARG_ENABLE(documentation, AC_HELP_STRING([--disable-documentation], [Omit building and installing the documentation. (default=no)]),, [enable_documentation=yes]) AM_CONDITIONAL([DOCUMENTATION], [test x$enable_documentation = xyes]) AC_PROG_LN_S AC_OUTPUT parallel-20141022/src/0000755000175000017500000000000012424527407013725 5ustar rbritorbritoparallel-20141022/src/sql0000755000175000017500000007450512422006235014452 0ustar rbritorbrito#!/usr/bin/perl -w =head1 NAME sql - execute a command on a database determined by a dburl =head1 SYNOPSIS B [options] I [I] B [options] I < commandfile B<#!/usr/bin/sql> B<--shebang> [options] I =head1 DESCRIPTION GNU B aims to give a simple, unified interface for accessing databases through all the different databases' command line clients. So far the focus has been on giving a common way to specify login information (protocol, username, password, hostname, and port number), size (database and table size), and running queries. The database is addressed using a DBURL. If I are left out you will get that database's interactive shell. GNU B is often used in combination with GNU B. =over 9 =item I A DBURL has the following syntax: [sql:]vendor:// [[user][:password]@][host][:port]/[database][?sqlquery] See the section DBURL below. =item I The SQL commands to run. Each argument will have a newline appended. Example: "SELECT * FROM foo;" "SELECT * FROM bar;" If the arguments contain '\n' or '\x0a' this will be replaced with a newline: Example: "SELECT * FROM foo;\n SELECT * FROM bar;" If no commands are given SQL is read from the keyboard or STDIN. Example: echo 'SELECT * FROM foo;' | sql mysql:/// =item B<--db-size> =item B<--dbsize> Size of database. Show the size of the database on disk. For Oracle this requires access to read the table I - the user I has that. =item B<--help> =item B<-h> Print a summary of the options to GNU B and exit. =item B<--html> HTML output. Turn on HTML tabular output. =item B<--show-processlist> =item B<--proclist> =item B<--listproc> Show the list of running queries. =item B<--show-databases> =item B<--showdbs> =item B<--list-databases> =item B<--listdbs> List the databases (table spaces) in the database. =item B<--show-tables> =item B<--list-tables> =item B<--table-list> List the tables in the database. =item B<--noheaders> =item B<--no-headers> =item B<-n> Remove headers and footers and print only tuples. Bug in Oracle: it still prints number of rows found. =item B<-p> I The string following -p will be given to the database connection program as arguments. Multiple -p's will be joined with space. Example: pass '-U' and the user name to the program: I<-p "-U scott"> can also be written I<-p -U -p scott>. =item B<-r> Try 3 times. Short version of I<--retries 3>. =item B<--retries> I Try I times. If the client program returns with an error, retry the command. Default is I<--retries 1>. =item B<--sep> I =item B<-s> I Field separator. Use I as separator between columns. =item B<--skip-first-line> Do not use the first line of input (used by GNU B itself when called with B<--shebang>). =item B<--table-size> =item B<--tablesize> Size of tables. Show the size of the tables in the database. =item B<--verbose> =item B<-v> Print which command is sent. =item B<--version> =item B<-V> Print the version GNU B and exit. =item B<--shebang> =item B<-Y> GNU B can be called as a shebang (#!) command as the first line of a script. Like this: #!/usr/bin/sql -Y mysql:/// SELECT * FROM foo; For this to work B<--shebang> or B<-Y> must be set as the first option. =back =head1 DBURL A DBURL has the following syntax: [sql:]vendor:// [[user][:password]@][host][:port]/[database][?sqlquery] To quote special characters use %-encoding specified in http://tools.ietf.org/html/rfc3986#section-2.1 (E.g. a password containing '/' would contain '%2F'). Examples: mysql://scott:tiger@my.example.com/mydb sql:oracle://scott:tiger@ora.example.com/xe postgresql://scott:tiger@pg.example.com/pgdb pg:/// postgresqlssl://scott@pg.example.com:3333/pgdb sql:sqlite2:////tmp/db.sqlite?SELECT * FROM foo; sqlite3:///../db.sqlite3?SELECT%20*%20FROM%20foo; Currently supported vendors: MySQL (mysql), MySQL with SSL (mysqls, mysqlssl), Oracle (oracle, ora), PostgreSQL (postgresql, pg, pgsql, postgres), PostgreSQL with SSL (postgresqlssl, pgs, pgsqlssl, postgresssl, pgssl, postgresqls, pgsqls, postgress), SQLite2 (sqlite, sqlite2), SQLite3 (sqlite3). Aliases must start with ':' and are read from /etc/sql/aliases and ~/.sql/aliases. The user's own ~/.sql/aliases should only be readable by the user. Example of aliases: :myalias1 pg://scott:tiger@pg.example.com/pgdb :myalias2 ora://scott:tiger@ora.example.com/xe # Short form of mysql://`whoami`:nopassword@localhost:3306/`whoami` :myalias3 mysql:/// # Short form of mysql://`whoami`:nopassword@localhost:33333/mydb :myalias4 mysql://:33333/mydb # Alias for an alias :m :myalias4 # the sortest alias possible : sqlite2:////tmp/db.sqlite # Including an SQL query :query sqlite:////tmp/db.sqlite?SELECT * FROM foo; =head1 EXAMPLES =head2 Get an interactive prompt The most basic use of GNU B is to get an interactive prompt: B If you have setup an alias you can do: B =head2 Run a query To run a query directly from the command line: B Oracle requires newlines after each statement. This can be done like this: B Or this: B =head2 Copy a PostgreSQL database To copy a PostgreSQL database use pg_dump to generate the dump and GNU B to import it: B =head2 Empty all tables in a MySQL database Using GNU B it is easy to empty all tables without dropping them: B =head2 Drop all tables in a PostgreSQL database To drop all tables in a PostgreSQL database do: B =head2 Run as a script Instead of doing: B you can combine the sqlfile with the DBURL to make a UNIX-script. Create a script called I: B<#!/usr/bin/sql -Y mysql:///> B