From 53ebf4dcd0ef63fd24400cf17f54372e00552a89 Mon Sep 17 00:00:00 2001 From: Ole Tange Date: Thu, 23 Apr 2015 01:12:00 +0200 Subject: [PATCH] Passes testsuite. --- NEWS | 47 +++++++++++++++++++ configure | 20 ++++---- .../obs/home:tange/parallel/parallel.spec | 2 +- src/parallel | 2 +- testsuite/tests-to-run/parallel-local-mem.sh | 2 +- testsuite/wanted-results/parallel-tutorial | 4 +- 6 files changed, 62 insertions(+), 15 deletions(-) diff --git a/NEWS b/NEWS index fc67c81c..30356feb 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,50 @@ +20150422 + +New in this release: + +* Security fix. An attacker on the local system could make you overwrite one of your own files with a single byte. The problem exist when you use --compress or --tmux or --pipe or --cat or --fifo. The attacker must figure out the randomly chosen file name and create a symlink within a time window of 15 ms. + +* --shuf will generate all jobs, and shuffle them before running them. This is useful to get a quick preview of the results before running the full batch. + +* GNU Parallel now has a DOI: https://dx.doi.org/10.5281/zenodo.16303 + +* GNU Parallel was cited in: Scaling Machine Learning for Target Prediction in Drug Discovery using Apache Spark https://cris.cumulus.vub.ac.be/portal/files/5147244/spark.pdf + +* GNU Parallel was cited in: Bayesian inference of protein structure from chemical shift data https://peerj.com/articles/861/ + +* GNU Parallel was cited in: Toward Enhanced Metadata Quality of Large-Scale Digital Libraries: Estimating Volume Time Range https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf + +* GNU Parallel was cited in: Contrasting regional architectures of schizophrenia and other complex diseases using fast variance components analysis http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf + +* GNU Parallel was cited in: Experimental study on the Wind Farm Substation Cable Installation Problem http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf + +* GNU Parallel was used in: landsat-gifworks https://github.com/KAPPS-/landsat-gifworks + +* GNU Parallel was used in: https://github.com/exascience/elprep + +* GNU Parallel was used in: http://search.cpan.org/~jillrowe/HPC-Runner-GnuParallel-0.01/ + +* GNU Parallel was used in: http://search.cpan.org/~ajpage/Bio-Roary-2.0.7/lib/Bio/Roary/JobRunner/Parallel.pm + +* GNU Parallel was used in: Rapid haploid SNP calling https://github.com/tseemann/snippy + +* Pictures and Metadata http://www.ozzy.no/2015/02/05/pictures-and-metadata/ + +* Task automation with bash and parallel https://biowize.wordpress.com/2015/03/23/task-automation-with-bash-and-parallel/ + +* How To: Speed Up File Transfers in Linux using RSync with GNU Parallel http://www.yourownlinux.com/2015/04/speed-up-file-transfers-using-rsync-with-gnu-parallel.html + +* Mirroring a Git Repository https://avacariu.me/articles/mirroring-a-git-repository.html + +* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/ + +* GNU Parallel (Sebuah Uji Coba) http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/ + +* 你见过的最牛逼的命令行程序是什么？ http://www.zhihu.com/question/29257300 + +* Bug fixes and man page updates. + + 20150322 New in this release: diff --git a/configure b/configure index 5945e8a3..601383db 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for parallel 20150322. +# Generated by GNU Autoconf 2.69 for parallel 20150422. # # Report bugs to . # @@ -579,8 +579,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='parallel' PACKAGE_TARNAME='parallel' -PACKAGE_VERSION='20150322' -PACKAGE_STRING='parallel 20150322' +PACKAGE_VERSION='20150422' +PACKAGE_STRING='parallel 20150422' PACKAGE_BUGREPORT='bug-parallel@gnu.org' PACKAGE_URL='' @@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures parallel 20150322 to adapt to many kinds of systems. +\`configure' configures parallel 20150422 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1269,7 +1269,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of parallel 20150322:";; + short | recursive ) echo "Configuration of parallel 20150422:";; esac cat <<\_ACEOF @@ -1345,7 +1345,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -parallel configure 20150322 +parallel configure 20150422 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by parallel $as_me 20150322, which was +It was created by parallel $as_me 20150422, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2225,7 +2225,7 @@ fi # Define the identity of the package. PACKAGE='parallel' - VERSION='20150322' + VERSION='20150422' cat >>confdefs.h <<_ACEOF @@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by parallel $as_me 20150322, which was +This file was extended by parallel $as_me 20150422, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -2929,7 +2929,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -parallel config.status 20150322 +parallel config.status 20150422 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/packager/obs/home:tange/parallel/parallel.spec b/packager/obs/home:tange/parallel/parallel.spec index 8c1b855e..fe87f92e 100644 --- a/packager/obs/home:tange/parallel/parallel.spec +++ b/packager/obs/home:tange/parallel/parallel.spec @@ -1,6 +1,6 @@ Summary: Shell tool for executing jobs in parallel Name: parallel -Version: 20150322 +Version: 20150422 Release: 1 License: GPL Group: Productivity/File utilities diff --git a/src/parallel b/src/parallel index c31a0f8f..771890fb 100755 --- a/src/parallel +++ b/src/parallel @@ -3719,7 +3719,7 @@ sub reap_usleep { $SIG{CHLD} = sub { kill "ALRM", $$ }; usleep($ms); # --compress needs $SIG{CHLD} undefined - $SIG{CHLD} = undef; + delete $SIG{CHLD}; exit_if_disk_full(); if($opt::linebuffer) { for my $job (values %Global::running) { diff --git a/testsuite/tests-to-run/parallel-local-mem.sh b/testsuite/tests-to-run/parallel-local-mem.sh index 99748832..46f7ccd8 100755 --- a/testsuite/tests-to-run/parallel-local-mem.sh +++ b/testsuite/tests-to-run/parallel-local-mem.sh @@ -1,7 +1,7 @@ #!/bin/bash make stopvm - +mkdir -p $TMPDIR # Jobs that eat more than 2 GB RAM cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -vj1 -k --joblog /tmp/jl-`basename $0` -L1 echo '### Trouble reading a record > 2 GB for certain versions of Perl (substr($a,0,2G+1)="fails")' diff --git a/testsuite/wanted-results/parallel-tutorial b/testsuite/wanted-results/parallel-tutorial index a43af627..d6c1c5b3 100644 --- a/testsuite/wanted-results/parallel-tutorial +++ b/testsuite/wanted-results/parallel-tutorial @@ -931,7 +931,7 @@ This helps funding further development; and it won't cost you a cent. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. parallel --version -GNU parallel 20150419 +GNU parallel 20150422 Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015 Ole Tange and Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later @@ -943,7 +943,7 @@ Web site: http://www.gnu.org/software/parallel When using programs that use GNU Parallel to process data for publication please cite as described in 'parallel --bibtex'. parallel --minversion 20130722 && echo Your version is at least 20130722. -20150419 +20150422 Your version is at least 20130722. parallel --bibtex Academic tradition requires you to cite works you base your article on.