mirror of
https://git.savannah.gnu.org/git/parallel.git
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bug #42893: --block should not cause decimals in cat_partial.
tempfile must respect $TMPDIR. disk full check bug fixed and tested on multiple filesystems.
This commit is contained in:
Ole Tange
parent
cb3197582a
commit
64998ab628
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@ -217,60 +217,24 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
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Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
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Jesse Alama <jesse.alama@gmail.com>
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Subject: GNU Parallel 20140722 ('MH17') released
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Subject: GNU Parallel 20140822 ('Argentina/Gaza') released
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GNU Parallel 20140722 ('MH17') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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This release contains a major change in central parts of the code and should be considered beta quality. As always it passes the testsuite, so most functionality clearly works.
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Thanks to Malcolm Cook for the brilliant idea to use a general perl expression as a replacement string.
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GNU Parallel 20140822 ('Argentina/Gaza') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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Haiku of the month:
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Are you tired of
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>>>Are you tired of
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inflexible replacements?
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Use Perl expressions.
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-- Ole Tange
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New in this release:
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* {= 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.
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* GNU Parallel was cited in: A Web Service for Scholarly Big Data Information Extraction http://patshih.ist.psu.edu/publications/Williams-CiteSeerExtractor-ICWS14.pdf
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* Positional perl expressions (similar to {2}) are given as {=2 perl expression=} where 2 is the position.
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* GNU Parallel was covered in the webcast 2014-08-20: Data Science at the Command Line http://www.oreilly.com/pub/e/3115
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* One small backwards incompatability: {1}_{2} will replace {2} with the empty string if there is only one argument. Previously {2} would have been left untouched.
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* Replacement strings can be defined using --rpl. E.g. parallel --rpl '{.gz} s/\.gz$//' echo {.gz} ::: *.gz
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* The parenthesis around {= perl expression =} can be changed with --parens.
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* --tmux will direct the output to a tmux session instead of files. Each running jobs will be in its own window.
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* --halt 10% will stop spawning new jobs if 10% failed so far.
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* 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
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* 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
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* 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
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* GNU Parallel was cited in: Web-scale Content Reuse Detection www.isi.edu/~johnh/PAPERS/Ardi14a.pdf
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* 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
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* GNU Parallel all the things! http://longwayaround.org.uk/notes/gnu-parallel-all-the-things/
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* Shell command composition and dispatch http://lukeluo.blogspot.dk/2014/07/linux-virtual-console6-shell-command.html
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* Parallelising plink (or anything else) the easy way http://chrisladroue.com/2012/03/parallelising-plink-or-anything-else-the-easy-way/
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* Easy and cheap cluster building on AWS https://grapeot.me/easy-and-cheap-cluster-building-on-aws.html
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* Paralelizace běžných činností v konzoli pomocí GNU Parallel http://www.abclinuxu.cz/clanky/paralelizace-beznych-cinnosti-v-konzoli-pomoci-gnu-parallel
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* [原] Ubuntu 下使用 parallel 命令的注意事项 http://blog.ailms.me/2014/06/28/ubuntu-with-parallel.html
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* 简单的并行, 可使用GNU parallel http://jerkwin.github.io/2014/06/10/GNU-parallel/
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* Сборка GNU parallel для CentOS/RHEL http://www.stableit.ru/2014/07/gnu-parallel-centosrhel.html
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* Bug fixes and man page updates.
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58
src/parallel
58
src/parallel
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@ -230,6 +230,7 @@ sub find_split_positions {
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# @positions of block start/end
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my($file, $block, $headerlen) = @_;
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my $size = -s $file;
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$block = int $block;
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# The optimal dd blocksize for mint, redhat, solaris, openbsd = 2^17..2^20
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# The optimal dd blocksize for freebsd = 2^15..2^17
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my $dd_block_size = 131072; # 2^17
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@ -770,6 +771,7 @@ sub parse_options {
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$Global::trim = 'n';
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$Global::max_jobs_running = 0;
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$Global::job_already_run = '';
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$ENV{'TMPDIR'} ||= "/tmp";
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@ARGV=read_options();
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@ -1315,7 +1317,7 @@ sub read_args_from_command_line {
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# Group of arguments on the command line.
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# Put them into a file.
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# Create argfile
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my ($outfh,$name) = ::tempfile(SUFFIX => ".arg");
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my ($outfh,$name) = ::tmpfile(SUFFIX => ".arg");
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unlink($name);
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# Put args into argfile
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print $outfh map { $_,$/ } @group;
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@ -2173,7 +2175,7 @@ sub filter_hosts {
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# 'echo' is used to get the best possible value for an ssh login time
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push(@echo, $host."\t".$sshcmd." echo\n");
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}
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my ($fh, $tmpfile) = ::tempfile(SUFFIX => ".ssh");
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my ($fh, $tmpfile) = ::tmpfile(SUFFIX => ".ssh");
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print $fh @cores, @cpus, @maxline, @echo;
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close $fh;
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# --timeout 5: Setting up an SSH connection and running a simple
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@ -2289,7 +2291,7 @@ sub onall {
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if(not defined $joblog) {
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return undef;
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}
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my ($fh, $tmpfile) = ::tempfile(SUFFIX => ".log");
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my ($fh, $tmpfile) = ::tmpfile(SUFFIX => ".log");
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close $fh;
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return $tmpfile;
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}
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@ -2301,7 +2303,7 @@ sub onall {
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# Copy all @fhlist into tempfiles
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my @argfiles = ();
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for my $fh (@fhlist) {
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my ($outfh, $name) = ::tempfile(SUFFIX => ".all", UNLINK => 1);
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my ($outfh, $name) = ::tmpfile(SUFFIX => ".all", UNLINK => 1);
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print $outfh (<$fh>);
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close $outfh;
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push @argfiles, $name;
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@ -2857,6 +2859,9 @@ sub multiply_binary_prefix {
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return $s;
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}
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sub tmpfile {
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return ::tempfile(DIR=>$ENV{'TMPDIR'}, TEMPLATE => 'parXXXXX', @_);
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}
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sub __DEBUGGING__ {}
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sub debug {
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@ -3100,7 +3105,7 @@ sub swap_activity {
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# As the command can take long to run if run remote
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# save it to a tmp file before moving it to the correct file
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my $file = $self->{'swap_activity_file'};
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my ($dummy_fh, $tmpfile) = ::tempfile(SUFFIX => ".swp");
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my ($dummy_fh, $tmpfile) = ::tmpfile(SUFFIX => ".swp");
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::debug("swap", "\n", $swap_activity, "\n");
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qx{ ($swap_activity > $tmpfile && mv $tmpfile $file || rm $tmpfile) & };
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}
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@ -3322,7 +3327,7 @@ sub loadavg {
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# As the command can take long to run if run remote
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# save it to a tmp file before moving it to the correct file
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my $file = $self->{'loadavg_file'};
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my ($dummy_fh, $tmpfile) = ::tempfile(SUFFIX => ".loa");
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my ($dummy_fh, $tmpfile) = ::tmpfile(SUFFIX => ".loa");
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qx{ ($cmd > $tmpfile && mv $tmpfile $file || rm $tmpfile) & };
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}
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return $self->{'loadavg'};
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@ -4574,14 +4579,14 @@ sub openoutputfiles {
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if(@Global::tee_jobs) {
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# files must be removed when the tee is done
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} elsif($opt::files) {
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($outfhw, $outname) = ::tempfile(SUFFIX => ".par");
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($errfhw, $errname) = ::tempfile(SUFFIX => ".par");
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($outfhw, $outname) = ::tmpfile(SUFFIX => ".par");
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($errfhw, $errname) = ::tmpfile(SUFFIX => ".par");
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# --files => only remove stderr
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$self->set_fh(1,"unlink","");
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$self->set_fh(2,"unlink",$errname);
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} else {
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($outfhw, $outname) = ::tempfile(SUFFIX => ".par");
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($errfhw, $errname) = ::tempfile(SUFFIX => ".par");
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($outfhw, $outname) = ::tmpfile(SUFFIX => ".par");
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($errfhw, $errname) = ::tmpfile(SUFFIX => ".par");
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$self->set_fh(1,"unlink",$outname);
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$self->set_fh(2,"unlink",$errname);
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}
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@ -5320,7 +5325,7 @@ sub start {
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# Bug:
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# If the command does not read the first char, the temp file
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# is not deleted.
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my ($dummy_fh, $tmpfile) = ::tempfile(SUFFIX => ".chr");
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my ($dummy_fh, $tmpfile) = ::tmpfile(SUFFIX => ".chr");
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$command = qq{
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sh -c 'dd bs=1 count=1 of=$tmpfile 2>/dev/null';
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test \! -s "$tmpfile" && rm -f "$tmpfile" && exec true;
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@ -5406,7 +5411,7 @@ sub tmux_wrap {
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my $self = shift;
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my $actual_command = shift;
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# Temporary file name. Used for fifo to communicate exit val
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my ($fh, $tmpfile) = ::tempfile(SUFFIX => ".tmx");
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my ($fh, $tmpfile) = ::tmpfile(SUFFIX => ".tmx");
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$Global::unlink{$tmpfile}=1;
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close $fh;
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unlink $tmpfile;
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@ -5719,25 +5724,42 @@ sub set_exitsignal {
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}
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{
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my ($disk_full_fh,$error_printed);
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my ($disk_full_fh,$b8193);
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sub exit_if_disk_full {
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# Checks if $TMPDIR is full by writing 8kb to a tmpfile
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# If the disk is full: Exit immediately.
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# Returns:
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# N/A
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if(not $disk_full_fh) {
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$disk_full_fh = ::tempfile();
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$disk_full_fh = ::tmpfile(SUFFIX => ".df");
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$b8193 = "x"x8193;
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}
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my $pos = tell $disk_full_fh;
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print $disk_full_fh "x"x8193;
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# Linux does not discover if a disk is full if writing <= 8192
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# Tested on:
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# bfs btrfs cramfs ext2 ext3 ext4 ext4dev jffs2 jfs minix msdos
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# ntfs reiserfs tmpfs ubifs vfat xfs
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# TODO this should be tested on different OS similar to this:
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#
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# doit() {
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# sudo mount /dev/ram0 /mnt/loop; sudo chmod 1777 /mnt/loop
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# seq 100000 | parallel --tmpdir /mnt/loop/ true &
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# seq 6900000 > /mnt/loop/i && echo seq OK
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# seq 6980868 > /mnt/loop/i
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# seq 10000 > /mnt/loop/ii
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# sleep 3
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# sudo umount /mnt/loop/ || sudo umount -l /mnt/loop/
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# echo >&2
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# }
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print $disk_full_fh $b8193;
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if(not $disk_full_fh
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or
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tell $disk_full_fh == $pos) {
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::error("Output is incomplete. Cannot append to buffer file in \$TMPDIR. Is the disk full?\n");
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::error("Output is incomplete. Cannot append to buffer file in $ENV{'TMPDIR'}. Is the disk full?\n");
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::error("Change \$TMPDIR with --tmpdir or use --compress.\n");
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::wait_and_exit(255);
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}
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truncate $disk_full_fh, $pos;
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truncate $disk_full_fh, 0;
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}
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}
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@ -5802,7 +5824,7 @@ sub populate {
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if($opt::cat or $opt::fifo) {
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# Get a tempfile name
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my($outfh,$name) = ::tempfile(SUFFIX => ".pip");
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my($outfh,$name) = ::tmpfile(SUFFIX => ".pip");
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close $outfh;
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# Unlink is needed if: ssh otheruser@localhost
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unlink $name;
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@ -49,16 +49,21 @@ echo '### bug #42041: Implement $PARALLEL_JOBSLOT'
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echo '### bug #42363: --pipepart and --fifo/--cat does not work'
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seq 100 > /tmp/bug42363;
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parallel --pipepart --block 31 -a /tmp/bug42363 -k --fifo wc | perl -pe s:/tmp/...........pip:/tmp/XXXX: ;
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parallel --pipepart --block 31 -a /tmp/bug42363 -k --cat wc | perl -pe s:/tmp/...........pip:/tmp/XXXX: ;
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parallel --pipepart --block 31 -a /tmp/bug42363 -k --fifo wc | perl -pe s:/tmp/.........pip:/tmp/XXXX: ;
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parallel --pipepart --block 31 -a /tmp/bug42363 -k --cat wc | perl -pe s:/tmp/.........pip:/tmp/XXXX: ;
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echo '### bug #42055: --pipe -a bigfile should not require sequential reading of bigfile'
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parallel --pipepart -a /etc/passwd -L 1 should not be run
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parallel --pipepart -a /etc/passwd -N 1 should not be run
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parallel --pipepart -a /etc/passwd -l 1 should not be run
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echo '### --tmux test - check termination'
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perl -e 'map {printf "$_%o%c\n",$_,$_}1..255' | stdout parallel --tmux echo {} :::: - ::: a b | perl -pe 's/\d/0/g'
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# TODO This is too unstable
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# echo '### --tmux test - check termination'
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# perl -e 'map {printf "$_%o%c\n",$_,$_}1..255' | stdout parallel --tmux echo {} :::: - ::: a b | perl -pe 's/\d/0/g'
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echo '### bug #42893: --block should not cause decimals in cat_partial'
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seq 100000 >/tmp/parallel-decimal;
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parallel --dry-run -kvv --pipepart --block 0.12345M -a /tmp/parallel-decimal true;
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rm /tmp/parallel-decimal
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EOF
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@ -15,7 +15,7 @@ echo '**'
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echo "### Test --tmpdir running full. bug #40733 was caused by this"
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### Test --tmpdir running full. bug #40733 was caused by this
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stdout parallel -j1 --tmpdir $SHM cat /dev/zero ::: dummy
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parallel: Error: Output is incomplete. Cannot append to buffer file in $TMPDIR. Is the disk full?
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parallel: Error: Output is incomplete. Cannot append to buffer file in /tmp/shm/parallel. Is the disk full?
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parallel: Error: Change $TMPDIR with --tmpdir or use --compress.
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echo '**'
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**
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@ -47,7 +47,7 @@ echo '### bug #42041: Implement $PARALLEL_JOBSLOT'
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2
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echo '### bug #42363: --pipepart and --fifo/--cat does not work'
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### bug #42363: --pipepart and --fifo/--cat does not work
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seq 100 > /tmp/bug42363; parallel --pipepart --block 31 -a /tmp/bug42363 -k --fifo wc | perl -pe s:/tmp/...........pip:/tmp/XXXX: ; parallel --pipepart --block 31 -a /tmp/bug42363 -k --cat wc | perl -pe s:/tmp/...........pip:/tmp/XXXX: ; echo '### bug #42055: --pipe -a bigfile should not require sequential reading of bigfile'
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seq 100 > /tmp/bug42363; parallel --pipepart --block 31 -a /tmp/bug42363 -k --fifo wc | perl -pe s:/tmp/.........pip:/tmp/XXXX: ; parallel --pipepart --block 31 -a /tmp/bug42363 -k --cat wc | perl -pe s:/tmp/.........pip:/tmp/XXXX: ; echo '### bug #42055: --pipe -a bigfile should not require sequential reading of bigfile'
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13 14 32 /tmp/XXXX
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11 11 33 /tmp/XXXX
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11 11 33 /tmp/XXXX
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@ -73,7 +73,14 @@ parallel: Error: --pipepart is incompatible with --max-replace-args, --max-lines
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parallel: Error: --pipepart is incompatible with --max-replace-args, --max-lines, and -L.
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parallel --pipepart -a /etc/passwd -l 1 should not be run
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parallel: Error: --pipepart is incompatible with --max-replace-args, --max-lines, and -L.
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echo '### --tmux test - check termination'
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### --tmux test - check termination
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perl -e 'map {printf "$_%o%c\n",$_,$_}1..255' | stdout parallel --tmux echo {} :::: - ::: a b | perl -pe 's/\d/0/g'
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See output with: tmux attach -t p00000
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# TODO This is too unstable
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# echo '### --tmux test - check termination'
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# perl -e 'map {printf "$_%o%c\n",$_,$_}1..255' | stdout parallel --tmux echo {} :::: - ::: a b | perl -pe 's/\d/0/g'
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echo '### bug #42893: --block should not cause decimals in cat_partial'
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### bug #42893: --block should not cause decimals in cat_partial
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seq 100000 >/tmp/parallel-decimal; parallel --dry-run -kvv --pipepart --block 0.12345M -a /tmp/parallel-decimal true; rm /tmp/parallel-decimal
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</tmp/parallel-decimal perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 0 129449|(true)
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</tmp/parallel-decimal perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 129449 129450|(true)
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</tmp/parallel-decimal perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 258899 129450|(true)
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</tmp/parallel-decimal perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 388349 129450|(true)
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</tmp/parallel-decimal perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 517799 71096|(true)
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