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parallel: --compress passes tests.
This commit is contained in:
Ole Tange
parent
18ce76f598
commit
9aaa763447
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@ -33,7 +33,7 @@ if test "$GET" = ""; then
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fi
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LANG=C
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LATEST=$($GET http://ftpmirror.gnu.org/parallel | perl -ne '/(parallel-\d{8})/ and print $1."\n"' | sort | $TAIL -n1)
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LATEST=$($GET http://ftpmirror.gnu.org/parallel | perl -ne '/.*(parallel-\d{8})/ and print $1."\n"' | sort | $TAIL -n1)
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if test \! -e $LATEST.tar.bz2; then
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# Source tar does not exist
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rm -f $LATEST.tar.bz2 $LATEST.tar.bz2.sig
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@ -204,51 +204,52 @@ cc:Sandro Cazzaniga <kharec@mandriva.org>,
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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 20140222 ('Со́чи') released
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Subject: GNU Parallel 20140222 ('Со́чи/Euromaidan') released
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GNU Parallel 20140222 ('Со́чи') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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GNU Parallel 20140222 ('Со́чи/Euromaidan') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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Packagers that default to --tollef should take note that --tollef is now retired after a full year of being obsolete.
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The --compress change is so big that this release is of alpha quality.
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New in this release:
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* --tollef has been retired.
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* --compress has be redesigned due to bugs.
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* GNU Parallel was cited in: Speaker Verification and Keyword Spotting
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Systems for Forensic Applications
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http://lantana.tenet.res.in/website_files/thesis/Phd/srikanth.pdf
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* 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
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* GNU Parallel was cited in: Scaleable Code Clone Detection
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http://scg.unibe.ch/archive/phd/schwarz-phd.pdf
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* GNU Parallel was cited in: Scaleable Code Clone Detection http://scg.unibe.ch/archive/phd/schwarz-phd.pdf
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* GNU Parallel was used (unfortunately without citation) in:
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Performance and Energy Efficiency of Common Compression /
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Decompression Utilities
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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
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* GNU Parallel was cited in: Clone Detection that scales http://scg.unibe.ch/archive/masters/Vogt14a.pdf
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* GNU Parallel was recommended (without citation) in: Redesigning the
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Specificity of Protein-DNA Interactions with Rosetta
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http://link.springer.com/protocol/10.1007/978-1-62703-968-0_17
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* GNU Parallel was cited in: Scalable Positional Analysis for Studying Evolution of Nodes in Networks http://arxiv-web3.library.cornell.edu/pdf/1402.3797
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* GNU Parallel is co-distributed with RepeatExplorer
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http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
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* GNU Parallel was cited in: Aggregate Characterization of User Behavior in Twitter and Analysis of the Retweet Graph http://arxiv.org/pdf/1402.2671v1
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* Convert MP3 to a scrolling spectrum waterfall plot video
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http://jdesbonnet.blogspot.dk/2014/02/convert-mp3-to-scrolling-spectrum.html
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* 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
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* PHP wrapper class for the GNU Parallel tool
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https://github.com/geopal-solutions/gnu-parallel-wrapper/tree/master
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* 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
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* Exploratory Data Analysis
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http://www.slideshare.net/thinrhino/gnunify
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* 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
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* Single-Thread-Programme auf Multicore-Rechnern parallelisieren
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http://www.adlerweb.info/blog/2014/02/08/linux-single-thread-programme-auf-multicore-rechnern-parallelisieren
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* 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
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* Распараллеливаем процессы для ускорения вычислений и выполнения заданий в Linux
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http://savepearlharbor.com/?p=210480
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* GNU Parallel is co-distributed with RepeatExplorer http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
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* Convert MP3 to a scrolling spectrum waterfall plot video http://jdesbonnet.blogspot.dk/2014/02/convert-mp3-to-scrolling-spectrum.html
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* PHP wrapper class for the GNU Parallel tool https://github.com/geopal-solutions/gnu-parallel-wrapper/tree/master
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* Exploratory Data Analysis http://www.slideshare.net/thinrhino/gnunify
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* Copias de archivos con rsync y parallel http://linuxmanr4.com/2014/02/20/copias-de-archivos-con-rsync-y-parallel
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* Single-Thread-Programme auf Multicore-Rechnern parallelisieren http://www.adlerweb.info/blog/2014/02/08/linux-single-thread-programme-auf-multicore-rechnern-parallelisieren
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* Распараллеливаем процессы для ускорения вычислений и выполнения заданий в Linux http://savepearlharbor.com/?p=210480
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* Bug fixes and man page updates.
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62
src/parallel
62
src/parallel
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@ -4037,21 +4037,17 @@ sub seq {
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sub cattail {
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# Returns:
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# $cattail = perl program for: cattail "decompress program" [file_to_decompress or stdin]
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# $cattail = perl program for: cattail "decompress program" writerpid [file_to_decompress or stdin] [file_to_unlink]
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my $cattail = q{
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# cat followed by tail.
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# SIGHUP says there will be appended no more, so just finish after this round.
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# If $writerpid dead: finish after this round
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use Fcntl;
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$SIG{HUP} = sub { $Global::sighup = 1; };
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$|=1;
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$cmd = shift;
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if(@ARGV) {
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open(IN,"<",$ARGV[0]) || die("Cannot open $ARGV[0]");
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my ($cmd, $writerpid, $read_file, $unlink_file) = @ARGV;
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if($read_file) {
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open(IN,"<",$read_file) || die("cattail: Cannot open $read_file");
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} else {
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*IN = *STDIN;
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}
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@ -4060,14 +4056,16 @@ sub cattail {
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fcntl(IN, F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
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$flags |= O_NONBLOCK; # Add non-blocking to the flags
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fcntl(IN, F_SETFL, $flags) || die $!; # Set the flags on the filehandle
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open(OUT,"|-",$cmd) || die;
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open(OUT,"|-",$cmd) || die("cattail: Cannot run $cmd");
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while(1) {
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# clear EOF
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seek(IN,0,1);
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my $writer_running = kill 0, $writerpid;
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$read = sysread(IN,$buf,1_000_000);
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if($read) {
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# We can unlink the file now: The writer has written something
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-e $unlink_file and unlink $unlink_file;
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# Blocking print
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while($buf) {
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my $bytes_written = syswrite(OUT,$buf);
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@ -4077,12 +4075,14 @@ sub cattail {
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# Something printed: Wait less next time
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$sleep /= 2;
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} else {
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if(eof(IN) and $Global::sighup) {
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# SIGHUP received: There will never be more to read => exit
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if(eof(IN) and not $writer_running) {
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# Writer dead: There will never be more to read => exit
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exit;
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}
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# Nothing read: Wait longer next time
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$sleep = 1.05*$sleep + 0.01;
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# TODO This could probably be done more efficiently using select(2)
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# Nothing read: Wait longer before next read
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# Up to 30 milliseconds
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$sleep = ($sleep < 30) ? ($sleep * 1.001 + 0.01) : ($sleep);
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usleep($sleep);
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}
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}
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@ -4159,12 +4159,13 @@ sub openoutputfiles {
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# cattail get pid i $pid = $self->fh($fdno,'rpid');
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my $cattail = cattail();
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for my $fdno (1,2) {
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my $wpid = open(my $fdw,"|-","$opt::compress_program >".
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my $wpid = open(my $fdw,"|-","$opt::compress_program >>".
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$self->fh($fdno,'name')) || die $?;
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$self->set_fh($fdno,'w',$fdw);
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$self->set_fh($fdno,'wpid',$wpid);
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my $rpid = open(my $fdr, "-|", "perl", "-e", $cattail,
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$opt::decompress_program, $self->fh($fdno,'name')) || die $?;
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$opt::decompress_program, $wpid,
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$self->fh($fdno,'name'),$self->fh($fdno,'unlink')) || die $?;
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$self->set_fh($fdno,'r',$fdr);
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$self->set_fh($fdno,'rpid',$rpid);
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# Unlink if required but only when cattail and compress_program has started.
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@ -4927,7 +4928,6 @@ sub print {
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if($opt::pipe and $self->virgin()) {
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} else {
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if($Global::joblog) { $self->print_joblog() }
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}
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# Printing is only relevant for grouped output.
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$Global::grouped or return;
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@ -4950,6 +4950,7 @@ sub print {
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# so flush to avoid STDOUT being buffered
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flush STDOUT;
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}
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}
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for my $fdno (sort { $a <=> $b } keys %Global::fd) {
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# Sort by file descriptor numerically: 1,2,3,..,9,10,11
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$fdno == 0 and next;
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@ -4961,7 +4962,7 @@ sub print {
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}
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next;
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}
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::debug("File descriptor $fdno:");
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::debug("File descriptor $fdno (".$self->fh($fdno,"name")."):");
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if($opt::files) {
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# If --compress: $in_fh must be closed first.
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close $self->fh($fdno,"w");
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@ -4978,8 +4979,13 @@ sub print {
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} elsif($opt::linebuffer) {
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# Line buffered print out
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my $partial = \$self->{'partial_line',$fdno};
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if(defined $self->{'exitstatus'}) {
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# If the job is dead: close printing fh. Needed for --compress
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close $self->fh($fdno,"w");
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}
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# This seek will clear EOF
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seek $in_fh, tell($in_fh), 0;
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# The read is non-blocking: The $in_fh is set to non-blocking.
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while(read($in_fh,substr($$partial,length $$partial),1_000_000)) {
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# Append to $$partial
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# Find the last \n
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@ -5007,8 +5013,11 @@ sub print {
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}
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}
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if(defined $self->{'exitstatus'} and length $$partial > 0) {
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if($self->fh($fdno,"rpid") and kill 0, $self->fh($fdno,"rpid")) {
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# decompress still running
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} elsif(defined $self->{'exitstatus'} and length $$partial > 0) {
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# If the job is dead: print the remaining partial line
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# read remaining
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if($opt::tag or defined $opt::tagstring) {
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my $tag = $self->tag();
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$$partial =~ s/^/$tag/gm;
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@ -5021,16 +5030,7 @@ sub print {
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} else {
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my $buf;
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close $self->fh($fdno,"w");
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if($self->fh($fdno,"wpid")) {
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# This is --compress
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# Wait for $compress_program to finish
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waitpid($self->fh($fdno,"wpid"),0);
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# Then tell cattail this the last reading
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CORE::kill "HUP", $self->fh($fdno,"rpid");
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} else {
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# Seek to start
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seek $in_fh, 0, 0;
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}
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seek $in_fh, 0, 0;
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# $in_fh is now ready for reading at position 0
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if($opt::tag or defined $opt::tagstring) {
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my $tag = $self->tag();
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@ -5064,8 +5064,8 @@ sub print {
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close $in_fh;
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}
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flush $out_fd;
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::debug("<<joboutput $command\n");
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}
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::debug("<<joboutput $command\n");
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}
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sub print_joblog {
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@ -35,6 +35,12 @@ echo "### bug #41609: --compress fails"
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seq 12 | parallel --compress --compress-program bzip2 -k seq {} 1000000 | md5sum
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seq 12 | parallel --compress -k seq {} 1000000 | md5sum
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echo "### --compress race condition (use nice): Fewer than 400 would run"
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seq 400| nice parallel -j200 --compress echo | wc
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echo "### -v --pipe: Dont spawn too many - 1 is enough"
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seq 1 | parallel -j10 -v --pipe cat
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echo "### Test -I";
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seq 1 10 | parallel -k 'seq 1 {} | parallel -k -I :: echo {} ::'
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@ -41,6 +41,11 @@ echo 4
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### bug #41609: --compress fails
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24812dd0f24a26d08a780f988b9d5ad2 -
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24812dd0f24a26d08a780f988b9d5ad2 -
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### --compress race condition (use nice): Fewer than 400 would run
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400 400 1492
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### -v --pipe: Dont spawn too many - 1 is enough
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cat
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1
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### Test -I
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1 1
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2 1
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