parallel: --compress passes tests.

10seconds_install

@@ -33,7 +33,7 @@ if test "$GET" = ""; then
 fi
 
 LANG=C
-LATEST=$($GET http://ftpmirror.gnu.org/parallel | perl -ne '/(parallel-\d{8})/ and print $1."\n"' | sort | $TAIL -n1)
+LATEST=$($GET http://ftpmirror.gnu.org/parallel | perl -ne '/.*(parallel-\d{8})/ and print $1."\n"' | sort | $TAIL -n1)
 if test \! -e $LATEST.tar.bz2; then
   # Source tar does not exist
   rm -f $LATEST.tar.bz2 $LATEST.tar.bz2.sig

doc/release_new_version

@@ -204,51 +204,52 @@ cc:Sandro Cazzaniga <kharec@mandriva.org>,
    Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
    Jesse Alama <jesse.alama@gmail.com>
 
-Subject: GNU Parallel 20140222 ('Со́чи') released
+Subject: GNU Parallel 20140222 ('Со́чи/Euromaidan') released
 
-GNU Parallel 20140222 ('Со́чи') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
+GNU Parallel 20140222 ('Со́чи/Euromaidan') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
+
+Packagers that default to --tollef should take note that --tollef is now retired after a full year of being obsolete.
 
 The --compress change is so big that this release is of alpha quality.
 
+
 New in this release:
 
 * --tollef has been retired.
 
 * --compress has be redesigned due to bugs.
 
-* GNU Parallel was cited in: Speaker Verification and Keyword Spotting
+* 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
-  Systems for Forensic Applications
-  http://lantana.tenet.res.in/website_files/thesis/Phd/srikanth.pdf
 
-* GNU Parallel was cited in: Scaleable Code Clone Detection
+* GNU Parallel was cited in: Scaleable Code Clone Detection http://scg.unibe.ch/archive/phd/schwarz-phd.pdf
-  http://scg.unibe.ch/archive/phd/schwarz-phd.pdf
 
-* GNU Parallel was used (unfortunately without citation) in:
+* GNU Parallel was cited in: Clone Detection that scales http://scg.unibe.ch/archive/masters/Vogt14a.pdf
-  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 recommended (without citation) in: Redesigning the
+* GNU Parallel was cited in: Scalable Positional Analysis for Studying Evolution of Nodes in Networks http://arxiv-web3.library.cornell.edu/pdf/1402.3797
-  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
+* GNU Parallel was cited in: Aggregate Characterization of User Behavior in Twitter and Analysis of the Retweet Graph http://arxiv.org/pdf/1402.2671v1
-  http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
 
-* Convert MP3 to a scrolling spectrum waterfall plot video
+* 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
-  http://jdesbonnet.blogspot.dk/2014/02/convert-mp3-to-scrolling-spectrum.html
 
-* PHP wrapper class for the GNU Parallel tool
+* 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
-  https://github.com/geopal-solutions/gnu-parallel-wrapper/tree/master
 
-* Exploratory Data Analysis
+* 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
-  http://www.slideshare.net/thinrhino/gnunify
 
-* Single-Thread-Programme auf Multicore-Rechnern parallelisieren
+* 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
-  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
+* GNU Parallel is co-distributed with RepeatExplorer http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/repeatexplorer/README.txt
-  http://savepearlharbor.com/?p=210480
+
+* 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.
 

src/parallel

@@ -4037,21 +4037,17 @@ sub seq {
 
 sub cattail {
     # Returns:
-    #   $cattail = perl program for: cattail "decompress program" [file_to_decompress or stdin]
+    #   $cattail = perl program for: cattail "decompress program" writerpid [file_to_decompress or stdin] [file_to_unlink]
     my $cattail = q{
     # cat followed by tail.
-    # SIGHUP says there will be appended no more, so just finish after this round.
+    # If $writerpid dead: finish after this round
-    
     use Fcntl;
     
-    $SIG{HUP} = sub { $Global::sighup = 1; };
-    
     $|=1;
 
-    $cmd = shift;
+    my ($cmd, $writerpid, $read_file, $unlink_file) = @ARGV;
-    
+    if($read_file) {
-    if(@ARGV) {
+        open(IN,"<",$read_file) || die("cattail: Cannot open $read_file");
-        open(IN,"<",$ARGV[0]) || die("Cannot open $ARGV[0]");
     } else {
         *IN = *STDIN;
     }
@@ -4060,14 +4056,16 @@ sub cattail {
     fcntl(IN, F_GETFL, $flags) || die $!; # Get the current flags on the filehandle
     $flags |= O_NONBLOCK; # Add non-blocking to the flags
     fcntl(IN, F_SETFL, $flags) || die $!; # Set the flags on the filehandle
-    
+    open(OUT,"|-",$cmd) || die("cattail: Cannot run $cmd");
-    open(OUT,"|-",$cmd) || die;
 
     while(1) {
         # clear EOF
         seek(IN,0,1);
+        my $writer_running = kill 0, $writerpid;
         $read = sysread(IN,$buf,1_000_000);
         if($read) {
+            # We can unlink the file now: The writer has written something
+            -e $unlink_file and unlink $unlink_file;
 	    # Blocking print
             while($buf) {
                 my $bytes_written = syswrite(OUT,$buf);
@@ -4077,12 +4075,14 @@ sub cattail {
 	    # Something printed: Wait less next time
 	    $sleep /= 2;
         } else {
-	    if(eof(IN) and $Global::sighup) {
+	    if(eof(IN) and not $writer_running) {
-                # SIGHUP received: There will never be more to read => exit
+                # Writer dead: There will never be more to read => exit
                 exit;
             }
-	    # Nothing read: Wait longer next time
+            # TODO This could probably be done more efficiently using select(2)
-	    $sleep = 1.05*$sleep + 0.01;
+	    # Nothing read: Wait longer before next read
+            # Up to 30 milliseconds
+            $sleep = ($sleep < 30) ? ($sleep * 1.001 + 0.01) : ($sleep);
 	    usleep($sleep);
         }
     }
@@ -4159,12 +4159,13 @@ sub openoutputfiles {
 	# cattail get pid i  $pid = $self->fh($fdno,'rpid');
 	my $cattail = cattail();
 	for my $fdno (1,2) {
-	    my $wpid = open(my $fdw,"|-","$opt::compress_program >".
+	    my $wpid = open(my $fdw,"|-","$opt::compress_program >>".
 			    $self->fh($fdno,'name')) || die $?;
 	    $self->set_fh($fdno,'w',$fdw);
 	    $self->set_fh($fdno,'wpid',$wpid);
 	    my $rpid = open(my $fdr, "-|", "perl", "-e", $cattail, 
-			    $opt::decompress_program, $self->fh($fdno,'name')) || die $?;
+			    $opt::decompress_program, $wpid,
+			    $self->fh($fdno,'name'),$self->fh($fdno,'unlink')) || die $?;
 	    $self->set_fh($fdno,'r',$fdr);
 	    $self->set_fh($fdno,'rpid',$rpid);
 	    # Unlink if required but only when cattail and compress_program has started.
@@ -4927,7 +4928,6 @@ sub print {
     if($opt::pipe and $self->virgin()) {
     } else {
 	if($Global::joblog) { $self->print_joblog() }
-    }
 
     # Printing is only relevant for grouped output.
     $Global::grouped or return;
@@ -4950,6 +4950,7 @@ sub print {
 	# so flush to avoid STDOUT being buffered
 	flush STDOUT;
     }
+    }
     for my $fdno (sort { $a <=> $b } keys %Global::fd) {
 	# Sort by file descriptor numerically: 1,2,3,..,9,10,11
 	$fdno == 0 and next;
@@ -4961,7 +4962,7 @@ sub print {
 	    }
 	    next;
 	}
-	::debug("File descriptor $fdno:");
+	::debug("File descriptor $fdno (".$self->fh($fdno,"name")."):");
 	if($opt::files) {
 	    # If --compress: $in_fh must be closed first.
 	    close $self->fh($fdno,"w");
@@ -4978,8 +4979,13 @@ sub print {
 	} elsif($opt::linebuffer) {
 	    # Line buffered print out
 	    my $partial = \$self->{'partial_line',$fdno};
+	    if(defined $self->{'exitstatus'}) {
+		# If the job is dead: close printing fh. Needed for --compress
+		close $self->fh($fdno,"w");
+	    }
 	    # This seek will clear EOF
 	    seek $in_fh, tell($in_fh), 0;
+	    # The read is non-blocking: The $in_fh is set to non-blocking.
 	    while(read($in_fh,substr($$partial,length $$partial),1_000_000)) {
 		# Append to $$partial
 		# Find the last \n
@@ -5007,8 +5013,11 @@ sub print {
 		}
 	    }
 
-	    if(defined $self->{'exitstatus'} and length $$partial > 0) {
+	    if($self->fh($fdno,"rpid") and kill 0, $self->fh($fdno,"rpid")) {
+		# decompress still running
+	    } elsif(defined $self->{'exitstatus'} and length $$partial > 0) {
 		# If the job is dead: print the remaining partial line
+		# read remaining
 		if($opt::tag or defined $opt::tagstring) {
 		    my $tag = $self->tag();
 		    $$partial =~ s/^/$tag/gm;
@@ -5021,16 +5030,7 @@ sub print {
 	} else {
 	    my $buf;
 	    close $self->fh($fdno,"w");
-	    if($self->fh($fdno,"wpid")) {
-		# This is --compress
-		# Wait for $compress_program to finish
-		waitpid($self->fh($fdno,"wpid"),0);
-		# Then tell cattail this the last reading
-		CORE::kill "HUP", $self->fh($fdno,"rpid");
-	    } else {
-		# Seek to start
 	    seek $in_fh, 0, 0;
-	    }
 	    # $in_fh is now ready for reading at position 0
 	    if($opt::tag or defined $opt::tagstring) {
 		my $tag = $self->tag();
@@ -5064,8 +5064,8 @@ sub print {
 	    close $in_fh;   
 	}
 	flush $out_fd;
-	::debug("<<joboutput $command\n");
     }
+    ::debug("<<joboutput $command\n");
 }
 
 sub print_joblog {

testsuite/tests-to-run/parallel-local114.sh

@@ -35,6 +35,12 @@ echo "### bug #41609: --compress fails"
   seq 12 | parallel --compress --compress-program bzip2 -k seq {} 1000000 | md5sum
   seq 12 | parallel --compress -k seq {} 1000000 | md5sum
 
+echo "### --compress race condition (use nice): Fewer than 400 would run"
+  seq 400| nice parallel -j200 --compress echo | wc
+
+echo "### -v --pipe: Dont spawn too many - 1 is enough"
+  seq 1 | parallel -j10 -v --pipe cat
+
 echo "### Test -I"; 
   seq 1 10 | parallel -k 'seq 1 {} | parallel -k -I :: echo {} ::'
 

testsuite/wanted-results/parallel-local114

@@ -41,6 +41,11 @@ echo 4
 ### bug #41609: --compress fails
 24812dd0f24a26d08a780f988b9d5ad2  -
 24812dd0f24a26d08a780f988b9d5ad2  -
+### --compress race condition (use nice): Fewer than 400 would run
+    400     400    1492
+### -v --pipe: Dont spawn too many - 1 is enough
+cat
+1
 ### Test -I
 1 1
 2 1