Fixed bug #45025: --pipe --retries does not reschedule on other host

NEWS

@@ -1,30 +1,53 @@
 20151122
 
-* GNU Parallel packaged for CERN CentOS: http://linuxsoft.cern.ch/cern/centos/7/cern/x86_64/repoview/parallel.html
+* GNU Parallel packaged for CERN CentOS:
+  http://linuxsoft.cern.ch/cern/centos/7/cern/x86_64/repoview/parallel.html
 
-* GNU Parallel was cited in: The Outer Solar System Origins Survey: I. Design and First-Quarter Discoveries http://arxiv.org/pdf/1511.02895.pdf
+* GNU Parallel was cited in: The Outer Solar System Origins Survey:
+  I. Design and First-Quarter Discoveries
+  http://arxiv.org/pdf/1511.02895.pdf
 
-* GNU Parallel was cited in: Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3431.html
+* GNU Parallel was cited in: Contrasting genetic architectures of
+  schizophrenia and other complex diseases using fast
+  variance-components analysis
+  http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3431.html
 
-* GNU Parallel was cited in: Named-Entity Chunking for Norwegian Text using Support Vector Machines http://ojs.bibsys.no/index.php/NIK/article/viewFile/248/211
+* GNU Parallel was cited in: Named-Entity Chunking for Norwegian Text
+  using Support Vector Machines
+  http://ojs.bibsys.no/index.php/NIK/article/viewFile/248/211
 
-* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004381#pcbi.1004381.ref072
+* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics
+  Using Brownian Dynamics, Molecular Dynamics and Milestoning
+  http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004381#pcbi.1004381.ref072
 
-* GNU Parallel was cited in: A Detailed Characterization of Errors in Logic Circuits due to Single-Event Transients http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=7302348&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7302348
+* GNU Parallel was cited in: A Detailed Characterization of Errors in
+  Logic Circuits due to Single-Event Transients
+  http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=7302348&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7302348
 
-* GNU Parallel was cited in: Arabic Speaker Emotion Classification Using Rhythm Metrics and Neural Networks http://www.eurasip.org/Proceedings/Eusipco/Eusipco2015/papers/1570104855.pdf
+* GNU Parallel was cited in: Arabic Speaker Emotion Classification
+  Using Rhythm Metrics and Neural Networks
+  http://www.eurasip.org/Proceedings/Eusipco/Eusipco2015/papers/1570104855.pdf
 
-* GNU Parallel was cited in: Stride Search: a general algorithm for storm detection in high resolution climate data http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
+* GNU Parallel was cited in: Stride Search: a general algorithm for
+  storm detection in high resolution climate data
+  http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
 
-* GNU Parallel was cited in: Decomposing Digital Paintings into Layers via RGB-space Geometry http://arxiv.org/pdf/1509.03335.pdf
+* GNU Parallel was cited in: Decomposing Digital Paintings into Layers
+  via RGB-space Geometry http://arxiv.org/pdf/1509.03335.pdf
 
-* GNU Parallel was cited in: Structure and evolutionary history of a large family of NLR proteins in the zebrafish http://www.biorxiv.org/content/biorxiv/early/2015/09/18/027151.full.pdf
+* GNU Parallel was cited in: Structure and evolutionary history of a
+  large family of NLR proteins in the zebrafish
+  http://www.biorxiv.org/content/biorxiv/early/2015/09/18/027151.full.pdf
 
-* GNU Parallel was cited in: Evolution of movement strategies under competitive interactions http://digital.csic.es/bitstream/10261/115973/1/evolution_movement_strategies_Kiziridis.pdf
+* GNU Parallel was cited in: Evolution of movement strategies under
+  competitive interactions
+  http://digital.csic.es/bitstream/10261/115973/1/evolution_movement_strategies_Kiziridis.pdf
 
-* Automating large numbers of tasks https://rcc.uchicago.edu/docs/tutorials/kicp-tutorials/running-jobs.html
+* Automating large numbers of tasks
+  https://rcc.uchicago.edu/docs/tutorials/kicp-tutorials/running-jobs.html
 
-* Max out your IOPs with GNU Parallel http://blog.bitratchet.com/2015/11/11/max-out-your-iops-with-gnu-parallel/
+* Max out your IOPs with GNU Parallel
+  http://blog.bitratchet.com/2015/11/11/max-out-your-iops-with-gnu-parallel/
 
 * Bug fixes and man page updates.
 

doc/release_new_version

@@ -236,6 +236,17 @@ http://www.researchgate.net/profile/Christoph_Junghans/publication/276178326_TAD
 
 * << Update forventet juni Rachel har lige svaret >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
 
+* <<Citation needed: A Cache- and Memory-Aware Mapping Algorithm
+for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7323015>>
+
+* <<Citation needed: Introspecting for RSA Key Material to Assist Intrusion Detection http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7331177&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7331177>>
+
+* GNU Parallel was cited in: Evolution and Learning in Heterogeneous Environments http://research.gold.ac.uk/15078/1/COM_thesis_JonesD_2015.pdf
+
+* GNU Parallel was cited in: Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html
+
+* GNU Parallel was cited in: Efficient Retrieval of Key Material for Inspecting Potentially Malicious Traffic in the Cloud http://www.cs.bham.ac.uk/~bxb/Papres/2015.1.pdf 
+
 * GNU Parallel was cited in: Achieving Consistent Doppler Measurements from SDO/HMI Vector Field Inversions http://arxiv.org/pdf/1511.06500.pdf
 
 * 使用 GNU parallel 來平行運算http://mutolisp.logdown.com/posts/316959-using-gnu-parallel-to-parallel-computing

src/parallel

@@ -424,6 +424,23 @@ sub spreadstdin {
     # If there is anything left in the buffer write it
     write_record_to_pipe($chunk_number++,\$header,\$buf,$recstart,$recend,length $buf);
 
+    if($opt::retries) {
+	$Global::no_more_input = 1;
+	# We need to start no more jobs: At most we need to retry some
+	# of the already running.
+	my @running = values %Global::running;
+	# Stop any virgins.
+	for my $job (@running) {
+	    if(defined $job and $job->virgin()) {
+		close $job->fh(0,"w");
+	    }
+	}
+	# Wait for running jobs to be done
+	my $sleep =1;
+	while($Global::total_running > 0) {
+	    $sleep = ::reap_usleep($sleep);
+	}
+    }
     $Global::start_no_new_jobs ||= 1;
     if($opt::roundrobin) {
 	for my $job (values %Global::running) {
@@ -662,7 +679,20 @@ sub write_record_to_pipe {
     my $job = shift @Global::virgin_jobs;
     # Job is no longer virgin
     $job->set_virgin(0);
-    if(1) {
+
+    if($opt::retries) {
+	# Copy $buffer[0..$endpos] to $job->{'block'}
+	# Remove rec_sep
+	# Run $job->add_transfersize
+	$job->set_block($header_ref,$buffer_ref,$endpos,$recstart,$recend);
+	if(fork()) {
+	    # Skip
+	} else {
+	    $job->write($job->block_ref());
+	    close $job->fh(0,"w");
+	    exit(0);
+	}
+    } else {
 	# We ignore the removed rec_sep which is technically wrong.
 	$job->add_transfersize($endpos + length $$header_ref);
 	if(fork()) {
@@ -1075,10 +1105,14 @@ sub check_invalid_option_combinations {
 	::error("--timeout must be seconds or percentage.");
 	wait_and_exit(255);
     }
-    if(defined $opt::fifo and $opt::cat) {
+    if(defined $opt::fifo and defined $opt::cat) {
 	::error("--fifo cannot be combined with --cat.");
 	::wait_and_exit(255);
     }
+    if(defined $opt::retries and defined $opt::roundrobin) {
+	::error("--retries cannot be combined with --roundrobin.");
+	::wait_and_exit(255);
+    }
     if(defined $opt::pipepart and
        (defined $opt::L or defined $opt::max_lines
 	or defined $opt::max_replace_args)) {
@@ -2153,7 +2187,20 @@ sub init_run_jobs {
 		      $job->replaced(),"'\n");
 		if($job->start()) {
 		    if($opt::pipe) {
-			push(@Global::virgin_jobs,$job);
+			if($job->virgin()) {
+			    push(@Global::virgin_jobs,$job);
+			} else {
+			    # Block already set: This is a retry
+			    if(fork()) {
+				::debug("pipe","\n\nWriting ",length ${$job->block_ref()},
+					" to ", $job->seq(),"\n");
+				close $job->fh(0,"w");
+			    } else {
+				$job->write($job->block_ref());
+				close $job->fh(0,"w");
+				exit(0);
+			    }
+			}
 		    }
 		    debug("start", "Started as seq ", $job->seq(),
 			  " pid:", $job->pid(), "\n");
@@ -3501,7 +3548,7 @@ sub bibtex {
 	       "  volume = {36},",
 	       "  url = {http://www.gnu.org/s/parallel},",
 	       "  year = {2011},",
-	       "  pages = {42-47}",
+	       "  pages = {42-47},",
 	       "  doi = {10.5281/zenodo.16303}",
 	       "}",
 	       "",
@@ -6244,7 +6291,8 @@ sub set_block {
     #   N/A
     my $self = shift;
     my ($header_ref,$buffer_ref,$endpos,$recstart,$recend) = @_;
-    $self->{'block'} = ($self->virgin() ? $$header_ref : "").substr($$buffer_ref,0,$endpos);
+    $self->{'block'} = ($self->virgin() ? $$header_ref : "").
+	substr($$buffer_ref,0,$endpos);
     if($opt::remove_rec_sep) {
 	remove_rec_sep(\$self->{'block'},$recstart,$recend);
     }
@@ -7427,10 +7475,10 @@ sub should_be_retried {
     if (not $opt::retries) {
 	return 0;
     }
-    if(not $self->exitstatus()) {
+    if(not $self->exitstatus() and not $self->exitsignal()) {
 	# Completed with success. If there is a recorded failure: forget it
 	$self->reset_failed_here();
-	return 0
+	return 0;
     } else {
 	# The job failed. Should it be retried?
 	$self->add_failed_here();
@@ -7445,7 +7493,7 @@ sub should_be_retried {
 	    ::debug("run", "Retry ", $self->seq(), "\n");
 	    return 1;
 	}
-}
+    }
 }
 
 {
@@ -8641,10 +8689,11 @@ sub get {
 	$cmd_line->populate();
 	::debug("init","cmd_line->number_of_args ",
 		$cmd_line->number_of_args(), "\n");
-	if($opt::pipe or $opt::pipepart) {
+	if(not $Global::no_more_input and ($opt::pipe or $opt::pipepart)) {
 	    if($cmd_line->replaced() eq "") {
 		# Empty command - pipe requires a command
-		::error("--pipe/--pipepart must have a command to pipe into (e.g. 'cat').");
+		::error("--pipe/--pipepart must have a command to pipe into ".
+			"(e.g. 'cat').");
 		::wait_and_exit(255);
 	    }
 	} else {

testsuite/tests-to-run/parallel-local-ssh5.sh

@@ -21,4 +21,8 @@ echo '### --ssh autossh - add commands that fail here'
   parallel -S lo false ::: a || echo OK should fail; 
   touch foo_autossh; stdout parallel -S csh@lo --trc {}.out touch {}.out ::: foo_autossh; rm foo_autossh*;
 
+echo '### bug #45025: --pipe --retries does not reschedule on other host'
+  seq 1 300030| stdout parallel -k --retries 2 -S a.a,: --pipe 'wc;hostname'
+  stdout parallel --retries 2 --roundrobin echo ::: should fail
+
 EOF

testsuite/wanted-results/parallel-local-ssh5

@@ -84,3 +84,13 @@ Environment variables are:
 
 rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
 rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.1]
+echo '### bug #45025: --pipe --retries does not reschedule on other host'
+### bug #45025: --pipe --retries does not reschedule on other host
+  seq 1 300030| stdout parallel -k --retries 2 -S a.a,: --pipe 'wc;hostname'
+parallel: Warning: Could not figure out number of cpus on a.a (). Using 1.
+ 165668  165668 1048571
+aspire
+ 134362  134362  940534
+aspire
+  stdout parallel --retries 2 --roundrobin echo ::: should fail
+parallel: Error: --retries cannot be combined with --roundrobin.

testsuite/wanted-results/parallel-local-ssh6

@@ -0,0 +1,108 @@
+echo '### Test --onall';   parallel --onall --tag -k -S parallel@lo,csh@lo '(echo {1} {2}) | awk \{print\ \$2}' ::: a b c ::: 1 2
+### Test --onall
+csh@lo	1
+csh@lo	2
+csh@lo	1
+csh@lo	2
+csh@lo	1
+csh@lo	2
+parallel@lo	1
+parallel@lo	2
+parallel@lo	1
+parallel@lo	2
+parallel@lo	1
+parallel@lo	2
+echo '### Test | --onall';   seq 3 | parallel --onall --tag -k -S parallel@lo,csh@lo '(echo {1} {2}) | awk \{print\ \$2}' ::: a b c :::: -
+### Test | --onall
+csh@lo	1
+csh@lo	2
+csh@lo	3
+csh@lo	1
+csh@lo	2
+csh@lo	3
+csh@lo	1
+csh@lo	2
+csh@lo	3
+parallel@lo	1
+parallel@lo	2
+parallel@lo	3
+parallel@lo	1
+parallel@lo	2
+parallel@lo	3
+parallel@lo	1
+parallel@lo	2
+parallel@lo	3
+echo '### Test --onall -u';   parallel --onall -S parallel@lo,csh@lo -u '(echo {1} {2}) | awk \{print\ \$2}' ::: a b c ::: 1 2 3 | sort
+### Test --onall -u
+1
+1
+1
+1
+1
+1
+2
+2
+2
+2
+2
+2
+3
+3
+3
+3
+3
+3
+echo '### Test --nonall';   parallel --nonall -k -S parallel@lo,csh@lo pwd | sort
+### Test --nonall
+/home/csh
+/home/parallel
+echo '### Test --nonall -u - should be interleaved x y x y';   parallel --nonall -S parallel@lo,csh@lo -u 'pwd|grep -q csh && sleep 3; pwd;sleep 12;pwd;'
+### Test --nonall -u - should be interleaved x y x y
+/home/parallel
+/home/csh
+/home/parallel
+/home/csh
+echo '### Test read sshloginfile from STDIN';   echo parallel@lo,csh@lo | parallel -S - -k --nonall pwd;   echo parallel@lo,csh@lo | parallel --sshloginfile - -k --onall pwd\; echo ::: foo
+### Test read sshloginfile from STDIN
+/home/csh
+/home/parallel
+/home/csh
+foo
+/home/parallel
+foo
+echo '**'
+**
+echo '### Test --nonall --basefile';   touch tmp/nonall--basefile;   stdout parallel --nonall --basefile tmp/nonall--basefile -S parallel@lo,csh@lo ls tmp/nonall--basefile;   stdout parallel --nonall -S parallel@lo,csh@lo rm tmp/nonall--basefile;   stdout rm tmp/nonall--basefile
+### Test --nonall --basefile
+tmp/nonall--basefile
+tmp/nonall--basefile
+echo '**'
+**
+echo '### Test --onall --basefile';   touch tmp/onall--basefile;   stdout parallel --onall --basefile tmp/onall--basefile -S parallel@lo,csh@lo ls {} ::: tmp/onall--basefile;   stdout parallel --onall -S parallel@lo,csh@lo rm {} ::: tmp/onall--basefile;   stdout rm tmp/onall--basefile
+### Test --onall --basefile
+tmp/onall--basefile
+tmp/onall--basefile
+echo '**'
+**
+echo '### Test --nonall --basefile --cleanup (rm should fail)';   touch tmp/nonall--basefile--clean;   stdout parallel --nonall --basefile tmp/nonall--basefile--clean --cleanup -S parallel@lo,csh@lo ls tmp/nonall--basefile--clean;   stdout parallel --nonall -S parallel@lo,csh@lo rm tmp/nonall--basefile--clean;   stdout rm tmp/nonall--basefile--clean
+### Test --nonall --basefile --cleanup (rm should fail)
+tmp/nonall--basefile--clean
+tmp/nonall--basefile--clean
+rm: cannot remove ‘tmp/nonall--basefile--clean’: No such file or directory
+rm: cannot remove ‘tmp/nonall--basefile--clean’: No such file or directory
+echo '**'
+**
+echo '### Test --onall --basefile --cleanup (rm should fail)';   touch tmp/onall--basefile--clean;   stdout parallel --onall --basefile tmp/onall--basefile--clean --cleanup -S parallel@lo,csh@lo ls {} ::: tmp/onall--basefile--clean;   stdout parallel --onall -S parallel@lo,csh@lo rm {} ::: tmp/onall--basefile--clean;   stdout rm tmp/onall--basefile--clean
+### Test --onall --basefile --cleanup (rm should fail)
+tmp/onall--basefile--clean
+tmp/onall--basefile--clean
+rm: cannot remove ‘tmp/onall--basefile--clean’: No such file or directory
+rm: cannot remove ‘tmp/onall--basefile--clean’: No such file or directory
+echo '**'
+**
+echo '### Test --workdir .';   ssh parallel@lo mkdir -p mydir;   mkdir -p $HOME/mydir; cd $HOME/mydir;   parallel --workdir . -S parallel@lo ::: pwd
+### Test --workdir .
+/home/parallel/mydir
+echo '### Test --wd .';   ssh csh@lo mkdir -p mydir;   mkdir -p $HOME/mydir; cd $HOME/mydir;   parallel --workdir . -S csh@lo ::: pwd
+### Test --wd .
+/home/csh/mydir