parallel: Deal with {} as part of the command (not arg for the command).

doc/release_new_version

@@ -236,8 +236,12 @@ Haiku of the month:
 
 New in this release:
 
+* A semibig refactoring of big functions. All non-trivial functions are now less than 100 lines. The refactoring makes this release beta quality.
+
 * GNU Parallel was cited in: Parallel post-processing with MPI-Bash http://dl.acm.org/citation.cfm?id=2691137
 
+* GNU Parallel was cited in: Distinguishing cause from effect using observational data: methods and benchmarks http://arxiv-web3.library.cornell.edu/pdf/1412.3773.pdf
+
 * GNU Parallel: Open Source For You (OSFY) magazine, October 2013 edition http://www.shakthimaan.com/posts/2014/11/27/gnu-parallel/news.html
 
 * コマンドを並列に実行するGNU parallelがとても便利 http://bicycle1885.hatenablog.com/entry/2014/08/10/143612

src/parallel

@@ -2185,17 +2185,23 @@ sub progress {
 }
 
 sub get_job_with_sshlogin {
+    # Input:
+    #   $sshlogin = which host should the job be run on?
+    # Uses:
+    #   $opt::hostgroups
+    #   $Global::JobQueue
     # Returns:
-    #   next job object for $sshlogin if any available
+    #   $job = next job object for $sshlogin if any available
     my $sshlogin = shift;
-    my $job = undef;
+    my $job;
 
     if ($opt::hostgroups) {
 	my @other_hostgroup_jobs = ();
 
         while($job = $Global::JobQueue->get()) {
 	    if($sshlogin->in_hostgroups($job->hostgroups())) {
-		# Found a job for this hostgroup
+		# Found a job to be run on a hostgroup of this
+		# $sshlogin
 		last;
 	    } else {
 		# This job was not in the hostgroups of $sshlogin
@@ -2255,6 +2261,9 @@ sub get_job_with_sshlogin {
 sub __REMOTE_SSH__ {}
 
 sub read_sshloginfiles {
+    # Read a list of --slf's
+    # Input:
+    #   @files = files or symbolic file names to read
     # Returns: N/A
     for my $s (@_) {
 	read_sshloginfile(expand_slf_shorthand($s));
@@ -2262,6 +2271,11 @@ sub read_sshloginfiles {
 }
 
 sub expand_slf_shorthand {
+    # Expand --slf shorthand into a read file name
+    # Input:
+    #   $file = file or symbolic file name to read
+    # Returns:
+    #   $file = actual file name to read
     my $file = shift;
     if($file eq "-") {
 	# skip: It is stdin
@@ -2282,6 +2296,11 @@ sub expand_slf_shorthand {
 }
 
 sub read_sshloginfile {
+    # Read sshloginfile into @Global::sshlogin
+    # Input:
+    #   $file = file to read
+    # Uses:
+    #   @Global::sshlogin
     # Returns: N/A
     my $file = shift;
     my $close = 1;
@@ -2309,6 +2328,17 @@ sub read_sshloginfile {
 }
 
 sub parse_sshlogin {
+    # Parse @Global::sshlogin into %Global::host.
+    # Keep only hosts that are in one of the given ssh hostgroups.
+    # Uses:
+    #   @Global::sshlogin
+    #   $Global::minimal_command_line_length
+    #   %Global::host
+    #   $opt::transfer
+    #   @opt::return
+    #   $opt::cleanup
+    #   @opt::basefile
+    #   @opt::trc
     # Returns: N/A
     my @login;
     if(not @Global::sshlogin) { @Global::sshlogin = (":"); }
@@ -2385,6 +2415,8 @@ sub parse_sshlogin {
 
 sub remote_hosts {
     # Return sshlogins that are not ':'
+    # Uses:
+    #   %Global::host
     # Returns:
     #   list of sshlogins with ':' removed
     return grep !/^:$/, keys %Global::host;
@@ -2393,6 +2425,9 @@ sub remote_hosts {
 sub setup_basefile {
     # Transfer basefiles to each $sshlogin
     # This needs to be done before first jobs on $sshlogin is run
+    # Uses:
+    #   %Global::host
+    #   @opt::basefile
     # Returns: N/A
     my $cmd = "";
     my $rsync_destdir;
@@ -2415,6 +2450,9 @@ sub setup_basefile {
 
 sub cleanup_basefile {
     # Remove the basefiles transferred
+    # Uses:
+    #   %Global::host
+    #   @opt::basefile
     # Returns: N/A
     my $cmd="";
     my $workdir = Job->new("")->workdir();
@@ -2430,9 +2468,58 @@ sub cleanup_basefile {
 }
 
 sub filter_hosts {
+    # Remove down --sshlogins from active duty.
+    # Find ncpus, ncores, maxlen, time-to-login for each host.
+    # Uses:
+    #   %Global::host
+    #   $Global::minimal_command_line_length
+    #   $opt::use_cpus_instead_of_cores
+    # Returns:
+    #   N/A
     my (%ncores, %ncpus, %time_to_login, %maxlen, %echo, @down_hosts);
 
-    for (parallelized_host_filtering()) {
+    my ($ncores_ref, $ncpus_ref, $time_to_login_ref, $maxlen_ref,
+	$echo_ref, $down_hosts_ref) =
+	    parse_host_filtering(parallelized_host_filtering());
+    %ncores = %$ncores_ref;
+    %ncpus = %$ncpus_ref;
+    %time_to_login = %$time_to_login_ref;
+    %maxlen = %$maxlen_ref;
+    %echo = %$echo_ref;
+    @down_hosts = @$down_hosts_ref;
+
+    delete @Global::host{@down_hosts};
+    @down_hosts and ::warning("Removed @down_hosts\n");
+
+    $Global::minimal_command_line_length = 8_000_000;
+    while (my ($sshlogin, $obj) = each %Global::host) {
+	if($sshlogin eq ":") { next }
+	$ncpus{$sshlogin} or ::die_bug("ncpus missing: ".$obj->serverlogin());
+	$ncores{$sshlogin} or ::die_bug("ncores missing: ".$obj->serverlogin());
+	$time_to_login{$sshlogin} or ::die_bug("time_to_login missing: ".$obj->serverlogin());
+	$maxlen{$sshlogin} or ::die_bug("maxlen missing: ".$obj->serverlogin());
+	if($opt::use_cpus_instead_of_cores) {
+	    $obj->set_ncpus($ncpus{$sshlogin});
+	} else {
+	    $obj->set_ncpus($ncores{$sshlogin});
+	}
+	$obj->set_time_to_login($time_to_login{$sshlogin});
+        $obj->set_maxlength($maxlen{$sshlogin});
+	$Global::minimal_command_line_length =
+	    ::min($Global::minimal_command_line_length,
+		  int($maxlen{$sshlogin}/2));
+	::debug("init", "Timing from -S:$sshlogin ncpus:",$ncpus{$sshlogin},
+		" ncores:", $ncores{$sshlogin},
+		" time_to_login:", $time_to_login{$sshlogin},
+		" maxlen:", $maxlen{$sshlogin},
+		" min_max_len:", $Global::minimal_command_line_length,"\n");
+    }
+}
+
+sub parse_host_filtering {
+    my (%ncores, %ncpus, %time_to_login, %maxlen, %echo, @down_hosts);
+
+    for (@_) {
 	chomp;
 	my @col = split /\t/, $_;
 	if(defined $col[6]) {
@@ -2454,7 +2541,6 @@ sub filter_hosts {
 		# Remove sshlogin
 		::debug("init", "--filtered $host\n");
 		push(@down_hosts, $host);
-		@down_hosts = uniq(@down_hosts);
 	    } elsif($col[6] eq "127") {
 		# signal == 127: parallel not installed remote
 		# Set ncpus and ncores = 1
@@ -2500,31 +2586,8 @@ sub filter_hosts {
 	    ::die_bug("host check unmatched short jobline ($col[0]): $_");
 	}
     }
-    delete @Global::host{@down_hosts};
+    @down_hosts = uniq(@down_hosts);
-    @down_hosts and ::warning("Removed @down_hosts\n");
+    return(\%ncores, \%ncpus, \%time_to_login, \%maxlen, \%echo, \@down_hosts);
-    $Global::minimal_command_line_length = 8_000_000;
-    while (my ($sshlogin, $obj) = each %Global::host) {
-	if($sshlogin eq ":") { next }
-	$ncpus{$sshlogin} or ::die_bug("ncpus missing: ".$obj->serverlogin());
-	$ncores{$sshlogin} or ::die_bug("ncores missing: ".$obj->serverlogin());
-	$time_to_login{$sshlogin} or ::die_bug("time_to_login missing: ".$obj->serverlogin());
-	$maxlen{$sshlogin} or ::die_bug("maxlen missing: ".$obj->serverlogin());
-	if($opt::use_cpus_instead_of_cores) {
-	    $obj->set_ncpus($ncpus{$sshlogin});
-	} else {
-	    $obj->set_ncpus($ncores{$sshlogin});
-	}
-	$obj->set_time_to_login($time_to_login{$sshlogin});
-        $obj->set_maxlength($maxlen{$sshlogin});
-	$Global::minimal_command_line_length =
-	    ::min($Global::minimal_command_line_length,
-		  int($maxlen{$sshlogin}/2));
-	::debug("init", "Timing from -S:$sshlogin ncpus:",$ncpus{$sshlogin},
-		" ncores:", $ncores{$sshlogin},
-		" time_to_login:", $time_to_login{$sshlogin},
-		" maxlen:", $maxlen{$sshlogin},
-		" min_max_len:", $Global::minimal_command_line_length,"\n");
-    }
 }
 
 sub parallelized_host_filtering {
@@ -7066,6 +7129,7 @@ sub new {
     }
     # Replace replacement strings with {= perl expr =}
     @command = merge_rpl_parts(@command);
+
     # Protect matching inside {= perl expr =}
     # by replacing {= and =} with \257< and \257>
     for(@command) {
@@ -7106,8 +7170,15 @@ sub new {
 	    }
 	}
     }
+    # Add {} if no replacement strings in @command
     my($replacecount_ref, $len_ref, @command) =
 	replacement_counts_and_lengths(@command);
+    if("@command" =~ /^\S*\257</) {
+	# Replacement string is (part of) the command (and not just argument)
+	# E.g. parallel {}, parallel my_{= s/_//=}, parallel {2}
+	# Do no quote (Otherwise it will fail if the input contains spaces)
+	$Global::noquote = 1;
+    }
 
     return bless {
 	'unget' => \@unget,
@@ -7162,7 +7233,7 @@ sub replacement_counts_and_lengths {
     # Count the number of different replacement strings.
     # Find the lengths of context for context groups and non-context
     # groups.
-    # If no {} found: add it to the @command
+    # If no {} found in @command: add it to @command
     #
     # Input:
     #   @command = command template
@@ -7180,8 +7251,8 @@ sub replacement_counts_and_lengths {
 	for my $c (@cmd) {
 	    while($c =~ s/ \257<([^\257]*?)\257> /\000/x) {
 		# %replacecount = { "perlexpr" => number of times seen }
-		# e.g { "$_++" => 2 }
+		# e.g { "s/a/b/" => 2 }
-		$replacecount{$1} ++;
+		$replacecount{$1}++;
 		$sum++;
 	    }
 	    # Measure the length of the context around the {= perl expr =}
@@ -7202,13 +7273,13 @@ sub replacement_counts_and_lengths {
 		# %replacecount = { "perlexpr" => number of times seen }
 		# e.g { "$_++" => 2 }
 		# But for tagstring we just need to mark it as seen
-		$replacecount{$1}||=1;
+		$replacecount{$1} ||= 1;
 	    }
 	}
 	if($opt::bar) {
 	    # If the command does not contain {} force it to be computed
 	    # as it is being used by --bar
-	    $replacecount{""}||=1;
+	    $replacecount{""} ||= 1;
 	}
 
 	$len{'context'} = 0+$contextlen;
@@ -7219,11 +7290,9 @@ sub replacement_counts_and_lengths {
 		" Non: ", $len{'noncontext'}, " Ctxgrp: ", $len{'contextgroups'},
 		" NonCtxGrp: ", $len{'noncontextgroups'}, "\n");
 	if($sum == 0) {
-	    # Default command = {}
-	    # If not replacement string: append {}
 	    if(not @command) {
+		# Default command = {}
 		@command = ("\257<\257>");
-		$Global::noquote = 1;
 	    } elsif(($opt::pipe or $opt::pipepart)
 		    and not $opt::fifo and not $opt::cat) {
 		# With --pipe / --pipe-part you can have no replacement

testsuite/tests-to-run/parallel-local-0.3s.sh

@@ -30,7 +30,7 @@ echo '### Test bug #43376: {%} and {#} with --pipe'
 
 echo '**'
 
-echo '### {= and =} in different groups'
+echo '### {= and =} in different groups separated by space'
   parallel echo {= s/a/b/ =} ::: a
   parallel echo {= s/a/b/=} ::: a
   parallel echo {= s/a/b/=}{= s/a/b/=} ::: a
@@ -41,4 +41,15 @@ echo '### {= and =} in different groups'
   parallel echo {={= =} ::: a
   parallel echo {= {= =} ::: a
   parallel echo {= {= =} =} ::: a
+
+echo '**'
+
+echo '### {} as part of the command'
+  echo p /bin/ls | parallel l{= s/p/s/ =}
+  echo /bin/ls-p | parallel --colsep '-' l{=2 s/p/s/ =} {1}
+  echo s /bin/ls | parallel l{}
+  echo /bin/ls | parallel ls {}
+  echo ls /bin/ls | parallel {}
+  echo ls /bin/ls | parallel
+
 EOF

testsuite/wanted-results/parallel-local-0.3s

@@ -26,8 +26,8 @@ echo '### Test bug #43376: {%} and {#} with --pipe'
 1
 echo '**'
 **
-echo '### {= and =} in different groups'
+echo '### {= and =} in different groups separated by space'
-### {= and =} in different groups
+### {= and =} in different groups separated by space
   parallel echo {= s/a/b/ =} ::: a
 b
   parallel echo {= s/a/b/=} ::: a
@@ -48,3 +48,19 @@ b {=a
 {= a
   parallel echo {= {= =} =} ::: a
 {= a =}
+echo '**'
+**
+echo '### {} as part of the command'
+### {} as part of the command
+  echo p /bin/ls | parallel l{= s/p/s/ =}
+/bin/ls
+  echo /bin/ls-p | parallel --colsep '-' l{=2 s/p/s/ =} {1}
+/bin/ls
+  echo s /bin/ls | parallel l{}
+/bin/ls
+  echo /bin/ls | parallel ls {}
+/bin/ls
+  echo ls /bin/ls | parallel {}
+/bin/ls
+  echo ls /bin/ls | parallel
+/bin/ls