5 files changed, 949 insertions, 0 deletions
diff --git a/pro-train/Makefile.am b/pro-train/Makefile.am
new file mode 100644
index 00000000..945ed5c3
--- /dev/null
+++ b/pro-train/Makefile.am
@@ -0,0 +1,13 @@
+bin_PROGRAMS = \
+  mr_pro_map \
+  mr_pro_reduce
+
+TESTS = lo_test
+
+mr_pro_map_SOURCES = mr_pro_map.cc
+mr_pro_map_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
+
+mr_pro_reduce_SOURCES = mr_pro_reduce.cc
+mr_pro_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
+
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/pro-train/README.shared-mem b/pro-train/README.shared-mem
new file mode 100644
index 00000000..7728efc0
--- /dev/null
+++ b/pro-train/README.shared-mem
@@ -0,0 +1,9 @@
+If you want to run dist-vest.pl on a very large shared memory machine, do the
+following:
+
+  ./dist-vest.pl --use-make I --decode-nodes J --weights weights.init --source-file=dev.src --ref-files=dev.ref.* cdec.ini
+
+This will use I jobs for doing the line search and J jobs to run the decoder. Typically, since the
+decoder must load grammars, language models, etc., J should be smaller than I, but this will depend
+on the system you are running on and the complexity of the models used for decoding.
+
diff --git a/pro-train/dist-pro.pl b/pro-train/dist-pro.pl
new file mode 100755
index 00000000..35bccea4
--- /dev/null
+++ b/pro-train/dist-pro.pl
@@ -0,0 +1,735 @@
+#!/usr/bin/env perl
+use strict;
+my @ORIG_ARGV=@ARGV;
+use Cwd qw(getcwd);
+my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../environment"; }
+
+# Skip local config (used for distributing jobs) if we're running in local-only mode
+use LocalConfig;
+use Getopt::Long;
+use IPC::Open2;
+use POSIX ":sys_wait_h";
+my $QSUB_CMD = qsub_args(mert_memory());
+
+my $VEST_DIR="$SCRIPT_DIR/../vest";
+require "$VEST_DIR/libcall.pl";
+
+# Default settings
+my $srcFile;
+my $refFiles;
+my $bin_dir = $SCRIPT_DIR;
+die "Bin directory $bin_dir missing/inaccessible" unless -d $bin_dir;
+my $FAST_SCORE="$bin_dir/../mteval/fast_score";
+die "Can't execute $FAST_SCORE" unless -x $FAST_SCORE;
+my $MAPINPUT = "$bin_dir/mr_pro_generate_mapper_input";
+my $MAPPER = "$bin_dir/mr_pro_map";
+my $REDUCER = "$bin_dir/mr_pro_reduce";
+my $parallelize = "$VEST_DIR/parallelize.pl";
+my $libcall = "$VEST_DIR/libcall.pl";
+my $sentserver = "$VEST_DIR/sentserver";
+my $sentclient = "$VEST_DIR/sentclient";
+my $LocalConfig = "$SCRIPT_DIR/../environment/LocalConfig.pm";
+
+my $SCORER = $FAST_SCORE;
+die "Can't find $MAPPER" unless -x $MAPPER;
+my $cdec = "$bin_dir/../decoder/cdec";
+die "Can't find decoder in $cdec" unless -x $cdec;
+die "Can't find $parallelize" unless -x $parallelize;
+die "Can't find $libcall" unless -e $libcall;
+my $decoder = $cdec;
+my $lines_per_mapper = 400;
+my $rand_directions = 15;
+my $iteration = 1;
+my $run_local = 0;
+my $best_weights;
+my $max_iterations = 15;
+my $optimization_iters = 6;
+my $decode_nodes = 15;   # number of decode nodes
+my $pmem = "9g";
+my $disable_clean = 0;
+my %seen_weights;
+my $normalize;
+my $help = 0;
+my $epsilon = 0.0001;
+my $interval = 5;
+my $dryrun = 0;
+my $last_score = -10000000;
+my $metric = "ibm_bleu";
+my $dir;
+my $iniFile;
+my $weights;
+my $initialWeights;
+my $decoderOpt;
+my $noprimary;
+my $maxsim=0;
+my $oraclen=0;
+my $oracleb=20;
+my $bleu_weight=1;
+my $use_make;  # use make to parallelize line search
+my $dirargs='';
+my $density_prune;
+my $usefork;
+my $pass_suffix = '';
+my $cpbin=1;
+# Process command-line options
+Getopt::Long::Configure("no_auto_abbrev");
+if (GetOptions(
+	"decoder=s" => \$decoderOpt,
+	"decode-nodes=i" => \$decode_nodes,
+	"density-prune=f" => \$density_prune,
+	"dont-clean" => \$disable_clean,
+	"pass-suffix=s" => \$pass_suffix,
+        "use-fork" => \$usefork,
+	"dry-run" => \$dryrun,
+	"epsilon=s" => \$epsilon,
+	"help" => \$help,
+	"interval" => \$interval,
+	"iteration=i" => \$iteration,
+	"local" => \$run_local,
+	"use-make=i" => \$use_make,
+	"max-iterations=i" => \$max_iterations,
+	"normalize=s" => \$normalize,
+	"pmem=s" => \$pmem,
+        "cpbin!" => \$cpbin,
+	"rand-directions=i" => \$rand_directions,
+	"random_directions=i" => \$rand_directions,
+        "bleu_weight=s" => \$bleu_weight,
+        "no-primary!" => \$noprimary,
+        "max-similarity=s" => \$maxsim,
+        "oracle-directions=i" => \$oraclen,
+        "n-oracle=i" => \$oraclen,
+        "oracle-batch=i" => \$oracleb,
+        "directions-args=s" => \$dirargs,
+	"ref-files=s" => \$refFiles,
+	"metric=s" => \$metric,
+	"source-file=s" => \$srcFile,
+	"weights=s" => \$initialWeights,
+	"workdir=s" => \$dir,
+    "opt-iterations=i" => \$optimization_iters,
+) == 0 || @ARGV!=1 || $help) {
+	print_help();
+	exit;
+}
+
+if (defined $density_prune) {
+  die "--density_prune n: n must be greater than 1.0\n" unless $density_prune > 1.0;
+}
+
+if ($usefork) { $usefork = "--use-fork"; } else { $usefork = ''; }
+
+if ($metric =~ /^(combi|ter)$/i) {
+  $lines_per_mapper = 40;
+} elsif ($metric =~ /^meteor$/i) {
+  $lines_per_mapper = 2000;   # start up time is really high
+}
+
+($iniFile) = @ARGV;
+
+
+sub write_config;
+sub enseg;
+sub print_help;
+
+my $nodelist;
+my $host =check_output("hostname"); chomp $host;
+my $bleu;
+my $interval_count = 0;
+my $logfile;
+my $projected_score;
+
+# used in sorting scores
+my $DIR_FLAG = '-r';
+if ($metric =~ /^ter$|^aer$/i) {
+  $DIR_FLAG = '';
+}
+
+my $refs_comma_sep = get_comma_sep_refs('r',$refFiles);
+
+unless ($dir){
+	$dir = "vest";
+}
+unless ($dir =~ /^\//){  # convert relative path to absolute path
+	my $basedir = check_output("pwd");
+	chomp $basedir;
+	$dir = "$basedir/$dir";
+}
+
+if ($decoderOpt){ $decoder = $decoderOpt; }
+
+
+# Initializations and helper functions
+srand;
+
+my @childpids = ();
+my @cleanupcmds = ();
+
+sub cleanup {
+	print STDERR "Cleanup...\n";
+	for my $pid (@childpids){ unchecked_call("kill $pid"); }
+	for my $cmd (@cleanupcmds){ unchecked_call("$cmd"); }
+	exit 1;
+};
+# Always call cleanup, no matter how we exit
+*CORE::GLOBAL::exit = 
+    sub{ cleanup(); }; 
+$SIG{INT} = "cleanup";
+$SIG{TERM} = "cleanup";
+$SIG{HUP} = "cleanup";
+
+my $decoderBase = check_output("basename $decoder"); chomp $decoderBase;
+my $newIniFile = "$dir/$decoderBase.ini";
+my $inputFileName = "$dir/input";
+my $user = $ENV{"USER"};
+
+
+# process ini file
+-e $iniFile || die "Error: could not open $iniFile for reading\n";
+open(INI, $iniFile);
+
+use File::Basename qw(basename);
+#pass bindir, refs to vars holding bin
+sub modbin {
+    local $_;
+    my $bindir=shift;
+    check_call("mkdir -p $bindir");
+    -d $bindir || die "couldn't make bindir $bindir";
+    for (@_) {
+        my $src=$$_;
+        $$_="$bindir/".basename($src);
+        check_call("cp -p $src $$_");
+    }
+}
+sub dirsize {
+    opendir ISEMPTY,$_[0];
+    return scalar(readdir(ISEMPTY))-1;
+}
+if ($dryrun){
+	write_config(*STDERR);
+	exit 0;
+} else {
+	if (-e $dir && dirsize($dir)>1 && -e "$dir/hgs" ){ # allow preexisting logfile, binaries, but not dist-vest.pl outputs
+	  die "ERROR: working dir $dir already exists\n\n";
+	} else {
+		-e $dir || mkdir $dir;
+		mkdir "$dir/hgs";
+        modbin("$dir/bin",\$LocalConfig,\$cdec,\$SCORER,\$MAPINPUT,\$MAPPER,\$REDUCER,\$parallelize,\$sentserver,\$sentclient,\$libcall) if $cpbin;
+    mkdir "$dir/scripts";
+        my $cmdfile="$dir/rerun-vest.sh";
+        open CMD,'>',$cmdfile;
+        print CMD "cd ",&getcwd,"\n";
+#        print CMD &escaped_cmdline,"\n"; #buggy - last arg is quoted.
+        my $cline=&cmdline."\n";
+        print CMD $cline;
+        close CMD;
+        print STDERR $cline;
+        chmod(0755,$cmdfile);
+		unless (-e $initialWeights) {
+			print STDERR "Please specify an initial weights file with --initial-weights\n";
+			print_help();
+			exit;
+		}
+		check_call("cp $initialWeights $dir/weights.0");
+		die "Can't find weights.0" unless (-e "$dir/weights.0");
+	}
+	write_config(*STDERR);
+}
+
+
+# Generate initial files and values
+check_call("cp $iniFile $newIniFile");
+$iniFile = $newIniFile;
+
+my $newsrc = "$dir/dev.input";
+enseg($srcFile, $newsrc);
+$srcFile = $newsrc;
+my $devSize = 0;
+open F, "<$srcFile" or die "Can't read $srcFile: $!";
+while(<F>) { $devSize++; }
+close F;
+
+unless($best_weights){ $best_weights = $weights; }
+unless($projected_score){ $projected_score = 0.0; }
+$seen_weights{$weights} = 1;
+
+my $random_seed = int(time / 1000);
+my $lastWeightsFile;
+my $lastPScore = 0;
+# main optimization loop
+while (1){
+	print STDERR "\n\nITERATION $iteration\n==========\n";
+
+	if ($iteration > $max_iterations){
+		print STDERR "\nREACHED STOPPING CRITERION: Maximum iterations\n";
+		last;
+	}
+	# iteration-specific files
+	my $runFile="$dir/run.raw.$iteration";
+	my $onebestFile="$dir/1best.$iteration";
+	my $logdir="$dir/logs.$iteration";
+	my $decoderLog="$logdir/decoder.sentserver.log.$iteration";
+	my $scorerLog="$logdir/scorer.log.$iteration";
+	check_call("mkdir -p $logdir");
+
+
+	#decode
+	print STDERR "RUNNING DECODER AT ";
+	print STDERR unchecked_output("date");
+	my $im1 = $iteration - 1;
+	my $weightsFile="$dir/weights.$im1";
+	my $decoder_cmd = "$decoder -c $iniFile --weights$pass_suffix $weightsFile -O $dir/hgs";
+	if ($density_prune) {
+		$decoder_cmd .= " --density_prune $density_prune";
+	}
+	my $pcmd;
+	if ($run_local) {
+		$pcmd = "cat $srcFile |";
+	} elsif ($use_make) {
+	    # TODO: Throw error when decode_nodes is specified along with use_make
+		$pcmd = "cat $srcFile | $parallelize --use-fork -p $pmem -e $logdir -j $use_make --";
+	} else {
+		$pcmd = "cat $srcFile | $parallelize $usefork -p $pmem -e $logdir -j $decode_nodes --";
+	}
+	my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $runFile";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_bash_call($cmd);
+        my $num_hgs;
+        my $num_topbest;
+        my $retries = 0;
+	while($retries < 5) {
+	    $num_hgs = check_output("ls $dir/hgs/*.gz | wc -l");
+	    $num_topbest = check_output("wc -l < $runFile");
+	    print STDERR "NUMBER OF HGs: $num_hgs\n";
+	    print STDERR "NUMBER OF TOP-BEST HYPs: $num_topbest\n";
+	    if($devSize == $num_hgs && $devSize == $num_topbest) {
+		last;
+	    } else {
+		print STDERR "Incorrect number of hypergraphs or topbest. Waiting for distributed filesystem and retrying...\n";
+		sleep(3);
+	    }
+	    $retries++;
+	}
+	die "Dev set contains $devSize sentences, but we don't have topbest and hypergraphs for all these! Decoder failure? Check $decoderLog\n" if ($devSize != $num_hgs || $devSize != $num_topbest);
+	my $dec_score = check_output("cat $runFile | $SCORER $refs_comma_sep -l $metric");
+	chomp $dec_score;
+	print STDERR "DECODER SCORE: $dec_score\n";
+
+	# save space
+	check_call("gzip -f $runFile");
+	check_call("gzip -f $decoderLog");
+
+	# run optimizer
+	print STDERR "RUNNING OPTIMIZER AT ";
+	print STDERR unchecked_output("date");
+	my $mergeLog="$logdir/prune-merge.log.$iteration";
+
+	my $score = 0;
+	my $icc = 0;
+	my $inweights="$dir/weights.$im1";
+	for (my $opt_iter=1; $opt_iter<$optimization_iters; $opt_iter++) {
+		print STDERR "\nGENERATE OPTIMIZATION STRATEGY (OPT-ITERATION $opt_iter/$optimization_iters)\n";
+		print STDERR unchecked_output("date");
+		$icc++;
+		my $nop=$noprimary?"--no_primary":"";
+		my $targs=$oraclen ? "--decoder_translations='$runFile.gz' ".get_comma_sep_refs('-references',$refFiles):"";
+		my $bwargs=$bleu_weight!=1 ? "--bleu_weight=$bleu_weight":"";
+		$cmd="$MAPINPUT -w $inweights -r $dir/hgs $bwargs -s $devSize -d $rand_directions --max_similarity=$maxsim --oracle_directions=$oraclen --oracle_batch=$oracleb $targs $dirargs > $dir/agenda.$im1-$opt_iter";
+		print STDERR "COMMAND:\n$cmd\n";
+		check_call($cmd);
+		check_call("mkdir -p $dir/splag.$im1");
+		$cmd="split -a 3 -l $lines_per_mapper $dir/agenda.$im1-$opt_iter $dir/splag.$im1/mapinput.";
+		print STDERR "COMMAND:\n$cmd\n";
+		check_call($cmd);
+		opendir(DIR, "$dir/splag.$im1") or die "Can't open directory: $!";
+		my @shards = grep { /^mapinput\./ } readdir(DIR);
+		closedir DIR;
+		die "No shards!" unless scalar @shards > 0;
+		my $joblist = "";
+		my $nmappers = 0;
+		my @mapoutputs = ();
+		@cleanupcmds = ();
+		my %o2i = ();
+		my $first_shard = 1;
+		my $mkfile; # only used with makefiles
+		my $mkfilename;
+		if ($use_make) {
+			$mkfilename = "$dir/splag.$im1/domap.mk";
+			open $mkfile, ">$mkfilename" or die "Couldn't write $mkfilename: $!";
+			print $mkfile "all: $dir/splag.$im1/map.done\n\n";
+		}
+		my @mkouts = ();  # only used with makefiles
+		for my $shard (@shards) {
+			my $mapoutput = $shard;
+			my $client_name = $shard;
+			$client_name =~ s/mapinput.//;
+			$client_name = "vest.$client_name";
+			$mapoutput =~ s/mapinput/mapoutput/;
+			push @mapoutputs, "$dir/splag.$im1/$mapoutput";
+			$o2i{"$dir/splag.$im1/$mapoutput"} = "$dir/splag.$im1/$shard";
+			my $script = "$MAPPER -s $srcFile -l $metric $refs_comma_sep < $dir/splag.$im1/$shard | sort -t \$'\\t' -k 1 > $dir/splag.$im1/$mapoutput";
+			if ($run_local) {
+				print STDERR "COMMAND:\n$script\n";
+				check_bash_call($script);
+			} elsif ($use_make) {
+				my $script_file = "$dir/scripts/map.$shard";
+				open F, ">$script_file" or die "Can't write $script_file: $!";
+				print F "#!/bin/bash\n";
+				print F "$script\n";
+				close F;
+				my $output = "$dir/splag.$im1/$mapoutput";
+				push @mkouts, $output;
+				chmod(0755, $script_file) or die "Can't chmod $script_file: $!";
+				if ($first_shard) { print STDERR "$script\n"; $first_shard=0; }
+				print $mkfile "$output: $dir/splag.$im1/$shard\n\t$script_file\n\n";
+			} else {
+				my $script_file = "$dir/scripts/map.$shard";
+				open F, ">$script_file" or die "Can't write $script_file: $!";
+				print F "$script\n";
+				close F;
+				if ($first_shard) { print STDERR "$script\n"; $first_shard=0; }
+
+				$nmappers++;
+				my $qcmd = "$QSUB_CMD -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file";
+				my $jobid = check_output("$qcmd");
+				chomp $jobid;
+				$jobid =~ s/^(\d+)(.*?)$/\1/g;
+				$jobid =~ s/^Your job (\d+) .*$/\1/;
+		 	 	push(@cleanupcmds, "qdel $jobid 2> /dev/null");
+				print STDERR " $jobid";
+				if ($joblist == "") { $joblist = $jobid; }
+				else {$joblist = $joblist . "\|" . $jobid; }
+			}
+		}
+		if ($run_local) {
+			print STDERR "\nProcessing line search complete.\n";
+		} elsif ($use_make) {
+			print $mkfile "$dir/splag.$im1/map.done: @mkouts\n\ttouch $dir/splag.$im1/map.done\n\n";
+			close $mkfile;
+			my $mcmd = "make -j $use_make -f $mkfilename";
+			print STDERR "\nExecuting: $mcmd\n";
+			check_call($mcmd);
+		} else {
+			print STDERR "\nLaunched $nmappers mappers.\n";
+      			sleep 8;
+			print STDERR "Waiting for mappers to complete...\n";
+			while ($nmappers > 0) {
+			  sleep 5;
+			  my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat | grep -v ' C '")));
+			  $nmappers = scalar @livejobs;
+			}
+			print STDERR "All mappers complete.\n";
+		}
+		my $tol = 0;
+		my $til = 0;
+		for my $mo (@mapoutputs) {
+		  my $olines = get_lines($mo);
+		  my $ilines = get_lines($o2i{$mo});
+		  $tol += $olines;
+		  $til += $ilines;
+		  die "$mo: output lines ($olines) doesn't match input lines ($ilines)" unless $olines==$ilines;
+		}
+		print STDERR "Results for $tol/$til lines\n";
+		print STDERR "\nSORTING AND RUNNING VEST REDUCER\n";
+		print STDERR unchecked_output("date");
+		$cmd="sort -t \$'\\t' -k 1 @mapoutputs | $REDUCER -l $metric > $dir/redoutput.$im1";
+		print STDERR "COMMAND:\n$cmd\n";
+		check_bash_call($cmd);
+		$cmd="sort -nk3 $DIR_FLAG '-t|' $dir/redoutput.$im1 | head -1";
+		# sort returns failure even when it doesn't fail for some reason
+		my $best=unchecked_output("$cmd"); chomp $best;
+		print STDERR "$best\n";
+		my ($oa, $x, $xscore) = split /\|/, $best;
+		$score = $xscore;
+		print STDERR "PROJECTED SCORE: $score\n";
+		if (abs($x) < $epsilon) {
+			print STDERR "\nOPTIMIZER: no score improvement: abs($x) < $epsilon\n";
+			last;
+		}
+                my $psd = $score - $last_score;
+                $last_score = $score;
+		if (abs($psd) < $epsilon) {
+			print STDERR "\nOPTIMIZER: no score improvement: abs($psd) < $epsilon\n";
+			last;
+		}
+		my ($origin, $axis) = split /\s+/, $oa;
+
+		my %ori = convert($origin);
+		my %axi = convert($axis);
+
+		my $finalFile="$dir/weights.$im1-$opt_iter";
+		open W, ">$finalFile" or die "Can't write: $finalFile: $!";
+                my $norm = 0;
+		for my $k (sort keys %ori) {
+			my $dd = $ori{$k} + $axi{$k} * $x;
+                        $norm += $dd * $dd;
+		}
+                $norm = sqrt($norm);
+		$norm = 1;
+		for my $k (sort keys %ori) {
+			my $v = ($ori{$k} + $axi{$k} * $x) / $norm;
+			print W "$k $v\n";
+		}
+		check_call("rm $dir/splag.$im1/*");
+		$inweights = $finalFile;
+	}
+	$lastWeightsFile = "$dir/weights.$iteration";
+	check_call("cp $inweights $lastWeightsFile");
+	if ($icc < 2) {
+		print STDERR "\nREACHED STOPPING CRITERION: score change too little\n";
+		last;
+	}
+	$lastPScore = $score;
+	$iteration++;
+	print STDERR "\n==========\n";
+}
+
+print STDERR "\nFINAL WEIGHTS: $lastWeightsFile\n(Use -w <this file> with the decoder)\n\n";
+
+print STDOUT "$lastWeightsFile\n";
+
+exit 0;
+
+sub normalize_weights {
+  my ($rfn, $rpts, $feat) = @_;
+  my @feat_names = @$rfn;
+  my @pts = @$rpts;
+  my $z = 1.0;
+  for (my $i=0; $i < scalar @feat_names; $i++) {
+    if ($feat_names[$i] eq $feat) {
+      $z = $pts[$i];
+      last;
+    }
+  }
+  for (my $i=0; $i < scalar @feat_names; $i++) {
+    $pts[$i] /= $z;
+  }
+  print STDERR " NORM WEIGHTS: @pts\n";
+  return @pts;
+}
+
+sub get_lines {
+  my $fn = shift @_;
+  open FL, "<$fn" or die "Couldn't read $fn: $!";
+  my $lc = 0;
+  while(<FL>) { $lc++; }
+  return $lc;
+}
+
+sub get_comma_sep_refs {
+  my ($r,$p) = @_;
+  my $o = check_output("echo $p");
+  chomp $o;
+  my @files = split /\s+/, $o;
+  return "-$r " . join(" -$r ", @files);
+}
+
+sub read_weights_file {
+  my ($file) = @_;
+  open F, "<$file" or die "Couldn't read $file: $!";
+  my @r = ();
+  my $pm = -1;
+  while(<F>) {
+    next if /^#/;
+    next if /^\s*$/;
+    chomp;
+    if (/^(.+)\s+(.+)$/) {
+      my $m = $1;
+      my $w = $2;
+      die "Weights out of order: $m <= $pm" unless $m > $pm;
+      push @r, $w;
+    } else {
+      warn "Unexpected feature name in weight file: $_";
+    }
+  }
+  close F;
+  return join ' ', @r;
+}
+
+# subs
+sub write_config {
+	my $fh = shift;
+	my $cleanup = "yes";
+	if ($disable_clean) {$cleanup = "no";}
+
+	print $fh "\n";
+	print $fh "DECODER:          $decoder\n";
+	print $fh "INI FILE:         $iniFile\n";
+	print $fh "WORKING DIR:      $dir\n";
+	print $fh "SOURCE (DEV):     $srcFile\n";
+	print $fh "REFS (DEV):       $refFiles\n";
+	print $fh "EVAL METRIC:      $metric\n";
+	print $fh "START ITERATION:  $iteration\n";
+	print $fh "MAX ITERATIONS:   $max_iterations\n";
+	print $fh "DECODE NODES:     $decode_nodes\n";
+	print $fh "HEAD NODE:        $host\n";
+	print $fh "PMEM (DECODING):  $pmem\n";
+	print $fh "CLEANUP:          $cleanup\n";
+	print $fh "INITIAL WEIGHTS:  $initialWeights\n";
+}
+
+sub update_weights_file {
+  my ($neww, $rfn, $rpts) = @_;
+  my @feats = @$rfn;
+  my @pts = @$rpts;
+  my $num_feats = scalar @feats;
+  my $num_pts = scalar @pts;
+  die "$num_feats (num_feats) != $num_pts (num_pts)" unless $num_feats == $num_pts;
+  open G, ">$neww" or die;
+  for (my $i = 0; $i < $num_feats; $i++) {
+    my $f = $feats[$i];
+    my $lambda = $pts[$i];
+    print G "$f $lambda\n";
+  }
+  close G;
+}
+
+sub enseg {
+	my $src = shift;
+	my $newsrc = shift;
+	open(SRC, $src);
+	open(NEWSRC, ">$newsrc");
+	my $i=0;
+	while (my $line=<SRC>){
+		chomp $line;
+		if ($line =~ /^\s*<seg/i) {
+		    if($line =~ /id="[0-9]+"/) {
+			print NEWSRC "$line\n";
+		    } else {
+			die "When using segments with pre-generated <seg> tags, you must include a zero-based id attribute";
+		    }
+		} else {
+			print NEWSRC "<seg id=\"$i\">$line</seg>\n";
+		}
+		$i++;
+	}
+	close SRC;
+	close NEWSRC;
+}
+
+sub print_help {
+
+	my $executable = check_output("basename $0"); chomp $executable;
+    print << "Help";
+
+Usage: $executable [options] <ini file>
+
+	$executable [options] <ini file>
+		Runs a complete MERT optimization and test set decoding, using
+		the decoder configuration in ini file.  Note that many of the
+		options have default values that are inferred automatically
+		based on certain conventions.  For details, refer to descriptions
+		of the options --decoder, --weights, and --workdir.
+
+Options:
+
+	--local
+		Run the decoder and optimizer locally with a single thread.
+
+	--use-make <I>
+		Use make -j <I> to run the optimizer commands (useful on large
+		shared-memory machines where qsub is unavailable).
+
+	--decode-nodes <I>
+		Number of decoder processes to run in parallel. [default=15]
+
+	--decoder <decoder path>
+		Decoder binary to use.
+
+	--density-prune <N>
+		Limit the density of the hypergraph on each iteration to N times
+		the number of edges on the Viterbi path.
+
+	--help
+		Print this message and exit.
+
+	--iteration <I>
+		Starting iteration number.  If not specified, defaults to 1.
+
+	--max-iterations <M>
+		Maximum number of iterations to run.  If not specified, defaults
+		to 10.
+
+	--pass-suffix <S>
+		If the decoder is doing multi-pass decoding, the pass suffix "2",
+		"3", etc., is used to control what iteration of weights is set.
+
+	--pmem <N>
+		Amount of physical memory requested for parallel decoding jobs.
+
+	--ref-files <files>
+		Dev set ref files.  This option takes only a single string argument.
+		To use multiple files (including file globbing), this argument should
+		be quoted.
+
+	--metric <method>
+		Metric to optimize.
+		Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
+
+	--normalize <feature-name>
+		After each iteration, rescale all feature weights such that feature-
+		name has a weight of 1.0.
+
+	--rand-directions <num>
+		MERT will attempt to optimize along all of the principle directions,
+		set this parameter to explore other directions. Defaults to 5.
+
+	--source-file <file>
+		Dev set source file.
+
+	--weights <file>
+		A file specifying initial feature weights.  The format is
+		FeatureName_1 value1
+		FeatureName_2 value2
+
+	--workdir <dir>
+		Directory for intermediate and output files.  If not specified, the
+		name is derived from the ini filename.  Assuming that the ini
+		filename begins with the decoder name and ends with ini, the default
+		name of the working directory is inferred from the middle part of
+		the filename.  E.g. an ini file named decoder.foo.ini would have
+		a default working directory name foo.
+
+Help
+}
+
+sub convert {
+  my ($str) = @_;
+  my @ps = split /;/, $str;
+  my %dict = ();
+  for my $p (@ps) {
+    my ($k, $v) = split /=/, $p;
+    $dict{$k} = $v;
+  }
+  return %dict;
+}
+
+
+
+sub cmdline {
+    return join ' ',($0,@ORIG_ARGV);
+}
+
+#buggy: last arg gets quoted sometimes?
+my $is_shell_special=qr{[ \t\n\\><|&;"'`~*?{}$!()]};
+my $shell_escape_in_quote=qr{[\\"\$`!]};
+
+sub escape_shell {
+    my ($arg)=@_;
+    return undef unless defined $arg;
+    if ($arg =~ /$is_shell_special/) {
+        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
+        return "\"$arg\"";
+    }
+    return $arg;
+}
+
+sub escaped_shell_args {
+    return map {local $_=$_;chomp;escape_shell($_)} @_;
+}
+
+sub escaped_shell_args_str {
+    return join ' ',&escaped_shell_args(@_);
+}
+
+sub escaped_cmdline {
+    return "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
+}
diff --git a/pro-train/mr_pro_map.cc b/pro-train/mr_pro_map.cc
new file mode 100644
index 00000000..b046cdea
--- /dev/null
+++ b/pro-train/mr_pro_map.cc
@@ -0,0 +1,111 @@
+#include <sstream>
+#include <iostream>
+#include <fstream>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "sampler.h"
+#include "filelib.h"
+#include "stringlib.h"
+#include "scorer.h"
+#include "inside_outside.h"
+#include "hg_io.h"
+#include "kbest.h"
+#include "viterbi.h"
+
+// This is Figure 4 (Algorithm Sampler) from Hopkins&May (2011)
+
+using namespace std;
+namespace po = boost::program_options;
+
+boost::shared_ptr<MT19937> rng;
+
+void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+        ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation (tokenized text)")
+        ("source,s",po::value<string>(), "Source file (ignored, except for AER)")
+        ("loss_function,l",po::value<string>()->default_value("ibm_bleu"), "Loss function being optimized")
+        ("input,i",po::value<string>()->default_value("-"), "Input file to map (- is STDIN)")
+        ("weights,w",po::value<string>(), "[REQD] Current weights file")
+        ("kbest_size,k",po::value<unsigned>()->default_value(1500u), "Top k-hypotheses to extract")
+        ("candidate_pairs,G", po::value<unsigned>()->default_value(5000u), "Number of pairs to sample per hypothesis (Gamma)")
+        ("best_pairs,X", po::value<unsigned>()->default_value(50u), "Number of pairs, ranked by magnitude of objective delta, to retain (Xi)")
+        ("random_seed,S", po::value<uint32_t>(), "Random seed (if not specified, /dev/random will be used)")
+        ("help,h", "Help");
+  po::options_description dcmdline_options;
+  dcmdline_options.add(opts);
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  bool flag = false;
+  if (!conf->count("reference")) {
+    cerr << "Please specify one or more references using -r <REF.TXT>\n";
+    flag = true;
+  }
+  if (flag || conf->count("help")) {
+    cerr << dcmdline_options << endl;
+    exit(1);
+  }
+}
+
+struct HypInfo {
+  HypInfo(const vector<WordID>& h, const SparseVector<double>& feats) : hyp(h), g_(-1), x(feats) {}
+  double g() {
+    return g_;
+  }
+ private:
+  int sent_id;
+  vector<WordID> hyp;
+  double g_;
+ public:
+  SparseVector<double> x;
+};
+
+int main(int argc, char** argv) {
+  po::variables_map conf;
+  InitCommandLine(argc, argv, &conf);
+  if (conf.count("random_seed"))
+    rng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
+  else
+    rng.reset(new MT19937);
+  const string loss_function = conf["loss_function"].as<string>();
+  ScoreType type = ScoreTypeFromString(loss_function);
+  DocScorer ds(type, conf["reference"].as<vector<string> >(), conf["source"].as<string>());
+  cerr << "Loaded " << ds.size() << " references for scoring with " << loss_function << endl;
+  Hypergraph hg;
+  string last_file;
+  ReadFile in_read(conf["input"].as<string>());
+  istream &in=*in_read.stream();
+  const unsigned kbest_size = conf["kbest_size"].as<unsigned>();
+  const unsigned gamma = conf["candidate_pairs"].as<unsigned>();
+  const unsigned xi = conf["best_pairs"].as<unsigned>();
+  while(in) {
+    string line;
+    getline(in, line);
+    if (line.empty()) continue;
+    istringstream is(line);
+    int sent_id;
+    string file;
+    // path-to-file (JSON) sent_id
+    is >> file >> sent_id;
+    ReadFile rf(file);
+    HypergraphIO::ReadFromJSON(rf.stream(), &hg);
+    KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(hg, kbest_size);
+
+    vector<HypInfo> J_i;
+    for (int i = 0; i < kbest_size; ++i) {
+      const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
+        kbest.LazyKthBest(hg.nodes_.size() - 1, i);
+      if (!d) break;
+      float sentscore = ds[sent_id]->ScoreCandidate(d->yield)->ComputeScore();
+      // if (invert_score) sentscore *= -1.0;
+      // cerr << TD::GetString(d->yield) << " ||| " << d->score << " ||| " << sentscore << endl;
+      d->feature_values;
+      sentscore;
+    }
+  }
+  return 0;
+}
+
diff --git a/pro-train/mr_pro_reduce.cc b/pro-train/mr_pro_reduce.cc
new file mode 100644
index 00000000..3df52020
--- /dev/null
+++ b/pro-train/mr_pro_reduce.cc
@@ -0,0 +1,81 @@
+#include <sstream>
+#include <iostream>
+#include <fstream>
+#include <vector>
+
+#include <boost/program_options.hpp>
+#include <boost/program_options/variables_map.hpp>
+
+#include "sparse_vector.h"
+#include "error_surface.h"
+#include "line_optimizer.h"
+#include "b64tools.h"
+
+using namespace std;
+namespace po = boost::program_options;
+
+void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
+  po::options_description opts("Configuration options");
+  opts.add_options()
+        ("loss_function,l",po::value<string>(), "Loss function being optimized")
+        ("help,h", "Help");
+  po::options_description dcmdline_options;
+  dcmdline_options.add(opts);
+  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
+  bool flag = conf->count("loss_function") == 0;
+  if (flag || conf->count("help")) {
+    cerr << dcmdline_options << endl;
+    exit(1);
+  }
+}
+
+int main(int argc, char** argv) {
+  po::variables_map conf;
+  InitCommandLine(argc, argv, &conf);
+  const string loss_function = conf["loss_function"].as<string>();
+  ScoreType type = ScoreTypeFromString(loss_function);
+  LineOptimizer::ScoreType opt_type = LineOptimizer::MAXIMIZE_SCORE;
+  if (type == TER || type == AER) {
+    opt_type = LineOptimizer::MINIMIZE_SCORE;
+  }
+  string last_key;
+  vector<ErrorSurface> esv;
+  while(cin) {
+    string line;
+    getline(cin, line);
+    if (line.empty()) continue;
+    size_t ks = line.find("\t");
+    assert(string::npos != ks);
+    assert(ks > 2);
+    string key = line.substr(2, ks - 2);
+    string val = line.substr(ks + 1);
+    if (key != last_key) {
+      if (!last_key.empty()) {
+	float score;
+        double x = LineOptimizer::LineOptimize(esv, opt_type, &score);
+	cout << last_key << "|" << x << "|" << score << endl;
+      }
+      last_key = key;
+      esv.clear();
+    }
+    if (val.size() % 4 != 0) {
+      cerr << "B64 encoding error 1! Skipping.\n";
+      continue;
+    }
+    string encoded(val.size() / 4 * 3, '\0');
+    if (!B64::b64decode(reinterpret_cast<const unsigned char*>(&val[0]), val.size(), &encoded[0], encoded.size())) {
+      cerr << "B64 encoding error 2! Skipping.\n";
+      continue;
+    }
+    esv.push_back(ErrorSurface());
+    esv.back().Deserialize(type, encoded);
+  }
+  if (!esv.empty()) {
+    // cerr << "ESV=" << esv.size() << endl;
+    // for (int i = 0; i < esv.size(); ++i) { cerr << esv[i].size() << endl; }
+    float score;
+    double x = LineOptimizer::LineOptimize(esv, opt_type, &score);
+    cout << last_key << "|" << x << "|" << score << endl;
+  }
+  return 0;
+}