major restructure of the training code

39 files changed, 0 insertions, 3296 deletions

diff --git a/dpmert/Makefile.am b/dpmert/Makefile.am
deleted file mode 100644
index 00768271..00000000
--- a/dpmert/Makefile.am
+++ /dev/null
@@ -1,33 +0,0 @@
-bin_PROGRAMS = \
-  mr_dpmert_map \
-  mr_dpmert_reduce \
-  mr_dpmert_generate_mapper_input \
-  sentserver \
-  sentclient
-
-noinst_PROGRAMS = \
-  lo_test
-TESTS = lo_test
-
-sentserver_SOURCES = sentserver.c
-sentserver_LDFLAGS = -pthread
-
-sentclient_SOURCES = sentclient.c
-sentclient_LDFLAGS = -pthread
-
-mr_dpmert_generate_mapper_input_SOURCES = mr_dpmert_generate_mapper_input.cc line_optimizer.cc
-mr_dpmert_generate_mapper_input_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
-
-# nbest2hg_SOURCES = nbest2hg.cc
-# nbest2hg_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lfst -lz
-
-mr_dpmert_map_SOURCES = mert_geometry.cc ces.cc error_surface.cc mr_dpmert_map.cc line_optimizer.cc
-mr_dpmert_map_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
-
-mr_dpmert_reduce_SOURCES = error_surface.cc ces.cc mr_dpmert_reduce.cc line_optimizer.cc mert_geometry.cc
-mr_dpmert_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
-
-lo_test_SOURCES = lo_test.cc ces.cc mert_geometry.cc error_surface.cc line_optimizer.cc
-lo_test_LDADD = $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/mteval/libmteval.a $(top_srcdir)/utils/libutils.a -lz
-
-AM_CPPFLAGS = -DBOOST_TEST_DYN_LINK -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/utils -I$(top_srcdir)/decoder -I$(top_srcdir)/mteval
diff --git a/dpmert/README.shared-mem b/dpmert/README.shared-mem
deleted file mode 100644
index 7728efc0..00000000
--- a/dpmert/README.shared-mem
+++ /dev/null
@@ -1,9 +0,0 @@
-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/dpmert/ces.cc b/dpmert/ces.cc
deleted file mode 100644
index 157b2d17..00000000
--- a/dpmert/ces.cc
+++ /dev/null
@@ -1,90 +0,0 @@
-#include "ces.h"
-
-#include <vector>
-#include <sstream>
-#include <boost/shared_ptr.hpp>
-
-// TODO, if AER is to be optimized again, we will need this
-// #include "aligner.h"
-#include "lattice.h"
-#include "mert_geometry.h"
-#include "error_surface.h"
-#include "ns.h"
-
-using namespace std;
-
-const bool minimize_segments = true;    // if adjacent segments have equal scores, merge them
-
-void ComputeErrorSurface(const SegmentEvaluator& ss,
-                         const ConvexHull& ve,
-                         ErrorSurface* env,
-                         const EvaluationMetric* metric,
-                         const Hypergraph& hg) {
-  vector<WordID> prev_trans;
-  const vector<boost::shared_ptr<MERTPoint> >& ienv = ve.GetSortedSegs();
-  env->resize(ienv.size());
-  SufficientStats prev_score; // defaults to 0
-  int j = 0;
-  for (unsigned i = 0; i < ienv.size(); ++i) {
-    const MERTPoint& seg = *ienv[i];
-    vector<WordID> trans;
-#if 0
-    if (type == AER) {
-      vector<bool> edges(hg.edges_.size(), false);
-      seg.CollectEdgesUsed(&edges);  // get the set of edges in the viterbi
-                                     // alignment
-      ostringstream os;
-      const string* psrc = ss.GetSource();
-      if (psrc == NULL) {
-        cerr << "AER scoring in VEST requires source, but it is missing!\n";
-        abort();
-      }
-      size_t pos = psrc->rfind(" ||| ");
-      if (pos == string::npos) {
-        cerr << "Malformed source for AER: expected |||\nINPUT: " << *psrc << endl;
-        abort();
-      }
-      Lattice src;
-      Lattice ref;
-      LatticeTools::ConvertTextOrPLF(psrc->substr(0, pos), &src);
-      LatticeTools::ConvertTextOrPLF(psrc->substr(pos + 5), &ref);
-      AlignerTools::WriteAlignment(src, ref, hg, &os, true, 0, &edges);
-      string tstr = os.str();
-      TD::ConvertSentence(tstr.substr(tstr.rfind(" ||| ") + 5), &trans);
-    } else {
-#endif
-      seg.ConstructTranslation(&trans);
-    //}
-    //cerr << "Scoring: " << TD::GetString(trans) << endl;
-    if (trans == prev_trans) {
-      if (!minimize_segments) {
-        ErrorSegment& out = (*env)[j];
-        out.delta.fields.clear();
-        out.x = seg.x;
-	++j;
-      }
-      //cerr << "Identical translation, skipping scoring\n";
-    } else {
-      SufficientStats score;
-      ss.Evaluate(trans, &score);
-      // cerr << "score= " << score->ComputeScore() << "\n";
-      //string x1; score.Encode(&x1); cerr << "STATS: " << x1 << endl;
-      const SufficientStats delta = score - prev_score;
-      //string x2; delta.Encode(&x2); cerr << "DELTA: " << x2 << endl;
-      //string xx; delta.Encode(&xx); cerr << xx << endl;
-      prev_trans.swap(trans);
-      prev_score = score;
-      if ((!minimize_segments) || (!delta.IsAdditiveIdentity())) {
-        ErrorSegment& out = (*env)[j];
-        out.delta = delta;
-        out.x = seg.x;
-        ++j;
-      }
-    }
-  }
-  // cerr << " In segments: " << ienv.size() << endl;
-  // cerr << "Out segments: " << j << endl;
-  assert(j > 0);
-  env->resize(j);
-}
-
diff --git a/dpmert/ces.h b/dpmert/ces.h
deleted file mode 100644
index e4fa2080..00000000
--- a/dpmert/ces.h
+++ /dev/null
@@ -1,16 +0,0 @@
-#ifndef _CES_H_
-#define _CES_H_
-
-class ConvexHull;
-class Hypergraph;
-class SegmentEvaluator;
-class ErrorSurface;
-class EvaluationMetric;
-
-void ComputeErrorSurface(const SegmentEvaluator& ss,
-                         const ConvexHull& convex_hull,
-                         ErrorSurface* es,
-                         const EvaluationMetric* metric,
-                         const Hypergraph& hg);
-
-#endif
diff --git a/dpmert/decode-and-evaluate.pl b/dpmert/decode-and-evaluate.pl
deleted file mode 100755
index fe765d00..00000000
--- a/dpmert/decode-and-evaluate.pl
+++ /dev/null
@@ -1,246 +0,0 @@
-#!/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 File::Basename qw(basename);
-my $QSUB_CMD = qsub_args(mert_memory());
-
-require "libcall.pl";
-
-# Default settings
-my $default_jobs = env_default_jobs();
-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 $parallelize = "$bin_dir/parallelize.pl";
-my $libcall = "$bin_dir/libcall.pl";
-my $sentserver = "$bin_dir/sentserver";
-my $sentclient = "$bin_dir/sentclient";
-my $LocalConfig = "$SCRIPT_DIR/../environment/LocalConfig.pm";
-
-my $SCORER = $FAST_SCORE;
-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 $jobs = $default_jobs;   # number of decode nodes
-my $pmem = "9g";
-my $help = 0;
-my $config;
-my $test_set;
-my $weights;
-my $use_make = 1;
-my $useqsub;
-my $cpbin=1;
-# Process command-line options
-if (GetOptions(
-	"jobs=i" => \$jobs,
-	"help" => \$help,
-	"qsub" => \$useqsub,
-	"input=s" => \$test_set,
-        "config=s" => \$config,
-	"weights=s" => \$weights,
-) == 0 || @ARGV!=0 || $help) {
-	print_help();
-	exit;
-}
-
-if ($useqsub) {
-  $use_make = 0;
-  die "LocalEnvironment.pm does not have qsub configuration for this host. Cannot run with --qsub!\n" unless has_qsub();
-}
-
-my @missing_args = ();
-
-if (!defined $test_set) { push @missing_args, "--input"; }
-if (!defined $config) { push @missing_args, "--config"; }
-if (!defined $weights) { push @missing_args, "--weights"; }
-die "Please specify missing arguments: " . join (', ', @missing_args) . "\nUse --help for more information.\n" if (@missing_args);
-
-my @tf = localtime(time);
-my $tname = basename($test_set);
-$tname =~ s/\.(sgm|sgml|xml)$//i;
-my $dir = "eval.$tname." . sprintf('%d%02d%02d-%02d%02d%02d', 1900+$tf[5], $tf[4], $tf[3], $tf[2], $tf[1], $tf[0]);
-
-my $time = unchecked_output("date");
-
-check_call("mkdir -p $dir");
-
-split_devset($test_set, "$dir/test.input.raw", "$dir/test.refs");
-my $refs = "-r $dir/test.refs";
-my $newsrc = "$dir/test.input";
-enseg("$dir/test.input.raw", $newsrc);
-my $src_file = $newsrc;
-open F, "<$src_file" or die "Can't read $src_file: $!"; close F;
-
-my $test_trans="$dir/test.trans";
-my $logdir="$dir/logs";
-my $decoderLog="$logdir/decoder.sentserver.log";
-check_call("mkdir -p $logdir");
-
-#decode
-print STDERR "RUNNING DECODER AT ";
-print STDERR unchecked_output("date");
-my $decoder_cmd = "$decoder -c $config --weights $weights";
-my $pcmd;
-if ($use_make) {
-	$pcmd = "cat $src_file | $parallelize --workdir $dir --use-fork -p $pmem -e $logdir -j $jobs --";
-} else {
-	$pcmd = "cat $src_file | $parallelize --workdir $dir -p $pmem -e $logdir -j $jobs --";
-}
-my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $test_trans";
-check_bash_call($cmd);
-print STDERR "DECODER COMPLETED AT ";
-print STDERR unchecked_output("date");
-print STDERR "\nOUTPUT: $test_trans\n\n";
-my $bleu = check_output("cat $test_trans | $SCORER $refs -m ibm_bleu");
-chomp $bleu;
-print STDERR "BLEU: $bleu\n";
-my $ter = check_output("cat $test_trans | $SCORER $refs -m ter");
-chomp $ter;
-print STDERR " TER: $ter\n";
-open TR, ">$dir/test.scores" or die "Can't write $dir/test.scores: $!";
-print TR <<EOT;
-### SCORE REPORT #############################################################
-        OUTPUT=$test_trans
-  SCRIPT INPUT=$test_set
- DECODER INPUT=$src_file
-    REFERENCES=$dir/test.refs
-------------------------------------------------------------------------------
-          BLEU=$bleu
-           TER=$ter
-##############################################################################
-EOT
-close TR;
-my $sr = unchecked_output("cat $dir/test.scores");
-print STDERR "\n\n$sr\n(A copy of this report can be found in $dir/test.scores)\n\n";
-exit 0;
-
-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 = basename($0); chomp $executable;
-	print << "Help";
-
-Usage: $executable [options] <ini file>
-
-	$executable --config cdec.ini --weights weights.txt [--jobs N] [--qsub] <testset.in-ref>
-
-Options:
-
-	--help
-		Print this message and exit.
-
-	--config <file>
-		A path to the cdec.ini file.
-
-	--weights <file>
-		A file specifying feature weights.
-
-	--dir <dir>
-		Directory for intermediate and output files.
-
-Job control options:
-
-	--jobs <I>
-		Number of decoder processes to run in parallel. [default=$default_jobs]
-
-	--qsub
-		Use qsub to run jobs in parallel (qsub must be configured in
-		environment/LocalEnvironment.pm)
-
-	--pmem <N>
-		Amount of physical memory requested for parallel decoding jobs
-		(used with qsub requests only)
-
-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 "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
-}
-
-sub split_devset {
-  my ($infile, $outsrc, $outref) = @_;
-  open F, "<$infile" or die "Can't read $infile: $!";
-  open S, ">$outsrc" or die "Can't write $outsrc: $!";
-  open R, ">$outref" or die "Can't write $outref: $!";
-  while(<F>) {
-    chomp;
-    my ($src, @refs) = split /\s*\|\|\|\s*/;
-    die "Malformed devset line: $_\n" unless scalar @refs > 0;
-    print S "$src\n";
-    print R join(' ||| ', @refs) . "\n";
-  }
-  close R;
-  close S;
-  close F;
-}
-
diff --git a/dpmert/divide_refs.py b/dpmert/divide_refs.py
deleted file mode 100755
index b478f918..00000000
--- a/dpmert/divide_refs.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python
-import sys
-
-(numRefs, outPrefix) = sys.argv[1:]
-numRefs = int(numRefs)
-
-outs = [open(outPrefix+str(i), "w") for i in range(numRefs)]
-
-i = 0
-for line in sys.stdin:
-  outs[i].write(line)
-  i = (i + 1) % numRefs
-
-for out in outs:
-  out.close()
diff --git a/dpmert/dpmert.pl b/dpmert/dpmert.pl
deleted file mode 100755
index c4f98870..00000000
--- a/dpmert/dpmert.pl
+++ /dev/null
@@ -1,617 +0,0 @@
-#!/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 File::Basename qw(basename);
-require "libcall.pl";
-
-my $QSUB_CMD = qsub_args(mert_memory());
-
-# Default settings
-my $srcFile;  # deprecated
-my $refFiles; # deprecated
-my $default_jobs = env_default_jobs();
-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_dpmert_generate_mapper_input";
-my $MAPPER = "$bin_dir/mr_dpmert_map";
-my $REDUCER = "$bin_dir/mr_dpmert_reduce";
-my $parallelize = "$bin_dir/parallelize.pl";
-my $libcall = "$bin_dir/libcall.pl";
-my $sentserver = "$bin_dir/sentserver";
-my $sentclient = "$bin_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 = 200;
-my $rand_directions = 15;
-my $iteration = 1;
-my $best_weights;
-my $max_iterations = 15;
-my $optimization_iters = 6;
-my $jobs = $default_jobs;   # number of decode nodes
-my $pmem = "9g";
-my $disable_clean = 0;
-my %seen_weights;
-my $help = 0;
-my $epsilon = 0.0001;
-my $last_score = -10000000;
-my $metric = "ibm_bleu";
-my $dir;
-my $iniFile;
-my $weights;
-my $initialWeights;
-my $bleu_weight=1;
-my $use_make = 1;  # use make to parallelize line search
-my $useqsub;
-my $pass_suffix = '';
-my $devset;
-# Process command-line options
-if (GetOptions(
-	"config=s" => \$iniFile,
-	"weights=s" => \$initialWeights,
-        "devset=s" => \$devset,
-	"jobs=i" => \$jobs,
-	"pass-suffix=s" => \$pass_suffix,
-	"help" => \$help,
-	"qsub" => \$useqsub,
-	"iterations=i" => \$max_iterations,
-	"pmem=s" => \$pmem,
-	"random-directions=i" => \$rand_directions,
-	"metric=s" => \$metric,
-	"source-file=s" => \$srcFile,
-	"output-dir=s" => \$dir,
-) == 0 || @ARGV!=0 || $help) {
-	print_help();
-	exit;
-}
-
-if ($useqsub) {
-  $use_make = 0;
-  die "LocalEnvironment.pm does not have qsub configuration for this host. Cannot run with --qsub!\n" unless has_qsub();
-}
-
-my @missing_args = ();
-if (defined $srcFile || defined $refFiles) {
-  die <<EOT;
-
-  The options --ref-files and --source-file are no longer supported.
-  Please specify the input file and its reference translations with
-  --devset FILE
-
-EOT
-}
-
-if (!defined $iniFile) { push @missing_args, "--config"; }
-if (!defined $devset) { push @missing_args, "--devset"; }
-if (!defined $initialWeights) { push @missing_args, "--weights"; }
-die "Please specify missing arguments: " . join (', ', @missing_args) . "\nUse --help for more information.\n" if (@missing_args);
-
-if ($metric =~ /^(combi|ter)$/i) {
-  $lines_per_mapper = 40;
-} elsif ($metric =~ /^meteor$/i) {
-  $lines_per_mapper = 2000;   # start up time is really high for METEOR
-}
-
-
-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) {
-  $DIR_FLAG = '';
-}
-
-unless ($dir){
-	$dir = "dpmert";
-}
-unless ($dir =~ /^\//){  # convert relative path to absolute path
-	my $basedir = check_output("pwd");
-	chomp $basedir;
-	$dir = "$basedir/$dir";
-}
-
-
-# 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 $decoderBase = basename($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 $iniFile for reading\n";
-
-sub dirsize {
-    opendir ISEMPTY,$_[0];
-    return scalar(readdir(ISEMPTY))-1;
-}
-if (-e $dir) {
-	# allow preexisting logfile, binaries, but not dist-dpmert.pl outputs
-	die "ERROR: output directory $dir already exists (remove or use --output-dir dir)\n\n";
-} else {
-	mkdir "$dir" or die "Can't mkdir $dir: $!";
-	mkdir "$dir/hgs" or die;
-	mkdir "$dir/scripts" or die;
-	print STDERR <<EOT;
-	DECODER:          $decoder
-	INI FILE:         $iniFile
-	WORKING DIR:      $dir
-	DEVSET:           $devset
-	EVAL METRIC:      $metric
-	MAX ITERATIONS:   $max_iterations
-	PARALLEL JOBS:    $jobs
-	HEAD NODE:        $host
-	PMEM (DECODING):  $pmem
-	INITIAL WEIGHTS:  $initialWeights
-EOT
-}
-
-# Generate initial files and values
-check_call("cp $iniFile $newIniFile");
-check_call("cp $initialWeights $dir/weights.0");
-$iniFile = $newIniFile;
-
-split_devset($devset, "$dir/dev.input.raw", "$dir/dev.refs");
-my $refs = "-r $dir/dev.refs";
-my $newsrc = "$dir/dev.input";
-enseg("$dir/dev.input.raw", $newsrc);
-$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";
-	my $pcmd;
-	if ($use_make) {
-		$pcmd = "cat $srcFile | $parallelize --workdir $dir --use-fork -p $pmem -e $logdir -j $jobs --";
-	} else {
-		$pcmd = "cat $srcFile | $parallelize --workdir $dir -p $pmem -e $logdir -j $jobs --";
-	}
-	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 -m $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++;
-		$cmd="$MAPINPUT -w $inweights -r $dir/hgs -s $devSize -d $rand_directions > $dir/agenda.$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.//;
-			$client_name = "dpmert.$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 -m $metric $refs < $dir/splag.$im1/$shard | sort -t \$'\\t' -k 1 > $dir/splag.$im1/$mapoutput";
-			if ($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 . "\|" . $jobid; }
-			}
-		}
-		if ($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 $jobs -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 -m $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";
-}
-
-check_call("cp $lastWeightsFile $dir/weights.final");
-print STDERR "\nFINAL WEIGHTS: $dir/weights.final\n(Use -w <this file> with the decoder)\n\n";
-print STDOUT "$dir/weights.final\n";
-exit 0;
-
-
-sub get_lines {
-  my $fn = shift @_;
-  open FL, "<$fn" or die "Couldn't read $fn: $!";
-  my $lc = 0;
-  while(<FL>) { $lc++; }
-  return $lc;
-}
-
-sub read_weights_file {
-  my ($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: $_";
-    }
-  }
-  close F;
-  return join ' ', @r;
-}
-
-sub update_weights_file {
-  my ($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 = basename($0); chomp $executable;
-	print << "Help";
-
-Usage: $executable [options] <ini file>
-
-	$executable [options]
-		Runs a complete MERT optimization. Required options are --weights,
-		--devset, and --config.
-
-Options:
-
-	--config <file>   [-c <file>]
-		The decoder configuration file.
-
-	--devset <file>   [-d <file>]
-		The source *and* references for the development set.
-
-	--weights <file>  [-w <file>]
-		A file specifying initial feature weights.  The format is
-		FeatureName_1 value1
-		FeatureName_2 value2
-		**All and only the weights listed in <file> will be optimized!**
-
-	--metric <name>
-		Metric to optimize.
-		Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
-
-	--iterations <M>
-		Maximum number of iterations to run.  If not specified, defaults
-		to 10.
-
-	--pass-suffix <S>
-		If the decoder is doing multi-pass decoding, the pass suffix "2",
-		"3", etc., is used to control what iteration of weights is set.
-
-	--rand-directions <num>
-		MERT will attempt to optimize along all of the principle directions,
-		set this parameter to explore other directions. Defaults to 5.
-
-	--output-dir <dir>
-		Directory for intermediate and output files.
-
-	--help
-		Print this message and exit.
-
-Job control options:
-
-	--jobs <I>
-		Number of decoder processes to run in parallel. [default=$default_jobs]
-
-	--qsub
-		Use qsub to run jobs in parallel (qsub must be configured in
-		environment/LocalEnvironment.pm)
-
-	--pmem <N>
-		Amount of physical memory requested for parallel decoding jobs
-		(used with qsub requests only)
-
-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 "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
-}
-
-sub split_devset {
-  my ($infile, $outsrc, $outref) = @_;
-  open F, "<$infile" or die "Can't read $infile: $!";
-  open S, ">$outsrc" or die "Can't write $outsrc: $!";
-  open R, ">$outref" or die "Can't write $outref: $!";
-  while(<F>) {
-    chomp;
-    my ($src, @refs) = split /\s*\|\|\|\s*/;
-    die "Malformed devset line: $_\n" unless scalar @refs > 0;
-    print S "$src\n";
-    print R join(' ||| ', @refs) . "\n";
-  }
-  close R;
-  close S;
-  close F;
-}
-
diff --git a/dpmert/error_surface.cc b/dpmert/error_surface.cc
deleted file mode 100644
index 515b67f8..00000000
--- a/dpmert/error_surface.cc
+++ /dev/null
@@ -1,42 +0,0 @@
-#include "error_surface.h"
-
-#include <cassert>
-#include <sstream>
-
-using namespace std;
-
-ErrorSurface::~ErrorSurface() {}
-
-void ErrorSurface::Serialize(std::string* out) const {
-  const int segments = this->size();
-  ostringstream os(ios::binary);
-  os.write((const char*)&segments,sizeof(segments));
-  for (int i = 0; i < segments; ++i) {
-    const ErrorSegment& cur = (*this)[i];
-    string senc;
-    cur.delta.Encode(&senc);
-    assert(senc.size() < 1024);
-    unsigned char len = senc.size();
-    os.write((const char*)&cur.x, sizeof(cur.x));
-    os.write((const char*)&len, sizeof(len));
-    os.write((const char*)&senc[0], len);
-  }
-  *out = os.str();
-}
-
-void ErrorSurface::Deserialize(const std::string& in) {
-  istringstream is(in, ios::binary);
-  int segments;
-  is.read((char*)&segments, sizeof(segments));
-  this->resize(segments);
-  for (int i = 0; i < segments; ++i) {
-    ErrorSegment& cur = (*this)[i];
-    unsigned char len;
-    is.read((char*)&cur.x, sizeof(cur.x));
-    is.read((char*)&len, sizeof(len));
-    string senc(len, '\0'); assert(senc.size() == len);
-    is.read((char*)&senc[0], len);
-    cur.delta = SufficientStats(senc);
-  }
-}
-
diff --git a/dpmert/error_surface.h b/dpmert/error_surface.h
deleted file mode 100644
index bb65847b..00000000
--- a/dpmert/error_surface.h
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _ERROR_SURFACE_H_
-#define _ERROR_SURFACE_H_
-
-#include <vector>
-#include <string>
-
-#include "ns.h"
-
-class Score;
-
-struct ErrorSegment {
-  double x;
-  SufficientStats delta;
-  ErrorSegment() : x(0), delta() {}
-};
-
-class ErrorSurface : public std::vector<ErrorSegment> {
- public:
-  ~ErrorSurface();
-  void Serialize(std::string* out) const;
-  void Deserialize(const std::string& in);
-};
-
-#endif
diff --git a/dpmert/libcall.pl b/dpmert/libcall.pl
deleted file mode 100644
index c7d0f128..00000000
--- a/dpmert/libcall.pl
+++ /dev/null
@@ -1,71 +0,0 @@
-use IPC::Open3;
-use Symbol qw(gensym);
-
-$DUMMY_STDERR = gensym();
-$DUMMY_STDIN = gensym();
-
-# Run the command and ignore failures
-sub unchecked_call {
-    system("@_")
-}
-
-# Run the command and return its output, if any ignoring failures
-sub unchecked_output {
-    return `@_`
-}
-
-# WARNING: Do not use this for commands that will return large amounts
-# of stdout or stderr -- they might block indefinitely
-sub check_output {
-    print STDERR "Executing and gathering output: @_\n";
-
-    my $pid = open3($DUMMY_STDIN, \*PH, $DUMMY_STDERR, @_);
-    my $proc_output = "";
-    while( <PH> ) {
-	$proc_output .= $_;
-    }
-    waitpid($pid, 0);
-    # TODO: Grab signal that the process died from
-    my $child_exit_status = $? >> 8;
-    if($child_exit_status == 0) {
-	return $proc_output;
-    } else {
-	print STDERR "ERROR: Execution of @_ failed.\n";
-	exit(1);
-    }
-}
-
-# Based on Moses' safesystem sub
-sub check_call {
-    print STDERR "Executing: @_\n";
-    system(@_);
-    my $exitcode = $? >> 8;
-    if($exitcode == 0) {
-	return 0;
-    } elsif ($? == -1) {
-	print STDERR "ERROR: Failed to execute: @_\n  $!\n";
-	exit(1);
-
-    } elsif ($? & 127) {
-      printf STDERR "ERROR: Execution of: @_\n  died with signal %d, %s coredump\n",
-      ($? & 127),  ($? & 128) ? 'with' : 'without';
-      exit(1);
-
-    } else {
-	print STDERR "Failed with exit code: $exitcode\n" if $exitcode;
-	exit($exitcode);
-    }
-}
-
-sub check_bash_call {
-    my @args = ( "bash", "-auxeo", "pipefail", "-c", "@_");
-    check_call(@args);
-}
-
-sub check_bash_output {
-    my @args = ( "bash", "-auxeo", "pipefail", "-c", "@_");
-    return check_output(@args);
-}
-
-# perl module weirdness...
-return 1;
diff --git a/dpmert/line_mediator.pl b/dpmert/line_mediator.pl
deleted file mode 100755
index bc2bb24c..00000000
--- a/dpmert/line_mediator.pl
+++ /dev/null
@@ -1,116 +0,0 @@
-#!/usr/bin/perl -w
-#hooks up two processes, 2nd of which has one line of output per line of input, expected by the first, which starts off the communication
-
-# if you don't know how to fork/exec in a C program, this could be helpful under limited cirmustances (would be ok to liaise with sentserver)
-
-#WARNING: because it waits for the result from command 2 after sending every line, and especially if command 1 does the same, using sentserver as command 2 won't actually buy you any real parallelism.
-
-use strict;
-use IPC::Open2;
-use POSIX qw(pipe dup2 STDIN_FILENO STDOUT_FILENO);
-
-my $quiet=!$ENV{DEBUG};
-$quiet=1 if $ENV{QUIET};
-sub info {
-    local $,=' ';
-    print STDERR @_ unless $quiet;
-}
-
-my $mode='CROSS';
-my $ser='DIRECT';
-$mode='PIPE' if $ENV{PIPE};
-$mode='SNAKE' if $ENV{SNAKE};
-$mode='CROSS' if $ENV{CROSS};
-$ser='SERIAL' if $ENV{SERIAL};
-$ser='DIRECT' if $ENV{DIRECT};
-$ser='SERIAL' if $mode eq 'SNAKE';
-info("mode: $mode\n");
-info("connection: $ser\n");
-
-
-my @c1;
-if (scalar @ARGV) {
-    do {
-        push @c1,shift
-    } while scalar @ARGV && $c1[$#c1] ne '--';
-}
-pop @c1;
-my @c2=@ARGV;
-@ARGV=();
-(scalar @c1 && scalar @c2) || die qq{
-usage: $0 cmd1 args -- cmd2 args
-all options are environment variables.
-DEBUG=1 env var enables debugging output.
-CROSS=1 hooks up two processes, 2nd of which has one line of output per line of input, expected by the first, which starts off the communication.  crosses stdin/stderr of cmd1 and cmd2 line by line (both must flush on newline and output.  cmd1 initiates the conversation (sends the first line).    default: attempts to cross stdin/stdout of c1 and c2 directly (via two unidirectional posix pipes created before fork).
-SERIAL=1: (no parallelism possible) but lines exchanged are logged if DEBUG.
-if SNAKE then stdin -> c1 -> c2 -> c1 -> stdout.
-if PIPE then stdin -> c1 -> c2 -> stdout (same as shell c1|c2, but with SERIAL you can see the intermediate in real time; you could do similar with c1 | tee /dev/fd/2 |c2.
-DIRECT=1 (default) will override SERIAL=1.
-CROSS=1 (default) will override SNAKE or PIPE.
-};
-
-info("1 cmd:",@c1,"\n");
-info("2 cmd:",@c2,"\n");
-
-sub lineto {
-    select $_[0];
-    $|=1;
-    shift;
-    print @_;
-}
-
-if ($ser eq 'SERIAL') {
-    my ($R1,$W1,$R2,$W2);
-    my $c1p=open2($R1,$W1,@c1); # Open2 R W backward from Open3.
-    my $c2p=open2($R2,$W2,@c2);
-    if ($mode eq 'CROSS') {
-        while(<$R1>) {
-            info("1:",$_);
-            lineto($W2,$_);
-            last unless defined ($_=<$R2>);
-            info("1|2:",$_);
-            lineto($W1,$_);
-        }
-    } else {
-        my $snake=$mode eq 'SNAKE';
-        while(<STDIN>) {
-            info("IN:",$_);
-            lineto($W1,$_);
-            last unless defined ($_=<$R1>);
-            info("IN|1:",$_);
-            lineto($W2,$_);
-            last unless defined ($_=<$R2>);
-            info("IN|1|2:",$_);
-            if ($snake) {
-                lineto($W1,$_);
-                last unless defined ($_=<$R1>);
-                info("IN|1|2|1:",$_);
-            }
-            lineto(*STDOUT,$_);
-        }
-    }
-} else {
-    info("DIRECT mode\n");
-    my @rw1=POSIX::pipe();
-    my @rw2=POSIX::pipe();
-    my $pid=undef;
-    $SIG{CHLD} = sub { wait };
-    while (not defined ($pid=fork())) {
-        sleep 1;
-    }
-    my $pipe = $mode eq 'PIPE';
-    unless ($pipe) {
-        POSIX::close(STDOUT_FILENO);
-        POSIX::close(STDIN_FILENO);
-    }
-    if ($pid) {
-        POSIX::dup2($rw1[1],STDOUT_FILENO);
-        POSIX::dup2($rw2[0],STDIN_FILENO) unless $pipe;
-        exec @c1;
-    } else {
-        POSIX::dup2($rw2[1],STDOUT_FILENO) unless $pipe;
-        POSIX::dup2($rw1[0],STDIN_FILENO);
-        exec @c2;
-    }
-    while (wait()!=-1) {}
-}
diff --git a/dpmert/line_optimizer.cc b/dpmert/line_optimizer.cc
deleted file mode 100644
index 9cf33502..00000000
--- a/dpmert/line_optimizer.cc
+++ /dev/null
@@ -1,114 +0,0 @@
-#include "line_optimizer.h"
-
-#include <limits>
-#include <algorithm>
-
-#include "sparse_vector.h"
-#include "ns.h"
-
-using namespace std;
-
-typedef ErrorSurface::const_iterator ErrorIter;
-
-// sort by increasing x-ints
-struct IntervalComp {
-  bool operator() (const ErrorIter& a, const ErrorIter& b) const {
-    return a->x < b->x;
-  }
-};
-
-double LineOptimizer::LineOptimize(
-    const EvaluationMetric* metric,
-    const vector<ErrorSurface>& surfaces,
-    const LineOptimizer::ScoreType type,
-    float* best_score,
-    const double epsilon) {
-  // cerr << "MIN=" << MINIMIZE_SCORE << " MAX=" << MAXIMIZE_SCORE << "  MINE=" << type << endl;
-  vector<ErrorIter> all_ints;
-  for (vector<ErrorSurface>::const_iterator i = surfaces.begin();
-       i != surfaces.end(); ++i) {
-    const ErrorSurface& surface = *i;
-    for (ErrorIter j = surface.begin(); j != surface.end(); ++j)
-      all_ints.push_back(j);
-  }
-  sort(all_ints.begin(), all_ints.end(), IntervalComp());
-  double last_boundary = all_ints.front()->x;
-  SufficientStats acc;
-  float& cur_best_score = *best_score;
-  cur_best_score = (type == MAXIMIZE_SCORE ?
-    -numeric_limits<float>::max() : numeric_limits<float>::max());
-  bool left_edge = true;
-  double pos = numeric_limits<double>::quiet_NaN();
-  for (vector<ErrorIter>::iterator i = all_ints.begin();
-       i != all_ints.end(); ++i) {
-    const ErrorSegment& seg = **i;
-    if (seg.x - last_boundary > epsilon) {
-      float sco = metric->ComputeScore(acc);
-      if ((type == MAXIMIZE_SCORE && sco > cur_best_score) ||
-          (type == MINIMIZE_SCORE && sco < cur_best_score) ) {
-        cur_best_score = sco;
-	if (left_edge) {
-	  pos = seg.x - 0.1;
-	  left_edge = false;
-	} else {
-	  pos = last_boundary + (seg.x - last_boundary) / 2;
-	}
-	//cerr << "NEW BEST: " << pos << "  (score=" << cur_best_score << ")\n";
-      }
-      // string xx = metric->DetailedScore(acc); cerr << "---- " << xx;
-#undef SHOW_ERROR_SURFACES
-#ifdef SHOW_ERROR_SURFACES
-      cerr << "x=" << seg.x << "\ts=" << sco << "\n";
-#endif
-      last_boundary = seg.x;
-    }
-    // cerr << "x-boundary=" << seg.x << "\n";
-    //string x2; acc.Encode(&x2); cerr << "   ACC: " << x2 << endl;
-    //string x1; seg.delta.Encode(&x1); cerr << " DELTA: " << x1 << endl;
-    acc += seg.delta;
-  }
-  float sco = metric->ComputeScore(acc);
-  if ((type == MAXIMIZE_SCORE && sco > cur_best_score) ||
-      (type == MINIMIZE_SCORE && sco < cur_best_score) ) {
-    cur_best_score = sco;
-    if (left_edge) {
-      pos = 0;
-    } else {
-      pos = last_boundary + 1000.0;
-    }
-  }
-  return pos;
-}
-
-void LineOptimizer::RandomUnitVector(const vector<int>& features_to_optimize,
-                                     SparseVector<double>* axis,
-                                     RandomNumberGenerator<boost::mt19937>* rng) {
-  axis->clear();
-  for (int i = 0; i < features_to_optimize.size(); ++i)
-    axis->set_value(features_to_optimize[i], rng->NextNormal(0.0,1.0));
-  (*axis) /= axis->l2norm();
-}
-
-void LineOptimizer::CreateOptimizationDirections(
-     const vector<int>& features_to_optimize,
-     int additional_random_directions,
-     RandomNumberGenerator<boost::mt19937>* rng,
-     vector<SparseVector<double> >* dirs
-     , bool include_orthogonal
-  ) {
-  dirs->clear();
-  typedef SparseVector<double> Dir;
-  vector<Dir> &out=*dirs;
-  int i=0;
-  if (include_orthogonal)
-    for (;i<features_to_optimize.size();++i) {
-      Dir d;
-      d.set_value(features_to_optimize[i],1.);
-      out.push_back(d);
-    }
-  out.resize(i+additional_random_directions);
-  for (;i<out.size();++i)
-     RandomUnitVector(features_to_optimize, &out[i], rng);
-  cerr << "Generated " << out.size() << " total axes to optimize along.\n";
-}
-
diff --git a/dpmert/line_optimizer.h b/dpmert/line_optimizer.h
deleted file mode 100644
index 83819f41..00000000
--- a/dpmert/line_optimizer.h
+++ /dev/null
@@ -1,48 +0,0 @@
-#ifndef LINE_OPTIMIZER_H_
-#define LINE_OPTIMIZER_H_
-
-#include <vector>
-
-#include "sparse_vector.h"
-#include "error_surface.h"
-#include "sampler.h"
-
-class EvaluationMetric;
-class Weights;
-
-struct LineOptimizer {
-
-  // use MINIMIZE_SCORE for things like TER, WER
-  // MAXIMIZE_SCORE for things like BLEU
-  enum ScoreType { MAXIMIZE_SCORE, MINIMIZE_SCORE };
-
-  // merge all the error surfaces together into a global
-  // error surface and find (the middle of) the best segment
-  static double LineOptimize(
-     const EvaluationMetric* metric,
-     const std::vector<ErrorSurface>& envs,
-     const LineOptimizer::ScoreType type,
-     float* best_score,
-     const double epsilon = 1.0/65536.0);
-
-  // return a random vector of length 1 where all dimensions
-  // not listed in dimensions will be 0.
-  static void RandomUnitVector(const std::vector<int>& dimensions,
-                               SparseVector<double>* axis,
-                               RandomNumberGenerator<boost::mt19937>* rng);
-
-  // generate a list of directions to optimize; the list will
-  // contain the orthogonal vectors corresponding to the dimensions in
-  // primary and then additional_random_directions directions in those
-  // dimensions as well.  All vectors will be length 1.
-  static void CreateOptimizationDirections(
-     const std::vector<int>& primary,
-     int additional_random_directions,
-     RandomNumberGenerator<boost::mt19937>* rng,
-     std::vector<SparseVector<double> >* dirs
-     , bool include_primary=true
-    );
-
-};
-
-#endif
diff --git a/dpmert/lo_test.cc b/dpmert/lo_test.cc
deleted file mode 100644
index 95a08d3d..00000000
--- a/dpmert/lo_test.cc
+++ /dev/null
@@ -1,229 +0,0 @@
-#define BOOST_TEST_MODULE LineOptimizerTest
-#include <boost/test/unit_test.hpp>
-#include <boost/test/floating_point_comparison.hpp>
-
-#include <cmath>
-#include <iostream>
-#include <fstream>
-
-#include <boost/shared_ptr.hpp>
-
-#include "ns.h"
-#include "ns_docscorer.h"
-#include "ces.h"
-#include "fdict.h"
-#include "hg.h"
-#include "kbest.h"
-#include "hg_io.h"
-#include "filelib.h"
-#include "inside_outside.h"
-#include "viterbi.h"
-#include "mert_geometry.h"
-#include "line_optimizer.h"
-
-using namespace std;
-
-const char* ref11 = "australia reopens embassy in manila";
-const char* ref12 = "( afp , manila , january 2 ) australia reopened its embassy in the philippines today , which was shut down about seven weeks ago due to what was described as a specific threat of a terrorist attack .";
-const char* ref21 = "australia reopened manila embassy";
-const char* ref22 = "( agence france-presse , manila , 2nd ) - australia reopened its embassy in the philippines today . the embassy was closed seven weeks ago after what was described as a specific threat of a terrorist attack .";
-const char* ref31 = "australia to reopen embassy in manila";
-const char* ref32 = "( afp report from manila , january 2 ) australia reopened its embassy in the philippines today . seven weeks ago , the embassy was shut down due to so - called confirmed terrorist attack threats .";
-const char* ref41 = "australia to re - open its embassy to manila";
-const char* ref42 = "( afp , manila , thursday ) australia reopens its embassy to manila , which was closed for the so - called \" clear \" threat of terrorist attack 7 weeks ago .";
-
-BOOST_AUTO_TEST_CASE( TestCheckNaN) {
-  double x = 0;
-  double y = 0;
-  double z = x / y;
-  BOOST_CHECK_EQUAL(true, std::isnan(z));
-}
-
-BOOST_AUTO_TEST_CASE(TestConvexHull) {
-  boost::shared_ptr<MERTPoint> a1(new MERTPoint(-1, 0));
-  boost::shared_ptr<MERTPoint> b1(new MERTPoint(1, 0));
-  boost::shared_ptr<MERTPoint> a2(new MERTPoint(-1, 1));
-  boost::shared_ptr<MERTPoint> b2(new MERTPoint(1, -1));
-  vector<boost::shared_ptr<MERTPoint> > sa; sa.push_back(a1); sa.push_back(b1);
-  vector<boost::shared_ptr<MERTPoint> > sb; sb.push_back(a2); sb.push_back(b2);
-  ConvexHull a(sa);
-  cerr << a << endl;
-  ConvexHull b(sb);
-  ConvexHull c = a;
-  c *= b;
-  cerr << a << " (*) " << b << " = " << c << endl;
-  BOOST_CHECK_EQUAL(3, c.size());
-}
-
-BOOST_AUTO_TEST_CASE(TestConvexHullInside) {
-  const string json = "{\"rules\":[1,\"[X] ||| a\",2,\"[X] ||| A [1]\",3,\"[X] ||| c\",4,\"[X] ||| C [1]\",5,\"[X] ||| [1] B [2]\",6,\"[X] ||| [1] b [2]\",7,\"[X] ||| X [1]\",8,\"[X] ||| Z [1]\"],\"features\":[\"f1\",\"f2\",\"Feature_1\",\"Feature_0\",\"Model_0\",\"Model_1\",\"Model_2\",\"Model_3\",\"Model_4\",\"Model_5\",\"Model_6\",\"Model_7\"],\"edges\":[{\"tail\":[],\"feats\":[],\"rule\":1}],\"node\":{\"in_edges\":[0]},\"edges\":[{\"tail\":[0],\"feats\":[0,-0.8,1,-0.1],\"rule\":2}],\"node\":{\"in_edges\":[1]},\"edges\":[{\"tail\":[],\"feats\":[1,-1],\"rule\":3}],\"node\":{\"in_edges\":[2]},\"edges\":[{\"tail\":[2],\"feats\":[0,-0.2,1,-0.1],\"rule\":4}],\"node\":{\"in_edges\":[3]},\"edges\":[{\"tail\":[1,3],\"feats\":[0,-1.2,1,-0.2],\"rule\":5},{\"tail\":[1,3],\"feats\":[0,-0.5,1,-1.3],\"rule\":6}],\"node\":{\"in_edges\":[4,5]},\"edges\":[{\"tail\":[4],\"feats\":[0,-0.5,1,-0.8],\"rule\":7},{\"tail\":[4],\"feats\":[0,-0.7,1,-0.9],\"rule\":8}],\"node\":{\"in_edges\":[6,7]}}";
-  Hypergraph hg;
-  istringstream instr(json);
-  HypergraphIO::ReadFromJSON(&instr, &hg);
-  SparseVector<double> wts;
-  wts.set_value(FD::Convert("f1"), 0.4);
-  wts.set_value(FD::Convert("f2"), 1.0);
-  hg.Reweight(wts);
-  vector<pair<vector<WordID>, prob_t> > list;
-  std::vector<SparseVector<double> > features;
-  KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(hg, 10);
-  for (int i = 0; i < 10; ++i) {
-    const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
-      kbest.LazyKthBest(hg.nodes_.size() - 1, i);
-    if (!d) break;
-    cerr << log(d->score) << " ||| " << TD::GetString(d->yield) << " ||| " << d->feature_values << endl;
-  }
-  SparseVector<double> dir; dir.set_value(FD::Convert("f1"), 1.0);
-  ConvexHullWeightFunction wf(wts, dir);
-  ConvexHull env = Inside<ConvexHull, ConvexHullWeightFunction>(hg, NULL, wf);
-  cerr << env << endl;
-  const vector<boost::shared_ptr<MERTPoint> >& segs = env.GetSortedSegs();
-  dir *= segs[1]->x;
-  wts += dir;
-  hg.Reweight(wts);
-  KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest2(hg, 10);
-  for (int i = 0; i < 10; ++i) {
-    const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
-      kbest2.LazyKthBest(hg.nodes_.size() - 1, i);
-    if (!d) break;
-    cerr << log(d->score) << " ||| " << TD::GetString(d->yield) << " ||| " << d->feature_values << endl;
-  }
-  for (unsigned i = 0; i < segs.size(); ++i) {
-    cerr << "seg=" << i << endl;
-    vector<WordID> trans;
-    segs[i]->ConstructTranslation(&trans);
-    cerr << TD::GetString(trans) << endl;
-  }
-}
-
-BOOST_AUTO_TEST_CASE( TestS1) {
-  int fPhraseModel_0 = FD::Convert("PhraseModel_0");
-  int fPhraseModel_1 = FD::Convert("PhraseModel_1");
-  int fPhraseModel_2 = FD::Convert("PhraseModel_2");
-  int fLanguageModel = FD::Convert("LanguageModel");
-  int fWordPenalty = FD::Convert("WordPenalty");
-  int fPassThrough = FD::Convert("PassThrough");
-  SparseVector<double> wts;
-  wts.set_value(fWordPenalty, 4.25);
-  wts.set_value(fLanguageModel, -1.1165);
-  wts.set_value(fPhraseModel_0, -0.96);
-  wts.set_value(fPhraseModel_1, -0.65);
-  wts.set_value(fPhraseModel_2, -0.77);
-  wts.set_value(fPassThrough, -10.0);
-
-  vector<int> to_optimize;
-  to_optimize.push_back(fWordPenalty);
-  to_optimize.push_back(fLanguageModel);
-  to_optimize.push_back(fPhraseModel_0);
-  to_optimize.push_back(fPhraseModel_1);
-  to_optimize.push_back(fPhraseModel_2);
-
-  std::string path(boost::unit_test::framework::master_test_suite().argc == 2 ? boost::unit_test::framework::master_test_suite().argv[1] : "test_data");
-
-  Hypergraph hg;
-  ReadFile rf(path + "/0.json.gz");
-  HypergraphIO::ReadFromJSON(rf.stream(), &hg);
-  hg.Reweight(wts);
-
-  Hypergraph hg2;
-  ReadFile rf2(path + "/1.json.gz");
-  HypergraphIO::ReadFromJSON(rf2.stream(), &hg2);
-  hg2.Reweight(wts);
-
-  vector<vector<WordID> > refs1(4);
-  TD::ConvertSentence(ref11, &refs1[0]);
-  TD::ConvertSentence(ref21, &refs1[1]);
-  TD::ConvertSentence(ref31, &refs1[2]);
-  TD::ConvertSentence(ref41, &refs1[3]);
-  vector<vector<WordID> > refs2(4);
-  TD::ConvertSentence(ref12, &refs2[0]);
-  TD::ConvertSentence(ref22, &refs2[1]);
-  TD::ConvertSentence(ref32, &refs2[2]);
-  TD::ConvertSentence(ref42, &refs2[3]);
-  vector<ConvexHull> envs(2);
-
-  RandomNumberGenerator<boost::mt19937> rng;
-
-  vector<SparseVector<double> > axes; // directions to search
-  LineOptimizer::CreateOptimizationDirections(
-     to_optimize,
-     10,
-     &rng,
-     &axes);
-  assert(axes.size() == 10 + to_optimize.size());
-  for (unsigned i = 0; i < axes.size(); ++i)
-    cerr << axes[i] << endl;
-  const SparseVector<double>& axis = axes[0];
-
-  cerr << "Computing Viterbi envelope using inside algorithm...\n";
-  cerr << "axis: " << axis << endl;
-  clock_t t_start=clock();
-  ConvexHullWeightFunction wf(wts, axis);  // wts = starting point, axis = search direction
-  envs[0] = Inside<ConvexHull, ConvexHullWeightFunction>(hg, NULL, wf);
-  envs[1] = Inside<ConvexHull, ConvexHullWeightFunction>(hg2, NULL, wf);
-
-  vector<ErrorSurface> es(2);
-  EvaluationMetric* metric = EvaluationMetric::Instance("IBM_BLEU");
-  boost::shared_ptr<SegmentEvaluator> scorer1 = metric->CreateSegmentEvaluator(refs1);
-  boost::shared_ptr<SegmentEvaluator> scorer2 = metric->CreateSegmentEvaluator(refs2);
-  ComputeErrorSurface(*scorer1, envs[0], &es[0], metric, hg);
-  ComputeErrorSurface(*scorer2, envs[1], &es[1], metric, hg2);
-  cerr << envs[0].size() << " " << envs[1].size() << endl;
-  cerr << es[0].size() << " " << es[1].size() << endl;
-  envs.clear();
-  clock_t t_env=clock();
-  float score;
-  double m = LineOptimizer::LineOptimize(metric,es, LineOptimizer::MAXIMIZE_SCORE, &score);
-  clock_t t_opt=clock();
-  cerr << "line optimizer returned: " << m << " (SCORE=" << score << ")\n";
-  BOOST_CHECK_CLOSE(0.48719698, score, 1e-5);
-  SparseVector<double> res = axis;
-  res *= m;
-  res += wts;
-  cerr << "res: " << res << endl;
-  cerr << "ENVELOPE PROCESSING=" << (static_cast<double>(t_env - t_start) / 1000.0) << endl;
-  cerr << "  LINE OPTIMIZATION=" << (static_cast<double>(t_opt - t_env) / 1000.0) << endl;
-  hg.Reweight(res);
-  hg2.Reweight(res);
-  vector<WordID> t1,t2;
-  ViterbiESentence(hg, &t1);
-  ViterbiESentence(hg2, &t2);
-  cerr << TD::GetString(t1) << endl;
-  cerr << TD::GetString(t2) << endl;
-}
-
-BOOST_AUTO_TEST_CASE(TestZeroOrigin) {
-  const string json = "{\"rules\":[1,\"[X7] ||| blA ||| without ||| LHSProb=3.92173 LexE2F=2.90799 LexF2E=1.85003 GenerativeProb=10.5381 RulePenalty=1 XFE=2.77259 XEF=0.441833 LabelledEF=2.63906 LabelledFE=4.96981 LogRuleCount=0.693147\",2,\"[X7] ||| blA ||| except ||| LHSProb=4.92173 LexE2F=3.90799 LexF2E=1.85003 GenerativeProb=11.5381 RulePenalty=1 XFE=2.77259 XEF=1.44183 LabelledEF=2.63906 LabelledFE=4.96981 LogRuleCount=1.69315\",3,\"[S] ||| [X7,1] ||| [1] ||| GlueTop=1\",4,\"[X28] ||| EnwAn ||| title ||| LHSProb=3.96802 LexE2F=2.22462 LexF2E=1.83258 GenerativeProb=10.0863 RulePenalty=1 XFE=0 XEF=1.20397 LabelledEF=1.20397 LabelledFE=-1.98341e-08 LogRuleCount=1.09861\",5,\"[X0] ||| EnwAn ||| funny ||| LHSProb=3.98479 LexE2F=1.79176 LexF2E=3.21888 GenerativeProb=11.1681 RulePenalty=1 XFE=0 XEF=2.30259 LabelledEF=2.30259 LabelledFE=0 LogRuleCount=0 SingletonRule=1\",6,\"[X8] ||| [X7,1] EnwAn ||| entitled [1] ||| LHSProb=3.82533 LexE2F=3.21888 LexF2E=2.52573 GenerativeProb=11.3276 RulePenalty=1 XFE=1.20397 XEF=1.20397 LabelledEF=2.30259 LabelledFE=2.30259 LogRuleCount=0 SingletonRule=1\",7,\"[S] ||| [S,1] [X28,2] ||| [1] [2] ||| Glue=1\",8,\"[S] ||| [S,1] [X0,2] ||| [1] [2] ||| Glue=1\",9,\"[S] ||| [X8,1] ||| [1] ||| GlueTop=1\",10,\"[Goal] ||| [S,1] ||| [1]\"],\"features\":[\"PassThrough\",\"Glue\",\"GlueTop\",\"LanguageModel\",\"WordPenalty\",\"LHSProb\",\"LexE2F\",\"LexF2E\",\"GenerativeProb\",\"RulePenalty\",\"XFE\",\"XEF\",\"LabelledEF\",\"LabelledFE\",\"LogRuleCount\",\"SingletonRule\"],\"edges\":[{\"tail\":[],\"spans\":[0,1,-1,-1],\"feats\":[5,3.92173,6,2.90799,7,1.85003,8,10.5381,9,1,10,2.77259,11,0.441833,12,2.63906,13,4.96981,14,0.693147],\"rule\":1},{\"tail\":[],\"spans\":[0,1,-1,-1],\"feats\":[5,4.92173,6,3.90799,7,1.85003,8,11.5381,9,1,10,2.77259,11,1.44183,12,2.63906,13,4.96981,14,1.69315],\"rule\":2}],\"node\":{\"in_edges\":[0,1],\"cat\":\"X7\"},\"edges\":[{\"tail\":[0],\"spans\":[0,1,-1,-1],\"feats\":[2,1],\"rule\":3}],\"node\":{\"in_edges\":[2],\"cat\":\"S\"},\"edges\":[{\"tail\":[],\"spans\":[1,2,-1,-1],\"feats\":[5,3.96802,6,2.22462,7,1.83258,8,10.0863,9,1,11,1.20397,12,1.20397,13,-1.98341e-08,14,1.09861],\"rule\":4}],\"node\":{\"in_edges\":[3],\"cat\":\"X28\"},\"edges\":[{\"tail\":[],\"spans\":[1,2,-1,-1],\"feats\":[5,3.98479,6,1.79176,7,3.21888,8,11.1681,9,1,11,2.30259,12,2.30259,15,1],\"rule\":5}],\"node\":{\"in_edges\":[4],\"cat\":\"X0\"},\"edges\":[{\"tail\":[0],\"spans\":[0,2,-1,-1],\"feats\":[5,3.82533,6,3.21888,7,2.52573,8,11.3276,9,1,10,1.20397,11,1.20397,12,2.30259,13,2.30259,15,1],\"rule\":6}],\"node\":{\"in_edges\":[5],\"cat\":\"X8\"},\"edges\":[{\"tail\":[1,2],\"spans\":[0,2,-1,-1],\"feats\":[1,1],\"rule\":7},{\"tail\":[1,3],\"spans\":[0,2,-1,-1],\"feats\":[1,1],\"rule\":8},{\"tail\":[4],\"spans\":[0,2,-1,-1],\"feats\":[2,1],\"rule\":9}],\"node\":{\"in_edges\":[6,7,8],\"cat\":\"S\"},\"edges\":[{\"tail\":[5],\"spans\":[0,2,-1,-1],\"feats\":[],\"rule\":10}],\"node\":{\"in_edges\":[9],\"cat\":\"Goal\"}}";
-  Hypergraph hg;
-  istringstream instr(json);
-  HypergraphIO::ReadFromJSON(&instr, &hg);
-  SparseVector<double> wts;
-  wts.set_value(FD::Convert("PassThrough"), -0.929201533002898);
-  hg.Reweight(wts);
-
-  vector<pair<vector<WordID>, prob_t> > list;
-  std::vector<SparseVector<double> > features;
-  KBest::KBestDerivations<vector<WordID>, ESentenceTraversal> kbest(hg, 10);
-  for (int i = 0; i < 10; ++i) {
-    const KBest::KBestDerivations<vector<WordID>, ESentenceTraversal>::Derivation* d =
-      kbest.LazyKthBest(hg.nodes_.size() - 1, i);
-    if (!d) break;
-    cerr << log(d->score) << " ||| " << TD::GetString(d->yield) << " ||| " << d->feature_values << endl;
-  }
- 
-  SparseVector<double> axis; axis.set_value(FD::Convert("Glue"),1.0);
-  ConvexHullWeightFunction wf(wts, axis);  // wts = starting point, axis = search direction
-  vector<ConvexHull> envs(1);
-  envs[0] = Inside<ConvexHull, ConvexHullWeightFunction>(hg, NULL, wf);
-
-  vector<vector<WordID> > mr(4);
-  TD::ConvertSentence("untitled", &mr[0]);
-  TD::ConvertSentence("with no title", &mr[1]);
-  TD::ConvertSentence("without a title", &mr[2]);
-  TD::ConvertSentence("without title", &mr[3]);
-  EvaluationMetric* metric = EvaluationMetric::Instance("IBM_BLEU");
-  boost::shared_ptr<SegmentEvaluator> scorer1 = metric->CreateSegmentEvaluator(mr);
-  vector<ErrorSurface> es(1);
-  ComputeErrorSurface(*scorer1, envs[0], &es[0], metric, hg);
-}
-
diff --git a/dpmert/mert_geometry.cc b/dpmert/mert_geometry.cc
deleted file mode 100644
index d6973658..00000000
--- a/dpmert/mert_geometry.cc
+++ /dev/null
@@ -1,185 +0,0 @@
-#include "mert_geometry.h"
-
-#include <cassert>
-#include <limits>
-
-using namespace std;
-
-ConvexHull::ConvexHull(int i) {
-  if (i == 0) {
-    // do nothing - <>
-  } else if (i == 1) {
-    points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(0, 0, 0, boost::shared_ptr<MERTPoint>(), boost::shared_ptr<MERTPoint>())));
-    assert(this->IsMultiplicativeIdentity());
-  } else {
-    cerr << "Only can create ConvexHull semiring 0 and 1 with this constructor!\n";
-    abort();
-  }
-}
-
-const ConvexHull ConvexHullWeightFunction::operator()(const Hypergraph::Edge& e) const {
-  const double m = direction.dot(e.feature_values_);
-  const double b = origin.dot(e.feature_values_);
-  MERTPoint* point = new MERTPoint(m, b, e);
-  return ConvexHull(1, point);
-}
-
-ostream& operator<<(ostream& os, const ConvexHull& env) {
-  os << '<';
-  const vector<boost::shared_ptr<MERTPoint> >& points = env.GetSortedSegs();
-  for (int i = 0; i < points.size(); ++i)
-    os << (i==0 ? "" : "|") << "x=" << points[i]->x << ",b=" << points[i]->b << ",m=" << points[i]->m << ",p1=" << points[i]->p1 << ",p2=" << points[i]->p2;
-  return os << '>';
-}
-
-#define ORIGINAL_MERT_IMPLEMENTATION 1
-#ifdef ORIGINAL_MERT_IMPLEMENTATION
-
-struct SlopeCompare {
-  bool operator() (const boost::shared_ptr<MERTPoint>& a, const boost::shared_ptr<MERTPoint>& b) const {
-    return a->m < b->m;
-  }
-};
-
-const ConvexHull& ConvexHull::operator+=(const ConvexHull& other) {
-  if (!other.is_sorted) other.Sort();
-  if (points.empty()) {
-    points = other.points;
-    return *this;
-  }
-  is_sorted = false;
-  int j = points.size();
-  points.resize(points.size() + other.points.size());
-  for (int i = 0; i < other.points.size(); ++i)
-    points[j++] = other.points[i];
-  assert(j == points.size());
-  return *this;
-}
-
-void ConvexHull::Sort() const {
-  sort(points.begin(), points.end(), SlopeCompare());
-  const int k = points.size();
-  int j = 0;
-  for (int i = 0; i < k; ++i) {
-    MERTPoint l = *points[i];
-    l.x = kMinusInfinity;
-    // cerr << "m=" << l.m << endl;
-    if (0 < j) {
-      if (points[j-1]->m == l.m) {   // lines are parallel
-        if (l.b <= points[j-1]->b) continue;
-        --j;
-      }
-      while(0 < j) {
-        l.x = (l.b - points[j-1]->b) / (points[j-1]->m - l.m);
-        if (points[j-1]->x < l.x) break;
-        --j;
-      }
-      if (0 == j) l.x = kMinusInfinity;
-    }
-    *points[j++] = l;
-  }
-  points.resize(j);
-  is_sorted = true;
-}
-
-const ConvexHull& ConvexHull::operator*=(const ConvexHull& other) {
-  if (other.IsMultiplicativeIdentity()) { return *this; }
-  if (this->IsMultiplicativeIdentity()) { (*this) = other; return *this; }
-
-  if (!is_sorted) Sort();
-  if (!other.is_sorted) other.Sort();
-
-  if (this->IsEdgeEnvelope()) {
-//    if (other.size() > 1)
-//      cerr << *this << " (TIMES) " << other << endl;
-    boost::shared_ptr<MERTPoint> edge_parent = points[0];
-    const double& edge_b = edge_parent->b;
-    const double& edge_m = edge_parent->m;
-    points.clear();
-    for (int i = 0; i < other.points.size(); ++i) {
-      const MERTPoint& p = *other.points[i];
-      const double m = p.m + edge_m;
-      const double b = p.b + edge_b;
-      const double& x = p.x;       // x's don't change with *
-      points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(x, m, b, edge_parent, other.points[i])));
-      assert(points.back()->p1->edge);
-    }
-//    if (other.size() > 1)
-//      cerr << " = " << *this << endl;
-  } else {
-    vector<boost::shared_ptr<MERTPoint> > new_points;
-    int this_i = 0;
-    int other_i = 0;
-    const int this_size  = points.size();
-    const int other_size = other.points.size();
-    double cur_x = kMinusInfinity;   // moves from left to right across the
-                                     // real numbers, stopping for all inter-
-                                     // sections
-    double this_next_val  = (1 < this_size  ? points[1]->x       : kPlusInfinity);
-    double other_next_val = (1 < other_size ? other.points[1]->x : kPlusInfinity);
-    while (this_i < this_size && other_i < other_size) {
-      const MERTPoint& this_point = *points[this_i];
-      const MERTPoint& other_point= *other.points[other_i];
-      const double m = this_point.m + other_point.m;
-      const double b = this_point.b + other_point.b;
- 
-      new_points.push_back(boost::shared_ptr<MERTPoint>(new MERTPoint(cur_x, m, b, points[this_i], other.points[other_i])));
-      int comp = 0;
-      if (this_next_val < other_next_val) comp = -1; else
-        if (this_next_val > other_next_val) comp = 1;
-      if (0 == comp) {  // the next values are equal, advance both indices
-        ++this_i;
-	++other_i;
-        cur_x = this_next_val;  // could be other_next_val (they're equal!)
-        this_next_val  = (this_i+1  < this_size  ? points[this_i+1]->x        : kPlusInfinity);
-        other_next_val = (other_i+1 < other_size ? other.points[other_i+1]->x : kPlusInfinity);
-      } else {  // advance the i with the lower x, update cur_x
-        if (-1 == comp) {
-          ++this_i;
-          cur_x = this_next_val;
-          this_next_val =  (this_i+1  < this_size  ? points[this_i+1]->x        : kPlusInfinity);
-        } else {
-          ++other_i;
-          cur_x = other_next_val;
-          other_next_val = (other_i+1 < other_size ? other.points[other_i+1]->x : kPlusInfinity);
-        }
-      }
-    }
-    points.swap(new_points);
-  }
-  //cerr << "Multiply: result=" << (*this) << endl;
-  return *this;
-}
-
-// recursively construct translation
-void MERTPoint::ConstructTranslation(vector<WordID>* trans) const {
-  const MERTPoint* cur = this;
-  vector<vector<WordID> > ant_trans;
-  while(!cur->edge) {
-    ant_trans.resize(ant_trans.size() + 1);
-    cur->p2->ConstructTranslation(&ant_trans.back());
-    cur = cur->p1.get();
-  }
-  size_t ant_size = ant_trans.size();
-  vector<const vector<WordID>*> pants(ant_size);
-  assert(ant_size == cur->edge->tail_nodes_.size());
-  --ant_size;
-  for (int i = 0; i < pants.size(); ++i) pants[ant_size - i] = &ant_trans[i];
-  cur->edge->rule_->ESubstitute(pants, trans);
-}
-
-void MERTPoint::CollectEdgesUsed(std::vector<bool>* edges_used) const {
-  if (edge) {
-    assert(edge->id_ < edges_used->size());
-    (*edges_used)[edge->id_] = true;
-  }
-  if (p1) p1->CollectEdgesUsed(edges_used);
-  if (p2) p2->CollectEdgesUsed(edges_used);
-}
-
-#else
-
-// THIS IS THE NEW FASTER IMPLEMENTATION OF THE MERT SEMIRING OPERATIONS
-
-#endif
-
diff --git a/dpmert/mert_geometry.h b/dpmert/mert_geometry.h
deleted file mode 100644
index a8b6959e..00000000
--- a/dpmert/mert_geometry.h
+++ /dev/null
@@ -1,81 +0,0 @@
-#ifndef _MERT_GEOMETRY_H_
-#define _MERT_GEOMETRY_H_
-
-#include <vector>
-#include <iostream>
-#include <boost/shared_ptr.hpp>
-
-#include "hg.h"
-#include "sparse_vector.h"
-
-static const double kMinusInfinity = -std::numeric_limits<double>::infinity();
-static const double kPlusInfinity = std::numeric_limits<double>::infinity();
-
-struct MERTPoint {
-  MERTPoint() : x(), m(), b(), edge() {}
-  MERTPoint(double _m, double _b) :
-    x(kMinusInfinity), m(_m), b(_b), edge() {}
-  MERTPoint(double _x, double _m, double _b, const boost::shared_ptr<MERTPoint>& p1_, const boost::shared_ptr<MERTPoint>& p2_) :
-    x(_x), m(_m), b(_b), p1(p1_), p2(p2_), edge() {}
-  MERTPoint(double _m, double _b, const Hypergraph::Edge& edge) :
-    x(kMinusInfinity), m(_m), b(_b), edge(&edge) {}
-
-  double x;                   // x intersection with previous segment in env, or -inf if none
-  double m;                   // this line's slope
-  double b;                   // intercept with y-axis
-
-  // we keep a pointer to the "parents" of this segment so we can reconstruct
-  // the Viterbi translation corresponding to this segment
-  boost::shared_ptr<MERTPoint> p1;
-  boost::shared_ptr<MERTPoint> p2;
-
-  // only MERTPoints created from an edge using the ConvexHullWeightFunction
-  // have rules
-  // TRulePtr rule;
-  const Hypergraph::Edge* edge;
-
-  // recursively recover the Viterbi translation that will result from setting
-  // the weights to origin + axis * x, where x is any value from this->x up
-  // until the next largest x in the containing ConvexHull
-  void ConstructTranslation(std::vector<WordID>* trans) const;
-  void CollectEdgesUsed(std::vector<bool>* edges_used) const;
-};
-
-// this is the semiring value type,
-// it defines constructors for 0, 1, and the operations + and *
-struct ConvexHull {
-  // create semiring zero
-  ConvexHull() : is_sorted(true) {}  // zero
-  // for debugging:
-  ConvexHull(const std::vector<boost::shared_ptr<MERTPoint> >& s) : points(s) { Sort(); }
-  // create semiring 1 or 0
-  explicit ConvexHull(int i);
-  ConvexHull(int n, MERTPoint* point) : is_sorted(true), points(n, boost::shared_ptr<MERTPoint>(point)) {}
-  const ConvexHull& operator+=(const ConvexHull& other);
-  const ConvexHull& operator*=(const ConvexHull& other);
-  bool IsMultiplicativeIdentity() const {
-    return size() == 1 && (points[0]->b == 0.0 && points[0]->m == 0.0) && (!points[0]->edge) && (!points[0]->p1) && (!points[0]->p2); }
-  const std::vector<boost::shared_ptr<MERTPoint> >& GetSortedSegs() const {
-    if (!is_sorted) Sort();
-    return points;
-  }
-  size_t size() const { return points.size(); }
-
- private:
-  bool IsEdgeEnvelope() const {
-    return points.size() == 1 && points[0]->edge; }
-  void Sort() const;
-  mutable bool is_sorted;
-  mutable std::vector<boost::shared_ptr<MERTPoint> > points;
-};
-std::ostream& operator<<(std::ostream& os, const ConvexHull& env);
-
-struct ConvexHullWeightFunction {
-  ConvexHullWeightFunction(const SparseVector<double>& ori,
-                           const SparseVector<double>& dir) : origin(ori), direction(dir) {}
-  const ConvexHull operator()(const Hypergraph::Edge& e) const;
-  const SparseVector<double> origin;
-  const SparseVector<double> direction;
-};
-
-#endif
diff --git a/dpmert/mr_dpmert_generate_mapper_input.cc b/dpmert/mr_dpmert_generate_mapper_input.cc
deleted file mode 100644
index 199cd23a..00000000
--- a/dpmert/mr_dpmert_generate_mapper_input.cc
+++ /dev/null
@@ -1,81 +0,0 @@
-#include <iostream>
-#include <vector>
-
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "filelib.h"
-#include "weights.h"
-#include "line_optimizer.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()
-        ("dev_set_size,s",po::value<unsigned>(),"[REQD] Development set size (# of parallel sentences)")
-        ("forest_repository,r",po::value<string>(),"[REQD] Path to forest repository")
-        ("weights,w",po::value<string>(),"[REQD] Current feature weights file")
-        ("optimize_feature,o",po::value<vector<string> >(), "Feature to optimize (if none specified, all weights listed in the weights file will be optimized)")
-        ("random_directions,d",po::value<unsigned int>()->default_value(20),"Number of random directions to run the line optimizer in")
-        ("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("dev_set_size") == 0) {
-    cerr << "Please specify the size of the development set using -d N\n";
-    flag = true;
-  }
-  if (conf->count("weights") == 0) {
-    cerr << "Please specify the starting-point weights using -w <weightfile.txt>\n";
-    flag = true;
-  }
-  if (conf->count("forest_repository") == 0) {
-    cerr << "Please specify the forest repository location using -r <DIR>\n";
-    flag = true;
-  }
-  if (flag || conf->count("help")) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-int main(int argc, char** argv) {
-  RandomNumberGenerator<boost::mt19937> rng;
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  vector<string> features;
-  SparseVector<weight_t> origin;
-  vector<weight_t> w;
-  Weights::InitFromFile(conf["weights"].as<string>(), &w, &features);
-  Weights::InitSparseVector(w, &origin);
-  const string forest_repository = conf["forest_repository"].as<string>();
-  if (!DirectoryExists(forest_repository)) {
-    cerr << "Forest repository directory " << forest_repository << " not found!\n";
-    return 1;
-  }
-  if (conf.count("optimize_feature") > 0)
-    features=conf["optimize_feature"].as<vector<string> >();
-  vector<SparseVector<weight_t> > directions;
-  vector<int> fids(features.size());
-  for (unsigned i = 0; i < features.size(); ++i)
-    fids[i] = FD::Convert(features[i]);
-  LineOptimizer::CreateOptimizationDirections(
-     fids,
-     conf["random_directions"].as<unsigned int>(),
-     &rng,
-     &directions);
-  unsigned dev_set_size = conf["dev_set_size"].as<unsigned>();
-  for (unsigned i = 0; i < dev_set_size; ++i) {
-    for (unsigned j = 0; j < directions.size(); ++j) {
-      cout << forest_repository << '/' << i << ".json.gz " << i << ' ';
-      print(cout, origin, "=", ";");
-      cout << ' ';
-      print(cout, directions[j], "=", ";");
-      cout << endl;
-    }
-  }
-  return 0;
-}
diff --git a/dpmert/mr_dpmert_map.cc b/dpmert/mr_dpmert_map.cc
deleted file mode 100644
index d1efcf96..00000000
--- a/dpmert/mr_dpmert_map.cc
+++ /dev/null
@@ -1,112 +0,0 @@
-#include <sstream>
-#include <iostream>
-#include <fstream>
-#include <vector>
-
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "ns.h"
-#include "ns_docscorer.h"
-#include "ces.h"
-#include "filelib.h"
-#include "stringlib.h"
-#include "sparse_vector.h"
-#include "mert_geometry.h"
-#include "inside_outside.h"
-#include "error_surface.h"
-#include "b64tools.h"
-#include "hg_io.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()
-        ("reference,r",po::value<vector<string> >(), "[REQD] Reference translation (tokenized text)")
-        ("source,s",po::value<string>(), "Source file (ignored, except for AER)")
-        ("evaluation_metric,m",po::value<string>()->default_value("ibm_bleu"), "Evaluation metric being optimized")
-        ("input,i",po::value<string>()->default_value("-"), "Input file to map (- is STDIN)")
-        ("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);
-  }
-}
-
-bool ReadSparseVectorString(const string& s, SparseVector<double>* v) {
-#if 0
-  // this should work, but untested.
-  std::istringstream i(s);
-  i>>*v;
-#else
-  vector<string> fields;
-  Tokenize(s, ';', &fields);
-  if (fields.empty()) return false;
-  for (unsigned i = 0; i < fields.size(); ++i) {
-    vector<string> pair(2);
-    Tokenize(fields[i], '=', &pair);
-    if (pair.size() != 2) {
-      cerr << "Error parsing vector string: " << fields[i] << endl;
-      return false;
-    }
-    v->set_value(FD::Convert(pair[0]), atof(pair[1].c_str()));
-  }
-  return true;
-#endif
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  const string evaluation_metric = conf["evaluation_metric"].as<string>();
-  EvaluationMetric* metric = EvaluationMetric::Instance(evaluation_metric);
-  DocumentScorer ds(metric, conf["reference"].as<vector<string> >());
-  cerr << "Loaded " << ds.size() << " references for scoring with " << evaluation_metric << endl;
-  Hypergraph hg;
-  string last_file;
-  ReadFile in_read(conf["input"].as<string>());
-  istream &in=*in_read.stream();
-  while(in) {
-    string line;
-    getline(in, line);
-    if (line.empty()) continue;
-    istringstream is(line);
-    int sent_id;
-    string file, s_origin, s_direction;
-    // path-to-file (JSON) sent_ed starting-point search-direction
-    is >> file >> sent_id >> s_origin >> s_direction;
-    SparseVector<double> origin;
-    ReadSparseVectorString(s_origin, &origin);
-    SparseVector<double> direction;
-    ReadSparseVectorString(s_direction, &direction);
-    // cerr << "File: " << file << "\nDir: " << direction << "\n   X: " << origin << endl;
-    if (last_file != file) {
-      last_file = file;
-      ReadFile rf(file);
-      HypergraphIO::ReadFromJSON(rf.stream(), &hg);
-    }
-    const ConvexHullWeightFunction wf(origin, direction);
-    const ConvexHull hull = Inside<ConvexHull, ConvexHullWeightFunction>(hg, NULL, wf);
-
-    ErrorSurface es;
-    ComputeErrorSurface(*ds[sent_id], hull, &es, metric, hg);
-    //cerr << "Viterbi envelope has " << ve.size() << " segments\n";
-    // cerr << "Error surface has " << es.size() << " segments\n";
-    string val;
-    es.Serialize(&val);
-    cout << 'M' << ' ' << s_origin << ' ' << s_direction << '\t';
-    B64::b64encode(val.c_str(), val.size(), &cout);
-    cout << endl << flush;
-  }
-  return 0;
-}
diff --git a/dpmert/mr_dpmert_reduce.cc b/dpmert/mr_dpmert_reduce.cc
deleted file mode 100644
index 31512a03..00000000
--- a/dpmert/mr_dpmert_reduce.cc
+++ /dev/null
@@ -1,77 +0,0 @@
-#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"
-#include "stringlib.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()
-        ("evaluation_metric,m",po::value<string>(), "Evaluation metric (IBM_BLEU, etc.)")
-        ("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("evaluation_metric") == 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 evaluation_metric = conf["evaluation_metric"].as<string>();
-  EvaluationMetric* metric = EvaluationMetric::Instance(evaluation_metric);
-  LineOptimizer::ScoreType opt_type = LineOptimizer::MAXIMIZE_SCORE;
-  if (metric->IsErrorMetric())
-    opt_type = LineOptimizer::MINIMIZE_SCORE;
-
-  vector<ErrorSurface> esv;
-  string last_key, line, key, val;
-  while(getline(cin, line)) {
-    size_t ks = line.find("\t");
-    assert(string::npos != ks);
-    assert(ks > 2);
-    key = line.substr(2, ks - 2);
-    val = line.substr(ks + 1);
-    if (key != last_key) {
-      if (!last_key.empty()) {
-	float score;
-        double x = LineOptimizer::LineOptimize(metric, esv, opt_type, &score);
-	cout << last_key << "|" << x << "|" << score << endl;
-      }
-      last_key.swap(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(encoded);
-  }
-  if (!esv.empty()) {
-    float score;
-    double x = LineOptimizer::LineOptimize(metric, esv, opt_type, &score);
-    cout << last_key << "|" << x << "|" << score << endl;
-  }
-  return 0;
-}
diff --git a/dpmert/parallelize.pl b/dpmert/parallelize.pl
deleted file mode 100755
index d2ebaeea..00000000
--- a/dpmert/parallelize.pl
+++ /dev/null
@@ -1,423 +0,0 @@
-#!/usr/bin/env perl
-
-# Author: Adam Lopez
-#
-# This script takes a command that processes input
-# from stdin one-line-at-time, and parallelizes it
-# on the cluster using David Chiang's sentserver/
-# sentclient architecture.
-#
-# Prerequisites: the command *must* read each line
-# without waiting for subsequent lines of input
-# (for instance, a command which must read all lines
-# of input before processing will not work) and
-# return it to the output *without* buffering
-# multiple lines.
-
-#TODO: if -j 1, run immediately, not via sentserver?  possible differences in environment might make debugging harder
-
-#ANNOYANCE: if input is shorter than -j n lines, or at the very last few lines, repeatedly sleeps.  time cut down to 15s from 60s
-
-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"; }
-use LocalConfig;
-
-use Cwd qw/ abs_path cwd getcwd /; 
-use File::Temp qw/ tempfile /;
-use Getopt::Long;
-use IPC::Open2;
-use strict;
-use POSIX ":sys_wait_h";
-
-use File::Basename;
-my $myDir = dirname(__FILE__);
-print STDERR __FILE__." -> $myDir\n";
-push(@INC, $myDir);
-require "libcall.pl";
-
-my $tailn=5; # +0 = concatenate all the client logs.  5 = last 5 lines
-my $recycle_clients;    # spawn new clients when previous ones terminate
-my $stay_alive;      # dont let server die when having zero clients
-my $joblist = "";
-my $errordir="";
-my $multiline;
-my $workdir = '.';
-my $numnodes = 8;
-my $user = $ENV{"USER"};
-my $pmem = "9g";
-my $basep=50300;
-my $randp=300;
-my $tryp=50;
-my $no_which;
-my $no_cd;
-
-my $DEBUG=$ENV{DEBUG};
-print STDERR "DEBUG=$DEBUG output enabled.\n" if $DEBUG;
-my $verbose = 1;
-sub verbose {
-    if ($verbose) {
-        print STDERR @_,"\n";
-    }
-}
-sub debug {
-    if ($DEBUG) {
-        my ($package, $filename, $line) = caller;
-        print STDERR "DEBUG: $filename($line): ",join(' ',@_),"\n";
-    }
-}
-my $is_shell_special=qr.[ \t\n\\><|&;"'`~*?{}$!()].;
-my $shell_escape_in_quote=qr.[\\"\$`!].;
-sub escape_shell {
-    my ($arg)=@_;
-    return undef unless defined $arg;
-    return '""' unless $arg;
-    if ($arg =~ /$is_shell_special/) {
-        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
-        return "\"$arg\"";
-    }
-    return $arg;
-}
-sub preview_files {
-    my ($l,$skipempty,$footer,$n)=@_;
-    $n=$tailn unless defined $n;
-    my @f=grep { ! ($skipempty && -z $_) } @$l;
-    my $fn=join(' ',map {escape_shell($_)} @f);
-    my $cmd="tail -n $n $fn";
-    unchecked_output("$cmd").($footer?"\nNONEMPTY FILES:\n$fn\n":"");
-}
-sub prefix_dirname($) {
-    #like `dirname but if ends in / then return the whole thing
-    local ($_)=@_;
-    if (/\/$/) {
-        $_;
-    } else {
-        s#/[^/]$##;
-        $_ ? $_ : '';
-    }
-}
-sub ensure_final_slash($) {
-    local ($_)=@_;
-    m#/$# ? $_ : ($_."/");
-}
-sub extend_path($$;$$) {
-    my ($base,$ext,$mkdir,$baseisdir)=@_;
-    if (-d $base) {
-        $base.="/";
-    } else {
-        my $dir;
-        if ($baseisdir) {
-            $dir=$base;
-            $base.='/' unless $base =~ /\/$/;
-        } else {
-            $dir=prefix_dirname($base);
-        }
-        my @cmd=("/bin/mkdir","-p",$dir);
-        check_call(@cmd) if $mkdir;
-    }
-    return $base.$ext;
-}
-
-my $abscwd=abs_path(&getcwd);
-sub print_help;
-
-my $use_fork;
-my @pids;
-
-# Process command-line options
-unless (GetOptions(
-      "stay-alive" => \$stay_alive,
-      "recycle-clients" => \$recycle_clients,
-      "error-dir=s" => \$errordir,
-      "multi-line" => \$multiline,
-      "workdir=s" => \$workdir,
-      "use-fork" => \$use_fork,
-      "verbose" => \$verbose,
-      "jobs=i" => \$numnodes,
-      "pmem=s" => \$pmem,
-        "baseport=i" => \$basep,
-#       "iport=i" => \$randp, #for short name -i
-        "no-which!" => \$no_which,
-            "no-cd!" => \$no_cd,
-            "tailn=s" => \$tailn,
-) && scalar @ARGV){
-  print_help();
-    die "bad options.";
-}
-
-my $cmd = "";
-my $prog=shift;
-if ($no_which) {
-    $cmd=$prog;
-} else {
-    $cmd=check_output("which $prog");
-    chomp $cmd;
-    die "$prog not found - $cmd" unless $cmd;
-}
-#$cmd=abs_path($cmd);
-for my $arg (@ARGV) {
-    $cmd .= " ".escape_shell($arg);
-}
-die "Please specify a command to parallelize\n" if $cmd eq '';
-
-my $cdcmd=$no_cd ? '' : ("cd ".escape_shell($abscwd)."\n");
-
-my $executable = $cmd;
-$executable =~ s/^\s*(\S+)($|\s.*)/$1/;
-$executable=check_output("basename $executable");
-chomp $executable;
-
-
-print STDERR "Parallelizing ($numnodes ways): $cmd\n\n";
-
-# create -e dir and save .sh
-use File::Temp qw/tempdir/;
-unless ($errordir) {
-    $errordir=tempdir("$executable.XXXXXX",CLEANUP=>1);
-}
-if ($errordir) {
-    my $scriptfile=extend_path("$errordir/","$executable.sh",1,1);
-    -d $errordir || die "should have created -e dir $errordir";
-    open SF,">",$scriptfile || die;
-    print SF "$cdcmd$cmd\n";
-    close SF;
-    chmod 0755,$scriptfile;
-    $errordir=abs_path($errordir);
-    &verbose("-e dir: $errordir");
-}
-
-# set cleanup handler
-my @cleanup_cmds;
-sub cleanup;
-sub cleanup_and_die;
-$SIG{INT} = "cleanup_and_die";
-$SIG{TERM} = "cleanup_and_die";
-$SIG{HUP} = "cleanup_and_die";
-
-# other subs:
-sub numof_live_jobs;
-sub launch_job_on_node;
-
-
-# vars
-my $mydir = check_output("dirname $0"); chomp $mydir;
-my $sentserver = "$mydir/sentserver";
-my $sentclient = "$mydir/sentclient";
-my $host = check_output("hostname");
-chomp $host;
-
-
-# find open port
-srand;
-my $port = 50300+int(rand($randp));
-my $endp=$port+$tryp;
-sub listening_port_lines {
-    my $quiet=$verbose?'':'2>/dev/null';
-    return unchecked_output("netstat -a -n $quiet | grep LISTENING | grep -i tcp");
-}
-my $netstat=&listening_port_lines;
-
-if ($verbose){ print STDERR "Testing port $port...";}
-
-while ($netstat=~/$port/ || &listening_port_lines=~/$port/){
-  if ($verbose){ print STDERR "port is busy\n";}
-  $port++;
-  if ($port > $endp){
-    die "Unable to find open port\n";
-  }
-  if ($verbose){ print STDERR "Testing port $port... "; }
-}
-if ($verbose){
-  print STDERR "port $port is available\n";
-}
-
-my $key = int(rand()*1000000);
-
-my $multiflag = "";
-if ($multiline){ $multiflag = "-m"; print STDERR "expecting multiline output.\n"; }
-my $stay_alive_flag = "";
-if ($stay_alive){ $stay_alive_flag = "--stay-alive"; print STDERR "staying alive while no clients are connected.\n"; }
-
-my $node_count = 0;
-my $script = "";
-# fork == one thread runs the sentserver, while the
-# other spawns the sentclient commands.
-my $pid = fork;
-if ($pid == 0) { # child
-  sleep 8; # give other thread time to start sentserver
-  $script = "$cdcmd$sentclient $host:$port:$key $cmd";
-
-  if ($verbose){
-    print STDERR "Client script:\n====\n";
-    print STDERR $script;
-    print STDERR "====\n";
-  }
-  for (my $jobn=0; $jobn<$numnodes; $jobn++){
-    launch_job();
-  }
-  if ($recycle_clients) {
-    my $ret;
-    my $livejobs;
-    while (1) {
-      $ret = waitpid($pid, WNOHANG);
-      #print STDERR "waitpid $pid ret = $ret \n";
-      last if ($ret != 0);
-      $livejobs = numof_live_jobs();
-      if ($numnodes >= $livejobs ) {  # a client terminated, OR # lines of input was less than -j
-        print STDERR "num of requested nodes = $numnodes; num of currently live jobs = $livejobs; Client terminated - launching another.\n";
-        launch_job();
-      } else {
-        sleep 15;
-      }
-    }
-  }
-  print STDERR "CHILD PROCESSES SPAWNED ... WAITING\n";
-  for my $p (@pids) {
-    waitpid($p, 0);
-  }
-} else {
-#  my $todo = "$sentserver -k $key $multiflag $port ";
-  my $todo = "$sentserver -k $key $multiflag $port $stay_alive_flag ";
-  if ($verbose){ print STDERR "Running: $todo\n"; }
-  check_call($todo);
-  print STDERR "Call to $sentserver returned.\n";
-  cleanup();
-  exit(0);
-}
-
-sub numof_live_jobs {
-  if ($use_fork) {
-    die "not implemented";
-  } else {
-    # We can probably continue decoding if the qstat error is only temporary
-    my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat")));
-    return ($#livejobs + 1);
-  }
-}
-my (@errors,@outs,@cmds);
-
-sub launch_job {
-    if ($use_fork) { return launch_job_fork(); }
-    my $errorfile = "/dev/null";
-    my $outfile = "/dev/null";
-    $node_count++;
-    my $clientname = $executable;
-    $clientname =~ s/^(.{4}).*$/$1/;
-    $clientname = "$clientname.$node_count";
-    if ($errordir){
-      $errorfile = "$errordir/$clientname.ER";
-      $outfile = "$errordir/$clientname.OU";
-      push @errors,$errorfile;
-      push @outs,$outfile;
-    }
-    my $todo = qsub_args($pmem) . " -N $clientname -o $outfile -e $errorfile";
-    push @cmds,$todo;
-
-    print STDERR "Running: $todo\n";
-    local(*QOUT, *QIN);
-    open2(\*QOUT, \*QIN, $todo) or die "Failed to open2: $!";
-    print QIN $script;
-    close QIN;
-    while (my $jobid=<QOUT>){
-      chomp $jobid;
-      if ($verbose){ print STDERR "Launched client job: $jobid"; }
-      $jobid =~ s/^(\d+)(.*?)$/\1/g;
-            $jobid =~ s/^Your job (\d+) .*$/\1/;
-      print STDERR " short job id $jobid\n";
-            if ($verbose){
-                print STDERR "cd: $abscwd\n";
-                print STDERR "cmd: $cmd\n";
-            }
-      if ($joblist == "") { $joblist = $jobid; }
-      else {$joblist = $joblist . "\|" . $jobid; }
-      my $cleanfn="qdel $jobid 2> /dev/null";
-      push(@cleanup_cmds, $cleanfn);
-    }
-    close QOUT;
-}
-
-sub launch_job_fork {
-  my $errorfile = "/dev/null";
-  my $outfile = "/dev/null";
-  $node_count++;
-  my $clientname = $executable;
-  $clientname =~ s/^(.{4}).*$/$1/;
-  $clientname = "$clientname.$node_count";
-  if ($errordir){
-    $errorfile = "$errordir/$clientname.ER";
-    $outfile = "$errordir/$clientname.OU";
-    push @errors,$errorfile;
-    push @outs,$outfile;
-  }
-  my $pid = fork;
-  if ($pid == 0) {
-    my ($fh, $scr_name) = get_temp_script();
-    print $fh $script;
-    close $fh;
-    my $todo = "/bin/bash -xeo pipefail $scr_name 1> $outfile 2> $errorfile";
-    print STDERR "EXEC: $todo\n";
-    my $out = check_output("$todo");
-    unlink $scr_name or warn "Failed to remove $scr_name";
-    exit 0;
-  } else {
-    push @pids, $pid;
-  }
-}
-
-sub get_temp_script {
-  my ($fh, $filename) = tempfile( "$workdir/workXXXX", SUFFIX => '.sh');
-  return ($fh, $filename);
-}
-
-sub cleanup_and_die {
-  cleanup();
-  die "\n";
-}
-
-sub cleanup {
-  print STDERR "Cleaning up...\n";
-  for $cmd (@cleanup_cmds){
-    print STDERR "  Cleanup command: $cmd\n";
-    eval $cmd;
-  }
-  print STDERR "outputs:\n",preview_files(\@outs,1),"\n";
-  print STDERR "errors:\n",preview_files(\@errors,1),"\n";
-  print STDERR "cmd:\n",$cmd,"\n";
-  print STDERR " cat $errordir/*.ER\nfor logs.\n";
-  print STDERR "Cleanup finished.\n";
-}
-
-sub print_help
-{
-  my $name = check_output("basename $0"); chomp $name;
-  print << "Help";
-
-usage: $name [options]
-
-  Automatic black-box parallelization of commands.
-
-options:
-
-  --use-fork
-    Instead of using qsub, use fork.
-
-  -e, --error-dir <dir>
-    Retain output files from jobs in <dir>, rather
-    than silently deleting them.
-
-  -m, --multi-line
-    Expect that command may produce multiple output
-    lines for a single input line.  $name makes a
-    reasonable attempt to obtain all output before
-    processing additional inputs.  However, use of this
-    option is inherently unsafe.
-
-  -v, --verbose
-    Print diagnostic informatoin on stderr.
-
-  -j, --jobs
-    Number of jobs to use.
-
-  -p, --pmem
-    pmem setting for each job.
-
-Help
-}
diff --git a/dpmert/sentclient.c b/dpmert/sentclient.c
deleted file mode 100644
index 91d994ab..00000000
--- a/dpmert/sentclient.c
+++ /dev/null
@@ -1,76 +0,0 @@
-/* Copyright (c) 2001 by David Chiang. All rights reserved.*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <sys/socket.h>
-#include <sys/types.h>
-#include <netinet/in.h>
-#include <netdb.h>
-#include <string.h>
-
-#include "sentserver.h"
-
-int main (int argc, char *argv[]) {
-  int sock, port;
-  char *s, *key;
-  struct hostent *hp;
-  struct sockaddr_in server;
-  int errors = 0;
-
-  if (argc < 3) {
-    fprintf(stderr, "Usage: sentclient host[:port[:key]] command [args ...]\n");
-    exit(1);
-  }
-
-  s = strchr(argv[1], ':');
-  key = NULL;
-
-  if (s == NULL) {
-    port = DEFAULT_PORT;
-  } else {
-    *s = '\0';
-    s+=1;
-	/* dumb hack */
-	key = strchr(s, ':');
-	if (key != NULL){
-		*key = '\0';
-		key += 1;
-	}
-    port = atoi(s);
-  }
-
-  sock = socket(AF_INET, SOCK_STREAM, 0);
-
-  hp = gethostbyname(argv[1]);
-  if (hp == NULL) {
-    fprintf(stderr, "unknown host %s\n", argv[1]);
-    exit(1);
-  }
-
-  bzero((char *)&server, sizeof(server));
-  bcopy(hp->h_addr, (char *)&server.sin_addr, hp->h_length);
-  server.sin_family = hp->h_addrtype;
-  server.sin_port = htons(port);
-
-  while (connect(sock, (struct sockaddr *)&server, sizeof(server)) < 0) {
-    perror("connect()");
-    sleep(1);
-    errors++;
-    if (errors > 5)
-      exit(1);
-  }
-
-  close(0);
-  close(1);
-  dup2(sock, 0);
-  dup2(sock, 1);
-
-  if (key != NULL){
-	write(1, key, strlen(key));
-	write(1, "\n", 1);
-  }
-
-  execvp(argv[2], argv+2);
-  return 0;
-}
diff --git a/dpmert/sentserver.c b/dpmert/sentserver.c
deleted file mode 100644
index c20b4fa6..00000000
--- a/dpmert/sentserver.c
+++ /dev/null
@@ -1,515 +0,0 @@
-/* Copyright (c) 2001 by David Chiang. All rights reserved.*/
-
-#include <string.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <fcntl.h>
-#include <stdio.h>
-#include <sys/socket.h>
-#include <sys/types.h>
-#include <sys/time.h>
-#include <netinet/in.h>
-#include <sched.h>
-#include <pthread.h>
-#include <errno.h>
-
-#include "sentserver.h"
-
-#define MAX_CLIENTS 64
-
-struct clientinfo {
-  int s;
-  struct sockaddr_in sin;
-};
-
-struct line {
-  int id;
-  char *s;
-  int status;
-  struct line *next;
-} *head, **ptail;
-
-int n_sent = 0, n_received=0, n_flushed=0;
-
-#define STATUS_RUNNING 0
-#define STATUS_ABORTED 1
-#define STATUS_FINISHED 2
-
-pthread_mutex_t queue_mutex = PTHREAD_MUTEX_INITIALIZER;
-pthread_mutex_t clients_mutex = PTHREAD_MUTEX_INITIALIZER;
-pthread_mutex_t input_mutex = PTHREAD_MUTEX_INITIALIZER;
-
-int n_clients = 0;
-int s;
-int expect_multiline_output = 0;
-int log_mutex = 0;
-int stay_alive = 0;		/* dont panic and die with zero clients */
-
-void queue_finish(struct line *node, char *s, int fid);
-char * read_line(int fd, int multiline);
-void done (int code);
-
-struct line * queue_get(int fid) {
-	struct line *cur;
-	char *s, *synch;
-
-	if (log_mutex) fprintf(stderr, "Getting for data for fid %d\n", fid);
-	if (log_mutex) fprintf(stderr, "Locking queue mutex (%d)\n", fid);
-	pthread_mutex_lock(&queue_mutex);
-
-	/* First, check for aborted sentences. */
-
-	if (log_mutex) fprintf(stderr, "  Checking queue for aborted jobs (fid %d)\n", fid);
-	for (cur = head; cur != NULL; cur = cur->next) {
-		if (cur->status == STATUS_ABORTED) {
-			cur->status = STATUS_RUNNING;
-
-			if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-			pthread_mutex_unlock(&queue_mutex);
-
-			return cur;
-		}
-	}
-	if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-	pthread_mutex_unlock(&queue_mutex);
-
-	/* Otherwise, read a new one. */
-	if (log_mutex) fprintf(stderr, "Locking input mutex (%d)\n", fid);
-	if (log_mutex) fprintf(stderr, "  Reading input for new data (fid %d)\n", fid);
-	pthread_mutex_lock(&input_mutex);
-	s = read_line(0,0);
-
-	while (s) {
-		if (log_mutex) fprintf(stderr, "Locking queue mutex (%d)\n", fid);
-		pthread_mutex_lock(&queue_mutex);
-		if (log_mutex) fprintf(stderr, "Unlocking input mutex (%d)\n", fid);
-		pthread_mutex_unlock(&input_mutex);
-
-		cur = malloc(sizeof (struct line));
-		cur->id = n_sent;
-		cur->s = s;
-		cur->next = NULL;
-
-		*ptail = cur;
-		ptail = &cur->next;
-
-		n_sent++;
-
-		if (strcmp(s,"===SYNCH===\n")==0){
-			fprintf(stderr, "Received ===SYNCH=== signal (fid %d)\n", fid);
-			// Note: queue_finish calls free(cur->s).
-			// Therefore we need to create a new string here.
-			synch = malloc((strlen("===SYNCH===\n")+2) * sizeof (char));
-			synch = strcpy(synch, s);
-
-			if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-			pthread_mutex_unlock(&queue_mutex);
-			queue_finish(cur, synch, fid); /* handles its own lock */
-
-			if (log_mutex) fprintf(stderr, "Locking input mutex (%d)\n", fid);
-			if (log_mutex) fprintf(stderr, "  Reading input for new data (fid %d)\n", fid);
-			pthread_mutex_lock(&input_mutex);
-
-			s = read_line(0,0);
-		} else {
-			if (log_mutex) fprintf(stderr, "  Received new data %d (fid %d)\n", cur->id, fid);
-			cur->status = STATUS_RUNNING;
-			if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-			pthread_mutex_unlock(&queue_mutex);
-			return cur;
-		}
-	}
-
-	if (log_mutex) fprintf(stderr, "Unlocking input mutex (%d)\n", fid);
-	pthread_mutex_unlock(&input_mutex);
-	/* Only way to reach this point: no more output */
-
-	if (log_mutex) fprintf(stderr, "Locking queue mutex (%d)\n", fid);
-	pthread_mutex_lock(&queue_mutex);
-	if (head == NULL) {
-		fprintf(stderr, "Reached end of file. Exiting.\n");
-		done(0);
-	} else
-		ptail = NULL; /* This serves as a signal that there is no more input */
-	if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-	pthread_mutex_unlock(&queue_mutex);
-
-	return NULL;
-}
-
-void queue_panic() {
-	struct line *next;
-	while (head && head->status == STATUS_FINISHED) {
-		/* Write out finished sentences */
-		if (head->status == STATUS_FINISHED) {
-			fputs(head->s, stdout);
-			fflush(stdout);
-		}
-		/* Write out blank line for unfinished sentences */
-		if (head->status == STATUS_ABORTED) {
-			fputs("\n", stdout);
-			fflush(stdout);
-		}
-		/* By defition, there cannot be any RUNNING sentences, since
-		function is only called when n_clients == 0 */
-		free(head->s);
-		next = head->next;
-		free(head);
-		head = next;
-		n_flushed++;
-	}
-	fclose(stdout);
-	fprintf(stderr, "All clients died. Panicking, flushing completed sentences and exiting.\n");
-	done(1);
-}
-
-void queue_abort(struct line *node, int fid) {
-	if (log_mutex) fprintf(stderr, "Locking queue mutex (%d)\n", fid);
-	pthread_mutex_lock(&queue_mutex);
-	node->status = STATUS_ABORTED;
-	if (n_clients == 0) {
-		if (stay_alive) {
-			fprintf(stderr, "Warning! No live clients detected! Staying alive, will retry soon.\n");
-		} else {
-			queue_panic();
-		}
-	}
-	if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-	pthread_mutex_unlock(&queue_mutex);
-}
-
-
-void queue_print() {
-  struct line *cur;
-
-  fprintf(stderr, "  Queue\n");
-
-  for (cur = head; cur != NULL; cur = cur->next) {
-    switch(cur->status) {
-    case STATUS_RUNNING:
-      fprintf(stderr, "    %d running  ", cur->id); break;
-    case STATUS_ABORTED:
-      fprintf(stderr, "    %d aborted  ", cur->id); break;
-    case STATUS_FINISHED:
-      fprintf(stderr, "    %d finished ", cur->id); break;
-
-    }
-	fprintf(stderr, "\n");
-    //fprintf(stderr, cur->s);
-  }
-}
-
-void queue_finish(struct line *node, char *s, int fid) {
-  struct line *next;
-  if (log_mutex) fprintf(stderr, "Locking queue mutex (%d)\n", fid);
-  pthread_mutex_lock(&queue_mutex);
-
-  free(node->s);
-  node->s = s;
-  node->status = STATUS_FINISHED;
-  n_received++;
-
-  /* Flush out finished nodes */
-  while (head && head->status == STATUS_FINISHED) {
-
-    if (log_mutex) fprintf(stderr, "  Flushing finished node %d\n", head->id);
-
-    fputs(head->s, stdout);
-    fflush(stdout);
-    if (log_mutex) fprintf(stderr, "  Flushed node %d\n", head->id);
-    free(head->s);
-
-    next = head->next;
-    free(head);
-
-    head = next;
-
-    n_flushed++;
-
-    if (head == NULL) { /* empty queue */
-      if (ptail == NULL) { /* This can only happen if set in queue_get as signal that there is no more input. */
-        fprintf(stderr, "All sentences finished. Exiting.\n");
-        done(0);
-      } else /* ptail pointed at something which was just popped off the stack -- reset to head*/
-        ptail = &head;
-    }
-  }
-
-  if (log_mutex) fprintf(stderr, "  Flushing output %d\n", head->id);
-  fflush(stdout);
-  fprintf(stderr, "%d sentences sent, %d sentences finished, %d sentences flushed\n", n_sent, n_received, n_flushed);
-
-  if (log_mutex) fprintf(stderr, "Unlocking queue mutex (%d)\n", fid);
-  pthread_mutex_unlock(&queue_mutex);
-
-}
-
-char * read_line(int fd, int multiline) {
-  int size = 80;
-  char errorbuf[100];
-  char *s = malloc(size+2);
-  int result, errors=0;
-  int i = 0;
-
-  result = read(fd, s+i, 1);
-
-  while (1) {
-    if (result < 0) {
-      perror("read()");
-      sprintf(errorbuf, "Error code: %d\n", errno);
-      fprintf(stderr, errorbuf);
-      errors++;
-      if (errors > 5) {
-	free(s);
-	return NULL;
-      } else {
-	sleep(1); /* retry after delay */
-      }
-    } else if (result == 0) {
-      break;
-    } else if (multiline==0 && s[i] == '\n') {
-      break;
-    } else {
-      if (s[i] == '\n'){
-	/* if we've reached this point,
-	   then multiline must be 1, and we're
-	   going to poll the fd for an additional
-	   line of data.  The basic design is to
-	   run a select on the filedescriptor fd.
-	   Select will return under two conditions:
-	   if there is data on the fd, or if a
-	   timeout is reached.  We'll select on this
-	   fd.  If select returns because there's data
-	   ready, keep going; else assume there's no
-	   more and return the data we already have.
-	*/
-
-	fd_set set;
-	FD_ZERO(&set);
-	FD_SET(fd, &set);
-
-	struct timeval timeout;
-	timeout.tv_sec = 3; // number of seconds for timeout
-	timeout.tv_usec = 0;
-
-	int ready = select(FD_SETSIZE, &set, NULL, NULL, &timeout);
-	if (ready<1){
-	  break; // no more data, stop looping
-	}
-      }
-      i++;
-
-      if (i == size) {
-	size = size*2;
-	s = realloc(s, size+2);
-      }
-    }
-
-    result = read(fd, s+i, 1);
-  }
-
-  if (result == 0 && i == 0) { /* end of file */
-    free(s);
-    return NULL;
-  }
-
-  s[i] = '\n';
-  s[i+1] = '\0';
-
-  return s;
-}
-
-void * new_client(void *arg) {
-  struct clientinfo *client = (struct clientinfo *)arg;
-  struct line *cur;
-  int result;
-  char *s;
-  char errorbuf[100];
-
-  pthread_mutex_lock(&clients_mutex);
-  n_clients++;
-  pthread_mutex_unlock(&clients_mutex);
-
-  fprintf(stderr, "Client connected (%d connected)\n", n_clients);
-
-  for (;;) {
-
-    cur = queue_get(client->s);
-
-    if (cur) {
-      /* fprintf(stderr, "Sending to client: %s", cur->s); */
-      fprintf(stderr, "Sending data %d to client (fid %d)\n", cur->id, client->s);
-      result = write(client->s, cur->s, strlen(cur->s));
-      if (result < strlen(cur->s)){
-        perror("write()");
-        sprintf(errorbuf, "Error code: %d\n", errno);
-        fprintf(stderr, errorbuf);
-
-        pthread_mutex_lock(&clients_mutex);
-        n_clients--;
-        pthread_mutex_unlock(&clients_mutex);
-
-        fprintf(stderr, "Client died (%d connected)\n", n_clients);
-        queue_abort(cur, client->s);
-
-        close(client->s);
-        free(client);
-
-        pthread_exit(NULL);
-      }
-    } else {
-      close(client->s);
-      pthread_mutex_lock(&clients_mutex);
-      n_clients--;
-      pthread_mutex_unlock(&clients_mutex);
-      fprintf(stderr, "Client dismissed (%d connected)\n", n_clients);
-      pthread_exit(NULL);
-    }
-
-    s = read_line(client->s,expect_multiline_output);
-    if (s) {
-      /* fprintf(stderr, "Client (fid %d) returned: %s", client->s, s); */
-      fprintf(stderr, "Client (fid %d) returned data %d\n", client->s, cur->id);
-//      queue_print();
-      queue_finish(cur, s, client->s);
-    } else {
-      pthread_mutex_lock(&clients_mutex);
-      n_clients--;
-      pthread_mutex_unlock(&clients_mutex);
-
-      fprintf(stderr, "Client died (%d connected)\n", n_clients);
-      queue_abort(cur, client->s);
-
-      close(client->s);
-      free(client);
-
-      pthread_exit(NULL);
-    }
-
-  }
-  return 0;
-}
-
-void done (int code) {
-  close(s);
-  exit(code);
-}
-
-
-
-int main (int argc, char *argv[]) {
-  struct sockaddr_in sin, from;
-  int g;
-  socklen_t len;
-  struct clientinfo *client;
-  int port;
-  int opt;
-  int errors = 0;
-  int argi;
-  char *key = NULL, *client_key;
-  int use_key = 0;
-  /* the key stuff here doesn't provide any
-  real measure of security, it's mainly to keep
-  jobs from bumping into each other.  */
-
-  pthread_t tid;
-  port = DEFAULT_PORT;
-
-  for (argi=1; argi < argc; argi++){
-    if (strcmp(argv[argi], "-m")==0){
-      expect_multiline_output = 1;
-    } else if (strcmp(argv[argi], "-k")==0){
-      argi++;
-      if (argi == argc){
-      	fprintf(stderr, "Key must be specified after -k\n");
-      	exit(1);
-      }
-      key = argv[argi];
-      use_key = 1;
-    } else if (strcmp(argv[argi], "--stay-alive")==0){
-      stay_alive = 1;    /* dont panic and die with zero clients */
-    } else {
-      port = atoi(argv[argi]);
-    }
-  }
-
-  /* Initialize data structures */
-  head = NULL;
-  ptail = &head;
-
-  /* Set up listener */
-  s = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP);
-  opt = 1;
-  setsockopt(s, SOL_SOCKET, SO_REUSEADDR, &opt, sizeof(opt));
-
-  sin.sin_family = AF_INET;
-  sin.sin_addr.s_addr = htonl(INADDR_ANY);
-  sin.sin_port = htons(port);
-  while (bind(s, (struct sockaddr *) &sin, sizeof(sin)) < 0) {
-	perror("bind()");
-	sleep(1);
-	errors++;
-	if (errors > 100)
-	  exit(1);
-  }
-
-  len = sizeof(sin);
-  getsockname(s, (struct sockaddr *) &sin, &len);
-
-  fprintf(stderr, "Listening on port %hu\n", ntohs(sin.sin_port));
-
-  while (listen(s, MAX_CLIENTS) < 0) {
-	perror("listen()");
-	sleep(1);
-	errors++;
-	if (errors > 100)
-	  exit(1);
-  }
-
-  for (;;) {
-    len = sizeof(from);
-    g = accept(s, (struct sockaddr *)&from, &len);
-    if (g < 0) {
-      perror("accept()");
-      sleep(1);
-      continue;
-    }
-    client = malloc(sizeof(struct clientinfo));
-    client->s = g;
-    bcopy(&from, &client->sin, len);
-
-	if (use_key){
-		fd_set set;
-		FD_ZERO(&set);
-		FD_SET(client->s, &set);
-
-		struct timeval timeout;
-		timeout.tv_sec = 3; // number of seconds for timeout
-		timeout.tv_usec = 0;
-
-		int ready = select(FD_SETSIZE, &set, NULL, NULL, &timeout);
-		if (ready<1){
-			fprintf(stderr, "Prospective client failed to respond with correct key.\n");
-			close(client->s);
-			free(client);
-		} else {
-			client_key = read_line(client->s,0);
-			client_key[strlen(client_key)-1]='\0'; /* chop trailing newline */
-			if (strcmp(key, client_key)==0){
-				pthread_create(&tid, NULL, new_client, client);
-			} else {
-				fprintf(stderr, "Prospective client failed to respond with correct key.\n");
-				close(client->s);
-				free(client);
-			}
-			free(client_key);
-		}
-	} else {
-		pthread_create(&tid, NULL, new_client, client);
-	}
-  }
-
-}
-
-
-
diff --git a/dpmert/sentserver.h b/dpmert/sentserver.h
deleted file mode 100644
index cd17a546..00000000
--- a/dpmert/sentserver.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef SENTSERVER_H
-#define SENTSERVER_H
-
-#define DEFAULT_PORT 50000
-
-#endif
diff --git a/dpmert/test_aer/README b/dpmert/test_aer/README
deleted file mode 100644
index 819b2e32..00000000
--- a/dpmert/test_aer/README
+++ /dev/null
@@ -1,8 +0,0 @@
-To run the test:
-
-../dist-vest.pl --local --metric aer cdec.ini --source-file corpus.src --ref-files=ref.0 --weights weights
-
-This will optimize the parameters of the tiny lexical translation model
-so as to minimize the AER of the Viterbi alignment on the development
-set in corpus.src according to the reference alignments in ref.0.
-
diff --git a/dpmert/test_aer/cdec.ini b/dpmert/test_aer/cdec.ini
deleted file mode 100644
index 08187848..00000000
--- a/dpmert/test_aer/cdec.ini
+++ /dev/null
@@ -1,3 +0,0 @@
-formalism=lextrans
-grammar=grammar
-aligner=true
diff --git a/dpmert/test_aer/corpus.src b/dpmert/test_aer/corpus.src
deleted file mode 100644
index 31b23971..00000000
--- a/dpmert/test_aer/corpus.src
+++ /dev/null
@@ -1,3 +0,0 @@
-el gato negro ||| the black cat
-el gato ||| the cat
-el libro ||| the book
diff --git a/dpmert/test_aer/grammar b/dpmert/test_aer/grammar
deleted file mode 100644
index 9d857824..00000000
--- a/dpmert/test_aer/grammar
+++ /dev/null
@@ -1,12 +0,0 @@
-el ||| cat ||| F1=1
-el ||| the ||| F2=1
-el ||| black ||| F3=1
-el ||| book ||| F11=1
-gato ||| cat ||| F4=1 NN=1
-gato ||| black ||| F5=1
-gato ||| the ||| F6=1
-negro ||| the ||| F7=1
-negro ||| cat ||| F8=1
-negro ||| black ||| F9=1
-libro ||| the ||| F10=1
-libro ||| book ||| F12=1 NN=1
diff --git a/dpmert/test_aer/ref.0 b/dpmert/test_aer/ref.0
deleted file mode 100644
index 734a9c5b..00000000
--- a/dpmert/test_aer/ref.0
+++ /dev/null
@@ -1,3 +0,0 @@
-0-0 1-2 2-1
-0-0 1-1
-0-0 1-1
diff --git a/dpmert/test_aer/weights b/dpmert/test_aer/weights
deleted file mode 100644
index afc9282e..00000000
--- a/dpmert/test_aer/weights
+++ /dev/null
@@ -1,13 +0,0 @@
-F1 0.1
-F2 -.5980815
-F3 0.24235
-F4 0.625
-F5 0.4514
-F6 0.112316
-F7 -0.123415
-F8 -0.25390285
-F9 -0.23852
-F10 0.646
-F11 0.413141
-F12 0.343216
-NN -0.1215
diff --git a/dpmert/test_data/0.json.gz b/dpmert/test_data/0.json.gz
deleted file mode 100644
index 30f8dd77..00000000
--- a/dpmert/test_data/0.json.gz
+++ /dev/null
diff --git a/dpmert/test_data/1.json.gz b/dpmert/test_data/1.json.gz
deleted file mode 100644
index c82cc179..00000000
--- a/dpmert/test_data/1.json.gz
+++ /dev/null
diff --git a/dpmert/test_data/c2e.txt.0 b/dpmert/test_data/c2e.txt.0
deleted file mode 100644
index 12c4abe9..00000000
--- a/dpmert/test_data/c2e.txt.0
+++ /dev/null
@@ -1,2 +0,0 @@
-australia reopens embassy in manila
-( afp , manila , january 2 ) australia reopened its embassy in the philippines today , which was shut down about seven weeks ago due to what was described as a specific threat of a terrorist attack .
diff --git a/dpmert/test_data/c2e.txt.1 b/dpmert/test_data/c2e.txt.1
deleted file mode 100644
index 4ac12df1..00000000
--- a/dpmert/test_data/c2e.txt.1
+++ /dev/null
@@ -1,2 +0,0 @@
-australia reopened manila embassy
-( agence france-presse , manila , 2nd ) - australia reopened its embassy in the philippines today . the embassy was closed seven weeks ago after what was described as a specific threat of a terrorist attack .
diff --git a/dpmert/test_data/c2e.txt.2 b/dpmert/test_data/c2e.txt.2
deleted file mode 100644
index 2f67b72f..00000000
--- a/dpmert/test_data/c2e.txt.2
+++ /dev/null
@@ -1,2 +0,0 @@
-australia to reopen embassy in manila
-( afp report from manila , january 2 ) australia reopened its embassy in the philippines today . seven weeks ago , the embassy was shut down due to so-called confirmed terrorist attack threats .
diff --git a/dpmert/test_data/c2e.txt.3 b/dpmert/test_data/c2e.txt.3
deleted file mode 100644
index 5483cef6..00000000
--- a/dpmert/test_data/c2e.txt.3
+++ /dev/null
@@ -1,2 +0,0 @@
-australia to re - open its embassy to manila
-( afp , manila , thursday ) australia reopens its embassy to manila , which was closed for the so-called " clear " threat of terrorist attack 7 weeks ago .
diff --git a/dpmert/test_data/re.txt.0 b/dpmert/test_data/re.txt.0
deleted file mode 100644
index 86eff087..00000000
--- a/dpmert/test_data/re.txt.0
+++ /dev/null
@@ -1,5 +0,0 @@
-erdogan states turkey to reject any pressures to urge it to recognize cyprus
-ankara 12 - 1 ( afp ) - turkish prime minister recep tayyip erdogan announced today , wednesday , that ankara will reject any pressure by the european union to urge it to recognize cyprus . this comes two weeks before the summit of european union state and government heads who will decide whether or nor membership negotiations with ankara should be opened .
-erdogan told " ntv " television station that " the european union cannot address us by imposing new conditions on us with regard to cyprus .
-we will discuss this dossier in the course of membership negotiations . "
-he added " let me be clear , i cannot sidestep turkey , this is something we cannot accept . "
diff --git a/dpmert/test_data/re.txt.1 b/dpmert/test_data/re.txt.1
deleted file mode 100644
index 2140f198..00000000
--- a/dpmert/test_data/re.txt.1
+++ /dev/null
@@ -1,5 +0,0 @@
-erdogan confirms turkey will resist any pressure to recognize cyprus
-ankara 12 - 1 ( afp ) - the turkish head of government , recep tayyip erdogan , announced today ( wednesday ) that ankara would resist any pressure the european union might exercise in order to force it into recognizing cyprus . this comes two weeks before a summit of european union heads of state and government , who will decide whether or not to open membership negotiations with ankara .
-erdogan said to the ntv television channel : " the european union cannot engage with us through imposing new conditions on us with regard to cyprus .
-we shall discuss this issue in the course of the membership negotiations . "
-he added : " let me be clear - i cannot confine turkey . this is something we do not accept . "
diff --git a/dpmert/test_data/re.txt.2 b/dpmert/test_data/re.txt.2
deleted file mode 100644
index 94e46286..00000000
--- a/dpmert/test_data/re.txt.2
+++ /dev/null
@@ -1,5 +0,0 @@
-erdogan confirms that turkey will reject any pressures to encourage it to recognize cyprus
-ankara , 12 / 1 ( afp ) - the turkish prime minister recep tayyip erdogan declared today , wednesday , that ankara will reject any pressures that the european union may apply on it to encourage to recognize cyprus . this comes two weeks before a summit of the heads of countries and governments of the european union , who will decide on whether or not to start negotiations on joining with ankara .
-erdogan told the ntv television station that " it is not possible for the european union to talk to us by imposing new conditions on us regarding cyprus .
-we shall discuss this dossier during the negotiations on joining . "
-and he added , " let me be clear . turkey's arm should not be twisted ; this is something we cannot accept . "
diff --git a/dpmert/test_data/re.txt.3 b/dpmert/test_data/re.txt.3
deleted file mode 100644
index f87c3308..00000000
--- a/dpmert/test_data/re.txt.3
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@@ -1,5 +0,0 @@
-erdogan stresses that turkey will reject all pressures to force it to recognize cyprus
-ankara 12 - 1 ( afp ) - turkish prime minister recep tayyip erdogan announced today , wednesday , that ankara would refuse all pressures applied on it by the european union to force it to recognize cyprus . that came two weeks before the summit of the presidents and prime ministers of the european union , who would decide on whether to open negotiations on joining with ankara or not .
-erdogan said to " ntv " tv station that the " european union can not communicate with us by imposing on us new conditions related to cyprus .
-we will discuss this file during the negotiations on joining . "
-he added , " let me be clear . turkey's arm should not be twisted . this is unacceptable to us . "