M mert/TerScorer.cpp

M    mert/BleuScorer.h
M    mert/ScorerFactory.h
M    mert/Scorer.h
M    mert/PerScorer.h
M    mert/TerScorer.h
M    mert/Makefile.am
AM   scripts/training/mert-moses-multi.pl


git-svn-id: https://mosesdecoder.svn.sourceforge.net/svnroot/mosesdecoder/trunk@4299 1f5c12ca-751b-0410-a591-d2e778427230

1 files changed, 1376 insertions, 0 deletions

diff --git a/scripts/training/mert-moses-multi.pl b/scripts/training/mert-moses-multi.pl
new file mode 100755
index 000000000..56ee9a91b
--- /dev/null
+++ b/scripts/training/mert-moses-multi.pl
@@ -0,0 +1,1376 @@
+#!/usr/bin/perl -w 
+# $Id$
+# Usage:
+# mert-moses.pl <foreign> <english> <decoder-executable> <decoder-config>
+# For other options see below or run 'mert-moses.pl --help'
+
+# Notes:
+# <foreign> and <english> should be raw text files, one sentence per line
+# <english> can be a prefix, in which case the files are <english>0, <english>1, etc. are used
+
+# Excerpts from revision history
+
+# Sept 2011   multi-threaded mert (Barry Haddow)
+# 3 Aug 2011  Added random directions, historic best, pairwise ranked (PK)
+# Jul 2011    simplifications (Ondrej Bojar)
+#             -- rely on moses' -show-weights instead of parsing moses.ini 
+#                ... so moses is also run once *before* mert starts, checking
+#                    the model to some extent
+#             -- got rid of the 'triples' mess;
+#                use --range to supply bounds for random starting values:
+#                --range tm:-3..3 --range lm:-3..3
+# 5 Aug 2009  Handling with different reference length policies (shortest, average, closest) for BLEU 
+#             and case-sensistive/insensitive evaluation (Nicola Bertoldi)
+# 5 Jun 2008  Forked previous version to support new mert implementation.
+# 13 Feb 2007 Better handling of default values for lambda, now works with multiple
+#             models and lexicalized reordering
+# 11 Oct 2006 Handle different input types through parameter --inputype=[0|1]
+#             (0 for text, 1 for confusion network, default is 0) (Nicola Bertoldi)
+# 10 Oct 2006 Allow skip of filtering of phrase tables (--no-filter-phrase-table)
+#             useful if binary phrase tables are used (Nicola Bertoldi)
+# 28 Aug 2006 Use either closest or average or shortest (default) reference
+#             length as effective reference length
+#             Use either normalization or not (default) of texts (Nicola Bertoldi)
+# 31 Jul 2006 move gzip run*.out to avoid failure wit restartings
+#             adding default paths
+# 29 Jul 2006 run-filter, score-nbest and mert run on the queue (Nicola; Ondrej had to type it in again)
+# 28 Jul 2006 attempt at foolproof usage, strong checking of input validity, merged the parallel and nonparallel version (Ondrej Bojar)
+# 27 Jul 2006 adding the safesystem() function to handle with process failure
+# 22 Jul 2006 fixed a bug about handling relative path of configuration file (Nicola Bertoldi) 
+# 21 Jul 2006 adapted for Moses-in-parallel (Nicola Bertoldi) 
+# 18 Jul 2006 adapted for Moses and cleaned up (PK)
+# 21 Jan 2005 unified various versions, thorough cleanup (DWC)
+#             now indexing accumulated n-best list solely by feature vectors
+# 14 Dec 2004 reimplemented find_threshold_points in C (NMD)
+# 25 Oct 2004 Use either average or shortest (default) reference
+#             length as effective reference length (DWC)
+# 13 Oct 2004 Use alternative decoders (DWC)
+# Original version by Philipp Koehn
+
+use FindBin qw($Bin);
+use File::Basename;
+use File::Path;
+my $SCRIPTS_ROOTDIR = $Bin;
+$SCRIPTS_ROOTDIR =~ s/\/training$//;
+$SCRIPTS_ROOTDIR = $ENV{"SCRIPTS_ROOTDIR"} if defined($ENV{"SCRIPTS_ROOTDIR"});
+
+## We preserve this bit of comments to keep the traditional weight ranges.
+#     "w" => [ [ 0.0, -1.0, 1.0 ] ],  # word penalty
+#     "d"  => [ [ 1.0, 0.0, 2.0 ] ],  # lexicalized reordering model
+#     "lm" => [ [ 1.0, 0.0, 2.0 ] ],  # language model
+#     "g"  => [ [ 1.0, 0.0, 2.0 ],    # generation model
+# 	      [ 1.0, 0.0, 2.0 ] ],
+#     "tm" => [ [ 0.3, 0.0, 0.5 ],    # translation model
+# 	      [ 0.2, 0.0, 0.5 ],
+# 	      [ 0.3, 0.0, 0.5 ],
+# 	      [ 0.2, 0.0, 0.5 ],
+# 	      [ 0.0,-1.0, 1.0 ] ],  # ... last weight is phrase penalty
+#     "lex"=> [ [ 0.1, 0.0, 0.2 ] ],  # global lexical model
+#     "I"  => [ [ 0.0,-1.0, 1.0 ] ],  # input lattice scores
+
+
+
+# moses.ini file uses FULL names for lambdas, while this training script
+# internally (and on the command line) uses ABBR names.
+my @ABBR_FULL_MAP = qw(d=weight-d lm=weight-l tm=weight-t w=weight-w
+  g=weight-generation lex=weight-lex I=weight-i);
+my %ABBR2FULL = map {split/=/,$_,2} @ABBR_FULL_MAP;
+my %FULL2ABBR = map {my ($a, $b) = split/=/,$_,2; ($b, $a);} @ABBR_FULL_MAP;
+
+my $minimum_required_change_in_weights = 0.00001;
+    # stop if no lambda changes more than this
+
+my $verbose = 0;
+my $usage = 0; # request for --help
+my $___WORKING_DIR = "mert-work";
+my $___DEV_F = undef; # required, input text to decode
+my $___DEV_E = undef; # required, basename of files with references
+my $___DECODER = undef; # required, pathname to the decoder executable
+my $___CONFIG = undef; # required, pathname to startup ini file
+my $___N_BEST_LIST_SIZE = 100;
+my $queue_flags = "-hard";  # extra parameters for parallelizer
+      # the -l ws0ssmt was relevant only to JHU 2006 workshop
+my $___JOBS = undef; # if parallel, number of jobs to use (undef or 0 -> serial)
+my $___DECODER_FLAGS = ""; # additional parametrs to pass to the decoder
+my $continue = 0; # should we try to continue from the last saved step?
+my $skip_decoder = 0; # and should we skip the first decoder run (assuming we got interrupted during mert)
+my $___FILTER_PHRASE_TABLE = 1; # filter phrase table
+my $___PREDICTABLE_SEEDS = 0;
+my $___START_WITH_HISTORIC_BESTS = 0; # use best settings from all previous iterations as starting points [Foster&Kuhn,2009]
+my $___RANDOM_DIRECTIONS = 0; # search in random directions only
+my $___NUM_RANDOM_DIRECTIONS = 0; # number of random directions, also works with default optimizer [Cer&al.,2008]
+my $___PAIRWISE_RANKED_OPTIMIZER = 0; # use Hopkins&May[2011]
+my $___PRO_STARTING_POINT = 0; # get a starting point from pairwise ranked optimizer
+my $___RANDOM_RESTARTS = 20;
+my $___HISTORIC_INTERPOLATION = 0; # interpolate optimize weights with previous iteration's weights [Hopkins&May,2011,5.4.3]
+my $__THREADS = 0;
+
+# Parameter for effective reference length when computing BLEU score
+# Default is to use shortest reference
+# Use "--shortest" to use shortest reference length
+# Use "--average" to use average reference length
+# Use "--closest" to use closest reference length
+# Only one between --shortest, --average and --closest can be set
+# If more than one choice the defualt (--shortest) is used
+my $___SHORTEST = 0;
+my $___AVERAGE = 0;
+my $___CLOSEST = 0;
+
+# Use "--nocase" to compute case-insensitive scores
+my $___NOCASE = 0;
+
+# Use "--nonorm" to non normalize translation before computing scores
+my $___NONORM = 0;
+
+# set 0 if input type is text, set 1 if input type is confusion network
+my $___INPUTTYPE = 0; 
+
+
+my $mertdir = undef; # path to new mert directory
+my $mertargs = undef; # args to pass through to mert & extractor
+my $mertmertargs = undef; # args to pass through to mert only
+my $filtercmd = undef; # path to filter-model-given-input.pl
+my $filterfile = undef;
+my $qsubwrapper = undef;
+my $moses_parallel_cmd = undef;
+my $scorer_config = "BLEU:1";
+my $old_sge = 0; # assume sge<6.0
+my $___CONFIG_ORIG = undef; # pathname to startup ini file before filtering
+my $___ACTIVATE_FEATURES = undef; # comma-separated (or blank-separated) list of features to work on 
+                                  # if undef work on all features
+                                  # (others are fixed to the starting values)
+my $___RANGES = undef;
+my $prev_aggregate_nbl_size = -1; # number of previous step to consider when loading data (default =-1)
+                                  # -1 means all previous, i.e. from iteration 1
+                                  # 0 means no previous data, i.e. from actual iteration
+                                  # 1 means 1 previous data , i.e. from the actual iteration and from the previous one
+                                  # and so on 
+my $maximum_iterations = 25;
+
+use strict;
+use Getopt::Long;
+GetOptions(
+  "working-dir=s" => \$___WORKING_DIR,
+  "input=s" => \$___DEV_F,
+  "inputtype=i" => \$___INPUTTYPE,
+  "refs=s" => \$___DEV_E,
+  "decoder=s" => \$___DECODER,
+  "config=s" => \$___CONFIG,
+  "nbest=i" => \$___N_BEST_LIST_SIZE,
+  "queue-flags=s" => \$queue_flags,
+  "jobs=i" => \$___JOBS,
+  "decoder-flags=s" => \$___DECODER_FLAGS,
+  "continue" => \$continue,
+  "skip-decoder" => \$skip_decoder,
+  "shortest" => \$___SHORTEST,
+  "average" => \$___AVERAGE,
+  "closest" => \$___CLOSEST,
+  "nocase" => \$___NOCASE,
+  "nonorm" => \$___NONORM,
+  "help" => \$usage,
+  "verbose" => \$verbose,
+  "mertdir=s" => \$mertdir,
+  "mertargs=s" => \$mertargs,
+  "mertmertargs=s" => \$mertmertargs,
+  "rootdir=s" => \$SCRIPTS_ROOTDIR,
+  "filtercmd=s" => \$filtercmd, # allow to override the default location
+  "filterfile=s" => \$filterfile, # input to filtering script (useful for lattices/confnets)
+  "qsubwrapper=s" => \$qsubwrapper, # allow to override the default location
+  "mosesparallelcmd=s" => \$moses_parallel_cmd, # allow to override the default location
+  "old-sge" => \$old_sge, #passed to moses-parallel
+  "filter-phrase-table!" => \$___FILTER_PHRASE_TABLE, # (dis)allow of phrase tables
+  "predictable-seeds" => \$___PREDICTABLE_SEEDS, # make random restarts deterministic
+  "historic-bests" => \$___START_WITH_HISTORIC_BESTS, # use best settings from all previous iterations as starting points
+  "random-directions" => \$___RANDOM_DIRECTIONS, # search only in random directions
+  "number-of-random-directions=i" => \$___NUM_RANDOM_DIRECTIONS, # number of random directions
+  "random-restarts=i" => \$___RANDOM_RESTARTS, # number of random restarts
+  "activate-features=s" => \$___ACTIVATE_FEATURES, #comma-separated (or blank-separated) list of features to work on (others are fixed to the starting values)
+  "range=s@" => \$___RANGES,
+  "prev-aggregate-nbestlist=i" => \$prev_aggregate_nbl_size, #number of previous step to consider when loading data (default =-1, i.e. all previous)
+  "maximum-iterations=i" => \$maximum_iterations,
+  "pairwise-ranked" => \$___PAIRWISE_RANKED_OPTIMIZER,
+  "pro-starting-point" => \$___PRO_STARTING_POINT,
+  "historic-interpolation=f" => \$___HISTORIC_INTERPOLATION,
+  "threads=i" => \$__THREADS,
+  "sc-config=s" => \$scorer_config
+) or exit(1);
+
+# the 4 required parameters can be supplied on the command line directly
+# or using the --options
+if (scalar @ARGV == 4) {
+  # required parameters: input_file references_basename decoder_executable
+  $___DEV_F = shift;
+  $___DEV_E = shift;
+  $___DECODER = shift;
+  $___CONFIG = shift;
+}
+
+if ($usage || !defined $___DEV_F || !defined $___DEV_E || !defined $___DECODER || !defined $___CONFIG) {
+  print STDERR "usage: $0 input-text references decoder-executable decoder.ini
+Options:
+  --working-dir=mert-dir ... where all the files are created
+  --nbest=100            ... how big nbestlist to generate
+  --jobs=N               ... set this to anything to run moses in parallel
+  --mosesparallelcmd=STR ... use a different script instead of moses-parallel
+  --queue-flags=STRING   ... anything you with to pass to qsub, eg.
+                             '-l ws06osssmt=true'. The default is: '-hard'
+                             To reset the parameters, please use 
+                             --queue-flags=' '
+                             (i.e. a space between the quotes).
+  --decoder-flags=STRING ... extra parameters for the decoder
+  --continue             ... continue from the last successful iteration
+  --skip-decoder         ... skip the decoder run for the first time,
+                             assuming that we got interrupted during
+                             optimization
+  --shortest --average --closest
+                         ... Use shortest/average/closest reference length
+                             as effective reference length (mutually exclusive)
+  --nocase               ... Do not preserve case information; i.e.
+                             case-insensitive evaluation (default is false).
+  --nonorm               ... Do not use text normalization (flag is not active,
+                             i.e. text is NOT normalized)
+  --filtercmd=STRING     ... path to filter-model-given-input.pl
+  --filterfile=STRING    ... path to alternative to input-text for filtering
+                             model. useful for lattice decoding
+  --rootdir=STRING       ... where do helpers reside (if not given explicitly)
+  --mertdir=STRING       ... path to new mert implementation
+  --mertargs=STRING      ... extra args for mert, eg. to specify scorer
+  --mertmertargs=STRING  ... extra args for mert only, 
+  --scorenbestcmd=STRING ... path to score-nbest.py
+  --old-sge              ... passed to parallelizers, assume Grid Engine < 6.0
+  --inputtype=[0|1|2]    ... Handle different input types: (0 for text,
+                             1 for confusion network, 2 for lattices,
+                             default is 0)
+  --no-filter-phrase-table ... disallow filtering of phrase tables
+                              (useful if binary phrase tables are available)
+  --random-restarts=INT  ... number of random restarts (default: 20)
+  --predictable-seeds    ... provide predictable seeds to mert so that random
+                             restarts are the same on every run
+  --range=tm:0..1,-1..1  ... specify min and max value for some features
+                             --range can be repeated as needed.
+                             The order of the various --range specifications
+                             is important only within a feature name.
+                             E.g.:
+                               --range=tm:0..1,-1..1 --range=tm:0..2
+                             is identical to:
+                               --range=tm:0..1,-1..1,0..2
+                             but not to:
+                               --range=tm:0..2 --range=tm:0..1,-1..1 
+  --activate-features=STRING  ... comma-separated list of features to optimize,
+                                  others are fixed to the starting values
+                                  default: optimize all features
+                                  example: tm_0,tm_4,d_0
+  --prev-aggregate-nbestlist=INT ... number of previous step to consider when
+                                     loading data (default = $prev_aggregate_nbl_size)
+                                    -1 means all previous, i.e. from iteration 1
+                                     0 means no previous data, i.e. only the
+                                       current iteration
+                                     N means this and N previous iterations
+
+  --maximum-iterations=ITERS ... Maximum number of iterations. Default: $maximum_iterations
+  --random-directions               ... search only in random directions
+  --number-of-random-directions=int ... number of random directions
+                                        (also works with regular optimizer, default: 0)
+  --pairwise-ranked         ... Use PRO for optimisation (Hopkins and May, emnlp 2011)
+  --pro-starting-point      ... Use PRO to get a starting point for MERT
+  --threads=NUMBER          ... Use multi-threaded mert (must be compiled in).
+  --historic-interpolation  ... Interpolate optimized weights with prior iterations' weight
+                                (parameter sets factor [0;1] given to current weights)
+  --sc-config=STRING     ... extra option to specify multiscoring.
+";
+  exit 1;
+}
+
+
+# Check validity of input parameters and set defaults if needed
+
+print STDERR "Using WORKING_DIR: $___WORKING_DIR\n";
+print STDERR "Using SCRIPTS_ROOTDIR: $SCRIPTS_ROOTDIR\n";
+
+# path of script for filtering phrase tables and running the decoder
+$filtercmd="$SCRIPTS_ROOTDIR/training/filter-model-given-input.pl" if !defined $filtercmd;
+
+if ( ! -x $filtercmd && ! $___FILTER_PHRASE_TABLE) {
+  print STDERR "Filtering command not found: $filtercmd.\n";
+  print STDERR "Use --filtercmd=PATH to specify a valid one or --no-filter-phrase-table\n";
+  exit 1;
+}
+
+$qsubwrapper="$SCRIPTS_ROOTDIR/generic/qsub-wrapper.pl" if !defined $qsubwrapper;
+
+$moses_parallel_cmd = "$SCRIPTS_ROOTDIR/generic/moses-parallel.pl"
+  if !defined $moses_parallel_cmd;
+
+if (!defined $mertdir) {
+  $mertdir = "$SCRIPTS_ROOTDIR/../mert";
+  print STDERR "Assuming --mertdir=$mertdir\n";
+}
+
+my $mert_extract_cmd = "$mertdir/extractor";
+my $mert_mert_cmd = "$mertdir/mert";
+
+die "Not executable: $mert_extract_cmd" if ! -x $mert_extract_cmd;
+die "Not executable: $mert_mert_cmd" if ! -x $mert_mert_cmd;
+
+my $pro_optimizer = "$mertdir/megam_i686.opt"; # or set to your installation
+if (($___PAIRWISE_RANKED_OPTIMIZER || $___PRO_STARTING_POINT) && ! -x $pro_optimizer) {
+  print "did not find $pro_optimizer, installing it in $mertdir\n";
+  `cd $mertdir; wget http://www.cs.utah.edu/~hal/megam/megam_i686.opt.gz;`;
+  `gunzip $pro_optimizer.gz`;
+  `chmod +x $pro_optimizer`;
+  die("ERROR: Installation of megam_i686.opt failed! Install by hand from http://www.cs.utah.edu/~hal/megam/") unless -x $pro_optimizer;
+}
+
+$mertargs = "" if !defined $mertargs;
+
+my $scconfig = undef;
+if ($mertargs =~ /\-\-scconfig\s+(.+?)(\s|$)/){
+  $scconfig=$1;
+  $scconfig =~ s/\,/ /g;
+  $mertargs =~ s/\-\-scconfig\s+(.+?)(\s|$)//;
+}
+
+# handling reference lengh strategy
+if (($___CLOSEST + $___AVERAGE + $___SHORTEST) > 1){
+  die "You can specify just ONE reference length strategy (closest or shortest or average) not both\n";
+}
+
+if ($___SHORTEST){
+  $scconfig .= " reflen:shortest";
+}elsif ($___AVERAGE){
+  $scconfig .= " reflen:average";
+}elsif ($___CLOSEST){
+  $scconfig .= " reflen:closest";
+}
+
+# handling case-insensitive flag
+if ($___NOCASE) {
+  $scconfig .= " case:false";
+}else{
+  $scconfig .= " case:true";
+}
+$scconfig =~ s/^\s+//;
+$scconfig =~ s/\s+$//;
+$scconfig =~ s/\s+/,/g;
+
+$scconfig = "--scconfig $scconfig" if ($scconfig);
+
+my $mert_extract_args=$mertargs;
+$mert_extract_args .=" $scconfig";
+
+$mertmertargs = "" if !defined $mertmertargs;
+
+my $mert_mert_args="$mertargs $mertmertargs";
+$mert_mert_args =~ s/\-+(binary|b)\b//;
+$mert_mert_args .=" $scconfig";
+if ($___ACTIVATE_FEATURES){ $mert_mert_args .=" -o \"$___ACTIVATE_FEATURES\""; }
+
+my ($just_cmd_filtercmd,$x) = split(/ /,$filtercmd);
+die "Not executable: $just_cmd_filtercmd" if ! -x $just_cmd_filtercmd;
+die "Not executable: $moses_parallel_cmd" if defined $___JOBS && ! -x $moses_parallel_cmd;
+die "Not executable: $qsubwrapper" if defined $___JOBS && ! -x $qsubwrapper;
+die "Not executable: $___DECODER" if ! -x $___DECODER;
+
+my $input_abs = ensure_full_path($___DEV_F);
+die "File not found: $___DEV_F (interpreted as $input_abs)."
+  if ! -e $input_abs;
+$___DEV_F = $input_abs;
+
+# Option to pass to qsubwrapper and moses-parallel
+my $pass_old_sge = $old_sge ? "-old-sge" : "";
+
+my $decoder_abs = ensure_full_path($___DECODER);
+die "File not executable: $___DECODER (interpreted as $decoder_abs)."
+  if ! -x $decoder_abs;
+$___DECODER = $decoder_abs;
+
+my $ref_abs = ensure_full_path($___DEV_E);
+# check if English dev set (reference translations) exist and store a list of all references
+my @references;
+if (-e $ref_abs) {
+  push @references, $ref_abs;
+}
+else {
+  # if multiple file, get a full list of the files
+    my $part = 0;
+    while (-e $ref_abs.$part) {
+        push @references, $ref_abs.$part;
+        $part++;
+    }
+    die("Reference translations not found: $___DEV_E (interpreted as $ref_abs)") unless $part;
+}
+
+my $config_abs = ensure_full_path($___CONFIG);
+die "File not found: $___CONFIG (interpreted as $config_abs)."
+  if ! -e $config_abs;
+$___CONFIG = $config_abs;
+
+# moses should use our config
+if ($___DECODER_FLAGS =~ /(^|\s)-(config|f) /
+|| $___DECODER_FLAGS =~ /(^|\s)-(ttable-file|t) /
+|| $___DECODER_FLAGS =~ /(^|\s)-(distortion-file) /
+|| $___DECODER_FLAGS =~ /(^|\s)-(generation-file) /
+|| $___DECODER_FLAGS =~ /(^|\s)-(lmodel-file) /
+|| $___DECODER_FLAGS =~ /(^|\s)-(global-lexical-file) /
+) {
+  die "It is forbidden to supply any of -config, -ttable-file, -distortion-file, -generation-file or -lmodel-file in the --decoder-flags.\nPlease use only the --config option to give the config file that lists all the supplementary files.";
+}
+
+# as weights are normalized in the next steps (by cmert)
+# normalize initial LAMBDAs, too
+my $need_to_normalize = 1;
+
+#store current directory and create the working directory (if needed)
+my $cwd = `pawd 2>/dev/null`; 
+if(!$cwd){$cwd = `pwd`;}
+chomp($cwd);
+
+mkpath($___WORKING_DIR);
+
+{
+# open local scope
+
+#chdir to the working directory
+chdir($___WORKING_DIR) or die "Can't chdir to $___WORKING_DIR";
+
+# fixed file names
+my $mert_outfile = "mert.out";
+my $mert_logfile = "mert.log";
+my $weights_in_file = "init.opt";
+my $weights_out_file = "weights.txt";
+
+# set start run
+my $start_run = 1;
+my $bestpoint = undef;
+my $devbleu = undef;
+my $sparse_weights_file = undef;
+
+my $prev_feature_file = undef;
+my $prev_score_file = undef;
+my $prev_init_file = undef;
+
+if ($___FILTER_PHRASE_TABLE) {
+  my $outdir = "filtered";
+  if (-e "$outdir/moses.ini") {
+    print STDERR "Assuming the tables are already filtered, reusing $outdir/moses.ini\n";
+  } 
+  else {
+    # filter the phrase tables with respect to input, use --decoder-flags
+    print STDERR "filtering the phrase tables... ".`date`;
+    my $___FILTER_F  = $___DEV_F;
+    $___FILTER_F = $filterfile if (defined $filterfile);
+    my $cmd = "$filtercmd ./$outdir $___CONFIG $___FILTER_F";
+    &submit_or_exec($cmd,"filterphrases.out","filterphrases.err");
+  }
+
+  # make a backup copy of startup ini filepath
+  $___CONFIG_ORIG = $___CONFIG;
+  # the decoder should now use the filtered model
+  $___CONFIG = "$outdir/moses.ini";
+}
+else{
+  # do not filter phrase tables (useful if binary phrase tables are available)
+  # use the original configuration file
+  $___CONFIG_ORIG = $___CONFIG;
+}
+
+# we run moses to check validity of moses.ini and to obtain all the feature
+# names
+my $featlist = get_featlist_from_moses($___CONFIG);
+$featlist = insert_ranges_to_featlist($featlist, $___RANGES);
+
+# Mark which features are disabled:
+if (defined $___ACTIVATE_FEATURES) {
+  my %enabled = map { ($_, 1) } split /[, ]+/, $___ACTIVATE_FEATURES;
+  my %cnt;
+  for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+    my $name = $featlist->{"names"}->[$i];
+    $cnt{$name} = 0 if !defined $cnt{$name};
+    $featlist->{"enabled"}->[$i] = $enabled{$name."_".$cnt{$name}};
+    $cnt{$name}++;
+  }
+} else {
+  # all enabled
+  for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+    $featlist->{"enabled"}->[$i] = 1;
+  }
+}
+
+print STDERR "MERT starting values and ranges for random generation:\n";
+for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+  my $name = $featlist->{"names"}->[$i];
+  my $val = $featlist->{"values"}->[$i];
+  my $min = $featlist->{"mins"}->[$i];
+  my $max = $featlist->{"maxs"}->[$i];
+  my $enabled = $featlist->{"enabled"}->[$i];
+  printf STDERR "  %5s = %7.3f", $name, $val;
+  if ($enabled) {
+    printf STDERR " (%5.2f .. %5.2f)\n", $min, $max;
+  } else {
+    print STDERR " --- inactive, not optimized ---\n";
+  }
+}
+
+if ($continue) {
+  # getting the last finished step
+  print STDERR "Trying to continue an interrupted optimization.\n";
+  open IN, "finished_step.txt" or die "Failed to find the step number, failed to read finished_step.txt";
+  my $step = <IN>;
+  chomp $step;
+  close IN;
+
+  print STDERR "Last finished step is $step\n";
+
+  # getting the first needed step
+  my $firststep;
+  if ($prev_aggregate_nbl_size==-1){
+    $firststep=1;
+  }
+  else{
+    $firststep=$step-$prev_aggregate_nbl_size+1;
+    $firststep=($firststep>0)?$firststep:1;
+  }
+
+#checking if all needed data are available
+  if ($firststep<=$step){
+    print STDERR "First previous needed data index is $firststep\n";
+    print STDERR "Checking whether all needed data (from step $firststep to step $step) are available\n";
+    
+    for (my $prevstep=$firststep; $prevstep<=$step;$prevstep++){
+      print STDERR "Checking whether data of step $prevstep are available\n";
+      if (! -e "run$prevstep.features.dat"){
+	die "Can't start from step $step, because run$prevstep.features.dat was not found!";
+      }else{
+	if (defined $prev_feature_file){
+	  $prev_feature_file = "${prev_feature_file},run$prevstep.features.dat";
+	}
+	else{
+	  $prev_feature_file = "run$prevstep.features.dat";
+	}
+      }
+      if (! -e "run$prevstep.scores.dat"){
+	die "Can't start from step $step, because run$prevstep.scores.dat was not found!";
+      }else{
+	if (defined $prev_score_file){
+	  $prev_score_file = "${prev_score_file},run$prevstep.scores.dat";
+	}
+	else{
+	  $prev_score_file = "run$prevstep.scores.dat";
+	}
+      }
+      if (! -e "run$prevstep.${weights_in_file}"){
+	die "Can't start from step $step, because run$prevstep.${weights_in_file} was not found!";
+      }else{
+        if (defined $prev_init_file){
+          $prev_init_file = "${prev_init_file},run$prevstep.${weights_in_file}";
+        }
+        else{
+          $prev_init_file = "run$prevstep.${weights_in_file}";
+        }
+      }
+    }
+    if (! -e "run$step.weights.txt"){
+      die "Can't start from step $step, because run$step.weights.txt was not found!";
+    }
+    if (! -e "run$step.$mert_logfile"){
+      die "Can't start from step $step, because run$step.$mert_logfile was not found!";
+    }
+    if (! -e "run$step.best$___N_BEST_LIST_SIZE.out.gz"){
+      die "Can't start from step $step, because run$step.best$___N_BEST_LIST_SIZE.out.gz was not found!";
+    }
+    print STDERR "All needed data are available\n";
+
+    print STDERR "Loading information from last step ($step)\n";
+    my %dummy; # sparse features
+    ($bestpoint,$devbleu) = &get_weights_from_mert("run$step.$mert_outfile","run$step.$mert_logfile",scalar @{$featlist->{"names"}},\%dummy);
+    die "Failed to parse mert.log, missed Best point there."
+      if !defined $bestpoint || !defined $devbleu;
+    print "($step) BEST at $step $bestpoint => $devbleu at ".`date`;
+    my @newweights = split /\s+/, $bestpoint;
+    
+    # Sanity check: order of lambdas must match
+    sanity_check_order_of_lambdas($featlist,
+      "gunzip -c < run$step.best$___N_BEST_LIST_SIZE.out.gz |");
+
+    # update my cache of lambda values
+    $featlist->{"values"} = \@newweights;
+  }
+  else{
+    print STDERR "No previous data are needed\n";
+  }
+
+  $start_run = $step +1;
+}
+
+###### MERT MAIN LOOP
+
+my $run=$start_run-1;
+
+my $oldallsorted = undef;
+my $allsorted = undef;
+
+my $nbest_file=undef;
+
+while(1) {
+  $run++;
+  if ($maximum_iterations && $run > $maximum_iterations) {
+      print "Maximum number of iterations exceeded - stopping\n";
+      last;
+  }
+  # run beamdecoder with option to output nbestlists
+  # the end result should be (1) @NBEST_LIST, a list of lists; (2) @SCORE, a list of lists of lists
+
+  print "run $run start at ".`date`;
+
+  # In case something dies later, we might wish to have a copy
+  create_config($___CONFIG, "./run$run.moses.ini", $featlist, $run, (defined$devbleu?$devbleu:"--not-estimated--"),$sparse_weights_file);
+
+
+  # skip running the decoder if the user wanted
+  if (!$skip_decoder) {
+      print "($run) run decoder to produce n-best lists\n";
+      $nbest_file = run_decoder($featlist, $run, $need_to_normalize);
+      $need_to_normalize = 0;
+      safesystem("gzip -f $nbest_file") or die "Failed to gzip run*out";
+      $nbest_file = $nbest_file.".gz";
+  }
+  else {
+      $nbest_file="run$run.best$___N_BEST_LIST_SIZE.out.gz";
+      print "skipped decoder run $run\n";
+      $skip_decoder = 0;
+      $need_to_normalize = 0;
+  }
+
+  # extract score statistics and features from the nbest lists
+  print STDERR "Scoring the nbestlist.\n";
+
+  my $base_feature_file = "features.dat";
+  my $base_score_file = "scores.dat";
+  my $feature_file = "run$run.${base_feature_file}";
+  my $score_file = "run$run.${base_score_file}";
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
+  my $cmd = "";
+  my $scorer_name;
+  my $scorer_weight;
+  $scorer_config=~s/ //g;
+  my @lists_scorer_config=split(",",$scorer_config);
+  $mert_mert_args=$mert_mert_args." --sctype MERGE ";
+  my $scorer_config_spec;
+  foreach $scorer_config_spec(@lists_scorer_config)
+  {
+#     print STDERR $scorer_config_spec."\n";
+    my @lists_scorer_config_spec=split(":",$scorer_config_spec);
+    $scorer_name=$lists_scorer_config_spec[0];
+    $scorer_weight=$lists_scorer_config_spec[1];
+#     print STDERR $scorer_name."\n";
+#     print STDERR $scorer_weight."\n";
+    $cmd = "$mert_extract_cmd $mert_extract_args --scfile $score_file.$scorer_name --ffile $feature_file.$scorer_name --sctype $scorer_name -r ".join(",", @references)." -n $nbest_file";
+#     print STDERR "LANCEMENT $scorer_name ********************************************\n";
+    &submit_or_exec($cmd,"extract.out.$scorer_name","extract.err.$scorer_name");
+#     print STDERR "FIN $scorer_name ************************************************** \n";
+#   print STDERR "executing $cmd\n";
+
+#   print STDERR "\n";
+#   safesystem("date"); 
+#   print STDERR "\n";
+
+#   if (defined $___JOBS) {
+#     safesystem("$qsubwrapper $pass_old_sge -command='$cmd' -queue-parameter=\"$queue_flags\" -stdout=extract.out.$scorer_name -stderr=extract.err.$scorer_name" )
+#       or die "$scorer_name Failed to submit extraction to queue (via $qsubwrapper)";
+#   } else {
+#     safesystem("$cmd > extract.out.$scorer_name 2> extract.err.$scorer_name") or die "$scorer_name Failed to do extraction of statistics.";
+#   }
+
+#   print FILE "$scorer_name $scorer_weight $score_file.$scorer_name $feature_file.$scorer_name\n";
+  }
+#   print STDERR "CREATION INI\n";
+  my @scorer_content;
+  my $fileIncrement=0;
+  open(FILE,">merge.init") || die ("File creation ERROR : merge.init");
+  foreach $scorer_config_spec(@lists_scorer_config)
+  {
+    my @lists_scorer_config_spec=split(":",$scorer_config_spec);
+    $scorer_name=$lists_scorer_config_spec[0];
+    $scorer_weight=$lists_scorer_config_spec[1];
+    print FILE "$scorer_name $scorer_weight $score_file.$scorer_name $feature_file.$scorer_name\n";
+    my @tmp_content=`/bin/cat $score_file.$scorer_name`;
+    $scorer_content[$fileIncrement] = [ @tmp_content ];
+    if ($fileIncrement==0)
+    {
+	`/bin/cp $feature_file.$scorer_name $feature_file`;
+    }
+    $fileIncrement++;
+  }
+  close(FILE);
+#   print STDERR "\n";
+#   safesystem("date");
+#   print STDERR "\n";
+  
+#   print STDERR "ON  VA RASSEMBLER dans $score_file\n";
+  open(SCOREFILE,">$score_file") || die ("File creation ERROR : $score_file");
+  my $newFileIncrement=0;
+  my $contentIncrement=0;
+  my $contentSize=scalar(@{$scorer_content[0]});
+#   print STDERR "TAILLE : ".$contentSize."|".$fileIncrement."\n";
+  while ($contentIncrement< $contentSize)
+  {
+      my $line="";
+      $newFileIncrement=0;
+      while($newFileIncrement< $fileIncrement)
+      {
+	 if (rindex($scorer_content[$newFileIncrement][$contentIncrement],"BEGIN")<0)
+	 {
+	    $line=$line." ".$scorer_content[$newFileIncrement][$contentIncrement];
+	    chomp($line);
+	 }
+	 else
+	 {
+	    my @split_line_input=split(" ",$scorer_content[$newFileIncrement][$contentIncrement]);
+	    my @split_line=split(" ",$line);
+	    if (scalar(@split_line)>0)
+	    {
+		$split_line_input[3]=$split_line[3]+$split_line_input[3];
+	    }
+	    $line=$split_line_input[0]." ".$split_line_input[1]." ".$split_line_input[2]." ".$split_line_input[3]." MERGE";
+	 }
+	 $newFileIncrement++;
+      }
+      $line=~s/^[ ]+//g;
+      $line=~s/[ ]+$//g;
+      $line=~s/[ ]+/ /g;
+#       print STDERR $line."\n";
+      print SCOREFILE $line."\n";
+      $contentIncrement++;
+  }
+  close(SCOREFILE);
+#   `/bin/cp `
+  
+#   $cmd="$mertdir/mergeWeights -c merge.init -s $score_file -f $feature_file";
+#   print STDERR "executing : $cmd\n";
+
+#   if (defined $___JOBS) {
+#     safesystem("$qsubwrapper $pass_old_sge -command='$cmd' -queue-parameter=\"$queue_flags\" -stdout=mergeWeight.out.MERGE -stderr=mergeWeight.err.MERGE" )
+#       or die "MERGE Failed to submit extraction to queue (via $qsubwrapper)";
+#   } else {
+#     safesystem("$cmd > mergeWeight.out.MERGE 2> mergeWeight.err.MERGE") or die "MERGE Failed to do extraction of statistics.";
+#   }
+
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
+
+#   my $cmd = "$mert_extract_cmd $mert_extract_args --scfile $score_file --ffile $feature_file -r ".join(",", @references)." -n $nbest_file";
+#   &submit_or_exec($cmd,"extract.out","extract.err");
+
+  # Create the initial weights file for mert: init.opt
+
+  my @MIN = @{$featlist->{"mins"}};
+  my @MAX = @{$featlist->{"maxs"}};
+  my @CURR = @{$featlist->{"values"}};
+  my @NAME = @{$featlist->{"names"}};
+  
+  open(OUT,"> $weights_in_file")
+    or die "Can't write $weights_in_file (WD now $___WORKING_DIR)";
+  print OUT join(" ", @CURR)."\n";
+  print OUT join(" ", @MIN)."\n";  # this is where we could pass MINS
+  print OUT join(" ", @MAX)."\n";  # this is where we could pass MAXS
+  close(OUT);
+  # print join(" ", @NAME)."\n";
+  
+  # make a backup copy labelled with this run number
+  safesystem("\\cp -f $weights_in_file run$run.$weights_in_file") or die;
+
+  my $DIM = scalar(@CURR); # number of lambdas
+
+  # run mert
+  $cmd = "$mert_mert_cmd -d $DIM $mert_mert_args";
+  
+  my $mert_settings = " -n $___RANDOM_RESTARTS";
+  if ($___PREDICTABLE_SEEDS) {
+      my $seed = $run * 1000;
+      $mert_settings .= " -r $seed";
+  }
+  if ($___RANDOM_DIRECTIONS) {
+    if ($___NUM_RANDOM_DIRECTIONS == 0) {
+      $mert_settings .= " -m 50";
+    }
+    $mert_settings .= " -t random-direction";
+  }
+  if ($___NUM_RANDOM_DIRECTIONS) {
+    $mert_settings .= " -m $___NUM_RANDOM_DIRECTIONS";
+  }
+  if ($__THREADS) {
+    $mert_settings .= " --threads $__THREADS";
+  }
+
+  my $file_settings = "";
+  if (defined $prev_feature_file) {
+    $file_settings .= " --ffile $prev_feature_file,$feature_file";
+  }
+  else{
+    $file_settings .= " --ffile $feature_file";
+  }
+  if (defined $prev_score_file) {
+    $file_settings .= " --scfile $prev_score_file,$score_file";
+  }
+  else{
+    $file_settings .= " --scfile $score_file";
+  }
+  if ($___START_WITH_HISTORIC_BESTS && defined $prev_init_file) {
+    $file_settings .= " --ifile $prev_init_file,run$run.$weights_in_file";
+  }
+  else{
+    $file_settings .= " --ifile run$run.$weights_in_file";
+  }
+
+  $cmd .= $file_settings;
+
+  # pro optimization
+  if ($___PAIRWISE_RANKED_OPTIMIZER) {
+    $cmd .= " --pro run$run.pro.data ; echo 'not used' > $weights_out_file; $pro_optimizer -fvals -maxi 30 -nobias binary run$run.pro.data";
+    &submit_or_exec($cmd,$mert_outfile,$mert_logfile);
+  }
+  # first pro, then mert
+  elsif ($___PRO_STARTING_POINT) {
+    # run pro...
+    my $pro_cmd = $cmd." --pro run$run.pro.data ; $pro_optimizer -fvals -maxi 30 -nobias binary run$run.pro.data";
+    &submit_or_exec($pro_cmd,"run$run.pro.out","run$run.pro.err");
+    # ... get results ...
+    my %dummy;
+    ($bestpoint,$devbleu) = &get_weights_from_mert("run$run.pro.out","run$run.pro.err",scalar @{$featlist->{"names"}},\%dummy);
+    open(PRO_START,">run$run.init.pro");
+    print PRO_START $bestpoint."\n";
+    close(PRO_START);
+    # ... and run mert
+    $cmd =~ s/(--ifile \S+)/$1,run$run.init.pro/;
+    &submit_or_exec($cmd.$mert_settings,$mert_outfile,$mert_logfile);
+  }
+  # just mert
+  else {
+    &submit_or_exec($cmd.$mert_settings,$mert_outfile,$mert_logfile);
+  }
+
+  die "Optimization failed, file $weights_out_file does not exist or is empty"
+    if ! -s $weights_out_file;
+
+  # backup copies
+  foreach my $extractFiles(`/bin/ls extract.*`)
+  {
+    chomp $extractFiles;
+    safesystem ("\\cp -f $extractFiles run$run.$extractFiles") or die;
+  }
+
+#  safesystem ("\\cp -f extract.err run$run.extract.err") or die;
+#  safesystem ("\\cp -f extract.out run$run.extract.out") or die;
+  safesystem ("\\cp -f $mert_outfile run$run.$mert_outfile") or die;
+  safesystem ("\\cp -f $mert_logfile run$run.$mert_logfile") or die;
+  safesystem ("touch $mert_logfile run$run.$mert_logfile") or die;
+  safesystem ("\\cp -f $weights_out_file run$run.$weights_out_file") or die; # this one is needed for restarts, too
+
+  print "run $run end at ".`date`;
+
+  my %sparse_weights; # sparse features
+  ($bestpoint,$devbleu) = &get_weights_from_mert("run$run.$mert_outfile","run$run.$mert_logfile",scalar @{$featlist->{"names"}},\%sparse_weights);
+
+  die "Failed to parse mert.log, missed Best point there."
+    if !defined $bestpoint || !defined $devbleu;
+
+  print "($run) BEST at $run: $bestpoint => $devbleu at ".`date`;
+
+  # update my cache of lambda values
+  my @newweights = split /\s+/, $bestpoint;
+
+  # interpolate with prior's interation weight, if historic-interpolation is specified
+  if ($___HISTORIC_INTERPOLATION>0 && $run>3) {
+    my %historic_sparse_weights;
+    if (-e "run$run.sparse-weights") {
+      open(SPARSE,"run$run.sparse-weights");
+      while(<SPARSE>) {
+        chop;
+        my ($feature,$weight) = split;
+        $historic_sparse_weights{$feature} = $weight;
+      }
+    }
+    my $prev = $run-1;
+    my @historic_weights = split /\s+/, `cat run$prev.$weights_out_file`;
+    for(my $i=0;$i<scalar(@newweights);$i++) {
+      $newweights[$i] = $___HISTORIC_INTERPOLATION * $newweights[$i] + (1-$___HISTORIC_INTERPOLATION) * $historic_weights[$i];
+    }
+    print "interpolate with ".join(",",@historic_weights)." to ".join(",",@newweights);
+    foreach (keys %sparse_weights) {
+      $sparse_weights{$_} *= $___HISTORIC_INTERPOLATION;
+      #print STDERR "sparse_weights{$_} *= $___HISTORIC_INTERPOLATION -> $sparse_weights{$_}\n";
+    }
+    foreach (keys %historic_sparse_weights) {
+      $sparse_weights{$_} += (1-$___HISTORIC_INTERPOLATION) * $historic_sparse_weights{$_};
+      #print STDERR "sparse_weights{$_} += (1-$___HISTORIC_INTERPOLATION) * $historic_sparse_weights{$_} -> $sparse_weights{$_}\n";
+    }
+  }
+  if ($___HISTORIC_INTERPOLATION>0) {
+    open(WEIGHTS,">run$run.$weights_out_file");
+    print WEIGHTS join(" ",@newweights);
+    close(WEIGHTS);
+  }
+
+  $featlist->{"values"} = \@newweights;
+
+  if (scalar keys %sparse_weights) {
+    $sparse_weights_file = "run".($run+1).".sparse-weights";
+    open(SPARSE,">".$sparse_weights_file);
+    foreach my $feature (keys %sparse_weights) {
+      print SPARSE "$feature $sparse_weights{$feature}\n";
+    }
+    close(SPARSE);
+  }
+
+  ## additional stopping criterion: weights have not changed
+  my $shouldstop = 1;
+  for(my $i=0; $i<@CURR; $i++) {
+    die "Lost weight! mert reported fewer weights (@newweights) than we gave it (@CURR)"
+      if !defined $newweights[$i];
+    if (abs($CURR[$i] - $newweights[$i]) >= $minimum_required_change_in_weights) {
+      $shouldstop = 0;
+      last;
+    }
+  }
+
+  open F, "> finished_step.txt" or die "Can't mark finished step";
+  print F $run."\n";
+  close F;
+
+  if ($shouldstop) {
+    print STDERR "None of the weights changed more than $minimum_required_change_in_weights. Stopping.\n";
+    last;
+  }
+
+  my $firstrun;
+  if ($prev_aggregate_nbl_size==-1){
+    $firstrun=1;
+  }
+  else{
+    $firstrun=$run-$prev_aggregate_nbl_size+1;
+    $firstrun=($firstrun>0)?$firstrun:1;
+  }
+  print "loading data from $firstrun to $run (prev_aggregate_nbl_size=$prev_aggregate_nbl_size)\n";
+  $prev_feature_file = undef;
+  $prev_score_file = undef;
+  $prev_init_file = undef;
+  for (my $i=$firstrun;$i<=$run;$i++){ 
+    if (defined $prev_feature_file){
+      $prev_feature_file = "${prev_feature_file},run${i}.${base_feature_file}";
+    }
+    else{
+      $prev_feature_file = "run${i}.${base_feature_file}";
+    }
+    if (defined $prev_score_file){
+      $prev_score_file = "${prev_score_file},run${i}.${base_score_file}";
+    }
+    else{
+      $prev_score_file = "run${i}.${base_score_file}";
+    }
+    if (defined $prev_init_file){
+      $prev_init_file = "${prev_init_file},run${i}.${weights_in_file}";
+    }
+    else{
+      $prev_init_file = "run${i}.${weights_in_file}";
+    }
+  }
+  print "loading data from $prev_feature_file\n" if defined($prev_feature_file);
+  print "loading data from $prev_score_file\n" if defined($prev_score_file);
+  print "loading data from $prev_init_file\n" if defined($prev_init_file);
+}
+print "Training finished at ".`date`;
+
+if (defined $allsorted){ safesystem ("\\rm -f $allsorted") or die; };
+
+safesystem("\\cp -f $weights_in_file run$run.$weights_in_file") or die;
+safesystem("\\cp -f $mert_logfile run$run.$mert_logfile") or die;
+
+create_config($___CONFIG_ORIG, "./moses.ini", $featlist, $run, $devbleu);
+
+# just to be sure that we have the really last finished step marked
+open F, "> finished_step.txt" or die "Can't mark finished step";
+print F $run."\n";
+close F;
+
+
+#chdir back to the original directory # useless, just to remind we were not there
+chdir($cwd);
+
+} # end of local scope
+
+sub get_weights_from_mert {
+  my ($outfile,$logfile,$weight_count,$sparse_weights) = @_;
+  my ($bestpoint,$devbleu);
+  if ($___PAIRWISE_RANKED_OPTIMIZER || ($___PRO_STARTING_POINT && $logfile =~ /pro/)) {
+    open(IN,$outfile) or die "Can't open $outfile";
+    my (@WEIGHT,$sum);
+    for(my $i=0;$i<$weight_count;$i++) { push @WEIGHT, 0; }
+    while(<IN>) {
+      # regular features
+      if (/^F(\d+) ([\-\.\de]+)/) {
+        $WEIGHT[$1] = $2;
+        $sum += abs($2);
+      }
+      # sparse features
+      elsif(/^(.+_.+) ([\-\.\de]+)/) {
+        $$sparse_weights{$1} = $2;
+      }
+    }
+    $devbleu = "unknown";
+    foreach (@WEIGHT) { $_ /= $sum; }
+    foreach (keys %{$sparse_weights}) { $$sparse_weights{$_} /= $sum; }
+    $bestpoint = join(" ",@WEIGHT);
+    close IN;
+  }
+  else {
+    open(IN,$logfile) or die "Can't open $logfile";
+    while (<IN>) {
+      if (/Best point:\s*([\s\d\.\-e]+?)\s*=> ([\-\d\.]+)/) {
+        $bestpoint = $1;
+        $devbleu = $2;
+        last;
+      }
+    }
+    close IN;
+  }
+  return ($bestpoint,$devbleu);
+}
+
+sub run_decoder {
+    my ($featlist, $run, $need_to_normalize) = @_;
+    my $filename_template = "run%d.best$___N_BEST_LIST_SIZE.out";
+    my $filename = sprintf($filename_template, $run);
+    
+    # user-supplied parameters
+    print "params = $___DECODER_FLAGS\n";
+
+    # parameters to set all model weights (to override moses.ini)
+    my @vals = @{$featlist->{"values"}};
+    if ($need_to_normalize) {
+      print STDERR "Normalizing lambdas: @vals\n";
+      my $totlambda=0;
+      grep($totlambda+=abs($_),@vals);
+      grep($_/=$totlambda,@vals);
+    }
+    # moses now does not seem accept "-tm X -tm Y" but needs "-tm X Y"
+    my %model_weights;
+    for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+      my $name = $featlist->{"names"}->[$i];
+      $model_weights{$name} = "-$name" if !defined $model_weights{$name};
+      $model_weights{$name} .= sprintf " %.6f", $vals[$i];
+    }
+    my $decoder_config = join(" ", values %model_weights);
+    print STDERR "DECODER_CFG = $decoder_config\n";
+    print "decoder_config = $decoder_config\n";
+
+    # run the decoder
+    my $nBest_cmd = "-n-best-size $___N_BEST_LIST_SIZE";
+    my $decoder_cmd;
+
+    if (defined $___JOBS && $___JOBS > 0) {
+      $decoder_cmd = "$moses_parallel_cmd $pass_old_sge -config $___CONFIG -inputtype $___INPUTTYPE -qsub-prefix mert$run -queue-parameters \"$queue_flags\" -decoder-parameters \"$___DECODER_FLAGS $decoder_config\" -n-best-list \"$filename $___N_BEST_LIST_SIZE\" -input-file $___DEV_F -jobs $___JOBS -decoder $___DECODER > run$run.out";
+    } else {
+      $decoder_cmd = "$___DECODER $___DECODER_FLAGS  -config $___CONFIG -inputtype $___INPUTTYPE $decoder_config -n-best-list $filename $___N_BEST_LIST_SIZE -input-file $___DEV_F > run$run.out";
+    }
+
+    safesystem($decoder_cmd) or die "The decoder died. CONFIG WAS $decoder_config \n";
+
+    sanity_check_order_of_lambdas($featlist, $filename);
+    return $filename;
+}
+
+
+sub insert_ranges_to_featlist {
+  my $featlist = shift;
+  my $ranges = shift;
+
+  $ranges = [] if !defined $ranges;
+
+  # first collect the ranges from options
+  my $niceranges;
+  foreach my $range (@$ranges) {
+    my $name = undef;
+    foreach my $namedpair (split /,/, $range) {
+      if ($namedpair =~ /^(.*?):/) {
+        $name = $1;
+        $namedpair =~ s/^.*?://;
+        die "Unrecognized name '$name' in --range=$range"
+          if !defined $ABBR2FULL{$name};
+      }
+      my ($min, $max) = split /\.\./, $namedpair;
+      die "Bad min '$min' in --range=$range" if $min !~ /^-?[0-9.]+$/;
+      die "Bad max '$max' in --range=$range" if $min !~ /^-?[0-9.]+$/;
+      die "No name given in --range=$range" if !defined $name;
+      push @{$niceranges->{$name}}, [$min, $max];
+    }
+  }
+
+  # now populate featlist
+  my $seen = undef;
+  for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+    my $name = $featlist->{"names"}->[$i];
+    $seen->{$name} ++;
+    my $min = 0.0;
+    my $max = 1.0;
+    if (defined $niceranges->{$name}) {
+      my $minmax = shift @{$niceranges->{$name}};
+      ($min, $max) = @$minmax if defined $minmax;
+    }
+    $featlist->{"mins"}->[$i] = $min;
+    $featlist->{"maxs"}->[$i] = $max;
+  }
+  return $featlist;
+}
+
+sub sanity_check_order_of_lambdas {
+  my $featlist = shift;
+  my $filename_or_stream = shift;
+
+  my @expected_lambdas = @{$featlist->{"names"}};
+  my @got = get_order_of_scores_from_nbestlist($filename_or_stream);
+  die "Mismatched lambdas. Decoder returned @got, we expected @expected_lambdas"
+    if "@got" ne "@expected_lambdas";
+}
+    
+
+sub get_featlist_from_moses {
+  # run moses with the given config file and return the list of features and
+  # their initial values
+  my $configfn = shift;
+  my $featlistfn = "./features.list";
+  if (-e $featlistfn) {
+    print STDERR "Using cached features list: $featlistfn\n";
+  } else {
+    print STDERR "Asking moses for feature names and values from $___CONFIG\n";
+    my $cmd = "$___DECODER $___DECODER_FLAGS -config $configfn  -inputtype $___INPUTTYPE -show-weights > $featlistfn";
+    safesystem($cmd) or die "Failed to run moses with the config $configfn";
+  }
+
+  # read feature list
+  my @names = ();
+  my @startvalues = ();
+  open(INI,$featlistfn) or die "Can't read $featlistfn";
+  my $nr = 0;
+  my @errs = ();
+  while (<INI>) {
+    $nr++;
+    chomp;
+    /^(.+) (\S+) (\S+)$/ || die("invalid feature: $_");
+    my ($longname, $feature, $value) = ($1,$2,$3);
+    next if $value eq "sparse";
+    push @errs, "$featlistfn:$nr:Bad initial value of $feature: $value\n"
+      if $value !~ /^[+-]?[0-9.e]+$/;
+    push @errs, "$featlistfn:$nr:Unknown feature '$feature', please add it to \@ABBR_FULL_MAP\n"
+      if !defined $ABBR2FULL{$feature};
+    push @names, $feature;
+    push @startvalues, $value;
+  }
+  close INI;
+  if (scalar @errs) {
+    print STDERR join("", @errs);
+    exit 1;
+  }
+  return {"names"=>\@names, "values"=>\@startvalues};
+}
+
+
+sub get_order_of_scores_from_nbestlist {
+  # read the first line and interpret the ||| label: num num num label2: num ||| column in nbestlist
+  # return the score labels in order
+  my $fname_or_source = shift;
+  # print STDERR "Peeking at the beginning of nbestlist to get order of scores: $fname_or_source\n";
+  open IN, $fname_or_source or die "Failed to get order of scores from nbestlist '$fname_or_source'";
+  my $line = <IN>;
+  close IN;
+  die "Line empty in nbestlist '$fname_or_source'" if !defined $line;
+  my ($sent, $hypo, $scores, $total) = split /\|\|\|/, $line;
+  $scores =~ s/^\s*|\s*$//g;
+  die "No scores in line: $line" if $scores eq "";
+
+  my @order = ();
+  my $label = undef;
+  my $sparse = 0; # we ignore sparse features here
+  foreach my $tok (split /\s+/, $scores) {
+    if ($tok =~ /.+_.+:/) {
+      $sparse = 1;
+    } elsif ($tok =~ /^([a-z][0-9a-z]*):/i) {
+      $label = $1;
+    } elsif ($tok =~ /^-?[-0-9.e]+$/) {
+      if (!$sparse) {
+        # a score found, remember it
+        die "Found a score but no label before it! Bad nbestlist '$fname_or_source'!"
+          if !defined $label;
+        push @order, $label;
+      }
+      $sparse = 0;
+    } else {
+      die "Not a label, not a score '$tok'. Failed to parse the scores string: '$scores' of nbestlist '$fname_or_source'";
+    }
+  }
+  print STDERR "The decoder returns the scores in this order: @order\n";
+  return @order;
+}
+
+sub create_config {
+    my $infn = shift; # source config
+    my $outfn = shift; # where to save the config
+    my $featlist = shift; # the lambdas we should write
+    my $iteration = shift;  # just for verbosity
+    my $bleu_achieved = shift; # just for verbosity
+    my $sparse_weights_file = shift; # only defined when optimizing sparse features
+
+    my %P; # the hash of all parameters we wish to override
+
+    # first convert the command line parameters to the hash
+    { # ensure local scope of vars
+	my $parameter=undef;
+	print "Parsing --decoder-flags: |$___DECODER_FLAGS|\n";
+        $___DECODER_FLAGS =~ s/^\s*|\s*$//;
+        $___DECODER_FLAGS =~ s/\s+/ /;
+	foreach (split(/ /,$___DECODER_FLAGS)) {
+	    if (/^\-([^\d].*)$/) {
+		$parameter = $1;
+		$parameter = $ABBR2FULL{$parameter} if defined($ABBR2FULL{$parameter});
+	    }
+	    else {
+                die "Found value with no -paramname before it: $_"
+                  if !defined $parameter;
+		push @{$P{$parameter}},$_;
+	    }
+	}
+    }
+
+    # First delete all weights params from the input, we're overwriting them.
+    # Delete both short and long-named version.
+    for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+      my $name = $featlist->{"names"}->[$i];
+      delete($P{$name});
+      delete($P{$ABBR2FULL{$name}});
+    }
+
+    # Convert weights to elements in P
+    for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
+      my $name = $featlist->{"names"}->[$i];
+      my $val = $featlist->{"values"}->[$i];
+      $name = defined $ABBR2FULL{$name} ? $ABBR2FULL{$name} : $name;
+        # ensure long name
+      push @{$P{$name}}, $val;
+    }
+
+    if (defined($sparse_weights_file)) {
+      push @{$P{"weights-file"}}, $___WORKING_DIR."/".$sparse_weights_file;
+    }
+
+    # create new moses.ini decoder config file by cloning and overriding the original one
+    open(INI,$infn) or die "Can't read $infn";
+    delete($P{"config"}); # never output 
+    print "Saving new config to: $outfn\n";
+    open(OUT,"> $outfn") or die "Can't write $outfn";
+    print OUT "# MERT optimized configuration\n";
+    print OUT "# decoder $___DECODER\n";
+    print OUT "# BLEU $bleu_achieved on dev $___DEV_F\n";
+    print OUT "# We were before running iteration $iteration\n";
+    print OUT "# finished ".`date`;
+    my $line = <INI>;
+    while(1) {
+	last unless $line;
+
+	# skip until hit [parameter]
+	if ($line !~ /^\[(.+)\]\s*$/) { 
+	    $line = <INI>;
+	    print OUT $line if $line =~ /^\#/ || $line =~ /^\s+$/;
+	    next;
+	}
+
+	# parameter name
+	my $parameter = $1;
+	$parameter = $ABBR2FULL{$parameter} if defined($ABBR2FULL{$parameter});
+	print OUT "[$parameter]\n";
+
+	# change parameter, if new values
+	if (defined($P{$parameter})) {
+	    # write new values
+	    foreach (@{$P{$parameter}}) {
+		print OUT $_."\n";
+	    }
+	    delete($P{$parameter});
+	    # skip until new parameter, only write comments
+	    while($line = <INI>) {
+		print OUT $line if $line =~ /^\#/ || $line =~ /^\s+$/;
+		last if $line =~ /^\[/;
+		last unless $line;
+	    }
+	    next;
+	}
+	
+	# unchanged parameter, write old
+	while($line = <INI>) {
+	    last if $line =~ /^\[/;
+	    print OUT $line;
+	}
+    }
+
+    # write all additional parameters
+    foreach my $parameter (keys %P) {
+	print OUT "\n[$parameter]\n";
+	foreach (@{$P{$parameter}}) {
+	    print OUT $_."\n";
+	}
+    }
+
+    close(INI);
+    close(OUT);
+    print STDERR "Saved: $outfn\n";
+}
+
+sub safesystem {
+  print STDERR "Executing: @_\n";
+  system(@_);
+  if ($? == -1) {
+      print STDERR "Failed to execute: @_\n  $!\n";
+      exit(1);
+  }
+  elsif ($? & 127) {
+      printf STDERR "Execution of: @_\n  died with signal %d, %s coredump\n",
+          ($? & 127),  ($? & 128) ? 'with' : 'without';
+      exit(1);
+  }
+  else {
+    my $exitcode = $? >> 8;
+    print STDERR "Exit code: $exitcode\n" if $exitcode;
+    return ! $exitcode;
+  }
+}
+sub ensure_full_path {
+    my $PATH = shift;
+$PATH =~ s/\/nfsmnt//;
+    return $PATH if $PATH =~ /^\//;
+    my $dir = `pawd 2>/dev/null`; 
+    if(!$dir){$dir = `pwd`;}
+    chomp($dir);
+    $PATH = $dir."/".$PATH;
+    $PATH =~ s/[\r\n]//g;
+    $PATH =~ s/\/\.\//\//g;
+    $PATH =~ s/\/+/\//g;
+    my $sanity = 0;
+    while($PATH =~ /\/\.\.\// && $sanity++<10) {
+        $PATH =~ s/\/+/\//g;
+        $PATH =~ s/\/[^\/]+\/\.\.\//\//g;
+    }
+    $PATH =~ s/\/[^\/]+\/\.\.$//;
+    $PATH =~ s/\/+$//;
+$PATH =~ s/\/nfsmnt//;
+    return $PATH;
+}
+
+sub submit_or_exec {
+  my ($cmd,$stdout,$stderr) = @_;
+  print STDERR "exec: $cmd\n";
+  if (defined $___JOBS && $___JOBS > 0) {
+    safesystem("$qsubwrapper $pass_old_sge -command='$cmd' -queue-parameter=\"$queue_flags\" -stdout=$stdout -stderr=$stderr" )
+      or die "ERROR: Failed to submit '$cmd' (via $qsubwrapper)";
+  } 
+  else {
+    safesystem("$cmd > $stdout 2> $stderr") or die "ERROR: Failed to run '$cmd'.";
+  }
+}