path: root/scripts/training/mert-moses.pl

#!/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 strict;
use FindBin qw($RealBin);
use File::Basename;
use File::Path;
use File::Spec;
use Cwd;

my $SCRIPTS_ROOTDIR = $RealBin;
$SCRIPTS_ROOTDIR =~ s/\/training$//;
$SCRIPTS_ROOTDIR = $ENV{"SCRIPTS_ROOTDIR"} if defined($ENV{"SCRIPTS_ROOTDIR"});

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

# We assume that if you don't specify working directory,
# we set the default is set to `pwd`/mert-work
my $___WORKING_DIR = File::Spec->catfile(Cwd::getcwd(), "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 $___LATTICE_SAMPLES = 0;
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 $___RANDOM_RESTARTS = 20;
my $___RETURN_BEST_DEV = 0; # return the best weights according to dev, not the last

# Flags related to PRO (Hopkins & May, 2011)
my $___PAIRWISE_RANKED_OPTIMIZER = 0; # flag to enable PRO.
my $___PRO_STARTING_POINT = 0; # get a starting point from pairwise ranked optimizer
my $___HISTORIC_INTERPOLATION = 0; # interpolate optimize weights with previous iteration's weights [Hopkins&May,2011,5.4.3]
# MegaM's options for PRO optimization.
# TODO: Should we also add these values to options of this script?
my $megam_default_options = "-fvals -maxi 30 -nobias binary";

# Flags related to Batch MIRA (Cherry & Foster, 2012)
my $___BATCH_MIRA = 0; # flg to enable batch MIRA

# Hypergraph mira 
my $___HG_MIRA = 0;

# Train phrase model mixture weights with PRO (Haddow, NAACL 2012)
my $__PROMIX_TRAINING = undef; # Location of main script (contrib/promix/main.py)
# The phrase tables. These should be gzip text format.
my @__PROMIX_TABLES;
# used to filter output
my $__REMOVE_SEGMENTATION = "$SCRIPTS_ROOTDIR/ems/support/remove-segmentation-markup.perl";

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, set 3 if input type is parse tree
my $___INPUTTYPE;


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 $extractorargs = undef; # args to pass through to extractor only
my $proargs = undef; # args to pass through to pro only

# Args to pass through to batch mira only.  This flags is useful to
# change MIRA's hyperparameters such as regularization parameter C,
# BLEU decay factor, and the number of iterations of MIRA.
my $batch_mira_args = undef;

my $filtercmd = undef; # path to filter-model-given-input.pl
my $filterfile = undef;
my $qsubwrapper = undef;
my $moses_parallel_cmd = undef;
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 $___USE_CONFIG_WEIGHTS_FIRST = 0; # use weights in configuration file for first iteration
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;

# Simulated post-editing
my $___MOSES_SIM_PE = "$SCRIPTS_ROOTDIR/generic/moses_sim_pe.py";
my $___DEV_SYMAL = undef;
my $dev_symal_abs = undef;
my $working_dir_abs = undef;

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,
  "lattice-samples=i" => \$___LATTICE_SAMPLES,
  "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,
  "extractorargs=s" => \$extractorargs,
  "proargs=s" => \$proargs,
  "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
  "return-best-dev" => \$___RETURN_BEST_DEV, # return the best weights according to dev, not the last
  "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,
  "use-config-weights-for-first-run" => \$___USE_CONFIG_WEIGHTS_FIRST, # use the weights in the configuration file when running the decoder for the first time
  "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,
  "batch-mira" => \$___BATCH_MIRA,
  "hg-mira" => \$___HG_MIRA,
  "batch-mira-args=s" => \$batch_mira_args,
  "promix-training=s" => \$__PROMIX_TRAINING,
  "promix-table=s" => \@__PROMIX_TABLES,
  "threads=i" => \$__THREADS,
  "spe-symal=s" => \$___DEV_SYMAL
) 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
  --lattice-samples      ... how many lattice samples (Chatterjee & Cancedda, emnlp 2010)
  --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 both extractor and mert
  --extractorargs=STRING ... extra args for extractor only
  --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
  --return-best-dev          ... Return the weights according to dev bleu, instead of returning
                                 the last iteration
  --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
  --batch-mira              ... Use Batch MIRA for optimisation (Cherry and Foster, NAACL 2012)
  --hg-mira                 ... Use hypergraph MIRA, ie batch mira with hypergraphs instead of kbests.
  --batch-mira-args=STRING  ... args to pass through to batch/hg MIRA. This flag is useful to
                                change MIRA's hyperparameters such as regularization parameter C,
                                BLEU decay factor, and the number of iterations of MIRA.
  --promix-training=STRING  ... PRO-based mixture model training (Haddow, NAACL 2013)
  --promix-tables=STRING    ... Phrase tables for PRO-based mixture model training.
  --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)
  --spe-symal=SYMAL      ... Use simulated post-editing when decoding.
                             (SYMAL aligns input to refs)
";
  exit 1;
}


# Check validity of input parameters and set defaults if needed

print STDERR "Using SCRIPTS_ROOTDIR: $SCRIPTS_ROOTDIR\n";

# path of script for filtering phrase tables and running the decoder
$filtercmd = File::Spec->catfile($SCRIPTS_ROOTDIR, "training", "filter-model-given-input.pl") if !defined $filtercmd;

# WHY ... ! ___FILTER_PHRASE_TABLE ??? This doesn't make sense! [UG]
# if ( ! -x $filtercmd && ! $___FILTER_PHRASE_TABLE) {
if ( ! -x $filtercmd && $___FILTER_PHRASE_TABLE) {
  warn "Filtering command not found: $filtercmd.";
  warn "Use --filtercmd=PATH to specify a valid one or --no-filter-phrase-table";
  exit 1;
}

$qsubwrapper = File::Spec->catfile($SCRIPTS_ROOTDIR, "generic", "qsub-wrapper.pl") if !defined $qsubwrapper;

$moses_parallel_cmd = File::Spec->catfile($SCRIPTS_ROOTDIR, "generic", "moses-parallel.pl")
  if !defined $moses_parallel_cmd;

if (!defined $mertdir) {
  $mertdir = File::Spec->catfile(File::Basename::dirname($SCRIPTS_ROOTDIR), "bin");
  die "mertdir does not exist: $mertdir" if ! -x $mertdir;
  print STDERR "Assuming --mertdir=$mertdir\n";
}

my $mert_extract_cmd = File::Spec->catfile($mertdir, "extractor");
my $mert_mert_cmd    = File::Spec->catfile($mertdir, "mert");
my $mert_pro_cmd     = File::Spec->catfile($mertdir, "pro");
my $mert_mira_cmd    = File::Spec->catfile($mertdir, "kbmira");
my $mert_eval_cmd    = File::Spec->catfile($mertdir, "evaluator");

die "Not executable: $mert_extract_cmd" if ! -x $mert_extract_cmd;
die "Not executable: $mert_mert_cmd"    if ! -x $mert_mert_cmd;
die "Not executable: $mert_pro_cmd"     if ! -x $mert_pro_cmd;
die "Not executable: $mert_mira_cmd"    if ! -x $mert_mira_cmd;
die "Not executable: $mert_eval_cmd"    if ! -x $mert_eval_cmd;

my $pro_optimizer = File::Spec->catfile($mertdir, "megam_i686.opt");  # or set to your installation

if (($___PAIRWISE_RANKED_OPTIMIZER || $___PRO_STARTING_POINT) && ! -x $pro_optimizer) {
  print "Could not find $pro_optimizer, installing it in $mertdir\n";
  my $megam_url = "http://hal3.name/megam";
  if (&is_mac_osx()) {
    die "Error: Sorry for Mac OS X users! Please get the source code of megam and compile by hand. Please see $megam_url for details.";
  }

  `cd $mertdir; wget $megam_url/megam_i686.opt.gz;`;
  `gunzip $pro_optimizer.gz`;
  `chmod +x $pro_optimizer`;
  die("ERROR: Installation of megam_i686.opt failed! Install by hand from $megam_url") unless -x $pro_optimizer;
}

if ($__PROMIX_TRAINING) {
  die "Not executable $__PROMIX_TRAINING" unless -x $__PROMIX_TRAINING;
  die "For promix training, specify the tables using --promix-table arguments" unless @__PROMIX_TABLES;
  die "For mixture model, need at least 2 tables" unless scalar(@__PROMIX_TABLES) > 1;
  
  for my $TABLE (@__PROMIX_TABLES) {
    die "Phrase table $TABLE not found" unless -r $TABLE;
  }
  die "To use promix training, need to specify a filter and binarisation command" unless   $filtercmd =~ /Binarizer/;
}

if (!defined $mertargs) {
  if (defined $batch_mira_args) {
    $mertargs = $batch_mira_args;
  }
  else {
    $mertargs = "";
  }
}

my $scconfig = undef;
if ($mertargs =~ /\-\-scconfig(?:\s+|=)(.+?)(\s|$)/) {
  $scconfig = $1;
  $scconfig =~ s/\,/ /g;
  $mertargs =~ s/\-\-scconfig(?:\s+|=)(.+?)(\s|$)//;
}

my $sctype = "--sctype BLEU";
if ($mertargs =~ /(\-\-sctype(?:\s+|=).+?)(\s|$)/) {
  $sctype = $1;
  $mertargs =~ s/(\-\-sctype(?:\s+|=)+.+?)(\s|$)//;
}


# handling reference lengh strategy
$scconfig .= &setup_reference_length_type();

# handling case-insensitive flag
$scconfig .= &setup_case_config();

$scconfig =~ s/^\s+//;
$scconfig =~ s/\s+$//;
$scconfig =~ s/\s+/,/g;

$scconfig = "--scconfig $scconfig" if ($scconfig);

my $mert_extract_args = "$sctype $scconfig";

$extractorargs = "" unless $extractorargs;
$mert_extract_args .= " $extractorargs";

$mertmertargs = "" if !defined $mertmertargs;

$proargs = "" unless $proargs;

my $mert_mert_args = "$mertargs $mertmertargs";
$mert_mert_args =~ s/\-+(binary|b)\b//;
$mert_mert_args .= "$sctype $scconfig";
if ($___ACTIVATE_FEATURES) {
  $mert_mert_args .= " -o \"$___ACTIVATE_FEATURES\"";
}

my ($just_cmd_filtercmd, $x) = split(/ /, $filtercmd);
die "Not executable: $just_cmd_filtercmd" if $___FILTER_PHRASE_TABLE && ! -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;
  if (! -e $ref_abs . "0" && -e $ref_abs . ".ref0") {
    $ref_abs .= ".ref";
  }
  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.";
}

# Paths needed for simulated post-editing
$working_dir_abs = ensure_full_path($___WORKING_DIR);
if (defined $___DEV_SYMAL) {
   $dev_symal_abs = ensure_full_path($___DEV_SYMAL);
}

# 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 = Cwd::getcwd();

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";
my $finished_step_file = "finished_step.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;
my @allnbests;

# If we're doing promix training, need to make sure the appropriate
# tables are in place
my @_PROMIX_TABLES_BIN;
if ($__PROMIX_TRAINING) {
  print STDERR "Training mixture model using promix\n";
  for (my $i = 0; $i < scalar(@__PROMIX_TABLES); ++$i) {
    # Create filtered, binarised tables
    my $filtered_config = "moses_$i.ini";
    substitute_ttable($___CONFIG, $filtered_config, $__PROMIX_TABLES[$i]); 
    #TODO: Remove reordering table from config, as we don't need to filter
    # and binarise it.
    my $filtered_path = "filtered_$i";
    my $___FILTER_F  = $___DEV_F;
    $___FILTER_F = $filterfile if (defined $filterfile);
    my $cmd = "$filtercmd ./$filtered_path $filtered_config $___FILTER_F";
    &submit_or_exec($cmd, "filterphrases_$i.out", "filterphrases_$i.err");
    push (@_PROMIX_TABLES_BIN,"$filtered_path/phrase-table.0-0.1.1");
  }
}
 
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) {
  $featlist->{"enabled"}    = undef;
  my %enabled = map { ($_, 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 my $fh, '<', $finished_step_file or die "$finished_step_file: $!";
  my $step = <$fh>;
  chomp $step;
  close $fh;

  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
    if (!$___HG_MIRA) {
      sanity_check_order_of_lambdas($featlist,
        "gunzip -c < run$step.best$___N_BEST_LIST_SIZE.out.gz |");
    } else {
      print STDERR "WARN: No sanity check of order of features in hypergraph mira\n";
    }

    # 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;
my $lsamp_file      = undef; # Lattice samples
my $hypergraph_dir  = undef;
my $orig_nbest_file = undef; # replaced if lattice sampling
# For mixture modelling
my @promix_weights;
my $num_mixed_phrase_features;
my $interpolated_config;
my $uninterpolated_config; # backup of config without interpolated ttable

while (1) {
  $run++;
  if ($maximum_iterations && $run > $maximum_iterations) {
    print "Maximum number of iterations exceeded - stopping\n";
    last;
  }
  print "run $run start at ".`date`;

  if ($__PROMIX_TRAINING) {
    # Need to create an ini file for the interpolated phrase table
    if (!@promix_weights) {
      # Create initial weights, distributing evenly between tables
      # total number of weights is 1 less than number of phrase features, multiplied
      # by the number of tables
      $num_mixed_phrase_features = (grep { $_ eq 'tm' } @{$featlist->{"names"}}) - 1;
  
      @promix_weights = (1.0/scalar(@__PROMIX_TABLES)) x 
        ($num_mixed_phrase_features * scalar(@__PROMIX_TABLES));
    }
    
    # backup orig config, so we always add the table into it
    $uninterpolated_config= $___CONFIG unless $uninterpolated_config; 

    # Interpolation
    my $interpolated_phrase_table = "interpolate";
    for my $itable (@_PROMIX_TABLES_BIN) {
      $interpolated_phrase_table .= " 1:$itable";
    }
    
    # Create an ini file for the interpolated phrase table
    $interpolated_config ="moses.interpolated.ini"; 
    substitute_ttable($uninterpolated_config, $interpolated_config, $interpolated_phrase_table, "99");

    # Append the multimodel weights
    open(ITABLE,">>$interpolated_config") || die "Failed to append weights to $interpolated_config";
    print ITABLE "\n";
    print ITABLE "[weight-t-multimodel]\n";
    #for my $feature (0..($num_mixed_phrase_features-1)) {
    #  for my $table (0..(scalar(@__PROMIX_TABLES)-1)) {
    #    print ITABLE $promix_weights[$table * $num_mixed_phrase_features + $feature];
    #    print ITABLE "\n";
    #  }
    #}
    for my $iweight (@promix_weights) {
      print ITABLE $iweight . "\n";
    }

    close ITABLE;

    # the decoder should now use the interpolated model
    $___CONFIG = "$interpolated_config";

  }

  # 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


  # 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);

  # Save dense weights to simplify best dev recovery
  {
    my $densefile = "run$run.dense";
    my @vals = @{$featlist->{"values"}};
    my @names = @{$featlist->{"names"}};
    open my $denseout, '>', $densefile or die "Can't write $densefile (WD now $___WORKING_DIR)";
    for (my $i = 0; $i < scalar(@{$featlist->{"names"}}); $i++) {
        print $denseout "$names[$i]= $vals[$i]\n";
    }
    close $denseout;
  }

  # skip running the decoder if the user wanted
  if (! $skip_decoder) {
    print "($run) run decoder to produce n-best lists\n";
    ($nbest_file, $lsamp_file, $hypergraph_dir) = run_decoder($featlist, $run, $need_to_normalize);
    $need_to_normalize = 0;
    if ($___LATTICE_SAMPLES) {
      my $combined_file = "$nbest_file.comb";
      safesystem("sort -k1,1n $nbest_file $lsamp_file > $combined_file") or
          die("failed to merge nbest and lattice samples");
      safesystem("gzip -f $nbest_file; gzip -f $lsamp_file") or
          die "Failed to gzip nbests and lattice samples";
      $orig_nbest_file = "$nbest_file.gz";
      $orig_nbest_file = "$nbest_file.gz";
      $lsamp_file      = "$lsamp_file.gz";
      $lsamp_file      = "$lsamp_file.gz";
      $nbest_file      = "$combined_file";
    }
    safesystem("gzip -f $nbest_file") or die "Failed to gzip run*out" unless $___HG_MIRA;
    $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 $cmd = "$mert_extract_cmd $mert_extract_args --scfile $score_file --ffile $feature_file -r " . join(",", @references) . " -n $nbest_file";

  if (! $___HG_MIRA) {
    $cmd .= " -d" if $__PROMIX_TRAINING; # Allow duplicates
    # remove segmentation
    $cmd .= " -l $__REMOVE_SEGMENTATION" if  $__PROMIX_TRAINING;
    $cmd = &create_extractor_script($cmd, $___WORKING_DIR);
    &submit_or_exec($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 my $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";
  my $seed_settings = "";
  if ($___PREDICTABLE_SEEDS) {
    my $seed = $run * 1000;
    $seed_settings .= " -r $seed";
  }
  $mert_settings .= $seed_settings;
  if ($___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 $ffiles = "";
  my $scfiles = "";

  if (defined $prev_feature_file) {
    $ffiles = "$prev_feature_file,$feature_file";
  } else{
    $ffiles = "$feature_file";
  }

  if (defined $prev_score_file) {
    $scfiles = "$prev_score_file,$score_file";
  } else{
    $scfiles = "$score_file";
  }

  my $mira_settings = "";
  if (($___BATCH_MIRA || $___HG_MIRA) && $batch_mira_args) {
    $mira_settings .= "$batch_mira_args ";
  }

  #$mira_settings .= " --dense-init run$run.$weights_in_file";
  $mira_settings .= " --dense-init run$run.dense";
  if (-e "run$run.sparse-weights") {
    $mira_settings .= " --sparse-init run$run.sparse-weights";
  }
  my $file_settings = " --ffile $ffiles --scfile $scfiles";
  my $pro_file_settings = "--ffile " . join(" --ffile ", split(/,/, $ffiles)) .
                          " --scfile " .  join(" --scfile ", split(/,/, $scfiles));

  push @allnbests, $nbest_file;
  my $promix_file_settings = 
                          "--scfile " .  join(" --scfile ", split(/,/, $scfiles)) .
                          " --nbest " . join(" --nbest ", @allnbests);

  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;

  my %sparse_weights; # sparse features
  my $pro_optimizer_cmd = "$pro_optimizer $megam_default_options run$run.pro.data";
  if ($___PAIRWISE_RANKED_OPTIMIZER) {  # pro optimization
    $cmd = "$mert_pro_cmd $proargs $seed_settings $pro_file_settings -o run$run.pro.data ; echo 'not used' > $weights_out_file; $pro_optimizer_cmd";
    &submit_or_exec($cmd, $mert_outfile, $mert_logfile);
  } elsif ($___PRO_STARTING_POINT) {  # First, run pro, then mert
    # run pro...
    my $pro_cmd = "$mert_pro_cmd $proargs $seed_settings $pro_file_settings -o run$run.pro.data ; $pro_optimizer_cmd";
    &submit_or_exec($pro_cmd, "run$run.pro.out", "run$run.pro.err");
    # ... get results ...
    ($bestpoint,$devbleu) = &get_weights_from_mert("run$run.pro.out","run$run.pro.err",scalar @{$featlist->{"names"}},\%sparse_weights, \@promix_weights);
    # Get the pro outputs ready for mert. Add the weight ranges,
    # and a weight and range for the single sparse feature
    $cmd =~ s/--ifile (\S+)/--ifile run$run.init.pro/;
    open(MERT_START,$1);
    open(PRO_START,">run$run.init.pro");
    print PRO_START $bestpoint." 1\n";
    my $mert_line = <MERT_START>;
    $mert_line = <MERT_START>;
    chomp $mert_line;
    print PRO_START $mert_line." 0\n";
    $mert_line = <MERT_START>;
    chomp $mert_line;
    print PRO_START $mert_line." 1\n";
    close(PRO_START);

    # Write the sparse weights to file so mert can use them
    open(SPARSE_WEIGHTS,">run$run.merge-weights");
    foreach my $fname (keys %sparse_weights) {
      print SPARSE_WEIGHTS "$fname $sparse_weights{$fname}\n";
    }
    close(SPARSE_WEIGHTS);
    $cmd = $cmd." --sparse-weights run$run.merge-weights";

    # ... and run mert
    $cmd =~ s/(--ifile \S+)/$1,run$run.init.pro/;
    &submit_or_exec($cmd . $mert_settings, $mert_outfile, $mert_logfile);
  } elsif ($___BATCH_MIRA) { # batch MIRA optimization
    safesystem("echo 'not used' > $weights_out_file") or die;
    $cmd = "$mert_mira_cmd $mira_settings $seed_settings $pro_file_settings -o $mert_outfile";
    &submit_or_exec($cmd, "run$run.mira.out", $mert_logfile);
  } elsif ($___HG_MIRA) {
    safesystem("echo 'not used' > $weights_out_file") or die;
    $mira_settings .= " --type hypergraph ";
    $mira_settings .= join(" ", map {"--reference $_"} @references);
    $mira_settings .= " --hgdir $hypergraph_dir ";
    #$mira_settings .= "--verbose "; 
    $cmd = "$mert_mira_cmd $mira_settings $seed_settings -o $mert_outfile";
    &submit_or_exec($cmd, "run$run.mira.out", $mert_logfile);
  } elsif ($__PROMIX_TRAINING) {
    # PRO trained  mixture model
    safesystem("echo 'not used' > $weights_out_file") or die;
    $cmd = "$__PROMIX_TRAINING $promix_file_settings";
    $cmd .= " -t mix ";
    $cmd .= join(" ", map {"-p $_"} @_PROMIX_TABLES_BIN);
    $cmd .= " -i $___DEV_F";
    print "Starting promix optimisation at " . `date`;
    &submit_or_exec($cmd, "$mert_outfile", $mert_logfile);
    print "Finished promix optimisation at " . `date`;
  } else {  # just mert
    &submit_or_exec($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
  if (! $___HG_MIRA) {
    safesystem("\\cp -f extract.err run$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.$weights_out_file") or die; # this one is needed for restarts, too
  if ($__PROMIX_TRAINING) {
    safesystem("\\cp -f $interpolated_config run$run.$interpolated_config") or die;
  }

  print "run $run end at ".`date`;

  ($bestpoint,$devbleu) = &get_weights_from_mert("run$run.$mert_outfile","run$run.$mert_logfile",scalar @{$featlist->{"names"}},\%sparse_weights,\@promix_weights);
  my $merge_weight = 0;
  if ($__PROMIX_TRAINING) {
    print "New mixture weights: " . join(" ", @promix_weights) . "\n";
  }

  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;

  if ($___PRO_STARTING_POINT) {
    $merge_weight = pop @newweights;
  }

  # 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 my $sparse_fh, '<', "run$run.sparse-weights" or die "run$run.sparse-weights: $!";
      while (<$sparse_fh>) {
        chop;
        my ($feature, $weight) = split;
        $historic_sparse_weights{$feature} = $weight;
      }
      close $sparse_fh;
    }
    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 my $weights_fh, '>', "run$run.$weights_out_file" or die "run$run.$weights_out_file: $!";
    print $weights_fh join(" ", @newweights);
    close $weights_fh;
  }

  $featlist->{"values"} = \@newweights;

  if (scalar keys %sparse_weights) {
    $sparse_weights_file = "run" . ($run + 1) . ".sparse-weights";
    open my $sparse_fh, '>', $sparse_weights_file or die "$sparse_weights_file: $!";
    foreach my $feature (keys %sparse_weights) {
      my $sparse_weight = $sparse_weights{$feature};
      if ($___PRO_STARTING_POINT) {
        $sparse_weight *= $merge_weight;
      }
      print $sparse_fh "$feature $sparse_weight\n";
    }
    close $sparse_fh;
  }

  ## 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;
    }
  }

  &save_finished_step($finished_step_file, $run);

  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);
}

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;

if($___RETURN_BEST_DEV) {
  my $bestit=1;
  my $bestbleu=0;
  my $evalout = "eval.out";
  for (my $i = 1; $i < $run; $i++) {
    my $candidate;
    if ($___HG_MIRA) {
      die "File not found: run$i.out" unless -r "run$i.out";
      $candidate = "--candidate run$i.out";
    }
    else {
      die "File not found: run$i.best$___N_BEST_LIST_SIZE.out.gz" unless -r "run$i.best$___N_BEST_LIST_SIZE.out.gz";
      $candidate = "--nbest run$i.best$___N_BEST_LIST_SIZE.out.gz";
    }
    my $cmd = "$mert_eval_cmd --reference " . join(",", @references) . " $mert_extract_args $candidate";
    $cmd .= " -l $__REMOVE_SEGMENTATION" if defined( $__PROMIX_TRAINING);
    safesystem("$cmd 2> /dev/null 1> $evalout");
    open my $fh, '<', $evalout or die "Can't read $evalout : $!";
    my $bleu = <$fh>;
    chomp $bleu;
    if($bleu > $bestbleu) {
      $bestbleu = $bleu;
      $bestit = $i;
    }
    close $fh;
  }
  print "copying weights from best iteration ($bestit, bleu=$bestbleu) to moses.ini\n";
  my $best_sparse_file = undef;
  if(defined $sparse_weights_file) {
      $best_sparse_file = "run$bestit.sparse-weights";
  }
  my $best_featlist = get_featlist_from_file("run$bestit.dense");
  $best_featlist->{"untuneables"} = $featlist->{"untuneables"};
  $best_featlist->{"allcomponentsuntuneable"} = $featlist->{"allcomponentsuntuneable"};
  $best_featlist->{"skippeduntuneablecomponents"} = $featlist->{"skippeduntuneablecomponents"};
  create_config($___CONFIG_ORIG, "./moses.ini", $best_featlist,
                $bestit, $bestbleu, $best_sparse_file);
}
else {
  create_config($___CONFIG_ORIG, "./moses.ini", $featlist, $run, $devbleu, $sparse_weights_file);
}

# just to be sure that we have the really last finished step marked
&save_finished_step($finished_step_file, $run);

#chdir back to the original directory # useless, just to remind we were not there
chdir($cwd);
print "Training finished at " . `date`;
} # end of local scope

sub get_weights_from_mert {
  my ($outfile, $logfile, $weight_count, $sparse_weights, $mix_weights) = @_;
  my ($bestpoint, $devbleu);
  if ($___PAIRWISE_RANKED_OPTIMIZER || ($___PRO_STARTING_POINT && $logfile =~ /pro/)
          || $___BATCH_MIRA || $__PROMIX_TRAINING || $___HG_MIRA) {
    open my $fh, '<', $outfile or die "Can't open $outfile: $!";
    my @WEIGHT;
    @$mix_weights = ();
    for (my $i = 0; $i < $weight_count; $i++) { push @WEIGHT, 0; }
    my $sum = 0.0;
    while (<$fh>) {
      if (/^F(\d+) ([\-\.\de]+)/) {     # regular features
        $WEIGHT[$1] = $2;
        $sum += abs($2);
      } elsif (/^M(\d+_\d+) ([\-\.\de]+)/) {     # mix weights
        push @$mix_weights,$2;
      } elsif (/^(.+_.+) ([\-\.\de]+)/) { # sparse features
        $$sparse_weights{$1} = $2;
      }
    }
    close $fh;
    die "It seems feature values are invalid or unable to read $outfile." if $sum < 1e-09;
  
    $devbleu = "unknown";
    foreach (@WEIGHT) { $_ /= $sum; }
    foreach (keys %{$sparse_weights}) { $$sparse_weights{$_} /= $sum; }
    $bestpoint = join(" ", @WEIGHT);

    if($___BATCH_MIRA || $___HG_MIRA) {
      open my $fh2, '<', $logfile or die "Can't open $logfile: $!";
      while(<$fh2>) {
        if(/Best BLEU = ([\-\d\.]+)/) {
          $devbleu = $1;
        }
      }
      close $fh2;
    }
  } else {
    open my $fh, '<', $logfile or die "Can't open $logfile: $!";
    while (<$fh>) {
      if (/Best point:\s*([\s\d\.\-e]+?)\s*=> ([\-\d\.]+)/) {
        $bestpoint = $1;
        $devbleu = $2;
        last;
      }
    }
    close $fh;
  }
  return ($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);
    my $hypergraph_dir = "hypergraph";
    my $lsamp_filename = undef;
    if ($___LATTICE_SAMPLES) {
      my $lsamp_filename_template = "run%d.lsamp$___LATTICE_SAMPLES.out";
      $lsamp_filename = sprintf($lsamp_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;
    my $valcnt = 0;
    my $offset = 0;
    for(my $i=0; $i<scalar(@{$featlist->{"names"}}); $i++) {
      my $name = $featlist->{"names"}->[$i];
      if (!defined $model_weights{$name}) {
        $model_weights{$name} = "$name=";
        $valcnt = 0;
        while (defined $featlist->{"skippeduntuneablecomponents"}->{$name}{$valcnt+$offset}) {
          #$model_weights{$name} .= sprintf " %.6f", $oldvalues{$name}{$valcnt+$offset};
          $model_weights{$name} .= sprintf " x";
          $offset++;
        }
      }
      $model_weights{$name} .= sprintf " %.6f", $vals[$i];
      $valcnt++;
      while (defined $featlist->{"skippeduntuneablecomponents"}->{$name}{$valcnt+$offset}) {
        #$model_weights{$name} .= sprintf " %.6f", $oldvalues{$name}{$valcnt+$offset};
        $model_weights{$name} .= sprintf " x";
        $offset++;
      }
    }
    my $decoder_config = "";
    $decoder_config = "-weight-overwrite '" . join(" ", values %model_weights) ."'" unless $___USE_CONFIG_WEIGHTS_FIRST && $run==1;
    $decoder_config .= " -weight-file run$run.sparse-weights" if -e "run$run.sparse-weights";
    $decoder_config .= " -report-segmentation" if $__PROMIX_TRAINING;
    print STDERR "DECODER_CFG = $decoder_config\n";
    print "decoder_config = $decoder_config\n";

    # run the decoder
    my $decoder_cmd;
    my $lsamp_cmd = "";
    if ($___LATTICE_SAMPLES) {
      $lsamp_cmd = " -lattice-samples $lsamp_filename $___LATTICE_SAMPLES ";
    }

    if (defined $___JOBS && $___JOBS > 0) {
      die "Hypergraph mira not supported by moses-parallel" if $___HG_MIRA;
      $decoder_cmd = "$moses_parallel_cmd $pass_old_sge -config $___CONFIG";
      $decoder_cmd .= " -inputtype $___INPUTTYPE" if defined($___INPUTTYPE); 
      $decoder_cmd .= " -qsub-prefix mert$run -queue-parameters \"$queue_flags\" -decoder-parameters \"$___DECODER_FLAGS $decoder_config\" $lsamp_cmd -n-best-list \"$filename $___N_BEST_LIST_SIZE distinct\" -input-file $___DEV_F -jobs $___JOBS -decoder $___DECODER > run$run.out";
    } else {
      my $nbest_list_cmd = "-n-best-list $filename $___N_BEST_LIST_SIZE distinct";
      if ($___HG_MIRA) {
        safesystem("rm -rf $hypergraph_dir");
        $nbest_list_cmd = "-output-search-graph-hypergraph true gz";
      }
      $decoder_cmd = "$___DECODER $___DECODER_FLAGS  -config $___CONFIG";
      $decoder_cmd .= " -inputtype $___INPUTTYPE" if defined($___INPUTTYPE);
      $decoder_cmd .= " $decoder_config $lsamp_cmd $nbest_list_cmd  -input-file $___DEV_F";
      if (defined $___DEV_SYMAL) {
        # If simulating post-editing, route command through moses_sim_pe.py
        # Always use single (first) reference.  Simulated post-editing undefined for multiple references.
        $decoder_cmd = "$___MOSES_SIM_PE $decoder_cmd -ref $references[0] -symal $dev_symal_abs -tmp $working_dir_abs > run$run.out";
      }
      $decoder_cmd .= " > run$run.out";
    }

    print STDERR "Executing: $decoder_cmd \n";
    safesystem($decoder_cmd) or die "The decoder died. CONFIG WAS $decoder_config \n";

    if (!$___HG_MIRA) {
      sanity_check_order_of_lambdas($featlist,$filename);
    } else {
      print STDERR "WARN: No sanity check of order of features in hypergraph mira\n";
    }
    return ($filename, $lsamp_filename, $hypergraph_dir);
}


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;
        $namedpair =~ s/^.*?://;
      }
      my ($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 && ! -z $featlistfn) {   # exists & not empty
    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";
    $cmd .= " -inputtype $___INPUTTYPE" if defined($___INPUTTYPE);
    $cmd .= " -show-weights > $featlistfn";
    print STDERR "Executing: $cmd\n";
    safesystem($cmd) or die "Failed to run moses with the config $configfn";
  }
  return get_featlist_from_file($featlistfn);
}

sub get_featlist_from_file {
  my $featlistfn = shift;
  # read feature list
  my @names = ();
  my @startvalues = ();
  my @untuneables = ();
  my @allcomponentsuntuneable = ();
  my %skippeduntuneablecomponents = ();
  open my $fh, '<', $featlistfn or die "Can't read $featlistfn : $!";
  my $nr = 0;
  my $i = 0;
  my @errs = ();
  while (<$fh>) {
    $nr++;
    chomp;
    if (/^(\S+)= (.+)$/) { # only for feature functions with dense features
      my ($longname, $valuesStr) = ($1, $2);
      next if (!defined($valuesStr));
    
      my @values = split(/ /, $valuesStr);
      my $valcnt = 0;
      my $hastuneablecomponent = 0;
      foreach my $value (@values) {
        if ($value =~ /^UNTUNEABLECOMPONENT$/) {
          $skippeduntuneablecomponents{$longname}{$valcnt} = 1;
          $i++;
          $valcnt++;
        } elsif ($value =~ /^[+-]?[0-9.\-e]+$/) {
          push @names, $longname;
          push @startvalues, $value;
          $i++;
          $valcnt++;
          $hastuneablecomponent = 1;
        } else {
          push @errs, "$featlistfn:$nr:Bad initial value of $longname: $value\n"
        }
      }
      if (!$hastuneablecomponent) {
        push @allcomponentsuntuneable, $longname;
      }
    }
    elsif (/^(\S+) UNTUNEABLE$/) {
      my ($longname) = ($1);
      push @untuneables, $longname;
    }
  }
  close $fh;

  if (scalar @errs) {
    warn join("", @errs);
    exit 1;
  }
  return {"names"=>\@names, "values"=>\@startvalues, "untuneables"=>\@untuneables, "allcomponentsuntuneable"=>\@allcomponentsuntuneable, "skippeduntuneablecomponents"=>\%skippeduntuneablecomponents};
}


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 my $fh, $fname_or_source or die "Failed to get order of scores from nbestlist '$fname_or_source': $!";
  my $line = <$fh>;
  close $fh;
  die "Line empty in nbestlist '$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 {
  # TODO: too many arguments. you might want to consider using hashes
  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 @keep_weights = ();

  for (my $i = 0; $i < scalar(@{$featlist->{"names"}}); $i++) {
    my $name = $featlist->{"names"}->[$i];
    my $val = $featlist->{"values"}->[$i];
    # ensure long name
		print STDERR "featlist: $name=$val \n";
  }

  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;
      } else {
				my $value = $_;
        die "Found value with no -paramname before it: $value"
            if !defined $parameter;
        push @{$P{$parameter}}, $value;
      }
    }
  }

  if (defined($sparse_weights_file)) {
    push @{$P{"weight-file"}}, File::Spec->catfile($___WORKING_DIR, $sparse_weights_file);
  }

  # create new moses.ini decoder config file by cloning and overriding the original one
  open my $ini_fh, '<', $infn or die "Can't read $infn: $!";
  delete($P{"config"}); # never output
  print "Saving new config to: $outfn\n";

  open my $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 %oldvalues = ();

  my $line = <$ini_fh>;
  while(1) {
    last unless $line;

    # skip until hit [parameter]
    if ($line !~ /^\[(.+)\]\s*$/) {
      $line = <$ini_fh>;
      print $out $line if $line =~ /^\#/ || $line =~ /^\s+$/;
      next;
    }

    # parameter name
    my $parameter = $1;

    if ($parameter eq "weight") {
      # leave weights 'til last. We're changing it
      while ($line = <$ini_fh>) {
        last if $line =~ /^\[/;
        if ($line =~ /^(\S+)= (.+)$/) {
          for( @{$featlist->{"untuneables"}} ){
            if ($1 eq $_ ) {# if weight is untuneable, copy it into new config
              push @keep_weights, $line;
            }
          }
          for( @{$featlist->{"allcomponentsuntuneable"}} ){
            if ($1 eq $_ ) {# if all dense weights are untuneable, copy it into new config
              push @keep_weights, $line;
            }
          }

          my ($longname, $valuesStr) = ($1, $2);
          next if (!defined($valuesStr));
          print $valuesStr;
          my @values = split(/ /, $valuesStr);
          my $valcnt = 0;
          foreach my $value (@values) {
            if ($value =~ /^[+-]?[0-9.\-e]+$/) {
              $oldvalues{$longname}{$valcnt} = $value;
            }
            $valcnt++;
          }
        }
      }
    }
    elsif (defined($P{$parameter})) {
      # found a param (thread, verbose etc) that we're overriding. Leave to the end
      while ($line = <$ini_fh>) {
        last if $line =~ /^\[/;
      }
    }
    else {
      # unchanged parameter, write old
      print $out "[$parameter]\n";
      while ($line = <$ini_fh>) {
        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";
    }
  }

  # write all weights
  print $out "[weight]\n";
  
  my $prevName = "";
  my $outStr = "";
  my $valcnt = 0;
  my $offset = 0;
  for (my $i = 0; $i < scalar(@{$featlist->{"names"}}); $i++) {
    my $name = $featlist->{"names"}->[$i];
    my $val = $featlist->{"values"}->[$i];
    
    if ($prevName ne $name) {
      print $out "$outStr\n";
      $valcnt = 0;
      $outStr = "$name=";
      $prevName = $name;
      while (defined $featlist->{"skippeduntuneablecomponents"}->{$name}{$valcnt+$offset}) {
        $outStr .= " $oldvalues{$name}{$valcnt+$offset}";
        $offset++;
      }
    }
    $outStr .= " $val";
    $valcnt++;
    while (defined $featlist->{"skippeduntuneablecomponents"}->{$name}{$valcnt+$offset}) {
      $outStr .= " $oldvalues{$name}{$valcnt+$offset}";
      $offset++;
    }
  }
  print $out "$outStr\n";

  for (@keep_weights) {
     print $out $_;
  }

  close $ini_fh;
  close $out;
  print STDERR "Saved: $outfn\n";
}

# Create a new ini file, with the first ttable replaced by the given one
# and its type set to text
sub substitute_ttable {
  my ($old_ini, $new_ini, $new_ttable, $ttable_type) = @_;
  $ttable_type = "0" unless defined($ttable_type);
  open(NEW_INI,">$new_ini") || die "Failed to create $new_ini";
  open(INI,$old_ini) || die "Failed to open $old_ini";
  while(<INI>) {
    if (/\[ttable-file\]/) {
      print NEW_INI "[ttable-file]\n";
      my $ttable_config = <INI>;
      chomp $ttable_config;
      my @ttable_fields = split /\s+/, $ttable_config;
      $ttable_fields[0] = $ttable_type;
      $ttable_fields[4] = $new_ttable;
      print NEW_INI join(" ", @ttable_fields) . "\n";
    } else {
      print NEW_INI;
    }
  }
  close NEW_INI;
  close INI;
}


sub safesystem {
  print STDERR "Executing: @_\n";
  system(@_);
  if ($? == -1) {
      warn "Failed to execute: @_\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;
    warn "Exit code: $exitcode\n" if $exitcode;
    return ! $exitcode;
  }
}

sub ensure_full_path {
  my $PATH = shift;
  $PATH =~ s/\/nfsmnt//;
  return $PATH if $PATH =~ /^\//;

  my $dir = Cwd::getcwd();
  $PATH = File::Spec->catfile($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'.";
  }
}

sub create_extractor_script() {
  my ($cmd, $outdir) = @_;
  my $script_path = File::Spec->catfile($outdir, "extractor.sh");

  open my $out, '>', $script_path
      or die "Couldn't open $script_path for writing: $!\n";
  print $out "#!/usr/bin/env bash\n";
  print $out "cd $outdir\n";
  print $out "$cmd\n";
  close $out;

  `chmod +x $script_path`;

  return $script_path;
}

sub save_finished_step {
  my ($filename, $step) = @_;
  open my $fh, '>', $filename or die "$filename: $!";
  print $fh $step . "\n";
  close $fh;
}

# It returns a config for mert/extractor.
sub setup_reference_length_type {
  if (($___CLOSEST + $___AVERAGE + $___SHORTEST) > 1) {
    die "You can specify just ONE reference length strategy (closest or shortest or average) not both\n";
  }

  if ($___SHORTEST) {
    return " reflen:shortest";
  } elsif ($___AVERAGE) {
    return " reflen:average";
  } elsif ($___CLOSEST) {
    return " reflen:closest";
  } else {
    return "";
  }
}

sub setup_case_config {
  if ($___NOCASE) {
    return " case:false";
  } else {
    return " case:true";
  }
}

sub is_mac_osx {
  return ($^O eq "darwin") ? 1 : 0;
}