Great - thanks. I modified a little to make it possible to pass a command to the new option. I hope I didn’t break anything. Maybe this modification could become part of the official moses package? |
#!/usr/bin/env perl # # This file is part of moses. Its use is licensed under the GNU Lesser General # Public License version 2.1 or, at your option, any later version.
# $Id$
# 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 warnings;
use strict;
use FindBin qw($RealBin);
use File::Basename;
use File::Path;
use File::Spec;
use File::Copy qw(move); ##(Anoop)
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 $___CACHE_MODEL = undef; # if models need to be copied to local disk from NFS
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 $___TRANSFORM_DECODED_FILE = 0; # Anoop: transform decoded file
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;
# Multiple instance parallelization
my $___MULTI_MOSES = "$SCRIPTS_ROOTDIR/generic/multi_moses.py";
my $___USE_MULTI_MOSES = undef;
# 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,
"cache-model=s" => \$___CACHE_MODEL,
"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
"transform-decoded-file=s" => \$___TRANSFORM_DECODED_FILE, # Anoop: transform decoded file to convert to standard word level format
"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,
"multi-moses" => \$___USE_MULTI_MOSES
) 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
--cache-model=STRING ... local directory into which copy model before running decoder
--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)
--multi-moses ... Use multiple instances of moses instead of threads for decoding
(Use with --decoder-flags='-threads N' to get N instances, each of
which uses a single thread (overrides threads in moses.ini))
";
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", 1);
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", 1);
}
# 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";
}
## Anoop: tranforming decoded file
if ($___TRANSFORM_DECODED_FILE) {
my $trans_file=$nbest_file.".transformed";
##Command to run: cat $nbest_file | sed 's, ||| ,""""",g' | awk -F '"""""' 'BEGIN{OFS=" ||| "}{gsub (" ", "", $2);gsub ("\\^"," ",$2);print}' > $trans_file
## my $trans_cmd="cat $nbest_file | sed 's, ||| ,!!!!!,g' | awk -F '!!!!!' 'BEGIN{OFS=\" ||| \"}{gsub (\" \", \"\", \$2);gsub (\"\\\\^\",\" \",\$2);print}' > $trans_file";
my $trans_cmd;
## check if the argument is a file or includes space
## if yes, then assume that it specifies the command to be run
if ((-e $___TRANSFORM_DECODED_FILE) || ($___TRANSFORM_DECODED_FILE=~/ /)){
$trans_cmd="cat $nbest_file | $___TRANSFORM_DECODED_FILE > $trans_file";
}
## otherwise assume BPE markup with @@
else{
$trans_cmd="cat $nbest_file | sed 's/\@\@ //g' > $trans_file";
}
print STDERR "Executing data transformation command: $trans_cmd \n";
safesystem($trans_cmd) or die "The data transformation failed \n";
move $trans_file, $nbest_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", 1);
}
# 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, $mert_logfile, 1);
} elsif ($___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", 1);
# ... 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, $mert_logfile, ($__THREADS ? $__THREADS : 1) );
} elsif ($___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", $mert_logfile, 1);
} elsif ($___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", $mert_logfile, 1);
} elsif ($__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", $mert_logfile, 1);
print "Finished promix optimisation at " . `date`;
} else { # just mert
&submit_or_exec($cmd . $mert_settings, $mert_outfile, $mert_logfile, ($__THREADS ? $__THREADS : 1) );
}
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( $__PROMIX_TRAINING);
&submit_or_exec($cmd, $evalout, "/dev/null", 1);
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 > 1) {
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 .= " -cache-model $___CACHE_MODEL" if defined($___CACHE_MODEL);
$decoder_cmd .= " -qsub-prefix mert$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 $___USE_MULTI_MOSES) {
# If requested, prefix full decoder command with multi-moses wrapper
$decoder_cmd = "$___MULTI_MOSES $decoder_cmd";
}
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 $cmd;
if ($___CACHE_MODEL) {
$cmd = "MOSES_INI=`$SCRIPTS_ROOTDIR/ems/support/cache-model.perl $configfn $___CACHE_MODEL` && ";
$configfn = "\$MOSES_INI";
}
$cmd .= "$___DECODER $___DECODER_FLAGS -config $configfn";
$cmd .= " -inputtype $___INPUTTYPE" if defined($___INPUTTYPE);
$cmd .= " -show-weights";
if (defined $___USE_MULTI_MOSES) {
# Pass moses command through multi-moses script to handle threads properly
$cmd = "$___MULTI_MOSES $cmd";
}
print STDERR "Executing: $cmd\n";
&submit_or_exec($cmd, $featlistfn, "/dev/null", 1);
}
return get_featlist_from_file($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 (sort 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, $threads) = @_;
print STDERR "exec: $cmd\n";
if (defined $___JOBS && $___JOBS > 1) {
# request fewer CPU slots, if not needed
my $queue_flags_for_this_command = $queue_flags;
$threads = 1 unless defined($threads);
$queue_flags_for_this_command =~ s/(\-pe smp) \d+/$1 $threads/;
safesystem("$qsubwrapper $pass_old_sge -command='$cmd' -queue-parameter=\"$queue_flags_for_this_command\" -stdout=$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;
}
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