fixed conflicts

1 files changed, 0 insertions, 540 deletions

diff --git a/minrisk/minrisk.pl b/minrisk/minrisk.pl
deleted file mode 100755
index d05b9595..00000000
--- a/minrisk/minrisk.pl
+++ /dev/null
@@ -1,540 +0,0 @@
-#!/usr/bin/env perl
-use strict;
-my @ORIG_ARGV=@ARGV;
-use Cwd qw(getcwd);
-my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../environment"; }
-
-# Skip local config (used for distributing jobs) if we're running in local-only mode
-use LocalConfig;
-use Getopt::Long;
-use IPC::Open2;
-use POSIX ":sys_wait_h";
-my $QSUB_CMD = qsub_args(mert_memory());
-my $default_jobs = env_default_jobs();
-
-my $VEST_DIR="$SCRIPT_DIR/../dpmert";
-require "$VEST_DIR/libcall.pl";
-
-# Default settings
-my $srcFile;
-my $refFiles;
-my $bin_dir = $SCRIPT_DIR;
-die "Bin directory $bin_dir missing/inaccessible" unless -d $bin_dir;
-my $FAST_SCORE="$bin_dir/../mteval/fast_score";
-die "Can't execute $FAST_SCORE" unless -x $FAST_SCORE;
-my $MAPINPUT = "$bin_dir/minrisk_generate_input.pl";
-my $MAPPER = "$bin_dir/minrisk_optimize";
-my $parallelize = "$VEST_DIR/parallelize.pl";
-my $libcall = "$VEST_DIR/libcall.pl";
-my $sentserver = "$VEST_DIR/sentserver";
-my $sentclient = "$VEST_DIR/sentclient";
-my $LocalConfig = "$SCRIPT_DIR/../environment/LocalConfig.pm";
-
-my $SCORER = $FAST_SCORE;
-die "Can't find $MAPPER" unless -x $MAPPER;
-my $cdec = "$bin_dir/../decoder/cdec";
-die "Can't find decoder in $cdec" unless -x $cdec;
-die "Can't find $parallelize" unless -x $parallelize;
-die "Can't find $libcall" unless -e $libcall;
-my $decoder = $cdec;
-my $lines_per_mapper = 30;
-my $iteration = 1;
-my $best_weights;
-my $psi = 1;
-my $default_max_iter = 30;
-my $max_iterations = $default_max_iter;
-my $jobs = $default_jobs;   # number of decode nodes
-my $pmem = "4g";
-my $disable_clean = 0;
-my %seen_weights;
-my $help = 0;
-my $epsilon = 0.0001;
-my $dryrun = 0;
-my $last_score = -10000000;
-my $metric = "ibm_bleu";
-my $dir;
-my $iniFile;
-my $weights;
-my $use_make = 1;  # use make to parallelize
-my $useqsub = 0;
-my $initial_weights;
-my $pass_suffix = '';
-my $cpbin=1;
-
-# regularization strength
-my $tune_regularizer = 0;
-my $reg = 500;
-my $reg_previous = 5000;
-my $dont_accum = 0;
-
-# Process command-line options
-Getopt::Long::Configure("no_auto_abbrev");
-if (GetOptions(
-	"jobs=i" => \$jobs,
-	"dont-clean" => \$disable_clean,
-	"dont-accumulate" => \$dont_accum,
-	"pass-suffix=s" => \$pass_suffix,
-        "qsub" => \$useqsub,
-	"dry-run" => \$dryrun,
-	"epsilon=s" => \$epsilon,
-	"help" => \$help,
-        "weights=s" => \$initial_weights,
-	"reg=f" => \$reg,
-	"use-make=i" => \$use_make,
-	"max-iterations=i" => \$max_iterations,
-	"pmem=s" => \$pmem,
-        "cpbin!" => \$cpbin,
-	"ref-files=s" => \$refFiles,
-	"metric=s" => \$metric,
-	"source-file=s" => \$srcFile,
-	"workdir=s" => \$dir,
-) == 0 || @ARGV!=1 || $help) {
-	print_help();
-	exit;
-}
-
-die "--tune-regularizer is no longer supported with --reg-previous and --reg. Please tune manually.\n" if $tune_regularizer;
-
-if ($useqsub) {
-  $use_make = 0;
-  die "LocalEnvironment.pm does not have qsub configuration for this host. Cannot run with --qsub!\n" unless has_qsub();
-}
-
-my @missing_args = ();
-if (!defined $srcFile) { push @missing_args, "--source-file"; }
-if (!defined $refFiles) { push @missing_args, "--ref-files"; }
-if (!defined $initial_weights) { push @missing_args, "--weights"; }
-die "Please specify missing arguments: " . join (', ', @missing_args) . "\n" if (@missing_args);
-
-if ($metric =~ /^(combi|ter)$/i) {
-  $lines_per_mapper = 5;
-}
-
-($iniFile) = @ARGV;
-
-
-sub write_config;
-sub enseg;
-sub print_help;
-
-my $nodelist;
-my $host =check_output("hostname"); chomp $host;
-my $bleu;
-my $interval_count = 0;
-my $logfile;
-my $projected_score;
-
-# used in sorting scores
-my $DIR_FLAG = '-r';
-if ($metric =~ /^ter$|^aer$/i) {
-  $DIR_FLAG = '';
-}
-
-my $refs_comma_sep = get_comma_sep_refs('r',$refFiles);
-
-unless ($dir){
-	$dir = "minrisk";
-}
-unless ($dir =~ /^\//){  # convert relative path to absolute path
-	my $basedir = check_output("pwd");
-	chomp $basedir;
-	$dir = "$basedir/$dir";
-}
-
-
-# Initializations and helper functions
-srand;
-
-my @childpids = ();
-my @cleanupcmds = ();
-
-sub cleanup {
-	print STDERR "Cleanup...\n";
-	for my $pid (@childpids){ unchecked_call("kill $pid"); }
-	for my $cmd (@cleanupcmds){ unchecked_call("$cmd"); }
-	exit 1;
-};
-# Always call cleanup, no matter how we exit
-*CORE::GLOBAL::exit = 
-    sub{ cleanup(); }; 
-$SIG{INT} = "cleanup";
-$SIG{TERM} = "cleanup";
-$SIG{HUP} = "cleanup";
-
-my $decoderBase = check_output("basename $decoder"); chomp $decoderBase;
-my $newIniFile = "$dir/$decoderBase.ini";
-my $inputFileName = "$dir/input";
-my $user = $ENV{"USER"};
-# process ini file
--e $iniFile || die "Error: could not open $iniFile for reading\n";
-open(INI, $iniFile);
-
-use File::Basename qw(basename);
-#pass bindir, refs to vars holding bin
-sub modbin {
-    local $_;
-    my $bindir=shift;
-    check_call("mkdir -p $bindir");
-    -d $bindir || die "couldn't make bindir $bindir";
-    for (@_) {
-        my $src=$$_;
-        $$_="$bindir/".basename($src);
-        check_call("cp -p $src $$_");
-    }
-}
-sub dirsize {
-    opendir ISEMPTY,$_[0];
-    return scalar(readdir(ISEMPTY))-1;
-}
-my @allweights;
-if ($dryrun){
-	write_config(*STDERR);
-	exit 0;
-} else {
-	if (-e $dir && dirsize($dir)>1 && -e "$dir/hgs" ){ # allow preexisting logfile, binaries, but not dist-pro.pl outputs
-	  die "ERROR: working dir $dir already exists\n\n";
-	} else {
-		-e $dir || mkdir $dir;
-		mkdir "$dir/hgs";
-        modbin("$dir/bin",\$LocalConfig,\$cdec,\$SCORER,\$MAPINPUT,\$MAPPER,\$parallelize,\$sentserver,\$sentclient,\$libcall) if $cpbin;
-    mkdir "$dir/scripts";
-        my $cmdfile="$dir/rerun-pro.sh";
-        open CMD,'>',$cmdfile;
-        print CMD "cd ",&getcwd,"\n";
-#        print CMD &escaped_cmdline,"\n"; #buggy - last arg is quoted.
-        my $cline=&cmdline."\n";
-        print CMD $cline;
-        close CMD;
-        print STDERR $cline;
-        chmod(0755,$cmdfile);
-	check_call("cp $initial_weights $dir/weights.0");
-	die "Can't find weights.0" unless (-e "$dir/weights.0");
-	}
-	write_config(*STDERR);
-}
-
-
-# Generate initial files and values
-check_call("cp $iniFile $newIniFile");
-$iniFile = $newIniFile;
-
-my $newsrc = "$dir/dev.input";
-enseg($srcFile, $newsrc);
-$srcFile = $newsrc;
-my $devSize = 0;
-open F, "<$srcFile" or die "Can't read $srcFile: $!";
-while(<F>) { $devSize++; }
-close F;
-
-unless($best_weights){ $best_weights = $weights; }
-unless($projected_score){ $projected_score = 0.0; }
-$seen_weights{$weights} = 1;
-my $kbest = "$dir/kbest";
-if ($dont_accum) {
-  $kbest = '';
-} else {
-  check_call("mkdir -p $kbest");
-  $kbest = "--kbest_repository $kbest";
-}
-
-my $random_seed = int(time / 1000);
-my $lastWeightsFile;
-my $lastPScore = 0;
-# main optimization loop
-while (1){
-	print STDERR "\n\nITERATION $iteration\n==========\n";
-
-	if ($iteration > $max_iterations){
-		print STDERR "\nREACHED STOPPING CRITERION: Maximum iterations\n";
-		last;
-	}
-	# iteration-specific files
-	my $runFile="$dir/run.raw.$iteration";
-	my $onebestFile="$dir/1best.$iteration";
-	my $logdir="$dir/logs.$iteration";
-	my $decoderLog="$logdir/decoder.sentserver.log.$iteration";
-	my $scorerLog="$logdir/scorer.log.$iteration";
-	check_call("mkdir -p $logdir");
-
-
-	#decode
-	print STDERR "RUNNING DECODER AT ";
-	print STDERR unchecked_output("date");
-	my $im1 = $iteration - 1;
-	my $weightsFile="$dir/weights.$im1";
-        push @allweights, "-w $dir/weights.$im1";
-        `rm -f $dir/hgs/*.gz`;
-	my $decoder_cmd = "$decoder -c $iniFile --weights$pass_suffix $weightsFile -O $dir/hgs";
-	my $pcmd;
-	if ($use_make) {
-		$pcmd = "cat $srcFile | $parallelize --use-fork -p $pmem -e $logdir -j $jobs --";
-	} else {
-		$pcmd = "cat $srcFile | $parallelize -p $pmem -e $logdir -j $jobs --";
-	}
-	my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $runFile";
-	print STDERR "COMMAND:\n$cmd\n";
-	check_bash_call($cmd);
-        my $num_hgs;
-        my $num_topbest;
-        my $retries = 0;
-	while($retries < 5) {
-	    $num_hgs = check_output("ls $dir/hgs/*.gz | wc -l");
-	    $num_topbest = check_output("wc -l < $runFile");
-	    print STDERR "NUMBER OF HGs: $num_hgs\n";
-	    print STDERR "NUMBER OF TOP-BEST HYPs: $num_topbest\n";
-	    if($devSize == $num_hgs && $devSize == $num_topbest) {
-		last;
-	    } else {
-		print STDERR "Incorrect number of hypergraphs or topbest. Waiting for distributed filesystem and retrying...\n";
-		sleep(3);
-	    }
-	    $retries++;
-	}
-	die "Dev set contains $devSize sentences, but we don't have topbest and hypergraphs for all these! Decoder failure? Check $decoderLog\n" if ($devSize != $num_hgs || $devSize != $num_topbest);
-	my $dec_score = check_output("cat $runFile | $SCORER $refs_comma_sep -m $metric");
-	chomp $dec_score;
-	print STDERR "DECODER SCORE: $dec_score\n";
-
-	# save space
-	check_call("gzip -f $runFile");
-	check_call("gzip -f $decoderLog");
-
-	# run optimizer
-	print STDERR "RUNNING OPTIMIZER AT ";
-	print STDERR unchecked_output("date");
-	print STDERR " - GENERATE TRAINING EXEMPLARS\n";
-	my $mergeLog="$logdir/prune-merge.log.$iteration";
-
-	my $score = 0;
-	my $icc = 0;
-	my $inweights="$dir/weights.$im1";
-	my $outweights="$dir/weights.$iteration";
-	$cmd="$MAPINPUT $dir/hgs > $dir/agenda.$im1";
-	print STDERR "COMMAND:\n$cmd\n";
-	check_call($cmd);
-	$cmd="$MAPPER $refs_comma_sep -m $metric -i $dir/agenda.$im1 $kbest -w $inweights > $outweights";
-	check_call($cmd);
-	$lastWeightsFile = $outweights;
-	$iteration++;
-	`rm hgs/*.gz`;
-	print STDERR "\n==========\n";
-}
-
-print STDERR "\nFINAL WEIGHTS: $lastWeightsFile\n(Use -w <this file> with the decoder)\n\n";
-
-print STDOUT "$lastWeightsFile\n";
-
-exit 0;
-
-sub get_lines {
-  my $fn = shift @_;
-  open FL, "<$fn" or die "Couldn't read $fn: $!";
-  my $lc = 0;
-  while(<FL>) { $lc++; }
-  return $lc;
-}
-
-sub get_comma_sep_refs {
-  my ($r,$p) = @_;
-  my $o = check_output("echo $p");
-  chomp $o;
-  my @files = split /\s+/, $o;
-  return "-$r " . join(" -$r ", @files);
-}
-
-sub read_weights_file {
-  my ($file) = @_;
-  open F, "<$file" or die "Couldn't read $file: $!";
-  my @r = ();
-  my $pm = -1;
-  while(<F>) {
-    next if /^#/;
-    next if /^\s*$/;
-    chomp;
-    if (/^(.+)\s+(.+)$/) {
-      my $m = $1;
-      my $w = $2;
-      die "Weights out of order: $m <= $pm" unless $m > $pm;
-      push @r, $w;
-    } else {
-      warn "Unexpected feature name in weight file: $_";
-    }
-  }
-  close F;
-  return join ' ', @r;
-}
-
-# subs
-sub write_config {
-	my $fh = shift;
-	my $cleanup = "yes";
-	if ($disable_clean) {$cleanup = "no";}
-
-	print $fh "\n";
-	print $fh "DECODER:          $decoder\n";
-	print $fh "INI FILE:         $iniFile\n";
-	print $fh "WORKING DIR:      $dir\n";
-	print $fh "SOURCE (DEV):     $srcFile\n";
-	print $fh "REFS (DEV):       $refFiles\n";
-	print $fh "EVAL METRIC:      $metric\n";
-	print $fh "MAX ITERATIONS:   $max_iterations\n";
-	print $fh "JOBS:             $jobs\n";
-	print $fh "HEAD NODE:        $host\n";
-	print $fh "PMEM (DECODING):  $pmem\n";
-	print $fh "CLEANUP:          $cleanup\n";
-}
-
-sub update_weights_file {
-  my ($neww, $rfn, $rpts) = @_;
-  my @feats = @$rfn;
-  my @pts = @$rpts;
-  my $num_feats = scalar @feats;
-  my $num_pts = scalar @pts;
-  die "$num_feats (num_feats) != $num_pts (num_pts)" unless $num_feats == $num_pts;
-  open G, ">$neww" or die;
-  for (my $i = 0; $i < $num_feats; $i++) {
-    my $f = $feats[$i];
-    my $lambda = $pts[$i];
-    print G "$f $lambda\n";
-  }
-  close G;
-}
-
-sub enseg {
-	my $src = shift;
-	my $newsrc = shift;
-	open(SRC, $src);
-	open(NEWSRC, ">$newsrc");
-	my $i=0;
-	while (my $line=<SRC>){
-		chomp $line;
-		if ($line =~ /^\s*<seg/i) {
-		    if($line =~ /id="[0-9]+"/) {
-			print NEWSRC "$line\n";
-		    } else {
-			die "When using segments with pre-generated <seg> tags, you must include a zero-based id attribute";
-		    }
-		} else {
-			print NEWSRC "<seg id=\"$i\">$line</seg>\n";
-		}
-		$i++;
-	}
-	close SRC;
-	close NEWSRC;
-	die "Empty dev set!" if ($i == 0);
-}
-
-sub print_help {
-
-	my $executable = check_output("basename $0"); chomp $executable;
-	print << "Help";
-
-Usage: $executable [options] <ini file>
-
-	$executable [options] <ini file>
-		Runs a complete PRO optimization using the ini file specified.
-
-Required:
-
-	--ref-files <files>
-		Dev set ref files.  This option takes only a single string argument.
-		To use multiple files (including file globbing), this argument should
-		be quoted.
-
-	--source-file <file>
-		Dev set source file.
-
-	--weights <file>
-		Initial weights file (use empty file to start from 0)
-
-General options:
-
-	--help
-		Print this message and exit.
-
-	--dont-accumulate
-		Don't accumulate k-best lists from multiple iterations.
-
-	--max-iterations <M>
-		Maximum number of iterations to run.  If not specified, defaults
-		to $default_max_iter.
-
-	--metric <method>
-		Metric to optimize.
-		Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
-
-	--pass-suffix <S>
-		If the decoder is doing multi-pass decoding, the pass suffix "2",
-		"3", etc., is used to control what iteration of weights is set.
-
-	--workdir <dir>
-		Directory for intermediate and output files.  If not specified, the
-		name is derived from the ini filename.  Assuming that the ini
-		filename begins with the decoder name and ends with ini, the default
-		name of the working directory is inferred from the middle part of
-		the filename.  E.g. an ini file named decoder.foo.ini would have
-		a default working directory name foo.
-
-Regularization options:
-
-	--reg <F>
-		l2 regularization strength [default=500]. The greater this value,
-		the closer to zero the weights will be.
-
-Job control options:
-
-	--jobs <I>
-		Number of decoder processes to run in parallel. [default=$default_jobs]
-
-	--qsub
-		Use qsub to run jobs in parallel (qsub must be configured in
-		environment/LocalEnvironment.pm)
-
-	--pmem <N>
-		Amount of physical memory requested for parallel decoding jobs
-		(used with qsub requests only)
-
-Help
-}
-
-sub convert {
-  my ($str) = @_;
-  my @ps = split /;/, $str;
-  my %dict = ();
-  for my $p (@ps) {
-    my ($k, $v) = split /=/, $p;
-    $dict{$k} = $v;
-  }
-  return %dict;
-}
-
-
-sub cmdline {
-    return join ' ',($0,@ORIG_ARGV);
-}
-
-#buggy: last arg gets quoted sometimes?
-my $is_shell_special=qr{[ \t\n\\><|&;"'`~*?{}$!()]};
-my $shell_escape_in_quote=qr{[\\"\$`!]};
-
-sub escape_shell {
-    my ($arg)=@_;
-    return undef unless defined $arg;
-    if ($arg =~ /$is_shell_special/) {
-        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
-        return "\"$arg\"";
-    }
-    return $arg;
-}
-
-sub escaped_shell_args {
-    return map {local $_=$_;chomp;escape_shell($_)} @_;
-}
-
-sub escaped_shell_args_str {
-    return join ' ',&escaped_shell_args(@_);
-}
-
-sub escaped_cmdline {
-    return "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
-}