fixed conflicts

1 files changed, 555 insertions, 0 deletions

diff --git a/training/pro/pro.pl b/training/pro/pro.pl
new file mode 100755
index 00000000..3b30c379
--- /dev/null
+++ b/training/pro/pro.pl
@@ -0,0 +1,555 @@
+#!/usr/bin/env perl
+use strict;
+use File::Basename qw(basename);
+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", "$SCRIPT_DIR/../utils"; }
+
+# 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 $UTILS_DIR="$SCRIPT_DIR/../utils";
+require "$UTILS_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/mr_pro_generate_mapper_input.pl";
+my $MAPPER = "$bin_dir/mr_pro_map";
+my $REDUCER = "$bin_dir/mr_pro_reduce";
+my $parallelize = "$UTILS_DIR/parallelize.pl";
+my $libcall = "$UTILS_DIR/libcall.pl";
+my $sentserver = "$UTILS_DIR/sentserver";
+my $sentclient = "$UTILS_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 $devset;
+
+# regularization strength
+my $reg = 500;
+my $reg_previous = 5000;
+
+# Process command-line options
+if (GetOptions(
+	"config=s" => \$iniFile,
+	"weights=s" => \$initial_weights,
+        "devset=s" => \$devset,
+	"jobs=i" => \$jobs,
+	"metric=s" => \$metric,
+	"pass-suffix=s" => \$pass_suffix,
+        "qsub" => \$useqsub,
+	"help" => \$help,
+	"reg=f" => \$reg,
+	"reg-previous=f" => \$reg_previous,
+	"output-dir=s" => \$dir,
+) == 0 || @ARGV!=0 || $help) {
+	print_help();
+	exit;
+}
+
+if ($useqsub) {
+  $use_make = 0;
+  die "LocalEnvironment.pm does not have qsub configuration for this host. Cannot run with --qsub!\n" unless has_qsub();
+}
+
+my @missing_args = ();
+if (!defined $iniFile) { push @missing_args, "--config"; }
+if (!defined $devset) { push @missing_args, "--devset"; }
+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;
+}
+
+my $host =check_output("hostname"); chomp $host;
+my $bleu;
+my $interval_count = 0;
+my $logfile;
+my $projected_score;
+
+# used in sorting scores
+my $DIR_FLAG = '-r';
+if ($metric =~ /^ter$|^aer$/i) {
+  $DIR_FLAG = '';
+}
+
+unless ($dir){
+	$dir = 'pro';
+}
+unless ($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);
+
+if (-e $dir) {
+	die "ERROR: working dir $dir already exists\n\n";
+} else {
+	mkdir "$dir" or die "Can't mkdir $dir: $!";
+	mkdir "$dir/hgs" or die;
+	mkdir "$dir/scripts" or die;
+	print STDERR <<EOT;
+	DECODER:          $decoder
+	INI FILE:         $iniFile
+	WORKING DIR:      $dir
+	DEVSET:           $devset
+	EVAL METRIC:      $metric
+	MAX ITERATIONS:   $max_iterations
+	PARALLEL JOBS:    $jobs
+	HEAD NODE:        $host
+	PMEM (DECODING):  $pmem
+	INITIAL WEIGHTS:  $initial_weights
+EOT
+}
+
+# Generate initial files and values
+check_call("cp $iniFile $newIniFile");
+check_call("cp $initial_weights $dir/weights.0");
+$iniFile = $newIniFile;
+
+my $refs = "$dir/dev.refs";
+split_devset($devset, "$dir/dev.input.raw", $refs);
+my $newsrc = "$dir/dev.input";
+enseg("$dir/dev.input.raw", $newsrc);
+$srcFile = $newsrc;
+my $devSize = 0;
+open F, "<$srcFile" or die "Can't read $srcFile: $!";
+while(<F>) { $devSize++; }
+close F;
+
+unless($best_weights){ $best_weights = $weights; }
+unless($projected_score){ $projected_score = 0.0; }
+$seen_weights{$weights} = 1;
+
+my $random_seed = int(time / 1000);
+my $lastWeightsFile;
+my $lastPScore = 0;
+# main optimization loop
+my @allweights;
+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 -r $refs -m $metric");
+	chomp $dec_score;
+	print STDERR "DECODER SCORE: $dec_score\n";
+
+	# save space
+	check_call("gzip -f $runFile");
+	check_call("gzip -f $decoderLog");
+
+	# run optimizer
+	print STDERR "RUNNING OPTIMIZER AT ";
+	print STDERR unchecked_output("date");
+	print STDERR " - GENERATE TRAINING EXEMPLARS\n";
+	my $mergeLog="$logdir/prune-merge.log.$iteration";
+
+	my $score = 0;
+	my $icc = 0;
+	my $inweights="$dir/weights.$im1";
+	$cmd="$MAPINPUT $dir/hgs > $dir/agenda.$im1";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_call($cmd);
+	check_call("mkdir -p $dir/splag.$im1");
+	$cmd="split -a 3 -l $lines_per_mapper $dir/agenda.$im1 $dir/splag.$im1/mapinput.";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_call($cmd);
+	opendir(DIR, "$dir/splag.$im1") or die "Can't open directory: $!";
+	my @shards = grep { /^mapinput\./ } readdir(DIR);
+	closedir DIR;
+	die "No shards!" unless scalar @shards > 0;
+	my $joblist = "";
+	my $nmappers = 0;
+	@cleanupcmds = ();
+	my %o2i = ();
+	my $first_shard = 1;
+	my $mkfile; # only used with makefiles
+	my $mkfilename;
+	if ($use_make) {
+		$mkfilename = "$dir/splag.$im1/domap.mk";
+		open $mkfile, ">$mkfilename" or die "Couldn't write $mkfilename: $!";
+		print $mkfile "all: $dir/splag.$im1/map.done\n\n";
+	}
+	my @mkouts = ();  # only used with makefiles
+	my @mapoutputs = ();
+	for my $shard (@shards) {
+		my $mapoutput = $shard;
+		my $client_name = $shard;
+		$client_name =~ s/mapinput.//;
+		$client_name = "pro.$client_name";
+		$mapoutput =~ s/mapinput/mapoutput/;
+		push @mapoutputs, "$dir/splag.$im1/$mapoutput";
+		$o2i{"$dir/splag.$im1/$mapoutput"} = "$dir/splag.$im1/$shard";
+		my $script = "$MAPPER -s $srcFile -m $metric -r $refs -w $inweights -K $dir/kbest < $dir/splag.$im1/$shard > $dir/splag.$im1/$mapoutput";
+		if ($use_make) {
+			my $script_file = "$dir/scripts/map.$shard";
+			open F, ">$script_file" or die "Can't write $script_file: $!";
+			print F "#!/bin/bash\n";
+			print F "$script\n";
+			close F;
+			my $output = "$dir/splag.$im1/$mapoutput";
+			push @mkouts, $output;
+			chmod(0755, $script_file) or die "Can't chmod $script_file: $!";
+			if ($first_shard) { print STDERR "$script\n"; $first_shard=0; }
+			print $mkfile "$output: $dir/splag.$im1/$shard\n\t$script_file\n\n";
+		} else {
+			my $script_file = "$dir/scripts/map.$shard";
+			open F, ">$script_file" or die "Can't write $script_file: $!";
+			print F "$script\n";
+			close F;
+			if ($first_shard) { print STDERR "$script\n"; $first_shard=0; }
+
+			$nmappers++;
+			my $qcmd = "$QSUB_CMD -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file";
+			my $jobid = check_output("$qcmd");
+			chomp $jobid;
+			$jobid =~ s/^(\d+)(.*?)$/\1/g;
+			$jobid =~ s/^Your job (\d+) .*$/\1/;
+		 	push(@cleanupcmds, "qdel $jobid 2> /dev/null");
+			print STDERR " $jobid";
+			if ($joblist == "") { $joblist = $jobid; }
+			else {$joblist = $joblist . "\|" . $jobid; }
+		}
+	}
+	my @dev_outs = ();
+	my @devtest_outs = ();
+	@dev_outs = @mapoutputs;
+	if ($use_make) {
+		print $mkfile "$dir/splag.$im1/map.done: @mkouts\n\ttouch $dir/splag.$im1/map.done\n\n";
+		close $mkfile;
+		my $mcmd = "make -j $jobs -f $mkfilename";
+		print STDERR "\nExecuting: $mcmd\n";
+		check_call($mcmd);
+	} else {
+		print STDERR "\nLaunched $nmappers mappers.\n";
+      		sleep 8;
+		print STDERR "Waiting for mappers to complete...\n";
+		while ($nmappers > 0) {
+		  sleep 5;
+		  my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat | grep -v ' C '")));
+		  $nmappers = scalar @livejobs;
+		}
+		print STDERR "All mappers complete.\n";
+	}
+	my $tol = 0;
+	my $til = 0;
+	my $dev_test_file = "$dir/splag.$im1/devtest.gz";
+	print STDERR "\nRUNNING CLASSIFIER (REDUCER)\n";
+	print STDERR unchecked_output("date");
+	$cmd="cat @dev_outs | $REDUCER -w $dir/weights.$im1 -C $reg -y $reg_previous --interpolate_with_weights $psi";
+        $cmd .= " > $dir/weights.$iteration";
+	print STDERR "COMMAND:\n$cmd\n";
+	check_bash_call($cmd);
+	$lastWeightsFile = "$dir/weights.$iteration";
+	$lastPScore = $score;
+	$iteration++;
+	print STDERR "\n==========\n";
+}
+
+
+check_call("cp $lastWeightsFile $dir/weights.final");
+print STDERR "\nFINAL WEIGHTS: $dir/weights.final\n(Use -w <this file> with the decoder)\n\n";
+print STDOUT "$dir/weights.final\n";
+
+exit 0;
+
+sub read_weights_file {
+  my ($file) = @_;
+  open F, "<$file" or die "Couldn't read $file: $!";
+  my @r = ();
+  my $pm = -1;
+  while(<F>) {
+    next if /^#/;
+    next if /^\s*$/;
+    chomp;
+    if (/^(.+)\s+(.+)$/) {
+      my $m = $1;
+      my $w = $2;
+      die "Weights out of order: $m <= $pm" unless $m > $pm;
+      push @r, $w;
+    } else {
+      warn "Unexpected feature name in weight file: $_";
+    }
+  }
+  close F;
+  return join ' ', @r;
+}
+
+sub 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 = basename($0); chomp $executable;
+	print << "Help";
+
+Usage: $executable [options]
+
+	$executable [options]
+		Runs a complete PRO optimization using the ini file specified.
+
+Required:
+
+	--config <cdec.ini>
+		Decoder configuration file.
+
+	--devset <files>
+		Dev set source and reference data.
+
+	--weights <file>
+		Initial weights file (use empty file to start from 0)
+
+General options:
+
+	--help
+		Print this message and exit.
+
+	--max-iterations <M>
+		Maximum number of iterations to run.  If not specified, defaults
+		to $default_max_iter.
+
+	--metric <method>
+		Metric to optimize.
+		Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
+
+	--pass-suffix <S>
+		If the decoder is doing multi-pass decoding, the pass suffix "2",
+		"3", etc., is used to control what iteration of weights is set.
+
+	--workdir <dir>
+		Directory for intermediate and output files.  If not specified, the
+		name is derived from the ini filename.  Assuming that the ini
+		filename begins with the decoder name and ends with ini, the default
+		name of the working directory is inferred from the middle part of
+		the filename.  E.g. an ini file named decoder.foo.ini would have
+		a default working directory name foo.
+
+Regularization options:
+
+	--reg <F>
+		l2 regularization strength [default=500]. The greater this value,
+		the closer to zero the weights will be.
+
+	--reg-previous <F>
+		l2 penalty for moving away from the weights from the previous
+		iteration. [default=5000]. The greater this value, the closer
+		to the previous iteration's weights the next iteration's weights
+		will be.
+
+Job control options:
+
+	--jobs <I>
+		Number of decoder processes to run in parallel. [default=$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)
+
+Deprecated options:
+
+	--interpolate-with-weights <F>
+		[deprecated] At each iteration the resulting weights are
+		interpolated with the weights from the previous iteration, with
+		this factor. [default=1.0, i.e., no effect]
+
+Help
+}
+
+sub convert {
+  my ($str) = @_;
+  my @ps = split /;/, $str;
+  my %dict = ();
+  for my $p (@ps) {
+    my ($k, $v) = split /=/, $p;
+    $dict{$k} = $v;
+  }
+  return %dict;
+}
+
+
+sub cmdline {
+    return join ' ',($0,@ORIG_ARGV);
+}
+
+#buggy: last arg gets quoted sometimes?
+my $is_shell_special=qr{[ \t\n\\><|&;"'`~*?{}$!()]};
+my $shell_escape_in_quote=qr{[\\"\$`!]};
+
+sub escape_shell {
+    my ($arg)=@_;
+    return undef unless defined $arg;
+    if ($arg =~ /$is_shell_special/) {
+        $arg =~ s/($shell_escape_in_quote)/\\$1/g;
+        return "\"$arg\"";
+    }
+    return $arg;
+}
+
+sub escaped_shell_args {
+    return map {local $_=$_;chomp;escape_shell($_)} @_;
+}
+
+sub escaped_shell_args_str {
+    return join ' ',&escaped_shell_args(@_);
+}
+
+sub escaped_cmdline {
+    return "$0 ".&escaped_shell_args_str(@ORIG_ARGV);
+}
+
+sub split_devset {
+  my ($infile, $outsrc, $outref) = @_;
+  open F, "<$infile" or die "Can't read $infile: $!";
+  open S, ">$outsrc" or die "Can't write $outsrc: $!";
+  open R, ">$outref" or die "Can't write $outref: $!";
+  while(<F>) {
+    chomp;
+    my ($src, @refs) = split /\s*\|\|\|\s*/;
+    die "Malformed devset line: $_\n" unless scalar @refs > 0;
+    print S "$src\n";
+    print R join(' ||| ', @refs) . "\n";
+  }
+  close R;
+  close S;
+  close F;
+}
+