initial check in

1 files changed, 642 insertions, 0 deletions

diff --git a/vest/dist-vest.pl b/vest/dist-vest.pl
new file mode 100755
index 00000000..5528838c
--- /dev/null
+++ b/vest/dist-vest.pl
@@ -0,0 +1,642 @@
+#!/usr/bin/env perl
+
+use Getopt::Long;
+use IPC::Open2;
+use strict;
+use POSIX ":sys_wait_h";
+
+my $mydir = `dirname $0`;
+chomp $mydir;
+# Default settings
+my $srcFile = "/fs/cliplab/mteval/Evaluation/Chinese-English/mt03.src.txt";
+my $refFiles = "/fs/cliplab/mteval/Evaluation/Chinese-English/mt03.ref.txt.*";
+my $bin_dir = "/fs/clip-software/cdec/bin";
+$bin_dir = "/Users/redpony/cdyer-svn-root/cdec/vest/bin_dir";
+die "Bin directory $bin_dir missing/inaccessible" unless -d $bin_dir;
+my $FAST_SCORE="$bin_dir/fast_score";
+die "Can't find $FAST_SCORE" unless -x $FAST_SCORE;
+my $MAPINPUT = "$bin_dir/mr_vest_generate_mapper_input";
+my $MAPPER = "$bin_dir/mr_vest_map";
+my $REDUCER = "$bin_dir/mr_vest_reduce";
+my $SCORER = $FAST_SCORE;
+die "Can't find $MAPPER" unless -x $MAPPER;
+my $forestUnion = "$bin_dir/union_forests";
+die "Can't find $forestUnion" unless -x $forestUnion;
+my $cdec = "$bin_dir/cdec";
+die "Can't find decoder in $cdec" unless -x $cdec;
+my $decoder = $cdec;
+my $lines_per_mapper = 440;
+my $rand_directions = 10;
+my $iteration = 1;
+my $run_local = 0;
+my $best_weights;
+my $max_iterations = 40;
+my $optimization_iters = 6;
+my $num_rand_points = 20;
+my $mert_nodes = join(" ", grep(/^c\d\d$/, split(/\n/, `pbsnodes -a`))); # "1 1 1 1 1" fails due to file staging conflicts
+my $decode_nodes = "1 1 1 1 1 1 1 1 1 1 1 1 1 1 1";  # start 15 jobs
+my $pmem = "3g";
+my $disable_clean = 0;
+my %seen_weights;
+my $normalize;
+my $help = 0;
+my $epsilon = 0.0001;
+my $interval = 5;
+my $dryrun = 0;
+my $ranges;
+my $restart = 0;
+my $metric = "ibm_bleu";
+my $dir;
+my $iniFile;
+my $weights;
+my $initialWeights;
+my $decoderOpt;
+
+# Process command-line options
+Getopt::Long::Configure("no_auto_abbrev");
+if (GetOptions(
+	"decoder=s" => \$decoderOpt,
+	"decode-nodes=s" => \$decode_nodes,
+	"dont-clean" => \$disable_clean,
+	"dry-run" => \$dryrun,
+	"epsilon" => \$epsilon,
+	"help" => \$help,
+	"interval" => \$interval,
+	"iteration=i" => \$iteration,
+	"local" => \$run_local,
+	"max-iterations=i" => \$max_iterations,
+	"mert-nodes=s" => \$mert_nodes,
+	"normalize=s" => \$normalize,
+	"pmem=s" => \$pmem,
+	"ranges=s" => \$ranges,
+	"rand-directions=i" => \$rand_directions,
+	"ref-files=s" => \$refFiles,
+	"metric=s" => \$metric,
+	"restart" => \$restart,
+	"source-file=s" => \$srcFile,
+	"weights=s" => \$initialWeights,
+	"workdir=s" => \$dir
+) == 0 || @ARGV!=1 || $help) {
+	print_help();
+	exit;
+}
+
+if ($metric =~ /^(combi|ter)$/i) {
+  $lines_per_mapper = 40;
+}
+
+($iniFile) = @ARGV;
+
+sub write_config;
+sub enseg;
+sub print_help;
+
+my $nodelist;
+my $host =`hostname`; chomp $host;
+my $bleu;
+my $best_bleu = 0.0;
+my $interval_count = 0;
+my $epsilon_bleu = $best_bleu + $epsilon;
+my $logfile;
+my $projected_score;
+
+my $refs_comma_sep = get_comma_sep_refs($refFiles);
+
+unless ($dir){ 
+	$dir = "vest";
+}
+unless ($dir =~ /^\//){  # convert relative path to absolute path
+	my $basedir = `pwd`;
+	chomp $basedir;
+	$dir = "$basedir/$dir";
+}
+if ($restart){
+	$iniFile = `ls $dir/*.ini`; chomp $iniFile;
+	unless (-e $iniFile){
+		die "ERROR: Could not find ini file in $dir to restart\n";
+	}
+	$logfile = "$dir/mert.log";
+	open(LOGFILE, ">>$logfile");
+	print LOGFILE "RESTARTING STOPPED OPTIMIZATION\n\n";
+
+	# figure out best weights so far and iteration number
+	open(LOG, "$dir/mert.log");
+	my $wi = 0;
+	while (my $line = <LOG>){
+		chomp $line;
+		if ($line =~ /ITERATION (\d+)/) {
+			$iteration = $1;
+		}
+	}
+
+	$iteration = $wi + 1;
+}
+
+if ($decoderOpt){ $decoder = $decoderOpt; }
+
+
+# Initializations and helper functions
+srand;
+
+my @childpids = ();
+my @cleanupcmds = ();
+
+sub cleanup {
+	print STDERR "Cleanup...\n";
+	for my $pid (@childpids){ `kill $pid`; }
+	for my $cmd (@cleanupcmds){`$cmd`; }
+	exit 1;
+};
+$SIG{INT} = "cleanup";
+$SIG{TERM} = "cleanup"; 
+$SIG{HUP} = "cleanup";
+
+my $decoderBase = `basename $decoder`; chomp $decoderBase;
+my $newIniFile = "$dir/$decoderBase.ini";
+my $parallelize = "$mydir/parallelize.pl";
+my $inputFileName = "$dir/input";
+my $user = $ENV{"USER"};
+
+# process ini file
+-e $iniFile || die "Error: could not open $iniFile for reading\n";
+open(INI, $iniFile);
+
+if ($dryrun){
+	write_config(*STDERR);
+	exit 0;
+} else {
+	if (-e $dir){
+		unless($restart){
+			die "ERROR: working dir $dir already exists\n\n";
+		}
+	} else {
+		mkdir $dir;
+		mkdir "$dir/hgs";
+		mkdir "$dir/hgs-current";
+		unless (-e $initialWeights) {
+			print STDERR "Please specify an initial weights file with --initial-weights\n";
+			print_help();
+			exit;
+		}
+		`cp $initialWeights $dir/weights.0`;
+		die "Can't find weights.0" unless (-e "$dir/weights.0");
+	}
+	unless($restart){
+		$logfile = "$dir/mert.log";
+		open(LOGFILE, ">$logfile");
+	}
+	write_config(*LOGFILE);
+}
+
+
+# Generate initial files and values
+unless ($restart){ `cp $iniFile $newIniFile`; }
+$iniFile = $newIniFile;
+
+my $newsrc = "$dir/dev.input";
+unless($restart){ enseg($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 $random_seed = int(time / 1000);
+my $lastWeightsFile;
+my $lastPScore = 0;
+# main optimization loop
+while (1){
+	print LOGFILE "\n\nITERATION $iteration\n==========\n";
+
+	# 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";
+	`mkdir -p $logdir`;
+
+	#decode
+	print LOGFILE "DECODE\n";
+	print LOGFILE `date`;
+	my $im1 = $iteration - 1;
+	my $weightsFile="$dir/weights.$im1";
+	my $decoder_cmd = "$decoder -c $iniFile -w $weightsFile -O $dir/hgs-current";
+	my $pcmd = "cat $srcFile | $parallelize -p $pmem -e $logdir -n \"$decode_nodes\" -- ";
+        if ($run_local) { $pcmd = "cat $srcFile |"; }
+        my $cmd = $pcmd . "$decoder_cmd 2> $decoderLog 1> $runFile";
+	print LOGFILE "COMMAND:\n$cmd\n";
+	my $result = 0;
+	$result = system($cmd);
+	unless ($result == 0){
+		cleanup();
+		print LOGFILE "ERROR: Parallel decoder returned non-zero exit code $result\n";
+		die;
+	}
+	my $dec_score = `cat $runFile | $SCORER $refs_comma_sep -l $metric`;
+	chomp $dec_score;
+	print LOGFILE "DECODER SCORE: $dec_score\n";
+
+	# save space
+	`gzip $runFile`;
+	`gzip $decoderLog`;
+
+	if ($iteration > $max_iterations){
+		print LOGFILE "\nREACHED STOPPING CRITERION: Maximum iterations\n";
+		last;
+	}
+	
+	# run optimizer
+	print LOGFILE "\nUNION FORESTS\n";
+	print LOGFILE `date`;
+	my $mergeLog="$logdir/prune-merge.log.$iteration";
+	$cmd = "$forestUnion -r $dir/hgs -n $dir/hgs-current -s $devSize";
+	print LOGFILE "COMMAND:\n$cmd\n";
+	$result = system($cmd);
+	unless ($result == 0){
+		cleanup();
+		print LOGFILE "ERROR: merge command returned non-zero exit code $result\n";
+		die;
+	}
+	`rm -f $dir/hgs-current/*.json.gz`; # clean up old HGs, they've been moved to the repository
+
+	my $score = 0;
+	my $icc = 0;
+	my $inweights="$dir/weights.$im1";
+	for (my $opt_iter=1; $opt_iter<$optimization_iters; $opt_iter++) {
+		print LOGFILE "\nGENERATE OPTIMIZATION STRATEGY (OPT-ITERATION $opt_iter/$optimization_iters)\n";
+		print LOGFILE `date`;
+		$icc++;
+		$cmd="$MAPINPUT -w $inweights -r $dir/hgs -s $devSize -d $rand_directions > $dir/agenda.$im1-$opt_iter";
+		print LOGFILE "COMMAND:\n$cmd\n";
+		$result = system($cmd);
+		unless ($result == 0){
+			cleanup();
+			print LOGFILE "ERROR: mapinput command returned non-zero exit code $result\n";
+			die;
+		}
+
+	        `mkdir $dir/splag.$im1`;
+		$cmd="split -a 3 -l $lines_per_mapper $dir/agenda.$im1-$opt_iter $dir/splag.$im1/mapinput.";
+		print LOGFILE "COMMAND:\n$cmd\n";
+		$result = system($cmd);
+		unless ($result == 0){
+			cleanup();
+			print LOGFILE "ERROR: split command returned non-zero exit code $result\n";
+			die;
+		}
+		opendir(DIR, "$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;
+		my @mapoutputs = ();
+		@cleanupcmds = ();
+		my %o2i = ();
+		my $first_shard = 1;
+		for my $shard (@shards) {
+			my $mapoutput = $shard;
+			my $client_name = $shard;
+			$client_name =~ s/mapinput.//;
+			$client_name = "fmert.$client_name";
+			$mapoutput =~ s/mapinput/mapoutput/;
+			push @mapoutputs, "$dir/splag.$im1/$mapoutput";
+			$o2i{"$dir/splag.$im1/$mapoutput"} = "$dir/splag.$im1/$shard";
+			my $script = "$MAPPER -l $metric $refs_comma_sep < $dir/splag.$im1/$shard | sort -k1 > $dir/splag.$im1/$mapoutput";
+			if ($run_local) {
+				print LOGFILE "COMMAND:\n$script\n";
+				$result = system($script);
+				unless ($result == 0){
+					cleanup();
+					print LOGFILE "ERROR: mapper returned non-zero exit code $result\n";
+					die;
+				}
+			} else {
+				my $todo = "qsub -q batch -l pmem=3000mb,walltime=5:00:00 -N $client_name -o /dev/null -e $logdir/$client_name.ER";
+				local(*QOUT, *QIN);
+				open2(\*QOUT, \*QIN, $todo);
+				print QIN $script;
+				if ($first_shard) { print LOGFILE "$script\n"; $first_shard=0; }
+				close QIN;
+				$nmappers++;
+				while (my $jobid=<QOUT>){
+	  				chomp $jobid;
+		  			push(@cleanupcmds, "`qdel $jobid 2> /dev/null`");
+					$jobid =~ s/^(\d+)(.*?)$/\1/g;
+					print STDERR "short job id $jobid\n";
+					if ($joblist == "") { $joblist = $jobid; }
+					else {$joblist = $joblist . "\|" . $jobid; }
+				}
+				close QOUT;
+			}
+		}
+		if ($run_local) {
+		} else {
+			print LOGFILE "Launched $nmappers mappers.\n";
+			print LOGFILE "Waiting for mappers to complete...\n";
+			while ($nmappers > 0) {
+			  sleep 5;
+			  my @livejobs = grep(/$joblist/, split(/\n/, `qstat`));
+			  $nmappers = scalar @livejobs;
+			}
+			print LOGFILE "All mappers complete.\n";
+		}
+		my $tol = 0;
+		my $til = 0;
+		for my $mo (@mapoutputs) {
+		  my $olines = get_lines($mo);
+		  my $ilines = get_lines($o2i{$mo});
+		  $tol += $olines;
+		  $til += $ilines;
+		  die "$mo: output lines ($olines) doesn't match input lines ($ilines)" unless $olines==$ilines;
+		}
+		print LOGFILE "Results for $tol/$til lines\n";
+		print LOGFILE "\nSORTING AND RUNNING FMERT REDUCER\n";
+		print LOGFILE `date`;
+		$cmd="sort -k1 @mapoutputs | $REDUCER > $dir/redoutput.$im1";
+		print LOGFILE "COMMAND:\n$cmd\n";
+		$result = system($cmd);
+		unless ($result == 0){
+			cleanup();
+			print LOGFILE "ERROR: reducer command returned non-zero exit code $result\n";
+			die;
+		}
+		$cmd="sort -rnk3 '-t|' $dir/redoutput.$im1 | head -1";
+		my $best=`$cmd`; chomp $best;
+		print LOGFILE "$best\n";
+		my ($oa, $x, $xscore) = split /\|/, $best;
+		$score = $xscore;
+		print LOGFILE "PROJECTED SCORE: $score\n";
+		if (abs($x) < $epsilon) {
+			print LOGFILE "\nOPTIMIZER: no score improvement: abs($x) < $epsilon\n";
+			last;
+		}
+		my ($origin, $axis) = split /\s+/, $oa;
+
+		my %ori = convert($origin);
+		my %axi = convert($axis);
+
+		my $finalFile="$dir/weights.$im1-$opt_iter";
+		open W, ">$finalFile" or die "Can't write: $finalFile: $!";
+		for my $k (sort keys %ori) {
+			my $v = $ori{$k} + $axi{$k} * $x;
+			print W "$k $v\n";
+		}
+
+		`rm -rf $dir/splag.$im1`;
+		$inweights = $finalFile;
+	}
+	$lastWeightsFile = "$dir/weights.$iteration";
+	`cp $inweights $lastWeightsFile`;
+	if ($icc < 2) {
+		print LOGFILE "\nREACHED STOPPING CRITERION: score change too little\n";
+		last;
+	}
+	$lastPScore = $score;
+	$iteration++;
+	print LOGFILE "\n==========\n";
+}
+
+print LOGFILE "\nFINAL WEIGHTS: $dir/$lastWeightsFile\n(Use -w <this file> with hiero)\n\n";
+
+sub normalize_weights {
+  my ($rfn, $rpts, $feat) = @_;
+  my @feat_names = @$rfn;
+  my @pts = @$rpts;
+  my $z = 1.0;
+  for (my $i=0; $i < scalar @feat_names; $i++) {
+    if ($feat_names[$i] eq $feat) {
+      $z = $pts[$i];
+      last;
+    }
+  }
+  for (my $i=0; $i < scalar @feat_names; $i++) {
+    $pts[$i] /= $z;
+  }
+  print LOGFILE " NORM WEIGHTS: @pts\n";
+  return @pts;
+}
+
+sub get_lines {
+  my $fn = shift @_;
+  open FL, "<$fn" or die "Couldn't read $fn: $!";
+  my $lc = 0;
+  while(<FL>) { $lc++; }
+  return $lc;
+}
+
+sub get_comma_sep_refs {
+  my ($p) = @_;
+  my $o = `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 "START ITERATION:  $iteration\n";
+	print $fh "MAX ITERATIONS:   $max_iterations\n";
+	print $fh "MERT NODES:       $mert_nodes\n";
+	print $fh "DECODE NODES:     $decode_nodes\n";
+	print $fh "HEAD NODE:        $host\n";
+	print $fh "PMEM (DECODING):  $pmem\n";
+	print $fh "CLEANUP:          $cleanup\n";
+	print $fh "INITIAL WEIGHTS:  $initialWeights\n";
+
+	if ($restart){
+		print $fh "PROJECTED BLEU:   $projected_score\n";
+		print $fh "BEST WEIGHTS:     $best_weights\n";
+		print $fh "BEST BLEU:        $best_bleu\n";
+	}
+}
+
+sub update_weights_file {
+  my ($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 $line;
+		print NEWSRC "<seg id=\"$i\">$line</seg>\n";
+		$i++;
+	}
+	close SRC;
+	close NEWSRC;
+}
+
+sub print_help {
+
+	my $executable = `basename $0`; chomp $executable;
+    print << "Help";
+
+Usage: $executable [options] <ini file>
+       $executable --restart <work dir>
+
+	$executable [options] <ini file> 
+		Runs a complete MERT optimization and test set decoding, using 
+		the decoder configuration in ini file.  Note that many of the
+		options have default values that are inferred automatically 
+		based on certain conventions.  For details, refer to descriptions
+		of the options --decoder, --weights, and --workdir. 
+
+	$executable --restart <work dir>
+		Continues an optimization run that was stopped for some reason,
+		using configuration information found in the working directory
+		left behind by the stopped run.
+
+Options:
+
+	--local
+		Run the decoder and optimizer locally.
+
+	--decoder <decoder path>
+		Decoder binary to use.
+
+	--decode-nodes <nodelist>
+		A list of nodes used for parallel decoding.  If specific nodes 
+		are not desired, use "1" for each node requested.  Defaults to 
+		"1 1 1 1 1 1 1 1 1 1 1 1 1 1 1", which indicates a request for 
+		15 nodes.
+
+	--dont-clean
+		 If present, this flag prevents intermediate files, including
+		 run files and cumulative files, from being automatically removed
+		 after a successful optimization run (these files are left if the
+		 run fails for any reason).  If used, a makefile containing
+		 cleanup commands is written to the directory.  To clean up
+		 the intermediate files, invoke make without any arguments.
+
+	--dry-run
+		Prints out the settings and exits without doing anything.
+
+	--epsilon <epsilon>
+		Require that the dev set BLEU score improve by at least <epsilon>
+		within <interval> iterations (controlled by parameter --interval).
+		If not specified, defaults to .002.
+
+	--help
+		Print this message and exit.
+
+	--interval <i>
+		Require that the dev set BLEU score improve by at least <epsilon>
+		(controlled by parameter --epsilon) within <interval> iterations.
+		If not specified, defaults to 5.
+
+	--iteration <I> 
+		Starting iteration number.  If not specified, defaults to 1.
+
+	--max-iterations <M> 
+		Maximum number of iterations to run.  If not specified, defaults
+		to 10.
+
+	--pmem <N>
+		Amount of physical memory requested for parallel decoding jobs,
+		in the format expected by qsub.  If not specified, defaults to
+		2g.
+
+	--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.  If not specified, defaults to
+		/fs/cliplab/mteval/Evaluation/Chinese-English/mt03.ref.txt.* 
+
+	--metric <method>
+		Metric to optimize.  See fmert's --metric option for values.
+		Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
+
+	--normalize <feature-name>
+		After each iteration, rescale all feature weights such that feature-
+		name has a weight of 1.0.
+
+	--rand-directions <num>
+		MERT will attempt to optimize along all of the principle directions,
+		set this parameter to explore other directions. Defaults to 5.
+
+	--source-file <file> 
+		Dev set source file.  If not specified, defaults to
+		/fs/cliplab/mteval/Evaluation/Chinese-English/mt03.src.txt
+
+	--weights <file> 
+		A file specifying initial feature weights.  The format is
+		FeatureName_1 value1
+		FeatureName_2 value2
+
+	--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.
+
+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;
+}
+
+