Merge remote-tracking branch 'upstream/master'

5 files changed, 32 insertions, 648 deletions

diff --git a/extractor/README.md b/extractor/README.md
index 575f5ca5..c9db8de8 100644
--- a/extractor/README.md
+++ b/extractor/README.md
@@ -2,7 +2,7 @@ C++ implementation of the online grammar extractor originally developed by [Adam
 
 To run the extractor you need to:
 
-    cdec/extractor/run_extractor -a <alignment> -b <parallel_corpus> -g <grammar_output_path> < <input_sentences> > <sgm_file>
+    cdec/extractor/run_extractor -t <num_threads> -a <alignment> -b <parallel_corpus> -g <grammar_output_path> < <input_sentences> > <sgm_file>
 
 To run unit tests you need first to configure `cdec` with the [Google Test](https://code.google.com/p/googletest/) and [Google Mock](https://code.google.com/p/googlemock/) libraries:
 
diff --git a/klm/search/Makefile.am b/klm/search/Makefile.am
index b8c8a050..b7f01c24 100644
--- a/klm/search/Makefile.am
+++ b/klm/search/Makefile.am
@@ -1,10 +1,22 @@
 noinst_LIBRARIES = libksearch.a
 
 libksearch_a_SOURCES = \
+  applied.hh \
+  config.hh \
+  context.hh \
+  dedupe.hh \
+  edge.hh \
   edge_generator.cc \
-	nbest.cc \
+  edge_generator.hh \
+  header.hh \
+  nbest.cc \
+  nbest.hh \
   rule.cc \
-  vertex.cc
+  rule.hh \
+  types.hh \
+  vertex.cc \
+  vertex.hh \
+  vertex_generator.hh
 
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I..
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare -I..
 
diff --git a/klm/util/Makefile.am b/klm/util/Makefile.am
index 7f873e96..5e650af7 100644
--- a/klm/util/Makefile.am
+++ b/klm/util/Makefile.am
@@ -19,40 +19,42 @@
 noinst_LIBRARIES = libklm_util.a
 
 libklm_util_a_SOURCES = \
+  bit_packing.cc \
   bit_packing.hh \
+  ersatz_progress.cc \
   ersatz_progress.hh \
+  exception.cc \
   exception.hh \
+  fake_ofstream.hh \
+  file.cc \
   file.hh \
+  file_piece.cc \
   file_piece.hh \
   getopt.hh \
   have.hh \
   joint_sort.hh \
+  mmap.cc \
   mmap.hh \
+  multi_intersection.hh \
+  murmur_hash.cc \
   murmur_hash.hh \
   pcqueue.hh \
+  pool.cc \
   pool.hh \
   probing_hash_table.hh \
   proxy_iterator.hh \
+  read_compressed.cc \
   read_compressed.hh \
+  scoped.cc \
   scoped.hh \
   sized_iterator.hh \
   sorted_uniform.hh \
+  string_piece.cc \
   string_piece.hh \
   string_piece_hash.hh \
   thread_pool.hh \
   tokenize_piece.hh \
-  usage.hh \
-  ersatz_progress.cc \
-  bit_packing.cc \
-  exception.cc \
-	file.cc \
-  file_piece.cc \
-  mmap.cc \
-  murmur_hash.cc \
-  pool.cc \
-	read_compressed.cc \
-  scoped.cc \
-  string_piece.cc \
-	usage.cc
+  usage.cc \
+  usage.hh
 
 AM_CPPFLAGS = -W -Wall -I$(top_srcdir)/klm -I$(top_srcdir)/klm/util/double-conversion
diff --git a/training/mira/mira.py b/training/mira/mira.py
index f031c313..29c51e1d 100755
--- a/training/mira/mira.py
+++ b/training/mira/mira.py
@@ -96,7 +96,7 @@ def main():
   parser.add_argument('-m', '--metric', default='ibm_bleu',
                       help='metric to optimize. Example values: '
                            'ibm_bleu, nist_bleu, Koehn_bleu, TER, Combi')
-  parser.add_argument('--max-iterations', type=int, default=10, metavar='N',
+  parser.add_argument('--max-iterations', type=int, default=20, metavar='N',
                       help='maximum number of iterations to run')
   parser.add_argument('--optimizer', type=int, default=2, choices=range(1,6),
                       help='learning method to use for weight update.'
diff --git a/training/mira/run_mira.pl b/training/mira/run_mira.pl
deleted file mode 100755
index d71590ba..00000000
--- a/training/mira/run_mira.pl
+++ /dev/null
@@ -1,630 +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 $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 $iteration = 0.0;
-my $max_iterations = 10;
-my $metric = "ibm_bleu";
-my $iniFile;
-my $weights;
-my $initialWeights;
-my $jobs = $default_jobs;   # number of decode nodes
-my $pmem = "1g";
-my $dir;
-
-my $SCORER = $FAST_SCORE;
-
-my $UTILS_DIR="$SCRIPT_DIR/../utils";
-require "$UTILS_DIR/libcall.pl";
-
-my $parallelize = "$UTILS_DIR/parallelize.pl";
-my $libcall = "$UTILS_DIR/libcall.pl";
-my $sentserver = "$UTILS_DIR/sentserver";
-my $sentclient = "$UTILS_DIR/sentclient";
-
-my $run_local = 0;
-my $pass_suffix = '';
-
-my $cdec ="$bin_dir/kbest_cut_mira"; 
-
-die "Can't find decoder in $cdec" unless -x $cdec;
-my $decoder = $cdec;
-my $decoderOpt;
-my $update_size;
-my $approx_score;
-my $kbest_size=250;
-my $metric_scale=1;
-my $optimizer=2;
-my $disable_clean = 0;
-my $use_make=0;  
-my $density_prune;
-my $cpbin=1;
-my $help = 0;
-my $epsilon = 0.0001;
-my $step_size = 0.01;
-my $gpref;
-my $unique_kbest;
-my $freeze;
-my $hopes=1;
-my $fears=1;
-my $sent_approx=0;
-my $pseudo_doc=0;
-
-my $range = 35000;
-my $minimum = 15000;
-my $portn = int(rand($range)) + $minimum;
-
-
-# Process command-line options
-Getopt::Long::Configure("no_auto_abbrev");
-if (GetOptions(
-        "decoder=s" => \$decoderOpt,
-        "jobs=i" => \$jobs,
-        "density-prune=f" => \$density_prune,
-        "dont-clean" => \$disable_clean,
-        "pass-suffix=s" => \$pass_suffix,
-        "epsilon=s" => \$epsilon,
-        "help" => \$help,
-        "local" => \$run_local,
-        "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,
-        "weights=s" => \$initialWeights,
-	"optimizer=i" => \$optimizer,
-	"metric-scale=i" => \$metric_scale,
-	"kbest-size=i" => \$kbest_size,
-	"update-size=i" => \$update_size,
-	"step-size=f" => \$step_size,
-	"hope-select=i" => \$hopes,
-	"fear-select=i" => \$fears,
-	"sent-approx" => \$sent_approx,
-        "pseudo-doc" => \$pseudo_doc,
-	"unique-kbest" => \$unique_kbest,
-        "grammar-prefix=s" => \$gpref,
-	"freeze" => \$freeze,
-        "workdir=s" => \$dir,
-	) == 0 || @ARGV!=1 || $help) {
-        print_help();
-        exit;
-}
-
-($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;
-
-
-#my $refs_comma_sep = get_comma_sep_refs($refFiles);
-my $refs_comma_sep = get_comma_sep_refs('r',$refFiles);
-
-#my $refs_comma_sep_4cdec = get_comma_sep_refs_4cdec($refFiles);
-
-unless ($dir){
-        $dir = "mira";
-}
-unless ($dir =~ /^\//){  # convert relative path to absolute path
-        my $basedir = check_output("pwd");
-        chomp $basedir;
-        $dir = "$basedir/$dir";
-}
-
-if ($decoderOpt){ $decoder = $decoderOpt; }
-
-# 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;
-}
-
-
-
-
-if (-e $dir && dirsize($dir)>1 && -e "$dir/weights" ){ # allow preexisting logfile, binaries, but not dist-vest.pl outputs
-    die "ERROR: working dir $dir already exists\n\n";
-} else {
-    -e $dir || mkdir $dir;
-    mkdir "$dir/scripts";
-    my $cmdfile="$dir/rerun-mira.sh";
-    open CMD,'>',$cmdfile;
-    print CMD "cd ",&getcwd,"\n";
-    my $cline=&cmdline."\n";
-    print CMD $cline;
-    close CMD;
-    print STDERR $cline;
-    chmod(0755,$cmdfile);
-    unless (-e $initialWeights) {
-        print STDERR "Please specify an initial weights file with --initial-weights\n";
-        print_help();
-        exit;
-    }
-    check_call("cp $initialWeights $dir/weights.0");
-    die "Can't find weights.0" unless (-e "$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, $gpref);
-
-$srcFile = $newsrc;
-my $devSize = 0;
-open F, "<$srcFile" or die "Can't read $srcFile: $!";
-while(<F>) { $devSize++; }
-close F;
-
-my $lastPScore = 0;
-my $lastWeightsFile;
-my $bestScoreIter=-1;
-my $bestScore=-1;
-unless ($update_size){$update_size = $kbest_size;}
-# main optimization loop
-#while (1){
-for (my $opt_iter=0; $opt_iter<$max_iterations; $opt_iter++) {
-
-	print STDERR "\n\nITERATION $opt_iter\n==========\n";
-	print STDERR "Using port $portn\n";
-
-	# iteration-specific files
-	my $runFile="$dir/run.raw.$opt_iter";
-	my $onebestFile="$dir/1best.$opt_iter";
-	my $logdir="$dir/logs.$opt_iter";
-	my $decoderLog="$logdir/decoder.sentserver.log.$opt_iter";
-	my $scorerLog="$logdir/scorer.log.$opt_iter";
-	my $weightdir="$dir/weights.pass$opt_iter/";
-	check_call("mkdir -p $logdir");
-	check_call("mkdir -p $weightdir");
-
-	#decode
-	print STDERR "RUNNING DECODER AT ";
-	print STDERR unchecked_output("date");
-#	my $im1 = $opt_iter - 1;
-	my $weightsFile="$dir/weights.$opt_iter";
-	print "ITER $iteration " ;
-	my $cur_pass = "-p 0$opt_iter";
-	my $decoder_cmd = "$decoder -c $iniFile -w $weightsFile $refs_comma_sep -m $metric -s $metric_scale -b $update_size -k $kbest_size -o $optimizer $cur_pass -O $weightdir -D $dir  -h $hopes -f $fears -C $step_size";
-	if($unique_kbest){
-		$decoder_cmd .= " -u";
-	}
-	if($sent_approx){
-		$decoder_cmd .= " -a";
-	}
-	if($pseudo_doc){
-                $decoder_cmd .= " -e";
-        }
-	if ($density_prune) {
-		$decoder_cmd .= " --density_prune $density_prune";
-	}
-	my $pcmd;
-	if ($run_local) {
-		$pcmd = "cat $srcFile |";
-	} elsif ($use_make) {
-	    # TODO: Throw error when jobs is speong with use_make
-		$pcmd = "cat $srcFile | $parallelize --use-fork -p $pmem -e $logdir -j $use_make --";
-	} 
-	else {
-	    $pcmd = "cat $srcFile | $parallelize -p $pmem -e $logdir -j $jobs --baseport $portn --";
-	}
-	my $cmd = "$pcmd $decoder_cmd 2> $decoderLog 1> $runFile";
-	print STDERR "COMMAND:\n$cmd\n";
-	check_bash_call($cmd);
-
-	my $retries = 0;
-        my $num_topbest;
-        while($retries < 6) {
-            $num_topbest = check_output("wc -l < $runFile");
-            print STDERR "NUMBER OF TOP-BEST HYPs: $num_topbest\n";
-            if($devSize == $num_topbest) {
-                last;
-            } else {
-                print STDERR "Incorrect number of topbest. Waiting for distributed filesystem and retrying...\n";
-                sleep(10);
-            }
-            $retries++;
-        }
-	 die "Dev set contains $devSize sentences, but we don't have topbest for all these! Decoder failure? Check $decoderLog\n" if ($devSize != $num_topbest);
-
-
-	#score the output from this iteration
-	open RUN, "<$runFile" or die "Can't read $runFile: $!";
-	open H, ">$runFile.H" or die;
-	open F, ">$runFile.F" or die;
-	open B, ">$runFile.B" or die;
-	while(<RUN>) {
-	    chomp();
-	    (my $hope,my $best,my $fear) = split(/ \|\|\| /);
-	    print H "$hope \n"; 	    
-	    print B "$best \n";
- 	    print F "$fear \n";
-	}
-	close RUN;
-	close F; close B; close H;
-	
-	my $dec_score = check_output("cat $runFile.B | $SCORER $refs_comma_sep -m $metric");
-	my $dec_score_h = check_output("cat $runFile.H | $SCORER $refs_comma_sep -m $metric");
-	my $dec_score_f = check_output("cat $runFile.F | $SCORER $refs_comma_sep -m $metric");
-	chomp $dec_score; chomp $dec_score_h; chomp $dec_score_f;
-	print STDERR "DECODER SCORE: $dec_score HOPE: $dec_score_h FEAR: $dec_score_f\n";
-	if ($dec_score> $bestScore){
-		$bestScoreIter=$opt_iter; 
-		$bestScore=$dec_score;
-	}
-	# save space
-	check_call("gzip -f $runFile");
-	check_call("gzip -f $decoderLog");
-		my $iter_filler="";
-	if($opt_iter < 10)
-	{$iter_filler="0";}
-
-	my $nextIter = $opt_iter + 1;
-	my $newWeightsFile = "$dir/weights.$nextIter";
-	$lastWeightsFile = "$dir/weights.$opt_iter";
-
-	average_weights("$weightdir/weights.mira-pass*.*[0-9].gz", $newWeightsFile, $logdir);
-	system("gzip -f $logdir/kbes*");
-	print STDERR "\n==========\n";
-	$iteration++;
-}
-print STDERR "\nBEST ITER: $bestScoreIter :: $bestScore\n\n\n";
-
-print STDOUT "$lastWeightsFile\n";
-
-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;
-}
-
-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 "DECODE NODES:     $jobs\n";
-	print $fh "HEAD NODE:        $host\n";
-	print $fh "PMEM (DECODING):  $pmem\n";
-	print $fh "CLEANUP:          $cleanup\n";
-	print $fh "INITIAL WEIGHTS:  $initialWeights\n";
-        print $fh "GRAMMAR PREFIX:   $gpref\n";
-}
-
-sub update_weights_file {
-  my ($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;
-    my $grammarpref = 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";
-	    }
-	}
-	elsif (defined $grammarpref) {
-	    print NEWSRC "<seg id=\"$i\" grammar=\"$grammarpref.$i.gz\">$line</seg>\n";}
-	else {
-	    print NEWSRC "<seg id=\"$i\">$line</seg>\n";
-	}
-	$i++;
-    }
-    close SRC;
-    close NEWSRC;
-}
-
-sub print_help {
- my $executable = check_output("basename $0"); chomp $executable;
-        print << "Help";
-
-Usage: $executable [options] <ini file>
-        Runs a complete MIRA optimization using the ini file specified.
-	Example invocation:
-	run_mira.pl \
-        --pmem 3g \
-        --max-iterations 20 \
-        --optimizer 2 \
-        --unique-kbest \
-        --jobs 15 \
-        --kbest-size 500 \
-        --hope-select 1 \
-        --fear-select 1  \
-        --ref-files "ref.0.soseos ref.1.soseos" \
-        --source-file src.soseos \
-        --weights weights.init \
-        --workdir workdir \
-        --grammar-prefix grammars/grammar \
-        --step-size 0.01 \
-        --metric-scale 10000 \
-
-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
-
-General options:
-
-        --help
-                Print this message and exit.
-
-       --max-iterations <M>
-                Maximum number of iterations to run.  If not specified, defaults
-                to $max_iterations.
-
-        --metric <method>
-                Metric to optimize.
-                Example values: IBM_BLEU, NIST_BLEU, Koehn_BLEU, TER, Combi
-
-        --workdir <dir>
-                Directory for intermediate and output files.  If not specified, the
-                name is derived from the ini filename.  Assuming that the ini
-                filename begins with the decoder name and ends with ini, the default
-                name of the working directory is inferred from the middle part of
-                the filename.  E.g. an ini file named decoder.foo.ini would have
-                a default working directory name foo.
-	--optimizer <I>
-		Learning method to use for weight update. Choice are 1) SGD, 2) PA MIRA with Selection from Cutting Plane, 3) Cutting Plane MIRA, 4) PA MIRA,5) nbest MIRA with hope, fear, and model constraints
-	--metric-scale <I>
-		Scale MT loss by this amount when computing hope/fear candidates
-	--kbest-size <I>
-		Size of k-best list to extract from forest
-	--update-size <I>
-		Size of k-best list to use for update (applies to optimizer 5)
-	--step-size <F>
-		Controls aggresiveness of update (C) 
-	--hope-select<I>
-		How to select hope candidate. Choices are 1) model score - cost, 2) min cost
-	--fear-select <I>
-		How to select fear candodate. Choices are 1) model score + cost, 2) max cost, 3) max score
-	--sent-approx
-		Use smoothed sentence-level MT metric
-	--pseudo-doc
-		Use pseudo document to approximate MT metric
-	--unique-kbest
-		Extract unique k-best from forest
-	--grammar-prefix <path>
-		Path to sentence-specific grammar files
-
-Job control options:
-
-        --jobs <I>
-                Number of decoder processes to run in parallel. [default=$default_jobs]
-
-        --pmem <N>
-                Amount of physical memory requested for parallel decoding jobs
-                (used with qsub requests only)
-
-	--local 
-		Run single learner
-	--use-make <I>
-		Run parallel learners on a single machine through fork.
-
-
-Help
-}
-
-
-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 average_weights {
-
-    my $path = shift;
-    my $out = shift;
-    my $logpath = shift;
-    print "AVERAGE $path $out\n";
-    my %feature_weights= ();
-    my $total =0;
-    my $total_mult =0;
-    sleep(10);
-    foreach my $file (glob "$path")
-    {
-	$file =~ /\/([^\/]+).gz$/;
-	my $fname = $1;
-	my $cmd = "gzip -d $file";
-	$file =~ s/\.gz//;
-	check_bash_call($cmd);
-	my $mult = 0;
-	print "FILE $file \n";
-	open SCORE, "< $file" or next;
-	$total++;
-	while( <SCORE> ) {
-	    my $line = $_;
-	    if ($line !~ m/^\#/)
-	    {
-		my @s = split(" ",$line);
-		$feature_weights{$s[0]}+= $mult * $s[1];
-	    }
-	    else
-	    {
-		(my $msg,my $ran,$mult) = split(/ \|\|\| /);
-		print "Processing $ran $mult\n";
-	    }
-	}
-	$total_mult += $mult;
-	
-	close SCORE;
-	$cmd = "gzip $file"; check_bash_call($cmd);
-    }
-    
-#print out new averaged weights
-    open OUT, "> $out" or next;
-    for my $f ( keys %feature_weights ) {
-	print "$f $feature_weights{$f} $total_mult\n";
-	my $ave = $feature_weights{$f} / $total_mult;
-	
-	print "Printing $f $ave ||| ";
-	print OUT "$f $ave\n";
-    }
-    
-}