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mosesdecoder/scripts/generic/moses-parallel.pl

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#! /usr/bin/perl
# $Id$
#######################
# Revision history
#
# 02 Aug 2006 added strict requirement
# 01 Aug 2006 fix bug about inputfile parameter
# fix bug about suffix index generation
# 31 Jul 2006 added parameter for reading queue parameters
# 29 Jul 2006 added code to handling consfusion networks
# 28 Jul 2006 added a better policy for removing jobs from the queue in case of killing signal (CTRL-C)
# added the parameter -qsub-prefix which sets the prefix for the name of submitted jobs
# 27 Jul 2006 added safesystem() function and other checks to handle with process failure
# added checks for existence of decoder and configuration file
# 26 Jul 2006 fix a bug related to the use of absolute path for srcfile and nbestfile
use strict;
#######################
#Customizable parameters
#parameters for submiiting processes through Sun GridEngine
my $queueparameters="";
#SGE-make-it-work:
# my $queueparameters="-l q1w -l mem_free=0.5G -hard";
# my $queueparameters="-l q1dm -pe pe_mth 2 -hard";
# etc.
# look for the correct pwdcmd
my $pwdcmd = getPwdCmd();
my $workingdir = `$pwdcmd`; chomp $workingdir;
my $tmpdir="$workingdir/tmp$$";
my $splitpfx="split$$";
$SIG{'INT'} = \&kill_all_and_quit; # catch exception for CTRL-C
#######################
#Default parameters
my $jobscript="$workingdir/job$$";
my $qsubout="$workingdir/out.job$$";
my $qsuberr="$workingdir/err.job$$";
my $mosesparameters="";
my $feed_moses_via_stdin = 0;
# a workaround, for a reason, the default "-input-file X" blocks
# my moses, while "< X" works fine.
my $cfgfile=""; #configuration file
my $version=undef;
my $help=0;
my $dbg=0;
my $jobs=4;
my $mosescmd="$ENV{MOSESBIN}/moses"; #decoder in use
my $inputlist=undef;
my $inputfile=undef;
my $inputtype=0;
my @nbestlist=();
my $nbestlist=undef;
my $nbestfile=undef;
my $oldnbestfile=undef;
my $oldnbest=undef;
my $nbestflag=0;
my @wordgraphlist=();
my $wordgraphlist=undef;
my $wordgraphfile=undef;
my $wordgraphflag=0;
my $robust=5; # resubmit crashed jobs robust-times
my $alifile=undef;
my $detailsfile=undef;
my $logfile="";
my $logflag="";
my $searchgraphlist="";
my $searchgraphfile="";
my $searchgraphflag=0;
my $qsubname="MOSES";
my $old_sge = 0; # assume old Sun Grid Engine (<6.0) where qsub does not
# implement -sync and -b
#SGE-make-it-work:
# my $old_sge = "1";
#######################
# Command line options processing
sub init(){
use Getopt::Long qw(:config pass_through no_ignore_case permute);
GetOptions('version'=>\$version,
'help'=>\$help,
'debug'=>\$dbg,
'jobs=i'=>\$jobs,
'decoder=s'=> \$mosescmd,
'robust=i' => \$robust,
'decoder-parameters=s'=> \$mosesparameters,
'feed-decoder-via-stdin'=> \$feed_moses_via_stdin,
'logfile=s'=> \$logfile,
'i|inputfile|input-file=s'=> \$inputlist,
'n-best-list=s'=> \$nbestlist,
'n-best-file=s'=> \$oldnbestfile,
'n-best-size=i'=> \$oldnbest,
'output-search-graph|osg=s'=> \$searchgraphlist,
'output-word-graph|owg=s'=> \$wordgraphlist,
'alignment-output-file=s'=> \$alifile,
'translation-details|T=s'=> \$detailsfile,
'qsub-prefix=s'=> \$qsubname,
'queue-parameters=s'=> \$queueparameters,
'inputtype=i'=> \$inputtype,
'config|f=s'=>\$cfgfile,
'old-sge' => \$old_sge,
) or exit(1);
getNbestParameters();
getSearchGraphParameters();
getWordGraphParameters();
getLogParameters();
#print_parameters();
#print STDERR "nbestflag:$nbestflag\n";
#print STDERR "searchgraphflag:$searchgraphflag\n";
print STDERR "wordgraphflag:$wordgraphflag\n";
#print STDERR "inputlist:$inputlist\n";
chomp($inputfile=`basename $inputlist`) if defined($inputlist);
$mosesparameters.="@ARGV -config $cfgfile -inputtype $inputtype";
}
#######################
##print version
sub version(){
# print STDERR "version 1.0 (15-07-2006)\n";
# print STDERR "version 1.1 (17-07-2006)\n";
# print STDERR "version 1.2 (18-07-2006)\n";
# print STDERR "version 1.3 (21-07-2006)\n";
# print STDERR "version 1.4 (26-07-2006)\n";
# print STDERR "version 1.5 (27-07-2006)\n";
# print STDERR "version 1.6 (28-07-2006)\n";
# print STDERR "version 1.7 (29-07-2006)\n";
# print STDERR "version 1.8 (31-07-2006)\n";
# print STDERR "version 1.9 (01-08-2006)\n";
# print STDERR "version 1.10 (02-08-2006)\n";
# print STDERR "version 1.11 (10-10-2006)\n";
# print STDERR "version 1.12 (27-12-2006)\n";
print STDERR "version 1.13 (29-12-2006)\n";
exit(1);
}
#usage
sub usage(){
print STDERR "moses-parallel.pl [parallel-options] [moses-options]\n";
print STDERR "Options marked (*) are required.\n";
print STDERR "Parallel options:\n";
print STDERR "* -decoder <file> Moses decoder to use\n";
print STDERR "* -i|inputfile|input-file <file> the input text to translate\n";
print STDERR "* -jobs <N> number of required jobs\n";
print STDERR " -logfile <file> file where storing log files of all jobs\n";
print STDERR " -qsub-prefix <string> name for sumbitte jobs\n";
print STDERR " -queue-parameters <string> specific requirements for queue\n";
print STDERR " -old-sge Assume Sun Grid Engine < 6.0\n";
print STDERR " -debug debug\n";
print STDERR " -version print version of the script\n";
print STDERR " -help this help\n";
print STDERR "Moses options:\n";
print STDERR " -inputtype <0|1|2> 0 for text, 1 for confusion networks, 2 for lattices\n";
print STDERR " -output-search-graph (osg) <file>: Output connected hypotheses of search into specified filename\n";
print STDERR " -output-word-graph (osg) '<file> <0|1>': Output stack info as word graph. Takes filename, 0=only hypos in stack, 1=stack + nbest hypos\n";
print STDERR " IMPORTANT NOTE: use single quote to group parameters of -output-word-graph\n";
print STDERR " This is different from standard moses\n";
print STDERR " -n-best-list '<file> <N> [distinct]' where\n";
print STDERR " <file>: file where storing nbest lists\n";
print STDERR " <N>: size of nbest lists\n";
print STDERR " distinct: (optional) to activate generation of distinct nbest alternatives\n";
print STDERR " IMPORTANT NOTE: use single quote to group parameters of -n-best-list\n";
print STDERR " This is different from standard moses\n";
print STDERR " IMPORTANT NOTE: The following two parameters are now OBSOLETE, and they are no more supported\n";
print STDERR " -n-best-file <file> file where storing nbet lists\n";
print STDERR " -n-best-size <N> size of nbest lists\n";
print STDERR " NOTE: -n-best-file-n-best-size are passed to the decoder as \"-n-best-list <file> <N>\"\n";
print STDERR "* -config (f) <cfgfile> configuration file\n";
print STDERR " -decoder-parameters <string> specific parameters for the decoder\n";
print STDERR "All other options are passed to Moses\n";
print STDERR " (This way to pass parameters is maintained for back compatibility\n";
print STDERR " but preferably use -decoder-parameters)\n";
exit(1);
}
#printparameters
sub print_parameters(){
print STDERR "Inputfile: $inputlist\n";
print STDERR "Configuration file: $cfgfile\n";
print STDERR "Decoder in use: $mosescmd\n";
print STDERR "Number of jobs:$jobs\n";
print STDERR "Nbest list: $nbestlist\n" if ($nbestflag);
print STDERR "Output Search Graph: $searchgraphlist\n" if ($searchgraphflag);
print STDERR "Output Word Graph: $wordgraphlist\n" if ($wordgraphflag);
print STDERR "LogFile:$logfile\n" if ($logflag);
print STDERR "Qsub name: $qsubname\n";
print STDERR "Queue parameters: $queueparameters\n";
print STDERR "Inputtype: text\n" if $inputtype == 0;
print STDERR "Inputtype: confusion network\n" if $inputtype == 1;
print STDERR "Inputtype: lattices\n" if $inputtype == 2;
print STDERR "parameters directly passed to Moses: $mosesparameters\n";
}
#get parameters for log file
sub getLogParameters(){
if ($logfile){ $logflag=1; }
}
#get parameters for nbest computation (possibly from configuration file)
sub getNbestParameters(){
if (!$nbestlist){
open (CFG, "$cfgfile");
while (chomp($_=<CFG>)){
if (/^\[n-best-list\]/){
my $tmp;
while (chomp($tmp=<CFG>)){
last if $tmp eq "" || $tmp=~/^\[/;
$nbestlist .= "$tmp ";
}
last;
}
}
close(CFG);
}
if ($nbestlist){
if ($oldnbestfile){
print STDERR "There is a conflict between NEW parameter -n-best-list and OBSOLETE parameter -n-best-file\n";
print STDERR "Please use only -nbest-list '<file> <N> [distinct]\n";
exit;
}
}
else{
if ($oldnbestfile){
print STDERR "You are using the OBSOLETE parameter -n-best-file\n";
print STDERR "Next time please use only -n-best-list '<file> <N> [distinct]\n";
$nbestlist="$oldnbestfile";
if ($oldnbest){ $nbestlist.=" $oldnbest"; }
else { $nbestlist.=" 1"; }
}
}
if ($nbestlist){
my @tmp=split(/[ \t]+/,$nbestlist);
@nbestlist = @tmp;
if ($nbestlist[0] eq '-'){ $nbestfile="nbest"; }
else{ chomp($nbestfile=`basename $nbestlist[0]`); }
$nbestflag=1;
}
}
#get parameters for search graph computation (possibly from configuration file)
sub getSearchGraphParameters(){
if (!$searchgraphlist){
open (CFG, "$cfgfile");
while (chomp($_=<CFG>)){
if (/^\[output-search-graph\]/ || /^\[osg\]/){
my $tmp;
while (chomp($tmp=<CFG>)){
last if $tmp eq "" || $tmp=~/^\[/;
$searchgraphlist = "$tmp";
}
last;
}
}
close(CFG);
}
if ($searchgraphlist){
if ($searchgraphlist eq '-'){ $searchgraphfile="searchgraph"; }
else{ chomp($searchgraphfile=`basename $searchgraphlist`); }
$searchgraphflag=1;
}
}
#get parameters for word graph computation (possibly from configuration file)
sub getWordGraphParameters(){
if (!$wordgraphlist){
open (CFG, "$cfgfile");
while (chomp($_=<CFG>)){
if (/^\[output-word-graph\]/ || /^\[owg\]/){
my $tmp;
while (chomp($tmp=<CFG>)){
last if $tmp eq "" || $tmp=~/^\[/;
$wordgraphlist .= "$tmp ";
}
last;
}
}
close(CFG);
}
if ($wordgraphlist){
my @tmp=split(/[ \t]+/,$wordgraphlist);
@wordgraphlist = @tmp;
if ($wordgraphlist[0] eq '-'){ $wordgraphfile="wordgraph"; }
else{ chomp($wordgraphfile=`basename $wordgraphlist[0]`); }
$wordgraphflag=1;
}
}
#######################
#Script starts here
init();
version() if $version;
usage() if $help;
if (!defined $inputlist || !defined $mosescmd || ! defined $cfgfile) {
print STDERR "Please specify -input-file, -decoder and -config\n";
usage();
}
#checking if inputfile exists
if (! -e ${inputlist} ){
print STDERR "Inputfile ($inputlist) does not exists\n";
usage();
}
#checking if decoder exists
if (! -e $mosescmd) {
print STDERR "Decoder ($mosescmd) does not exists\n";
usage();
}
#checking if configfile exists
if (! -e $cfgfile) {
print STDERR "Configuration file ($cfgfile) does not exists\n";
usage();
}
print_parameters(); # so that people know
exit(1) if $dbg; # debug mode: just print and do not run
#splitting test file in several parts
#$decimal="-d"; #split does not accept this options (on MAC OS)
my $decimal="";
my $cmd;
my $sentenceN;
my $splitN;
my @idxlist=();
if ($inputtype==0){ #text input
#getting the number of input sentences (one sentence per line)
chomp($sentenceN=`wc -l ${inputlist} | awk '{print \$1}' `);
#Reducing the number of jobs if less sentences to translate
if ($jobs>$sentenceN){ $jobs=$sentenceN; }
#Computing the number of sentences for each files
if ($sentenceN % $jobs == 0){ $splitN=int($sentenceN / $jobs); }
else{ $splitN=int($sentenceN /$jobs) + 1; }
if ($dbg){
print STDERR "There are $sentenceN sentences to translate\n";
print STDERR "There are at most $splitN sentences per job\n";
}
$cmd="split $decimal -a 2 -l $splitN $inputlist ${inputfile}.$splitpfx-";
safesystem("$cmd") or die;
}
elsif ($inputtype==1){ #confusion network input
my $tmpfile="/tmp/cnsplit$$";
$cmd="cat $inputlist | perl -pe 's/\\n/ _CNendline_ /g;' | perl -pe 's/_CNendline_ _CNendline_ /_CNendline_\\n/g;' > $tmpfile";
safesystem("$cmd") or die;
#getting the number of input CNs
chomp($sentenceN=`wc -l $tmpfile | awk '{print \$1}' `);
#Reducing the number of jobs if less CNs to translate
if ($jobs>$sentenceN){ $jobs=$sentenceN; }
#Computing the number of CNs for each files
if ($sentenceN % $jobs == 0){ $splitN=int($sentenceN / $jobs); }
else{ $splitN=int($sentenceN /$jobs) + 1; }
if ($dbg){
print STDERR "There are $sentenceN confusion networks to translate\n";
print STDERR "There are at most $splitN sentences per job\n";
}
$cmd="split $decimal -a 2 -l $splitN $tmpfile $tmpfile-";
safesystem("$cmd") or die;
my @idxlist=();
chomp(@idxlist=`ls $tmpfile-*`);
grep(s/.+(\-\S+)$/$1/e,@idxlist);
foreach my $idx (@idxlist){
$cmd="perl -pe 's/ _CNendline_ /\\n/g;s/ _CNendline_/\\n/g;'";
safesystem("cat $tmpfile$idx | $cmd > ${inputfile}.$splitpfx$idx ; \\rm -f $tmpfile$idx;");
}
}
elsif ($inputtype==2){ #confusion network input
#getting the number of input lattices (one lattice per line)
chomp($sentenceN=`wc -l ${inputlist} | awk '{print \$1}' `);
#Reducing the number of jobs if less lattices to translate
if ($jobs>$sentenceN){ $jobs=$sentenceN; }
#Computing the number of sentences for each files
if ($sentenceN % $jobs == 0){ $splitN=int($sentenceN / $jobs); }
else{ $splitN=int($sentenceN /$jobs) + 1; }
if ($dbg){
print STDERR "There are $sentenceN lattices to translate\n";
print STDERR "There are at most $splitN lattices per job\n";
}
$cmd="split $decimal -a 2 -l $splitN $inputlist ${inputfile}.$splitpfx-";
safesystem("$cmd") or die;
}
else{ #unknown input type
die "INPUTTYPE:$inputtype is unknown!\n";
}
chomp(@idxlist=`ls ${inputfile}.$splitpfx-*`);
grep(s/.+(\-\S+)$/$1/e,@idxlist);
safesystem("mkdir -p $tmpdir") or die;
preparing_script();
#launching process through the queue
my @sgepids =();
my @idx_todo = ();
foreach (@idxlist) { push @idx_todo,$_; }
# loop up to --robust times
while ($robust && scalar @idx_todo) {
$robust--;
my $failure=0;
foreach my $idx (@idx_todo){
my $batch_and_join = undef;
if ($old_sge) {
# old SGE understands -b no as the default and does not understand 'yes'
$batch_and_join = "-j y";
} else {
$batch_and_join = "-b no -j yes";
}
$cmd="qsub $queueparameters $batch_and_join -o $qsubout$idx -e $qsuberr$idx -N $qsubname$idx ${jobscript}${idx}.bash > ${jobscript}${idx}.log 2>&1";
print STDERR "$cmd\n" if $dbg;
safesystem($cmd) or die;
my ($res,$id);
open (IN,"${jobscript}${idx}.log")
or die "Can't read id of job ${jobscript}${idx}.log";
chomp($res=<IN>);
my @arrayStr = split(/\s+/,$res);
$id=$arrayStr[2];
die "Failed to guess job id from $jobscript$idx.log, got: $res"
if $id !~ /^[0-9]+$/;
close(IN);
push @sgepids, $id;
}
#waiting until all jobs have finished
my $hj = "-hold_jid " . join(" -hold_jid ", @sgepids);
if ($old_sge) {
# we need to implement our own waiting script
my $syncscript = "${jobscript}.sync_workaround_script.sh";
safesystem("echo 'date' > $syncscript") or kill_all_and_quit();
my $pwd = `$pwdcmd`; chomp $pwd;
my $checkpointfile = "${jobscript}.sync_workaround_checkpoint";
# delete previous checkpoint, if left from previous runs
safesystem("\\rm -f $checkpointfile") or kill_all_and_quit();
# start the 'hold' job, i.e. the job that will wait
$cmd="qsub -cwd $queueparameters $hj -o $checkpointfile -e /dev/null -N $qsubname.W $syncscript 2> $qsubname.W.log";
safesystem($cmd) or kill_all_and_quit();
# and wait for checkpoint file to appear
my $nr=0;
while (!-e $checkpointfile) {
sleep(10);
$nr++;
print STDERR "w" if $nr % 3 == 0;
}
print STDERR "End of waiting.\n";
safesystem("\\rm -f $checkpointfile $syncscript") or kill_all_and_quit();
my $failure = 1;
my $nr = 0;
while ($nr < 60 && $failure) {
$nr ++;
$failure=&check_exit_status();
if (!$failure) {
$failure = check_translation_old_sge();
}
last if !$failure;
print STDERR "Extra wait ($nr) for possibly unfinished processes.\n";
sleep 10;
}
} else {
# use the -sync option for qsub
$cmd="qsub $queueparameters -sync y $hj -j y -o /dev/null -e /dev/null -N $qsubname.W -b y /bin/ls > $qsubname.W.log";
safesystem($cmd) or kill_all_and_quit();
$failure=&check_exit_status();
}
kill_all_and_quit() if $failure && !$robust;
# check if some translations failed
my @idx_still_todo = check_translation();
if ($robust) {
# if robust, redo crashed jobs
if ((scalar @idx_still_todo) == (scalar @idxlist)) {
# ... but not if all crashed
print STDERR "everything crashed, not trying to resubmit jobs\n";
$robust = 0;
kill_all_and_quit();
}
@idx_todo = @idx_still_todo;
}
else {
if (scalar (@idx_still_todo)) {
print STDERR "some jobs crashed: ".join(" ",@idx_still_todo)."\n";
kill_all_and_quit();
}
}
}
#concatenating translations and removing temporary files
concatenate_1best();
concatenate_logs() if $logflag;
concatenate_ali() if defined $alifile;
concatenate_details() if defined $detailsfile;
concatenate_nbest() if $nbestflag;
safesystem("cat nbest$$ >> /dev/stdout") if $nbestlist[0] eq '-';
concatenate_searchgraph() if $searchgraphflag;
safesystem("cat searchgraph$$ >> /dev/stdout") if $searchgraphlist eq '-';
concatenate_wordgraph() if $wordgraphflag;
safesystem("cat wordgraph$$ >> /dev/stdout") if $wordgraphlist[0] eq '-';
remove_temporary_files();
#script creation
sub preparing_script(){
my $currStartTranslationId = 0;
foreach my $idx (@idxlist){
my $scriptheader="";
$scriptheader.="\#\! /bin/bash\n\n";
# !!! this is useless. qsub ignores the first line of the script.
# Pass '-S /bin/bash' to qsub instead.
#SGE-make-it-work:
# $scriptheader.="## Sun's Grid Engine parameters\n";
# $scriptheader.="# ... (see 'man qsub' for complete documentation)\n";
# $scriptheader.="# ... job name\n";
# $scriptheader.="#\$ -N mert-$qsubname\n";
# $scriptheader.="# ... make sure to use proper shell\n";
# $scriptheader.="#\$ -S /bin/bash\n";
# $scriptheader.="# ... e-mail address to send notifications\n";
# $scriptheader.="#\$ -M ww.xx\@yy.zz\n\n";
$scriptheader.="uname -a\n\n";
$scriptheader.="ulimit -c 0\n\n"; # avoid coredumps
$scriptheader.="cd $workingdir\n\n";
open (OUT, "> ${jobscript}${idx}.bash");
print OUT $scriptheader;
my $inputmethod = $feed_moses_via_stdin ? "<" : "-input-file";
my $tmpnbestlist="";
if ($nbestflag){
$tmpnbestlist="$tmpdir/$nbestfile.$splitpfx$idx $nbestlist[1]";
$tmpnbestlist = "$tmpnbestlist $nbestlist[2]" if scalar(@nbestlist)==3;
$tmpnbestlist = "-n-best-list $tmpnbestlist";
}
my $tmpalioutfile = "";
if (defined $alifile){
$tmpalioutfile="-alignment-output-file $tmpdir/$alifile.$splitpfx$idx";
}
my $tmpdetailsoutfile = "";
if (defined $detailsfile){
$tmpdetailsoutfile="-translation-details $tmpdir/$detailsfile.$splitpfx$idx";
}
my $tmpsearchgraphlist="";
if ($searchgraphflag){
$tmpsearchgraphlist="-output-search-graph $tmpdir/$searchgraphfile.$splitpfx$idx";
}
my $tmpwordgraphlist="";
if ($wordgraphflag){
$tmpwordgraphlist="-output-word-graph $tmpdir/$wordgraphfile.$splitpfx$idx $wordgraphlist[1]";
}
my $tmpStartTranslationId = ""; # "-start-translation-id $currStartTranslationId";
print OUT "$mosescmd $mosesparameters $tmpStartTranslationId $tmpalioutfile $tmpdetailsoutfile $tmpwordgraphlist $tmpsearchgraphlist $tmpnbestlist $inputmethod ${inputfile}.$splitpfx$idx > $tmpdir/${inputfile}.$splitpfx$idx.trans\n\n";
print OUT "echo exit status \$\?\n\n";
if (defined $alifile){
print OUT "\\mv -f $tmpdir/${alifile}.$splitpfx$idx .\n\n";
print OUT "echo exit status \$\?\n\n";
}
if (defined $detailsfile){
print OUT "\\mv -f $tmpdir/${detailsfile}.$splitpfx$idx .\n\n";
print OUT "echo exit status \$\?\n\n";
}
if ($nbestflag){
print OUT "\\mv -f $tmpdir/${nbestfile}.$splitpfx$idx .\n\n";
print OUT "echo exit status \$\?\n\n";
}
if ($searchgraphflag){
print OUT "\\mv -f $tmpdir/${searchgraphfile}.$splitpfx$idx .\n\n";
print OUT "echo exit status \$\?\n\n";
}
if ($wordgraphflag){
print OUT "\\mv -f $tmpdir/${wordgraphfile}.$splitpfx$idx .\n\n";
print OUT "echo exit status \$\?\n\n";
}
print OUT "\\mv -f $tmpdir/${inputfile}.$splitpfx$idx.trans .\n\n";
print OUT "echo exit status \$\?\n\n";
close(OUT);
#setting permissions of each script
chmod(oct(755),"${jobscript}${idx}.bash");
$currStartTranslationId += $splitN;
}
}
sub concatenate_wordgraph(){
my $oldcode="";
my $newcode=-1;
my %inplength = ();
my $offset = 0;
my $outwordgraph=$wordgraphlist[0];
if ($wordgraphlist[0] eq '-'){ $outwordgraph="wordgraph$$"; }
open (OUT, "> $outwordgraph");
foreach my $idx (@idxlist){
#computing the length of each input file
my @in=();
open (IN, "${inputfile}.${splitpfx}${idx}.trans");
@in=<IN>;
close(IN);
$inplength{$idx} = scalar(@in);
open (IN, "${wordgraphfile}.${splitpfx}${idx}");
while (<IN>){
my $code="";
if (/^UTTERANCE=/){
($code)=($_=~/^UTTERANCE=(\d+)/);
print STDERR "code:$code offset:$offset\n";
$code += $offset;
if ($code ne $oldcode){
# if there is a jump between two consecutive codes
# it means that an input sentence is not translated
# fill this hole with a "fictitious" list of wordgraphs
# comprising just one "_EMPTYSEARCHGRAPH_
while ($code - $oldcode > 1){
$oldcode++;
print OUT "UTTERANCE=$oldcode\n";
print STDERR " to OUT -> code:$oldcode\n";
print OUT "_EMPTYWORDGRAPH_\n";
}
}
$oldcode=$code;
print OUT "UTTERANCE=$oldcode\n";
next;
}
print OUT "$_";
}
close(IN);
$offset += $inplength{$idx};
while ($offset - $oldcode > 1){
$oldcode++;
print OUT "UTTERANCE=$oldcode\n";
print OUT "_EMPTYWORDGRAPH_\n";
}
}
close(OUT);
}
sub concatenate_searchgraph(){
my $oldcode="";
my $newcode=-1;
my %inplength = ();
my $offset = 0;
my $outsearchgraph=$searchgraphlist;
if ($searchgraphlist eq '-'){ $outsearchgraph="searchgraph$$"; }
open (OUT, "> $outsearchgraph");
foreach my $idx (@idxlist){
#computing the length of each input file
my @in=();
open (IN, "${inputfile}.${splitpfx}${idx}.trans");
@in=<IN>;
close(IN);
$inplength{$idx} = scalar(@in);
open (IN, "${searchgraphfile}.${splitpfx}${idx}");
while (<IN>){
my ($code,@extra)=split(/[ \t]+/,$_);
$code += $offset;
if ($code ne $oldcode){
# if there is a jump between two consecutive codes
# it means that an input sentence is not translated
# fill this hole with a "fictitious" list of searchgraphs
# comprising just one "_EMPTYSEARCHGRAPH_
while ($code - $oldcode > 1){
$oldcode++;
print OUT "$oldcode _EMPTYSEARCHGRAPH_\n";
}
}
$oldcode=$code;
print OUT join(" ",($oldcode,@extra));
}
close(IN);
$offset += $inplength{$idx};
while ($offset - $oldcode > 1){
$oldcode++;
print OUT "$oldcode _EMPTYSEARCHGRAPH_\n";
}
}
close(OUT);
}
sub concatenate_nbest(){
my $oldcode="";
my $newcode=-1;
my %inplength = ();
my $offset = 0;
# get the list of feature and set a fictitious string with zero scores
open (IN, "${nbestfile}.${splitpfx}$idxlist[0]");
my $str = <IN>;
chomp($str);
close(IN);
my ($code,$trans,$featurescores,$globalscore)=split(/\|\|\|/,$str);
my $emptytrans = " ";
my $emptyglobalscore = " 0.0";
my $emptyfeaturescores = $featurescores;
$emptyfeaturescores =~ s/[-0-9\.]+/0/g;
my $outnbest=$nbestlist[0];
if ($nbestlist[0] eq '-'){ $outnbest="nbest$$"; }
open (OUT, "> $outnbest");
foreach my $idx (@idxlist){
#computing the length of each input file
my @in=();
open (IN, "${inputfile}.${splitpfx}${idx}.trans");
@in=<IN>;
close(IN);
$inplength{$idx} = scalar(@in);
open (IN, "${nbestfile}.${splitpfx}${idx}");
while (<IN>){
my ($code,@extra)=split(/\|\|\|/,$_);
$code += $offset;
if ($code ne $oldcode){
# if there is a jump between two consecutive codes
# it means that an input sentence is not translated
# fill this hole with a "fictitious" list of translation
# comprising just one "emtpy translation" with zero scores
while ($code - $oldcode > 1){
$oldcode++;
print OUT join("\|\|\|",($oldcode,$emptytrans,$emptyfeaturescores,$emptyglobalscore)),"\n";
}
}
$oldcode=$code;
print OUT join("\|\|\|",($oldcode,@extra));
}
close(IN);
$offset += $inplength{$idx};
while ($offset - $oldcode > 1){
$oldcode++;
print OUT join("\|\|\|",($oldcode,$emptytrans,$emptyfeaturescores,$emptyglobalscore)),"\n";
}
}
close(OUT);
}
sub concatenate_1best(){
foreach my $idx (@idxlist){
my @in=();
open (IN, "${inputfile}.${splitpfx}${idx}.trans");
@in=<IN>;
print STDOUT "@in";
close(IN);
}
}
sub concatenate_logs(){
open (OUT, "> ${logfile}");
foreach my $idx (@idxlist){
my @in=();
open (IN, "$qsubout$idx");
@in=<IN>;
print OUT "@in";
close(IN);
}
close(OUT);
}
sub concatenate_ali(){
open (OUT, "> ${alifile}");
foreach my $idx (@idxlist){
my @in=();
open (IN, "$alifile.$splitpfx$idx");
@in=<IN>;
print OUT "@in";
close(IN);
}
close(OUT);
}
sub concatenate_details(){
open (OUT, "> ${detailsfile}");
foreach my $idx (@idxlist){
my @in=();
open (IN, "$detailsfile.$splitpfx$idx");
@in=<IN>;
print OUT "@in";
close(IN);
}
close(OUT);
}
sub check_exit_status(){
print STDERR "check_exit_status\n";
my $failure=0;
foreach my $idx (@idxlist){
print STDERR "check_exit_status of job $idx\n";
open(IN,"$qsubout$idx");
while (<IN>){
$failure=1 if (/exit status 1/);
}
close(IN);
}
return $failure;
}
sub kill_all_and_quit(){
print STDERR "Got interrupt or something failed.\n";
print STDERR "kill_all_and_quit\n";
foreach my $id (@sgepids){
print STDERR "qdel $id\n";
safesystem("qdel $id");
}
print STDERR "Translation was not performed correctly\n";
print STDERR "or some of the submitted jobs died.\n";
print STDERR "qdel function was called for all submitted jobs\n";
exit(1);
}
sub check_translation(){
#checking if all sentences were translated
my $inputN;
my $outputN;
my @failed = ();
foreach my $idx (@idx_todo){
if ($inputtype==0){#text input
chomp($inputN=`wc -l ${inputfile}.$splitpfx$idx | cut -d' ' -f1`);
}
elsif ($inputtype==1){#confusion network input
chomp($inputN=`cat ${inputfile}.$splitpfx$idx | perl -pe 's/\\n/ _CNendline_ /g;' | perl -pe 's/_CNendline_ _CNendline_ /_CNendline_\\n/g;' | wc -l | cut -d' ' -f1 `);
}
elsif ($inputtype==2){#lattice input
chomp($inputN=`wc -l ${inputfile}.$splitpfx$idx | cut -d' ' -f1`);
}
else{#unknown input
die "INPUTTYPE:$inputtype is unknown!\n";
}
chomp($outputN=`wc -l ${inputfile}.$splitpfx$idx.trans | cut -d' ' -f1`);
if ($inputN != $outputN){
print STDERR "Split ($idx) were not entirely translated\n";
print STDERR "outputN=$outputN inputN=$inputN\n";
print STDERR "outputfile=${inputfile}.$splitpfx$idx.trans inputfile=${inputfile}.$splitpfx$idx\n";
push @failed,$idx;
}
}
return @failed;
}
sub check_translation_old_sge(){
#checking if all sentences were translated
my $inputN;
my $outputN;
foreach my $idx (@idx_todo){
if ($inputtype==0){#text input
chomp($inputN=`wc -l ${inputfile}.$splitpfx$idx | cut -d' ' -f1`);
}
elsif ($inputtype==1){#confusion network input
chomp($inputN=`cat ${inputfile}.$splitpfx$idx | perl -pe 's/\\n/ _CNendline_ /g;' | perl -pe 's/_CNendline_ _CNendline_ /_CNendline_\\n/g;' | wc -l |
cut -d' ' -f1 `);
}
elsif ($inputtype==2){#lattice input
chomp($inputN=`wc -l ${inputfile}.$splitpfx$idx | cut -d' ' -f1`);
}
else{#unknown input
die "INPUTTYPE:$inputtype is unknown!\n";
}
chomp($outputN=`wc -l ${inputfile}.$splitpfx$idx.trans | cut -d' ' -f1`);
if ($inputN != $outputN){
print STDERR "Split ($idx) were not entirely translated\n";
print STDERR "outputN=$outputN inputN=$inputN\n";
print STDERR "outputfile=${inputfile}.$splitpfx$idx.trans inputfile=${inputfile}.$splitpfx$idx\n";
return 1;
}
}
return 0;
}
sub remove_temporary_files(){
#removing temporary files
foreach my $idx (@idxlist){
unlink("${inputfile}.${splitpfx}${idx}.trans");
unlink("${inputfile}.${splitpfx}${idx}");
if (defined $alifile){ unlink("${alifile}.${splitpfx}${idx}"); }
if (defined $detailsfile){ unlink("${detailsfile}.${splitpfx}${idx}"); }
if ($nbestflag){ unlink("${nbestfile}.${splitpfx}${idx}"); }
if ($searchgraphflag){ unlink("${searchgraphfile}.${splitpfx}${idx}"); }
if ($wordgraphflag){ unlink("${wordgraphfile}.${splitpfx}${idx}"); }
unlink("${jobscript}${idx}.bash");
unlink("${jobscript}${idx}.log");
unlink("$qsubname.W.log");
unlink("$qsubout$idx");
unlink("$qsuberr$idx");
rmdir("$tmpdir");
}
if ($nbestflag && $nbestlist[0] eq '-'){ unlink("${nbestfile}$$"); };
if ($searchgraphflag && $searchgraphlist eq '-'){ unlink("${searchgraphfile}$$"); };
if ($wordgraphflag && $wordgraphlist eq '-'){ unlink("${wordgraphfile}$$"); };
}
sub safesystem {
print STDERR "Executing: @_\n";
system(@_);
if ($? == -1) {
print STDERR "Failed to execute: @_\n $!\n";
exit(1);
}
elsif ($? & 127) {
printf STDERR "Execution of: @_\n died with signal %d, %s coredump\n",
($? & 127), ($? & 128) ? 'with' : 'without';
exit 1;
}
else {
my $exitcode = $? >> 8;
print STDERR "Exit code: $exitcode\n" if $exitcode;
return ! $exitcode;
}
}
# look for the correct pwdcmd (pwd by default, pawd if it exists)
# I assume that pwd always exists
sub getPwdCmd(){
my $pwdcmd="pwd";
my $a;
chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print $1}'`);
if ($a && -e $a){ $pwdcmd=$a; }
return $pwdcmd;
}
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