- gcc -shared -o $@ $(OBJ_DIR)/src/cwrapper.o $(OBJ_DIR)/init.o $(OBJ_DIR)/src/libKaldiLib.a $(OBJ_DIR)/src/init.o -lstdc++ -Wl,-rpath=$(LIB_PATH) -L$(LIB_PATH) -lnervcore -lluaT

- -rm $(OBJ_DIR)/src/*.o

-#include "../nerv/common.h"

- local raw = self.gconf.cumat_type.new_from_host(self.feat_repo:cur_utter(self.debug))

- local expanded = self.gconf.cumat_type(raw:nrow(), raw:ncol() * step)

- feat_utter = self.gconf.mmat_type(rearranged:nrow(), rearranged:ncol())

- rearranged:copy_toh(feat_utter)

-#include "nerv/common.h"

- extern Matrix *nerv_matrix_host_float_create(long nrow, long ncol, Status *status);

- Matrix *tnet_feature_repo_read_utterance(TNetFeatureRepo *repo, lua_State *L, int debug) {

- mat = nerv_matrix_host_float_create(n, m, &status);

- int debug) {

- mat = nerv_matrix_host_float_create(n, m, &status);

-#include "nerv/matrix/matrix.h"

-#include "nerv/common.h"

- Matrix *tnet_feature_repo_read_utterance(TNetFeatureRepo *repo, lua_State *L, int debug);

- int debug);

-#include "nerv/common.h"

- Matrix *utter = tnet_feature_repo_read_utterance(repo, L, debug);

- tnet_feature_repo_current_tag(feat_repo), L, debug);

- feat_utter = tnet_feature_repo_read_utterance(feat_repo, NULL, 1);

- 1);

-source path.sh

-source cmd.sh

-

-acwt=0.1

-dir=/slfs5/users/ymz09/chime/baseline/ASR/exp/nerv_seq/

-graph=/slfs5/users/ymz09/chime/baseline/ASR/exp/tri4a_dnn_tr05_multi_enhanced/graph_tgpr_5k

-data=/slfs5/users/ymz09/chime/baseline/ASR/data-fbank/et05_real_enhanced

-config=/slfs6/users/ymz09/nerv-project/nerv/nerv/examples/mpe_chime3.lua

-

-decode.sh --nj 4 --cmd "$decode_cmd" --config conf/decode_dnn.config --acwt $acwt \

- $graph $data $config \

- $dir/decode_tgpr_5k_et05_real_enhanced_nerv

-

-#!/bin/bash

-# "queue.pl" uses qsub. The options to it are

-# options to qsub. If you have GridEngine installed,

-# change this to a queue you have access to.

-# Otherwise, use "run.pl", which will run jobs locally

-# (make sure your --num-jobs options are no more than

-# the number of cpus on your machine.

-

-#a) JHU cluster options

-#export train_cmd="queue.pl -l arch=*64"

-#export decode_cmd="queue.pl -l arch=*64,mem_free=2G,ram_free=2G"

-#export mkgraph_cmd="queue.pl -l arch=*64,ram_free=4G,mem_free=4G"

-

-#export cuda_cmd="..."

-

-

-#b) BUT cluster options

-#export train_cmd="queue.pl -q all.q@@blade -l ram_free=1200M,mem_free=1200M"

-#export decode_cmd="queue.pl -q all.q@@blade -l ram_free=1700M,mem_free=1700M"

-#export decodebig_cmd="queue.pl -q all.q@@blade -l ram_free=4G,mem_free=4G"

-

-#export cuda_cmd="queue.pl -q long.q@@pco203 -l gpu=1"

-#export cuda_cmd="queue.pl -q long.q@pcspeech-gpu"

-#export mkgraph_cmd="queue.pl -q all.q@@servers -l ram_free=4G,mem_free=4G"

-

-#c) run it locally...

-export train_cmd=run.pl

-export decode_cmd=run.pl

-export cuda_cmd=run.pl

-export mkgraph_cmd=run.pl

-

-#export train_cmd='queue.pl'

-#export decode_cmd='queue.pl'

-#export cuda_cmd='queue.pl -l gpu=1 -l hostname="markov|date|hamming"'

-#export mkgraph_cmd='queue.pl"'

-

-beam=18.0 # beam for decoding. Was 13.0 in the scripts.

-lattice_beam=10.0 # this has most effect on size of the lattices.

-

-nnet_forward_opts="--prior-scale=1.0"

- echo "Usage: $0 [options] <graph-dir> <data-dir> <nerv-config> <decode-dir>"

-config=$3

-cmvn_opts=

-delta_opts=

- $cmd --num-threads $((num_threads+1)) JOB=1:$nj $dir/log/decode.JOB.log \

- ./src/nnet-forward $nnet_forward_opts --class-frame-counts=$class_frame_counts --use-gpu=$use_gpu $config "$feats" ark:- \| \

-#!/bin/bash

-# Copyright 2012 Johns Hopkins University (Author: Daniel Povey)

-# Apache 2.0

-

-[ -f ./path.sh ] && . ./path.sh

-

-# begin configuration section.

-cmd=run.pl

-stage=0

-decode_mbr=true

-reverse=false

-word_ins_penalty=0.0

-min_lmwt=5

-max_lmwt=20

-#end configuration section.

-

-[ -f ./path.sh ] && . ./path.sh

-. parse_options.sh || exit 1;

-

-if [ $# -ne 3 ]; then

- echo "Usage: local/score.sh [--cmd (run.pl|queue.pl...)] <data-dir> <lang-dir|graph-dir> <decode-dir>"

- echo " Options:"

- echo " --cmd (run.pl|queue.pl...) # specify how to run the sub-processes."

- echo " --stage (0|1|2) # start scoring script from part-way through."

- echo " --decode_mbr (true/false) # maximum bayes risk decoding (confusion network)."

- echo " --min_lmwt <int> # minumum LM-weight for lattice rescoring "

- echo " --max_lmwt <int> # maximum LM-weight for lattice rescoring "

- echo " --reverse (true/false) # score with time reversed features "

- exit 1;

-fi

-

-data=$1

-lang_or_graph=$2

-dir=$3

-

-symtab=$lang_or_graph/words.txt

-

-for f in $symtab $dir/lat.1.gz $data/text; do

- [ ! -f $f ] && echo "score.sh: no such file $f" && exit 1;

-done

-

-mkdir -p $dir/scoring/log

-

-cat $data/text | sed 's:<NOISE>::g' | sed 's:<SPOKEN_NOISE>::g' > $dir/scoring/test_filt.txt

-

-$cmd LMWT=$min_lmwt:$max_lmwt $dir/scoring/log/best_path.LMWT.log \

- lattice-scale --inv-acoustic-scale=LMWT "ark:gunzip -c $dir/lat.*.gz|" ark:- \| \

- lattice-add-penalty --word-ins-penalty=$word_ins_penalty ark:- ark:- \| \

- lattice-best-path --word-symbol-table=$symtab \

- ark:- ark,t:$dir/scoring/LMWT.tra || exit 1;

-

-if $reverse; then

- for lmwt in `seq $min_lmwt $max_lmwt`; do

- mv $dir/scoring/$lmwt.tra $dir/scoring/$lmwt.tra.orig

- awk '{ printf("%s ",$1); for(i=NF; i>1; i--){ printf("%s ",$i); } printf("\n"); }' \

- <$dir/scoring/$lmwt.tra.orig >$dir/scoring/$lmwt.tra

- done

-fi

-

-# Note: the double level of quoting for the sed command

-$cmd LMWT=$min_lmwt:$max_lmwt $dir/scoring/log/score.LMWT.log \

- cat $dir/scoring/LMWT.tra \| \

- utils/int2sym.pl -f 2- $symtab \| sed 's:\<UNK\>::g' \| \

- compute-wer --text --mode=present \

- ark:$dir/scoring/test_filt.txt ark,p:- ">&" $dir/wer_LMWT || exit 1;

-

-exit 0;

-export KALDI_ROOT=/slfs6/users/ymz09/kaldi/

-export PATH=$PWD/utils/:$KALDI_ROOT/src/bin:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/src/fstbin/:$KALDI_ROOT/src/gmmbin/:$KALDI_ROOT/src/featbin/:$KALDI_ROOT/src/lm/:$KALDI_ROOT/src/sgmmbin/:$KALDI_ROOT/src/sgmm2bin/:$KALDI_ROOT/src/fgmmbin/:$KALDI_ROOT/src/latbin/:$KALDI_ROOT/src/nnetbin:$KALDI_ROOT/src/nnet2bin/:$KALDI_ROOT/src/kwsbin:$PWD:$PATH

-export LC_ALL=C

-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/slhome/ymz09/mylibs/:.

-

-# Change KDIR to `kaldi-trunk' path (Kaldi must be compiled with --share)

-KDIR := /slfs6/users/ymz09/kaldi/

-NERVDIR := /slfs6/users/ymz09/nerv-project/nerv/

-CUDADIR := /usr/local/cuda/

-

-nnet-forward:

- g++ -msse -msse2 -Wall -I $(KDIR)/src/ -pthread -DKALDI_DOUBLEPRECISION=0 -DHAVE_POSIX_MEMALIGN -Wno-sign-compare -Wno-unused-local-typedefs -Winit-self -DHAVE_EXECINFO_H=1 -rdynamic -DHAVE_CXXABI_H -DHAVE_ATLAS -I $(KDIR)/tools/ATLAS/include -I $(KDIR)/tools/openfst/include -Wno-sign-compare -g -fPIC -DHAVE_CUDA -I $(CUDADIR)/include -DKALDI_NO_EXPF -I $(NERVDIR)/install//include/luajit-2.0/ -I $(NERVDIR)/install/include/ -DLUA_USE_APICHECK -c -o nnet-forward.o nnet-forward.cc

- g++ -rdynamic -Wl,-rpath=$(KDIR)/tools/openfst/lib -L$(CUDADIR)/lib64 -Wl,-rpath=$(CUDADIR)/lib64 -Wl,-rpath=$(KDIR)/src/lib -L. -L$(KDIR)/src/nnet/ -L$(KDIR)/src/cudamatrix/ -L$(KDIR)/src/lat/ -L$(KDIR)/src/hmm/ -L$(KDIR)/src/tree/ -L$(KDIR)/src/matrix/ -L$(KDIR)/src/util/ -L$(KDIR)/src/base/ nnet-forward.o $(KDIR)/src/nnet//libkaldi-nnet.so $(KDIR)/src/cudamatrix//libkaldi-cudamatrix.so $(KDIR)/src/lat//libkaldi-lat.so $(KDIR)/src/hmm//libkaldi-hmm.so $(KDIR)/src/tree//libkaldi-tree.so $(KDIR)/src/matrix//libkaldi-matrix.so $(KDIR)/src/util//libkaldi-util.so $(KDIR)/src/base//libkaldi-base.so -L$(KDIR)/tools/openfst/lib -lfst /usr/lib/liblapack.so /usr/lib/libcblas.so /usr/lib/libatlas.so /usr/lib/libf77blas.so -lm -lpthread -ldl -lcublas -lcudart -lkaldi-nnet -lkaldi-cudamatrix -lkaldi-lat -lkaldi-hmm -lkaldi-tree -lkaldi-matrix -lkaldi-util -lkaldi-base -lstdc++ -L$(NERVDIR)/install/lib -Wl,-rpath=$(NERVDIR)/install/lib -lnervcore -lluaT -rdynamic -Wl,-rpath=$(KDIR)//tools/openfst/lib -L$(CUDADIR)/lib64 -Wl,-rpath=$(CUDADIR)/lib64 -Wl,-rpath=$(KDIR)//src/lib -lfst -lm -lpthread -ldl -lcublas -lcudart -L $(NERVDIR)/luajit-2.0/src/ -lluajit -o nnet-forward

-

-clean:

- -rm nnet-forward.o nnet-forward

-

-package.path="/home/slhome/ymz09/.luarocks/share/lua/5.1/?.lua;/home/slhome/ymz09/.luarocks/share/lua/5.1/?/init.lua;/slfs6/users/ymz09/nerv-project/nerv/install/share/lua/5.1/?.lua;/slfs6/users/ymz09/nerv-project/nerv/install/share/lua/5.1/?/init.lua;"..package.path;

-package.cpath="/home/slhome/ymz09/.luarocks/lib/lua/5.1/?.so;/slfs6/users/ymz09/nerv-project/nerv/install/lib/lua/5.1/?.so;"..package.cpath;

-local k,l,_=pcall(require,"luarocks.loader") _=k and l.add_context("nerv","scm-1")

-require 'nerv'

-

-function build_trainer(ifname, feature)

- local param_repo = nerv.ParamRepo()

- param_repo:import(ifname, nil, gconf)

- local layer_repo = make_layer_repo(param_repo)

- local network = get_decode_network(layer_repo)

- local global_transf = get_global_transf(layer_repo)

- local input_order = get_input_order()

- local readers = make_readers(feature, layer_repo)

- network:init(1)

-

- local iterative_trainer = function()

- local data = nil

- for ri = 1, #readers, 1 do

- data = readers[ri].reader:get_data()

- if data ~= nil then

- break

- end

- end

-

- if data == nil then

- return "", nil

- end

-

- local input = {}

- for i, e in ipairs(input_order) do

- local id = e.id

- if data[id] == nil then

- nerv.error("input data %s not found", id)

- end

- local transformed

- if e.global_transf then

- local batch = gconf.cumat_type(data[id]:nrow(), data[id]:ncol())

- batch:copy_fromh(data[id])

- transformed = nerv.speech_utils.global_transf(batch,

- global_transf,

- gconf.frm_ext or 0, 0,

- gconf)

- else

- transformed = data[id]

- end

- table.insert(input, transformed)

- end

- local output = {nerv.CuMatrixFloat(input[1]:nrow(), network.dim_out[1])}

- network:batch_resize(input[1]:nrow())

- network:propagate(input, output)

-

- local utt = data["key"]

- if utt == nil then

- nerv.error("no key found.")

- end

-

- local mat = nerv.MMatrixFloat(output[1]:nrow(), output[1]:ncol())

- output[1]:copy_toh(mat)

-

- collectgarbage("collect")

- return utt, mat

- end

-

- return iterative_trainer

-end

-

-function init(config, feature)

- local tmp = io.write

- io.write = function(...)

- end

- dofile(config)

- trainer = build_trainer(gconf.decode_param, feature)

- io.write = tmp

-end

-

-function feed()

- local utt, mat = trainer()

- return utt, mat

-end

-#include "nerv/matrix/matrix.h"

-#include "nerv/common.h"

-#include "nerv/luaT/luaT.h"

- "Usage: nnet-forward [options] <nerv-config> <feature-rspecifier> <feature-wspecifier> [nerv4decode.lua]\n"

- nerv4decode = "src/nerv4decode.lua";

- if(po.NumArgs() >= 4)

- nerv4decode = po.GetArg(4);

- if(luaL_loadfile(L, nerv4decode.c_str()))

- KALDI_ERR << "luaL_loadfile() " << nerv4decode << " failed " << lua_tostring(L, -1);

-#!/usr/bin/env perl

-# Copyright 2010-2012 Microsoft Corporation Johns Hopkins University (Author: Daniel Povey)

-# Apache 2.0.

-

-undef $field_begin;

-undef $field_end;

-

-

-if ($ARGV[0] eq "-f") {

- shift @ARGV;

- $field_spec = shift @ARGV;

- if ($field_spec =~ m/^\d+$/) {

- $field_begin = $field_spec - 1; $field_end = $field_spec - 1;

- }

- if ($field_spec =~ m/^(\d*)[-:](\d*)/) { # accept e.g. 1:10 as a courtesty (properly, 1-10)

- if ($1 ne "") {

- $field_begin = $1 - 1; # Change to zero-based indexing.

- }

- if ($2 ne "") {

- $field_end = $2 - 1; # Change to zero-based indexing.

- }

- }

- if (!defined $field_begin && !defined $field_end) {

- die "Bad argument to -f option: $field_spec";

- }

-}

-$symtab = shift @ARGV;

-if(!defined $symtab) {

- print STDERR "Usage: sym2int.pl [options] symtab [input] > output\n" .

- "options: [-f (<field>|<field_start>-<field-end>)]\n" .

- "e.g.: -f 2, or -f 3-4\n";

- exit(1);

-}

-

-open(F, "<$symtab") || die "Error opening symbol table file $symtab";

-while(<F>) {

- @A = split(" ", $_);

- @A == 2 || die "bad line in symbol table file: $_";

- $int2sym{$A[1]} = $A[0];

-}

-

-sub int2sym {

- my $a = shift @_;

- my $pos = shift @_;

- if($a !~ m:^\d+$:) { # not all digits..

- $pos1 = $pos+1; # make it one-based.

- die "int2sym.pl: found noninteger token $a [in position $pos1]\n";

- }

- $s = $int2sym{$a};

- if(!defined ($s)) {

- die "int2sym.pl: integer $a not in symbol table $symtab.";

- }

- return $s;

-}

-

-$error = 0;

-while (<>) {

- @A = split(" ", $_);

- for ($pos = 0; $pos <= $#A; $pos++) {

- $a = $A[$pos];

- if ( (!defined $field_begin || $pos >= $field_begin)

- && (!defined $field_end || $pos <= $field_end)) {

- $a = int2sym($a, $pos);

- }

- print $a . " ";

- }

- print "\n";

-}

-

-

-

-#!/bin/bash

-

-# Copyright 2012 Johns Hopkins University (Author: Daniel Povey);

-# Arnab Ghoshal, Karel Vesely

-

-# Licensed under the Apache License, Version 2.0 (the "License");

-# you may not use this file except in compliance with the License.

-# You may obtain a copy of the License at

-#

-# http://www.apache.org/licenses/LICENSE-2.0

-#

-# THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY

-# KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED

-# WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,

-# MERCHANTABLITY OR NON-INFRINGEMENT.

-# See the Apache 2 License for the specific language governing permissions and

-# limitations under the License.

-

-

-# Parse command-line options.

-# To be sourced by another script (as in ". parse_options.sh").

-# Option format is: --option-name arg

-# and shell variable "option_name" gets set to value "arg."

-# The exception is --help, which takes no arguments, but prints the

-# $help_message variable (if defined).

-

-

-###

-### The --config file options have lower priority to command line

-### options, so we need to import them first...

-###

-

-# Now import all the configs specified by command-line, in left-to-right order

-for ((argpos=1; argpos<$#; argpos++)); do

- if [ "${!argpos}" == "--config" ]; then

- argpos_plus1=$((argpos+1))

- config=${!argpos_plus1}

- [ ! -r $config ] && echo "$0: missing config '$config'" && exit 1

- . $config # source the config file.

- fi

-done

-

-

-###

-### No we process the command line options

-###

-while true; do

- [ -z "${1:-}" ] && break; # break if there are no arguments

- case "$1" in

- # If the enclosing script is called with --help option, print the help

- # message and exit. Scripts should put help messages in $help_message

- --help|-h) if [ -z "$help_message" ]; then echo "No help found." 1>&2;

- else printf "$help_message\n" 1>&2 ; fi;

- exit 0 ;;

- --*=*) echo "$0: options to scripts must be of the form --name value, got '$1'"

- exit 1 ;;

- # If the first command-line argument begins with "--" (e.g. --foo-bar),

- # then work out the variable name as $name, which will equal "foo_bar".

- --*) name=`echo "$1" | sed s/^--// | sed s/-/_/g`;

- # Next we test whether the variable in question is undefned-- if so it's

- # an invalid option and we die. Note: $0 evaluates to the name of the

- # enclosing script.

- # The test [ -z ${foo_bar+xxx} ] will return true if the variable foo_bar

- # is undefined. We then have to wrap this test inside "eval" because

- # foo_bar is itself inside a variable ($name).

- eval '[ -z "${'$name'+xxx}" ]' && echo "$0: invalid option $1" 1>&2 && exit 1;

-

- oldval="`eval echo \\$$name`";

- # Work out whether we seem to be expecting a Boolean argument.

- if [ "$oldval" == "true" ] || [ "$oldval" == "false" ]; then

- was_bool=true;

- else

- was_bool=false;

- fi

-

- # Set the variable to the right value-- the escaped quotes make it work if

- # the option had spaces, like --cmd "queue.pl -sync y"

- eval $name=\"$2\";

-

- # Check that Boolean-valued arguments are really Boolean.

- if $was_bool && [[ "$2" != "true" && "$2" != "false" ]]; then

- echo "$0: expected \"true\" or \"false\": $1 $2" 1>&2

- exit 1;

- fi

- shift 2;

- ;;

- *) break;

- esac

-done

-

-

-# Check for an empty argument to the --cmd option, which can easily occur as a

-# result of scripting errors.

-[ ! -z "${cmd+xxx}" ] && [ -z "$cmd" ] && echo "$0: empty argument to --cmd option" 1>&2 && exit 1;

-

-

-true; # so this script returns exit code 0.

-#!/usr/bin/env perl

-use strict;

-use warnings;

-

-# Copyright 2012 Johns Hopkins University (Author: Daniel Povey).

-# 2014 Vimal Manohar (Johns Hopkins University)

-# Apache 2.0.

-

-use File::Basename;

-use Cwd;

-use Getopt::Long;

-

-# queue.pl has the same functionality as run.pl, except that

-# it runs the job in question on the queue (Sun GridEngine).

-# This version of queue.pl uses the task array functionality

-# of the grid engine. Note: it's different from the queue.pl

-# in the s4 and earlier scripts.

-

-# The script now supports configuring the queue system using a config file

-# (default in conf/queue.conf; but can be passed specified with --config option)

-# and a set of command line options.

-# The current script handles:

-# 1) Normal configuration arguments

-# For e.g. a command line option of "--gpu 1" could be converted into the option

-# "-q g.q -l gpu=1" to qsub. How the CLI option is handled is determined by a

-# line in the config file like

-# gpu=* -q g.q -l gpu=$0

-# $0 here in the line is replaced with the argument read from the CLI and the

-# resulting string is passed to qsub.

-# 2) Special arguments to options such as

-# gpu=0

-# If --gpu 0 is given in the command line, then no special "-q" is given.

-# 3) Default argument

-# default gpu=0

-# If --gpu option is not passed in the command line, then the script behaves as

-# if --gpu 0 was passed since 0 is specified as the default argument for that

-# option

-# 4) Arbitrary options and arguments.

-# Any command line option starting with '--' and its argument would be handled

-# as long as its defined in the config file.

-# 5) Default behavior

-# If the config file that is passed using is not readable, then the script

-# behaves as if the queue has the following config file:

-# $ cat conf/queue.conf

-# # Default configuration

-# command qsub -v PATH -cwd -S /bin/bash -j y -l arch=*64*

-# option mem=* -l mem_free=$0,ram_free=$0

-# option mem=0 # Do not add anything to qsub_opts

-# option num_threads=* -pe smp $0

-# option num_threads=1 # Do not add anything to qsub_opts

-# option max_jobs_run=* -tc $0

-# default gpu=0

-# option gpu=0 -q all.q

-# option gpu=* -l gpu=$0 -q g.q

-

-my $qsub_opts = "";

-my $sync = 0;

-my $num_threads = 1;

-my $gpu = 0;

-

-my $config = "conf/queue.conf";

-

-my %cli_options = ();

-

-my $jobname;

-my $jobstart;

-my $jobend;

-

-my $array_job = 0;

-

-sub print_usage() {

- print STDERR

- "Usage: queue.pl [options] [JOB=1:n] log-file command-line arguments...\n" .

- "e.g.: queue.pl foo.log echo baz\n" .

- " (which will echo \"baz\", with stdout and stderr directed to foo.log)\n" .

- "or: queue.pl -q all.q\@xyz foo.log echo bar \| sed s/bar/baz/ \n" .

- " (which is an example of using a pipe; you can provide other escaped bash constructs)\n" .

- "or: queue.pl -q all.q\@qyz JOB=1:10 foo.JOB.log echo JOB \n" .

- " (which illustrates the mechanism to submit parallel jobs; note, you can use \n" .

- " another string other than JOB)\n" .

- "Note: if you pass the \"-sync y\" option to qsub, this script will take note\n" .

- "and change its behavior. Otherwise it uses qstat to work out when the job finished\n" .

- "Options:\n" .

- " --config <config-file> (default: $config)\n" .

- " --mem <mem-requirement> (e.g. --mem 2G, --mem 500M, \n" .

- " also support K and numbers mean bytes)\n" .

- " --num-threads <num-threads> (default: $num_threads)\n" .

- " --max-jobs-run <num-jobs>\n" .

- " --gpu <0|1> (default: $gpu)\n";

- exit 1;

-}

-

-if (@ARGV < 2) {

- print_usage();

-}

-

-for (my $x = 1; $x <= 3; $x++) { # This for-loop is to

- # allow the JOB=1:n option to be interleaved with the

- # options to qsub.

- while (@ARGV >= 2 && $ARGV[0] =~ m:^-:) {

- my $switch = shift @ARGV;

-

- if ($switch eq "-V") {

- $qsub_opts .= "-V ";

- } else {

- my $argument = shift @ARGV;

- if ($argument =~ m/^--/) {

- print STDERR "WARNING: suspicious argument '$argument' to $switch; starts with '-'\n";

- }

- if ($switch eq "-sync" && $argument =~ m/^[yY]/) {

- $sync = 1;

- $qsub_opts .= "$switch $argument ";

- } elsif ($switch eq "-pe") { # e.g. -pe smp 5

- my $argument2 = shift @ARGV;

- $qsub_opts .= "$switch $argument $argument2 ";

- $num_threads = $argument2;

- } elsif ($switch =~ m/^--/) { # Config options

- # Convert CLI option to variable name

- # by removing '--' from the switch and replacing any

- # '-' with a '_'

- $switch =~ s/^--//;

- $switch =~ s/-/_/g;

- $cli_options{$switch} = $argument;

- } else { # Other qsub options - passed as is

- $qsub_opts .= "$switch $argument ";

- }

- }

- }

- if ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+):(\d+)$/) { # e.g. JOB=1:20

- $array_job = 1;

- $jobname = $1;

- $jobstart = $2;

- $jobend = $3;

- shift;

- if ($jobstart > $jobend) {

- die "queue.pl: invalid job range $ARGV[0]";

- }

- if ($jobstart <= 0) {

- die "run.pl: invalid job range $ARGV[0], start must be strictly positive (this is a GridEngine limitation).";

- }

- } elsif ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+)$/) { # e.g. JOB=1.

- $array_job = 1;

- $jobname = $1;

- $jobstart = $2;

- $jobend = $2;

- shift;

- } elsif ($ARGV[0] =~ m/.+\=.*\:.*$/) {

- print STDERR "Warning: suspicious first argument to queue.pl: $ARGV[0]\n";

- }

-}

-

-if (@ARGV < 2) {

- print_usage();

-}

-

-if (exists $cli_options{"config"}) {

- $config = $cli_options{"config"};

-}

-

-my $default_config_file = <<'EOF';

-# Default configuration

-command qsub -v PATH -cwd -S /bin/bash -j y -l arch=*64*

-option mem=* -l mem_free=$0,ram_free=$0

-option mem=0 # Do not add anything to qsub_opts

-option num_threads=* -pe smp $0

-option num_threads=1 # Do not add anything to qsub_opts

-option max_jobs_run=* -tc $0

-default gpu=0

-option gpu=0

-option gpu=* -l gpu=$0 -q g.q

-EOF

-

-# Here the configuration options specified by the user on the command line

-# (e.g. --mem 2G) are converted to options to the qsub system as defined in

-# the config file. (e.g. if the config file has the line

-# "option mem=* -l ram_free=$0,mem_free=$0"

-# and the user has specified '--mem 2G' on the command line, the options

-# passed to queue system would be "-l ram_free=2G,mem_free=2G

-# A more detailed description of the ways the options would be handled is at

-# the top of this file.

-

-my $opened_config_file = 1;

-

-open CONFIG, "<$config" or $opened_config_file = 0;

-

-my %cli_config_options = ();

-my %cli_default_options = ();

-

-if ($opened_config_file == 0 && exists($cli_options{"config"})) {

- print STDERR "Could not open config file $config\n";

- exit(1);

-} elsif ($opened_config_file == 0 && !exists($cli_options{"config"})) {

- # Open the default config file instead

- open (CONFIG, "echo '$default_config_file' |") or die "Unable to open pipe\n";

- $config = "Default config";

-}

-

-my $qsub_cmd = "";

-my $read_command = 0;

-

-while(<CONFIG>) {

- chomp;

- my $line = $_;

- $_ =~ s/\s*#.*//g;

- if ($_ eq "") { next; }

- if ($_ =~ /^command (.+)/) {

- $read_command = 1;

- $qsub_cmd = $1 . " ";

- } elsif ($_ =~ m/^option ([^=]+)=\* (.+)$/) {

- # Config option that needs replacement with parameter value read from CLI

- # e.g.: option mem=* -l mem_free=$0,ram_free=$0

- my $option = $1; # mem

- my $arg= $2; # -l mem_free=$0,ram_free=$0

- if ($arg !~ m:\$0:) {

- die "Unable to parse line '$line' in config file ($config)\n";

- }

- if (exists $cli_options{$option}) {

- # Replace $0 with the argument read from command line.

- # e.g. "-l mem_free=$0,ram_free=$0" -> "-l mem_free=2G,ram_free=2G"

- $arg =~ s/\$0/$cli_options{$option}/g;

- $cli_config_options{$option} = $arg;

- }

- } elsif ($_ =~ m/^option ([^=]+)=(\S+)\s?(.*)$/) {

- # Config option that does not need replacement

- # e.g. option gpu=0 -q all.q

- my $option = $1; # gpu

- my $value = $2; # 0

- my $arg = $3; # -q all.q

- if (exists $cli_options{$option}) {

- $cli_default_options{($option,$value)} = $arg;

- }

- } elsif ($_ =~ m/^default (\S+)=(\S+)/) {

- # Default options. Used for setting default values to options i.e. when

- # the user does not specify the option on the command line

- # e.g. default gpu=0

- my $option = $1; # gpu

- my $value = $2; # 0

- if (!exists $cli_options{$option}) {

- # If the user has specified this option on the command line, then we

- # don't have to do anything

- $cli_options{$option} = $value;

- }

- } else {

- print STDERR "queue.pl: unable to parse line '$line' in config file ($config)\n";

- exit(1);

- }

-}

-

-close(CONFIG);

-

-if ($read_command != 1) {

- print STDERR "queue.pl: config file ($config) does not contain the line \"command .*\"\n";

- exit(1);

-}

-

-for my $option (keys %cli_options) {

- if ($option eq "config") { next; }

- if ($option eq "max_jobs_run" && $array_job != 1) { next; }

- my $value = $cli_options{$option};

-

- if (exists $cli_default_options{($option,$value)}) {

- $qsub_opts .= "$cli_default_options{($option,$value)} ";

- } elsif (exists $cli_config_options{$option}) {

- $qsub_opts .= "$cli_config_options{$option} ";

- } else {

- if ($opened_config_file == 0) { $config = "default config file"; }

- die "queue.pl: Command line option $option not described in $config (or value '$value' not allowed)\n";

- }

-}

-

-my $cwd = getcwd();

-my $logfile = shift @ARGV;

-

-if ($array_job == 1 && $logfile !~ m/$jobname/

- && $jobend > $jobstart) {

- print STDERR "queue.pl: you are trying to run a parallel job but "

- . "you are putting the output into just one log file ($logfile)\n";

- exit(1);

-}

-

-#

-# Work out the command; quote escaping is done here.

-# Note: the rules for escaping stuff are worked out pretty

-# arbitrarily, based on what we want it to do. Some things that

-# we pass as arguments to queue.pl, such as "|", we want to be

-# interpreted by bash, so we don't escape them. Other things,

-# such as archive specifiers like 'ark:gunzip -c foo.gz|', we want

-# to be passed, in quotes, to the Kaldi program. Our heuristic

-# is that stuff with spaces in should be quoted. This doesn't

-# always work.

-#

-my $cmd = "";

-

-foreach my $x (@ARGV) {

- if ($x =~ m/^\S+$/) { $cmd .= $x . " "; } # If string contains no spaces, take

- # as-is.

- elsif ($x =~ m:\":) { $cmd .= "'$x' "; } # else if no dbl-quotes, use single

- else { $cmd .= "\"$x\" "; } # else use double.

-}

-

-#

-# Work out the location of the script file, and open it for writing.

-#

-my $dir = dirname($logfile);

-my $base = basename($logfile);

-my $qdir = "$dir/q";

-$qdir =~ s:/(log|LOG)/*q:/q:; # If qdir ends in .../log/q, make it just .../q.

-my $queue_logfile = "$qdir/$base";

-

-if (!-d $dir) { system "mkdir -p $dir 2>/dev/null"; } # another job may be doing this...

-if (!-d $dir) { die "Cannot make the directory $dir\n"; }

-# make a directory called "q",

-# where we will put the log created by qsub... normally this doesn't contain

-# anything interesting, evertyhing goes to $logfile.

-if (! -d "$qdir") {

- system "mkdir $qdir 2>/dev/null";

- sleep(5); ## This is to fix an issue we encountered in denominator lattice creation,

- ## where if e.g. the exp/tri2b_denlats/log/15/q directory had just been

- ## created and the job immediately ran, it would die with an error because nfs

- ## had not yet synced. I'm also decreasing the acdirmin and acdirmax in our

- ## NFS settings to something like 5 seconds.

-}

-

-my $queue_array_opt = "";

-if ($array_job == 1) { # It's an array job.

- $queue_array_opt = "-t $jobstart:$jobend";

- $logfile =~ s/$jobname/\$SGE_TASK_ID/g; # This variable will get

- # replaced by qsub, in each job, with the job-id.

- $cmd =~ s/$jobname/\$\{SGE_TASK_ID\}/g; # same for the command...

- $queue_logfile =~ s/\.?$jobname//; # the log file in the q/ subdirectory

- # is for the queue to put its log, and this doesn't need the task array subscript

- # so we remove it.

-}

-

-# queue_scriptfile is as $queue_logfile [e.g. dir/q/foo.log] but

-# with the suffix .sh.

-my $queue_scriptfile = $queue_logfile;

-($queue_scriptfile =~ s/\.[a-zA-Z]{1,5}$/.sh/) || ($queue_scriptfile .= ".sh");

-if ($queue_scriptfile !~ m:^/:) {

- $queue_scriptfile = $cwd . "/" . $queue_scriptfile; # just in case.

-}

-

-# We'll write to the standard input of "qsub" (the file-handle Q),

-# the job that we want it to execute.

-# Also keep our current PATH around, just in case there was something

-# in it that we need (although we also source ./path.sh)

-

-my $syncfile = "$qdir/done.$$";

-

-system("rm $queue_logfile $syncfile 2>/dev/null");

-#

-# Write to the script file, and then close it.

-#

-open(Q, ">$queue_scriptfile") || die "Failed to write to $queue_scriptfile";

-

-print Q "#!/bin/bash\n";

-print Q "cd $cwd\n";

-print Q ". ./path.sh\n";

-print Q "( echo '#' Running on \`hostname\`\n";

-print Q " echo '#' Started at \`date\`\n";

-print Q " echo -n '# '; cat <<EOF\n";

-print Q "$cmd\n"; # this is a way of echoing the command into a comment in the log file,

-print Q "EOF\n"; # without having to escape things like "|" and quote characters.

-print Q ") >$logfile\n";

-print Q "time1=\`date +\"%s\"\`\n";

-print Q " ( $cmd ) 2>>$logfile >>$logfile\n";

-print Q "ret=\$?\n";

-print Q "time2=\`date +\"%s\"\`\n";

-print Q "echo '#' Accounting: time=\$((\$time2-\$time1)) threads=$num_threads >>$logfile\n";

-print Q "echo '#' Finished at \`date\` with status \$ret >>$logfile\n";

-print Q "[ \$ret -eq 137 ] && exit 100;\n"; # If process was killed (e.g. oom) it will exit with status 137;

- # let the script return with status 100 which will put it to E state; more easily rerunnable.

-if ($array_job == 0) { # not an array job

- print Q "touch $syncfile\n"; # so we know it's done.

-} else {

- print Q "touch $syncfile.\$SGE_TASK_ID\n"; # touch a bunch of sync-files.

-}

-print Q "exit \$[\$ret ? 1 : 0]\n"; # avoid status 100 which grid-engine

-print Q "## submitted with:\n"; # treats specially.

-$qsub_cmd .= "-o $queue_logfile $qsub_opts $queue_array_opt $queue_scriptfile >>$queue_logfile 2>&1";

-print Q "# $qsub_cmd\n";

-if (!close(Q)) { # close was not successful... || die "Could not close script file $shfile";

- die "Failed to close the script file (full disk?)";

-}

-

-my $ret = system ($qsub_cmd);

-if ($ret != 0) {

- if ($sync && $ret == 256) { # this is the exit status when a job failed (bad exit status)

- if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/*/g; }

- print STDERR "queue.pl: job writing to $logfile failed\n";

- } else {

- print STDERR "queue.pl: error submitting jobs to queue (return status was $ret)\n";

- print STDERR "queue log file is $queue_logfile, command was $qsub_cmd\n";

- print STDERR `tail $queue_logfile`;

- }

- exit(1);

-}

-

-my $sge_job_id;

-if (! $sync) { # We're not submitting with -sync y, so we

- # need to wait for the jobs to finish. We wait for the

- # sync-files we "touched" in the script to exist.

- my @syncfiles = ();

- if (!defined $jobname) { # not an array job.

- push @syncfiles, $syncfile;

- } else {

- for (my $jobid = $jobstart; $jobid <= $jobend; $jobid++) {

- push @syncfiles, "$syncfile.$jobid";

- }

- }

- # We will need the sge_job_id, to check that job still exists

- { # Get the SGE job-id from the log file in q/

- open(L, "<$queue_logfile") || die "Error opening log file $queue_logfile";

- undef $sge_job_id;

- while (<L>) {

- if (m/Your job\S* (\d+)[. ].+ has been submitted/) {

- if (defined $sge_job_id) {

- die "Error: your job was submitted more than once (see $queue_logfile)";

- } else {

- $sge_job_id = $1;

- }

- }

- }

- close(L);

- if (!defined $sge_job_id) {

- die "Error: log file $queue_logfile does not specify the SGE job-id.";

- }

- }

- my $check_sge_job_ctr=1;

- #

- my $wait = 0.1;

- my $counter = 0;

- foreach my $f (@syncfiles) {

- # wait for them to finish one by one.

- while (! -f $f) {

- sleep($wait);

- $wait *= 1.2;

- if ($wait > 3.0) {

- $wait = 3.0; # never wait more than 3 seconds.

- # the following (.kick) commands are basically workarounds for NFS bugs.

- if (rand() < 0.25) { # don't do this every time...

- if (rand() > 0.5) {

- system("touch $qdir/.kick");

- } else {

- system("rm $qdir/.kick 2>/dev/null");

- }

- }

- if ($counter++ % 10 == 0) {

- # This seems to kick NFS in the teeth to cause it to refresh the

- # directory. I've seen cases where it would indefinitely fail to get

- # updated, even though the file exists on the server.

- # Only do this every 10 waits (every 30 seconds) though, or if there

- # are many jobs waiting they can overwhelm the file server.

- system("ls $qdir >/dev/null");

- }

- }

-

- # Check that the job exists in SGE. Job can be killed if duration

- # exceeds some hard limit, or in case of a machine shutdown.

- if (($check_sge_job_ctr++ % 10) == 0) { # Don't run qstat too often, avoid stress on SGE.

- if ( -f $f ) { next; }; #syncfile appeared: OK.

- $ret = system("qstat -j $sge_job_id >/dev/null 2>/dev/null");

- # system(...) : To get the actual exit value, shift $ret right by eight bits.

- if ($ret>>8 == 1) { # Job does not seem to exist

- # Don't consider immediately missing job as error, first wait some

- # time to make sure it is not just delayed creation of the syncfile.

-

- sleep(3);

- # Sometimes NFS gets confused and thinks it's transmitted the directory

- # but it hasn't, due to timestamp issues. Changing something in the

- # directory will usually fix that.

- system("touch $qdir/.kick");

- system("rm $qdir/.kick 2>/dev/null");

- if ( -f $f ) { next; } #syncfile appeared, ok

- sleep(7);

- system("touch $qdir/.kick");

- sleep(1);

- system("rm $qdir/.kick 2>/dev/null");

- if ( -f $f ) { next; } #syncfile appeared, ok

- sleep(60);

- system("touch $qdir/.kick");

- sleep(1);

- system("rm $qdir/.kick 2>/dev/null");

- if ( -f $f ) { next; } #syncfile appeared, ok

- $f =~ m/\.(\d+)$/ || die "Bad sync-file name $f";

- my $job_id = $1;

- if (defined $jobname) {

- $logfile =~ s/\$SGE_TASK_ID/$job_id/g;

- }

- my $last_line = `tail -n 1 $logfile`;

- if ($last_line =~ m/status 0$/ && (-M $logfile) < 0) {

- # if the last line of $logfile ended with "status 0" and

- # $logfile is newer than this program [(-M $logfile) gives the

- # time elapsed between file modification and the start of this

- # program], then we assume the program really finished OK,

- # and maybe something is up with the file system.

- print STDERR "**queue.pl: syncfile $f was not created but job seems\n" .

- "**to have finished OK. Probably your file-system has problems.\n" .

- "**This is just a warning.\n";

- last;

- } else {

- chop $last_line;

- print STDERR "queue.pl: Error, unfinished job no " .

- "longer exists, log is in $logfile, last line is '$last_line', " .

- "syncfile is $f, return status of qstat was $ret\n" .

- "Possible reasons: a) Exceeded time limit? -> Use more jobs!" .

- " b) Shutdown/Frozen machine? -> Run again!\n";

- exit(1);

- }

- } elsif ($ret != 0) {

- print STDERR "queue.pl: Warning: qstat command returned status $ret (qstat -j $sge_job_id,$!)\n";

- }

- }

- }

- }

- my $all_syncfiles = join(" ", @syncfiles);

- system("rm $all_syncfiles 2>/dev/null");

-}

-

-# OK, at this point we are synced; we know the job is done.

-# But we don't know about its exit status. We'll look at $logfile for this.

-# First work out an array @logfiles of file-locations we need to

-# read (just one, unless it's an array job).

-my @logfiles = ();

-if (!defined $jobname) { # not an array job.

- push @logfiles, $logfile;

-} else {

- for (my $jobid = $jobstart; $jobid <= $jobend; $jobid++) {

- my $l = $logfile;

- $l =~ s/\$SGE_TASK_ID/$jobid/g;

- push @logfiles, $l;

- }

-}

-

-my $num_failed = 0;

-my $status = 1;

-foreach my $l (@logfiles) {

- my @wait_times = (0.1, 0.2, 0.2, 0.3, 0.5, 0.5, 1.0, 2.0, 5.0, 5.0, 5.0, 10.0, 25.0);

- for (my $iter = 0; $iter <= @wait_times; $iter++) {

- my $line = `tail -10 $l 2>/dev/null`; # Note: although this line should be the last

- # line of the file, I've seen cases where it was not quite the last line because

- # of delayed output by the process that was running, or processes it had called.

- # so tail -10 gives it a little leeway.

- if ($line =~ m/with status (\d+)/) {

- $status = $1;

- last;

- } else {

- if ($iter < @wait_times) {

- sleep($wait_times[$iter]);

- } else {

- if (! -f $l) {

- print STDERR "Log-file $l does not exist.\n";

- } else {

- print STDERR "The last line of log-file $l does not seem to indicate the "

- . "return status as expected\n";

- }

- exit(1); # Something went wrong with the queue, or the

- # machine it was running on, probably.

- }

- }

- }

- # OK, now we have $status, which is the return-status of

- # the command in the job.

- if ($status != 0) { $num_failed++; }

-}

-if ($num_failed == 0) { exit(0); }

-else { # we failed.

- if (@logfiles == 1) {

- if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/$jobstart/g; }

- print STDERR "queue.pl: job failed with status $status, log is in $logfile\n";

- if ($logfile =~ m/JOB/) {

- print STDERR "queue.pl: probably you forgot to put JOB=1:\$nj in your script.\n";

- }

- } else {

- if (defined $jobname) { $logfile =~ s/\$SGE_TASK_ID/*/g; }

- my $numjobs = 1 + $jobend - $jobstart;

- print STDERR "queue.pl: $num_failed / $numjobs failed, log is in $logfile\n";

- }

- exit(1);

-}

-#!/usr/bin/env perl

-use warnings; #sed replacement for -w perl parameter

-

-# In general, doing

-# run.pl some.log a b c is like running the command a b c in

-# the bash shell, and putting the standard error and output into some.log.

-# To run parallel jobs (backgrounded on the host machine), you can do (e.g.)

-# run.pl JOB=1:4 some.JOB.log a b c JOB is like running the command a b c JOB

-# and putting it in some.JOB.log, for each one. [Note: JOB can be any identifier].

-# If any of the jobs fails, this script will fail.

-

-# A typical example is:

-# run.pl some.log my-prog "--opt=foo bar" foo \| other-prog baz

-# and run.pl will run something like:

-# ( my-prog '--opt=foo bar' foo | other-prog baz ) >& some.log

-#

-# Basically it takes the command-line arguments, quotes them

-# as necessary to preserve spaces, and evaluates them with bash.

-# In addition it puts the command line at the top of the log, and

-# the start and end times of the command at the beginning and end.

-# The reason why this is useful is so that we can create a different

-# version of this program that uses a queueing system instead.

-

-# use Data::Dumper;

-

-@ARGV < 2 && die "usage: run.pl log-file command-line arguments...";

-

-

-$max_jobs_run = -1;

-$jobstart = 1;

-$jobend = 1;

-$ignored_opts = ""; # These will be ignored.

-

-# First parse an option like JOB=1:4, and any

-# options that would normally be given to

-# queue.pl, which we will just discard.

-

-if (@ARGV > 0) {

- while (@ARGV >= 2 && $ARGV[0] =~ m:^-:) { # parse any options

- # that would normally go to qsub, but which will be ignored here.

- $switch = shift @ARGV;

- if ($switch eq "-V") {

- $ignored_opts .= "-V ";

- } elsif ($switch eq "--max-jobs-run" || $switch eq "-tc") {

- # we do support the option --max-jobs-run n, and its GridEngine form -tc n.

- $max_jobs_run = shift @ARGV;

- if (! ($max_jobs_run > 0)) {

- die "run.pl: invalid option --max-jobs-run $max_jobs_run";

- }

- } else {

- $option = shift @ARGV;

- if ($switch eq "-sync" && $option =~ m/^[yY]/) {

- $ignored_opts .= "-sync "; # Note: in the

- # corresponding code in queue.pl it says instead, just "$sync = 1;".

- }

- $ignored_opts .= "$switch $option ";

- if ($switch eq "-pe") { # e.g. -pe smp 5

- $option2 = shift @ARGV;

- $ignored_opts .= "$option2 ";

- }

- }

- }

- if ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+):(\d+)$/) { # e.g. JOB=1:10

- $jobname = $1;

- $jobstart = $2;

- $jobend = $3;

- shift;

- if ($jobstart > $jobend) {

- die "run.pl: invalid job range $ARGV[0]";

- }

- if ($jobstart <= 0) {

- die "run.pl: invalid job range $ARGV[0], start must be strictly positive (this is required for GridEngine compatibility).";

- }

- } elsif ($ARGV[0] =~ m/^([\w_][\w\d_]*)+=(\d+)$/) { # e.g. JOB=1.

- $jobname = $1;

- $jobstart = $2;

- $jobend = $2;

- shift;

- } elsif ($ARGV[0] =~ m/.+\=.*\:.*$/) {

- print STDERR "run.pl: Warning: suspicious first argument to run.pl: $ARGV[0]\n";

- }

-}

-

-# Users found this message confusing so we are removing it.

-# if ($ignored_opts ne "") {

-# print STDERR "run.pl: Warning: ignoring options \"$ignored_opts\"\n";

-# }

-

-if ($max_jobs_run == -1) { # If --max-jobs-run option not set,

- # then work out the number of processors if possible,

- # and set it based on that.

- $max_jobs_run = 0;

- if (open(P, "</proc/cpuinfo")) { # Linux

- while (<P>) { if (m/^processor/) { $max_jobs_run++; } }

- if ($max_jobs_run == 0) {

- print STDERR "run.pl: Warning: failed to detect any processors from /proc/cpuinfo\n";

- $max_jobs_run = 10; # reasonable default.

- }

- close(P);

- } elsif (open(P, "sysctl -a |")) { # BSD/Darwin

- while (<P>) {

- if (m/hw\.ncpu\s*[:=]\s*(\d+)/) { # hw.ncpu = 4, or hw.ncpu: 4

- $max_jobs_run = $1;

- last;

- }

- }

- close(P);

- if ($max_jobs_run == 0) {

- print STDERR "run.pl: Warning: failed to detect any processors from sysctl -a\n";

- $max_jobs_run = 10; # reasonable default.

- }

- } else {

- # allow at most 32 jobs at once, on non-UNIX systems; change this code

- # if you need to change this default.

- $max_jobs_run = 32;

- }

- # The just-computed value of $max_jobs_run is just the number of processors

- # (or our best guess); and if it happens that the number of jobs we need to

- # run is just slightly above $max_jobs_run, it will make sense to increase

- # $max_jobs_run to equal the number of jobs, so we don't have a small number

- # of leftover jobs.

- $num_jobs = $jobend - $jobstart + 1;

- if ($num_jobs > $max_jobs_run && $num_jobs < 1.4 * $max_jobs_run) {

- $max_jobs_run = $num_jobs;

- }

-}

-

-$logfile = shift @ARGV;

-

-if (defined $jobname && $logfile !~ m/$jobname/ &&

- $jobend > $jobstart) {

- print STDERR "run.pl: you are trying to run a parallel job but "

- . "you are putting the output into just one log file ($logfile)\n";

- exit(1);

-}

-

-$cmd = "";

-

-foreach $x (@ARGV) {

- if ($x =~ m/^\S+$/) { $cmd .= $x . " "; }

- elsif ($x =~ m:\":) { $cmd .= "'$x' "; }

- else { $cmd .= "\"$x\" "; }

-}

-

-#$Data::Dumper::Indent=0;

-$ret = 0;

-$numfail = 0;

-%active_pids=();

-

-use POSIX ":sys_wait_h";

-for ($jobid = $jobstart; $jobid <= $jobend; $jobid++) {

- if (scalar(keys %active_pids) >= $max_jobs_run) {

-

- # Lets wait for a change in any child's status

- # Then we have to work out which child finished

- $r = waitpid(-1, 0);

- $code = $?;

- if ($r < 0 ) { die "run.pl: Error waiting for child process"; } # should never happen.

- if ( defined $active_pids{$r} ) {

- $jid=$active_pids{$r};

- $fail[$jid]=$code;

- if ($code !=0) { $numfail++;}

- delete $active_pids{$r};

- # print STDERR "Finished: $r/$jid " . Dumper(\%active_pids) . "\n";

- } else {

- die "run.pl: Cannot find the PID of the chold process that just finished.";

- }

-

- # In theory we could do a non-blocking waitpid over all jobs running just

- # to find out if only one or more jobs finished during the previous waitpid()

- # However, we just omit this and will reap the next one in the next pass

- # through the for(;;) cycle

- }

- $childpid = fork();

- if (!defined $childpid) { die "run.pl: Error forking in run.pl (writing to $logfile)"; }

- if ($childpid == 0) { # We're in the child... this branch

- # executes the job and returns (possibly with an error status).

- if (defined $jobname) {

- $cmd =~ s/$jobname/$jobid/g;

- $logfile =~ s/$jobname/$jobid/g;

- }

- system("mkdir -p `dirname $logfile` 2>/dev/null");

- open(F, ">$logfile") || die "run.pl: Error opening log file $logfile";

- print F "# " . $cmd . "\n";

- print F "# Started at " . `date`;

- $starttime = `date +'%s'`;

- print F "#\n";

- close(F);

-

- # Pipe into bash.. make sure we're not using any other shell.

- open(B, "|bash") || die "run.pl: Error opening shell command";

- print B "( " . $cmd . ") 2>>$logfile >> $logfile";

- close(B); # If there was an error, exit status is in $?

- $ret = $?;

-

- $lowbits = $ret & 127;

- $highbits = $ret >> 8;

- if ($lowbits != 0) { $return_str = "code $highbits; signal $lowbits" }

- else { $return_str = "code $highbits"; }

-

- $endtime = `date +'%s'`;

- open(F, ">>$logfile") || die "run.pl: Error opening log file $logfile (again)";

- $enddate = `date`;

- chop $enddate;

- print F "# Accounting: time=" . ($endtime - $starttime) . " threads=1\n";

- print F "# Ended ($return_str) at " . $enddate . ", elapsed time " . ($endtime-$starttime) . " seconds\n";

- close(F);

- exit($ret == 0 ? 0 : 1);

- } else {

- $pid[$jobid] = $childpid;

- $active_pids{$childpid} = $jobid;

- # print STDERR "Queued: " . Dumper(\%active_pids) . "\n";

- }

-}

-

-# Now we have submitted all the jobs, lets wait until all the jobs finish

-foreach $child (keys %active_pids) {

- $jobid=$active_pids{$child};

- $r = waitpid($pid[$jobid], 0);

- $code = $?;

- if ($r == -1) { die "run.pl: Error waiting for child process"; } # should never happen.

- if ($r != 0) { $fail[$jobid]=$code; $numfail++ if $code!=0; } # Completed successfully

-}

-

-# Some sanity checks:

-# The $fail array should not contain undefined codes

-# The number of non-zeros in that array should be equal to $numfail

-# We cannot do foreach() here, as the JOB ids do not necessarily start by zero

-$failed_jids=0;

-for ($jobid = $jobstart; $jobid <= $jobend; $jobid++) {

- $job_return = $fail[$jobid];

- if (not defined $job_return ) {

- # print Dumper(\@fail);

-

- die "run.pl: Sanity check failed: we have indication that some jobs are running " .

- "even after we waited for all jobs to finish" ;

- }

- if ($job_return != 0 ){ $failed_jids++;}

-}

-if ($failed_jids != $numfail) {

- die "run.pl: Sanity check failed: cannot find out how many jobs failed ($failed_jids x $numfail)."

-}

-if ($numfail > 0) { $ret = 1; }

-

-if ($ret != 0) {

- $njobs = $jobend - $jobstart + 1;

- if ($njobs == 1) {

- if (defined $jobname) {

- $logfile =~ s/$jobname/$jobstart/; # only one numbered job, so replace name with

- # that job.

- }

- print STDERR "run.pl: job failed, log is in $logfile\n";

- if ($logfile =~ m/JOB/) {

- print STDERR "run.pl: probably you forgot to put JOB=1:\$nj in your script.";

- }

- }

- else {

- $logfile =~ s/$jobname/*/g;

- print STDERR "run.pl: $numfail / $njobs failed, log is in $logfile\n";

- }

-}

-

-

-exit ($ret);

-#!/bin/bash

-# Copyright 2010-2013 Microsoft Corporation

-# Johns Hopkins University (Author: Daniel Povey)

-

-# Licensed under the Apache License, Version 2.0 (the "License");

-# you may not use this file except in compliance with the License.

-# You may obtain a copy of the License at

-#

-# http://www.apache.org/licenses/LICENSE-2.0

-#

-# THIS CODE IS PROVIDED *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY

-# KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED

-# WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,

-# MERCHANTABLITY OR NON-INFRINGEMENT.

-# See the Apache 2 License for the specific language governing permissions and

-# limitations under the License.

-

-split_per_spk=true

-if [ "$1" == "--per-utt" ]; then

- split_per_spk=false

- shift

-fi

-

-if [ $# != 2 ]; then

- echo "Usage: split_data.sh [--per-utt] <data-dir> <num-to-split>"

- echo "This script will not split the data-dir if it detects that the output is newer than the input."

- echo "By default it splits per speaker (so each speaker is in only one split dir),"

- echo "but with the --per-utt option it will ignore the speaker information while splitting."

- exit 1

-fi

-

-data=$1

-numsplit=$2

-

-if [ $numsplit -le 0 ]; then

- echo "Invalid num-split argument $numsplit";

- exit 1;

-fi

-

-n=0;

-feats=""

-wavs=""

-utt2spks=""

-texts=""

-

-nu=`cat $data/utt2spk | wc -l`

-nf=`cat $data/feats.scp 2>/dev/null | wc -l`

-nt=`cat $data/text 2>/dev/null | wc -l` # take it as zero if no such file

-if [ -f $data/feats.scp ] && [ $nu -ne $nf ]; then

- echo "** split_data.sh: warning, #lines is (utt2spk,feats.scp) is ($nu,$nf); you can "

- echo "** use utils/fix_data_dir.sh $data to fix this."

-fi

-if [ -f $data/text ] && [ $nu -ne $nt ]; then

- echo "** split_data.sh: warning, #lines is (utt2spk,text) is ($nu,$nt); you can "

- echo "** use utils/fix_data_dir.sh to fix this."

-fi

-

-s1=$data/split$numsplit/1

-if [ ! -d $s1 ]; then

- need_to_split=true

-else

- need_to_split=false

- for f in utt2spk spk2utt spk2warp feats.scp text wav.scp cmvn.scp spk2gender \

- vad.scp segments reco2file_and_channel utt2lang; do

- if [[ -f $data/$f && ( ! -f $s1/$f || $s1/$f -ot $data/$f ) ]]; then

- need_to_split=true

- fi

- done

-fi

-

-if ! $need_to_split; then

- exit 0;

-fi

-

-for n in `seq $numsplit`; do

- mkdir -p $data/split$numsplit/$n

- utt2spks="$utt2spks $data/split$numsplit/$n/utt2spk"

-done

-

-if $split_per_spk; then

- utt2spk_opt="--utt2spk=$data/utt2spk"

-else

- utt2spk_opt=

-fi

-

-# If lockfile is not installed, just don't lock it. It's not a big deal.

-which lockfile >&/dev/null && lockfile -l 60 $data/.split_lock

-

-utils/split_scp.pl $utt2spk_opt $data/utt2spk $utt2spks || exit 1

-

-for n in `seq $numsplit`; do

- dsn=$data/split$numsplit/$n

- utils/utt2spk_to_spk2utt.pl $dsn/utt2spk > $dsn/spk2utt || exit 1;

-done

-

-maybe_wav_scp=

-if [ ! -f $data/segments ]; then

- maybe_wav_scp=wav.scp # If there is no segments file, then wav file is

- # indexed per utt.

-fi

-

-# split some things that are indexed by utterance.

-for f in feats.scp text vad.scp utt2lang $maybe_wav_scp; do

- if [ -f $data/$f ]; then

- utils/filter_scps.pl JOB=1:$numsplit \

- $data/split$numsplit/JOB/utt2spk $data/$f $data/split$numsplit/JOB/$f || exit 1;

- fi

-done

-

-# split some things that are indexed by speaker

-for f in spk2gender spk2warp cmvn.scp; do

- if [ -f $data/$f ]; then

- utils/filter_scps.pl JOB=1:$numsplit \

- $data/split$numsplit/JOB/spk2utt $data/$f $data/split$numsplit/JOB/$f || exit 1;

- fi

-done

-

-for n in `seq $numsplit`; do

- dsn=$data/split$numsplit/$n

- if [ -f $data/segments ]; then

- utils/filter_scp.pl $dsn/utt2spk $data/segments > $dsn/segments

- awk '{print $2;}' $dsn/segments | sort | uniq > $data/tmp.reco # recording-ids.

- if [ -f $data/reco2file_and_channel ]; then

- utils/filter_scp.pl $data/tmp.reco $data/reco2file_and_channel > $dsn/reco2file_and_channel

- fi

- if [ -f $data/wav.scp ]; then

- utils/filter_scp.pl $data/tmp.reco $data/wav.scp >$dsn/wav.scp

- fi

- rm $data/tmp.reco

- fi # else it would have been handled above, see maybe_wav.

-done

-

-rm -f $data/.split_lock

-

-exit 0

-# Change KDIR to `kaldi-trunk' path (Kaldi must be compiled with --share)

-KDIR := /slfs6/users/ymz09/kaldi/

-KL := $(KDIR)/src/feat/kaldi-feat.a $(KDIR)/src/matrix/kaldi-matrix.a $(KDIR)/src/base/kaldi-base.a $(KDIR)/src/util/kaldi-util.a $(KDIR)/src/hmm/kaldi-hmm.a $(KDIR)/src/tree/kaldi-tree.a -lcblas -llapack_atlas

-

- gcc -shared -fPIC -o $@ $(OBJ_DIR)/src/cwrapper_kaldi.o $(OBJ_DIR)/init.o $(OBJ_DIR)/src/init.o -lstdc++ -Wl,-rpath=$(LIB_PATH) -L$(LIB_PATH) -lnervcore -lluaT $(KL)

- -rm $(OBJ_DIR)/src/*.o

-#include "../nerv/common.h"

- local raw = self.gconf.cumat_type.new_from_host(self.feat_repo:cur_utter(self.debug))

- local expanded = self.gconf.cumat_type(raw:nrow(), raw:ncol() * step)

- feat_utter = self.gconf.mmat_type(rearranged:nrow(), rearranged:ncol())

- rearranged:copy_toh(feat_utter)

- -- need provide 'gconf.decoding = true' while decoding

- if not self.gconf.decoding and lab_utter == nil then

- nerv.info("[Kaldi IO] utterance %s alignment not found, skip it.", self.feat_repo:key())

- summary = "Kaldi I/O support (Kaldi I/O wrapper) for Nerv",

-#include "nerv/common.h"

- extern Matrix *nerv_matrix_host_float_create(long nrow, long ncol, Status *status);

- extern Matrix *nerv_matrix_host_double_create(long nrow, long ncol, Status *status);

- Matrix *kaldi_feature_repo_read_utterance(KaldiFeatureRepo *repo, lua_State *L, int debug) {

- mat = nerv_matrix_host_float_create(n, m, &status);

- mat = nerv_matrix_host_double_create(n, m, &status);

- kaldi::SequentialBaseFloatMatrixReader feature_reader = kaldi::SequentialBaseFloatMatrixReader(string(feature_rspecifier));

- for (; !feature_reader.Done(); feature_reader.Next())

- const std::string &key = feature_reader.Key();

- const kaldi::Matrix<BaseFloat> &feat = feature_reader.Value();

- kaldi::SequentialTokenVectorReader map_reader = kaldi::SequentialTokenVectorReader(string(map_rspecifier));

- for (; !map_reader.Done(); map_reader.Next())

- const std::vector<std::string> target = map_reader.Value();

- repo->map[map_reader.Key()] = *target.begin();

- Matrix *kaldi_lookup_feature_repo_read_utterance(KaldiLookupFeatureRepo *repo, KaldiFeatureRepo *frepo, int nframes, lua_State *L, int debug) {

- mat = nerv_matrix_host_float_create(n, m, &status);

- mat = nerv_matrix_host_double_create(n, m, &status);

- int debug) {

- else return mat;

- mat = nerv_matrix_host_float_create(n, m, &status);

- mat = nerv_matrix_host_double_create(n, m, &status);

-#include "nerv/matrix/matrix.h"

-#include "nerv/common.h"

- Matrix *kaldi_feature_repo_read_utterance(KaldiFeatureRepo *repo, lua_State *L, int debug);

- int debug);

- Matrix *kaldi_lookup_feature_repo_read_utterance(KaldiLookupFeatureRepo *repo, KaldiFeatureRepo *frepo, int nframes, lua_State *L, int debug);

-#include "nerv/common.h"

- Matrix *utter = kaldi_feature_repo_read_utterance(repo, L, debug);

- Matrix *utter = kaldi_lookup_feature_repo_read_utterance(repo, feat_repo, nframes, L, debug);

- Matrix *utter = kaldi_label_repo_read_utterance(repo, feat_repo, nframes, L, debug);

- mat = kaldi_feature_repo_read_utterance(repo, NULL, 1);

- mat = kaldi_feature_repo_read_utterance(repo, NULL, 1);

-double mat[4096][4096];

- fout.open(argv[1]);

- int cnt = 0;

- while (scanf("%s", token) != EOF)

- scanf("%d %d", &ncol, &nrow);

- scanf("%s %lf %s %lf %s %lf",

- scanf("%s", token);

- scanf("%lf", mat[i] + j);

- scanf("%s", token);

- if (scanf("%s", token) == 1 && *token == '[')

- scanf("%lf", mat[0] + j);

- scanf("%d %d", &ncol, &ncol);

- scanf("%s %lf",

- scanf("%s", token);

- scanf("%lf", mat[0] + j);

- scanf("%s", token);

--- usage: nerv config_file nerv_param_input tnet_output

-param_repo:import({arg[2], gconf.initialized_param[2]}, nil, gconf)

-# Change KDIR to `kaldi-trunk' path (Kaldi must be compiled with --share)

-KDIR := /slfs6/users/ymz09/kaldi/

-#include "../nerv/common.h"

-#include "nerv/common.h"

-#include "nerv/common.h"

- extern NervMatrix *nerv_matrix_host_float_create(long nrow, long ncol, Status *status);

-#include "nerv/matrix/matrix.h"

-#include "nerv/common.h"

-#include "nerv/common.h"

- extern NervMatrix *nerv_matrix_host_float_create(long nrow, long ncol, Status *status);

-#include "nerv/matrix/matrix.h"

-#include "nerv/common.h"

- expanded = gconf.cumat_type(output[1]:nrow() - frm_trim * 2, output[1]:ncol())

- expanded:copy_fromd(output[1], frm_trim, feat_utter:nrow() - frm_trim)