retrain_simple2.sh
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#!/bin/bash
# Copyright 2012-2014 Johns Hopkins University (Author: Daniel Povey).
# 2013 Xiaohui Zhang
# 2013 Guoguo Chen
# 2014 Vimal Manohar
# Apache 2.0.
# retrain_simple2.sh is a script for training a single-layer (softmax-only)
# neural network on top of activations dumped from an existing network; we'll
# later combine the networks to a single network.
# It differs from train_pnorm_simple2.sh in the same way that retrain_fast.sh
# differs from train_pnorm_fast.sh.
# Begin configuration section.
cmd=run.pl
num_epochs=5 # Number of epochs of training;
initial_learning_rate=0.04
final_learning_rate=0.004
minibatch_size=128 # by default use a smallish minibatch size for neural net
# training; this controls instability which would otherwise
# be a problem with multi-threaded update.
samples_per_iter=400000 # each iteration of training, see this many samples
# per job. This option is passed to get_egs.sh
num_jobs_nnet=4 # Number of neural net jobs to run in parallel. This option
# is passed to get_egs.sh.
prior_subset_size=10000 # 10k samples per job, for computing priors. Should be
# more than enough.
num_jobs_compute_prior=10 # these are single-threaded, run on CPU.
get_egs_stage=0
max_models_combine=20 # The "max_models_combine" is the maximum number of models we give
# to the final 'combine' stage, but these models will themselves be averages of
# iteration-number ranges.
shuffle_buffer_size=5000 # This "buffer_size" variable controls randomization of the samples
# on each iter. You could set it to 0 or to a large value for complete
# randomization, but this would both consume memory and cause spikes in
# disk I/O. Smaller is easier on disk and memory but less random. It's
# not a huge deal though, as samples are anyway randomized right at the start.
# (the point of this is to get data in different minibatches on different iterations,
# since in the preconditioning method, 2 samples in the same minibatch can
# affect each others' gradients.
stage=-4
alpha=4.0 # relates to online preconditioning.
update_period=4 # relates to online preconditioning: says how often we update the subspace.
num_samples_history=2000 # relates to online preconditioning
precondition_rank_in=20 # relates to online preconditioning
precondition_rank_out=80 # relates to online preconditioning
max_change_per_sample=0.075
mix_up=0 # Number of components to mix up to (should be > #tree leaves, if
# specified.)
num_threads=16
parallel_opts="--num-threads 16 --mem 1G"
# by default we use 16 threads; this lets the queue know.
# note: parallel_opts doesn't automatically get adjusted if you adjust num-threads.
combine_num_threads=8
combine_parallel_opts="--num-threads 8" # queue options for the "combine" stage.
cleanup=true
egs_dir=
egs_opts=
io_opts="--max-jobs-run 5" # for jobs with a lot of I/O, limits the number running at one time.
align_cmd= # The cmd that is passed to steps/nnet2/align.sh
align_use_gpu= # Passed to use_gpu in steps/nnet2/align.sh [yes/no]
realign_epochs= # List of epochs, the beginning of which realignment is done
num_jobs_align=30 # Number of jobs for realignment
# End configuration section.
echo "$0 $@" # Print the command line for logging
if [ -f path.sh ]; then . ./path.sh; fi
. parse_options.sh || exit 1;
if [ $# != 4 ]; then
echo "Usage: $0 [opts] <data> <lang> <ali-dir> <exp-dir>"
echo " e.g.: $0 data/train data/lang exp/tri3_ali exp/tri4_nnet"
echo ""
echo "Main options (for others, see top of script file)"
echo " --config <config-file> # config file containing options"
echo " --cmd (utils/run.pl|utils/queue.pl <queue opts>) # how to run jobs."
echo " --num-epochs <#epochs|5> # Number of epochs of training"
echo " --initial-learning-rate <initial-learning-rate|0.02> # Learning rate at start of training, e.g. 0.02 for small"
echo " # data, 0.01 for large data"
echo " --final-learning-rate <final-learning-rate|0.004> # Learning rate at end of training, e.g. 0.004 for small"
echo " # data, 0.001 for large data"
echo " --mix-up <#pseudo-gaussians|0> # Can be used to have multiple targets in final output layer,"
echo " # per context-dependent state. Try a number several times #states."
echo " --num-jobs-nnet <num-jobs|8> # Number of parallel jobs to use for main neural net"
echo " # training (will affect results as well as speed; try 8, 16)"
echo " # Note: if you increase this, you may want to also increase"
echo " # the learning rate."
echo " --num-threads <num-threads|16> # Number of parallel threads per job (will affect results"
echo " # as well as speed; may interact with batch size; if you increase"
echo " # this, you may want to decrease the batch size."
echo " --parallel-opts <opts|\"--num-threads 16 --mem 1G\"> # extra options to pass to e.g. queue.pl for processes that"
echo " # use multiple threads... "
echo " --io-opts <opts|\"--max-jobs-run 10\"> # Options given to e.g. queue.pl for jobs that do a lot of I/O."
echo " --minibatch-size <minibatch-size|128> # Size of minibatch to process (note: product with --num-threads"
echo " # should not get too large, e.g. >2k)."
echo " --samples-per-iter <#samples|400000> # Number of samples of data to process per iteration, per"
echo " # process."
echo " --realign-epochs <list-of-epochs|\"\"> # A list of space-separated epoch indices the beginning of which"
echo " # realignment is to be done"
echo " --align-cmd (utils/run.pl|utils/queue.pl <queue opts>) # passed to align.sh"
echo " --align-use-gpu (yes/no) # specify is gpu is to be used for realignment"
echo " --num-jobs-align <#njobs|30> # Number of jobs to perform realignment"
echo " --stage <stage|-4> # Used to run a partially-completed training process from somewhere in"
echo " # the middle."
exit 1;
fi
data=$1
lang=$2
alidir=$3
dir=$4
if [ ! -z "$realign_epochs" ]; then
[ -z "$align_cmd" ] && echo "$0: realign_epochs specified but align_cmd not specified" && exit 1
[ -z "$align_use_gpu" ] && echo "$0: realign_epochs specified but align_use_gpu not specified" && exit 1
fi
# Check some files.
for f in $data/feats.scp $lang/L.fst $alidir/ali.1.gz $alidir/final.mdl $alidir/tree; do
[ ! -f $f ] && echo "$0: no such file $f" && exit 1;
done
# Set some variables.
num_leaves=`tree-info $alidir/tree 2>/dev/null | grep num-pdfs | awk '{print $2}'` || exit 1
[ -z $num_leaves ] && echo "\$num_leaves is unset" && exit 1
[ "$num_leaves" -eq "0" ] && echo "\$num_leaves is 0" && exit 1
nj=`cat $alidir/num_jobs` || exit 1; # number of jobs in alignment dir...
# in this dir we'll have just one job.
sdata=$data/split$nj
utils/split_data.sh $data $nj
mkdir -p $dir/log
echo $nj > $dir/num_jobs
cp $alidir/tree $dir
utils/lang/check_phones_compatible.sh $lang/phones.txt $alidir/phones.txt || exit 1;
cp $lang/phones.txt $dir || exit 1;
if [ $stage -le -3 ] && [ -z "$egs_dir" ]; then
echo "$0: calling get_egs2.sh"
# set --frames-per-eg to 1 because there is no context, so there
# is no advantage in having multiple frames per eg.
steps/nnet2/get_egs2.sh --feat-type raw \
--frames-per-eg 1 --left-context 0 --right-context 0 \
--cmvn-opts "--norm-means=false --norm-vars=false" \
--io-opts "$io_opts" \
--samples-per-iter $samples_per_iter --stage $get_egs_stage \
--cmd "$cmd" $egs_opts $data $alidir $dir/egs || exit 1;
fi
if [ -z $egs_dir ]; then
egs_dir=$dir/egs
fi
frames_per_eg=$(cat $egs_dir/info/frames_per_eg) || { echo "error: no such file $egs_dir/info/frames_per_eg"; exit 1; }
num_archives=$(cat $egs_dir/info/num_archives) || { echo "error: no such file $egs_dir/info/frames_per_eg"; exit 1; }
# num_archives_expanded considers each separate label-position from
# 0..frames_per_eg-1 to be a separate archive.
num_archives_expanded=$[$num_archives*$frames_per_eg]
if [ $num_jobs_nnet -gt $num_archives_expanded ]; then
echo "$0: --num-jobs-nnet cannot exceed num-archives*frames-per-eg which is $num_archives_expanded"
echo "$0: setting --num-jobs-nnet to $num_archives_expanded"
num_jobs_nnet=$num_archives_expanded
fi
if [ $stage -le -2 ]; then
echo "$0: initializing neural net";
feat_dim=$(feat-to-dim scp:$data/feats.scp -) || exit 1;
online_preconditioning_opts="alpha=$alpha num-samples-history=$num_samples_history update-period=$update_period rank-in=$precondition_rank_in rank-out=$precondition_rank_out max-change-per-sample=$max_change_per_sample"
stddev=`perl -e "print 1.0/sqrt($pnorm_input_dim);"`
cat >$dir/nnet.config <<EOF
AffineComponentPreconditionedOnline input-dim=$feat_dim output-dim=$num_leaves $online_preconditioning_opts learning-rate=$initial_learning_rate param-stddev=0 bias-stddev=0
SoftmaxComponent dim=$num_leaves
EOF
$cmd $dir/log/nnet_init.log \
nnet-am-init $alidir/tree $lang/topo "nnet-init $dir/nnet.config -|" \
$dir/0.mdl || exit 1;
fi
if [ $stage -le -1 ]; then
echo "Training transition probabilities and setting priors"
$cmd $dir/log/train_trans.log \
nnet-train-transitions $dir/0.mdl "ark:gunzip -c $alidir/ali.*.gz|" $dir/0.mdl \
|| exit 1;
fi
# set num_iters so that as close as possible, we process the data $num_epochs
# times, i.e. $num_iters*$num_jobs_nnet == $num_epochs*$num_archives_expanded
num_iters=$[($num_epochs*$num_archives_expanded)/$num_jobs_nnet]
echo "$0: Will train for $num_epochs epochs = $num_iters iterations"
mix_up_iter=$[$num_iters/2]
if [ $num_threads -eq 1 ]; then
parallel_suffix="-simple" # this enables us to use GPU code if
# we have just one thread.
parallel_train_opts=
if ! cuda-compiled; then
echo "$0: WARNING: you are running with one thread but you have not compiled"
echo " for CUDA. You may be running a setup optimized for GPUs. If you have"
echo " GPUs and have nvcc installed, go to src/ and do ./configure; make"
fi
else
parallel_suffix="-parallel"
parallel_train_opts="--num-threads=$num_threads"
fi
approx_iters_per_epoch=$[$num_iters/$num_epochs]
# First work out how many models we want to combine over in the final
# nnet-combine-fast invocation. This equals
# min(max(max_models_combine, iters_per_epoch),
# 2/3 * iters_after_mixup)
num_models_combine=$max_models_combine
if [ $num_models_combine -lt $approx_iters_per_epoch ]; then
num_models_combine=$approx_iters_per_epoch
fi
iters_after_mixup_23=$[(($num_iters-$mix_up_iter-1)*2)/3]
if [ $num_models_combine -gt $iters_after_mixup_23 ]; then
num_models_combine=$iters_after_mixup_23
fi
first_model_combine=$[$num_iters-$num_models_combine+1]
x=0
for realign_epoch in $realign_epochs; do
# compare the equation below with the equation we use to set num_iters above.
# note, realign_epochs may be floating-point, which is why we don't use $[] to
# do the math.
realign_iter=$(perl -e 'print int(($ARGV[0]*$ARGV[1])/$ARGV[2]);' $realign_epoch $num_archives_expanded $num_jobs_nnet)
realign_this_iter[$realign_iter]=$realign_epoch
done
cur_egs_dir=$egs_dir
while [ $x -lt $num_iters ]; do
if [ ! -z "${realign_this_iter[$x]}" ]; then
prev_egs_dir=$cur_egs_dir
cur_egs_dir=$dir/egs_${realign_this_iter[$x]}
fi
if [ $x -ge 0 ] && [ $stage -le $x ]; then
if [ ! -z "${realign_this_iter[$x]}" ]; then
epoch=${realign_this_iter[$x]}
echo "Getting average posterior for purposes of adjusting the priors."
# Note: this just uses CPUs, using a smallish subset of data.
# always use the first egs archive, which makes the script simpler;
# we're using different random subsets of it.
rm $dir/post.$x.*.vec 2>/dev/null
$cmd JOB=1:$num_jobs_compute_prior $dir/log/get_post.$x.JOB.log \
nnet-copy-egs --srand=JOB --frame=random ark:$prev_egs_dir/egs.1.ark ark:- \| \
nnet-subset-egs --srand=JOB --n=$prior_subset_size ark:- ark:- \| \
nnet-compute-from-egs "nnet-to-raw-nnet $dir/$x.mdl -|" ark:- ark:- \| \
matrix-sum-rows ark:- ark:- \| vector-sum ark:- $dir/post.$x.JOB.vec || exit 1;
sleep 3; # make sure there is time for $dir/post.$x.*.vec to appear.
$cmd $dir/log/vector_sum.$x.log \
vector-sum $dir/post.$x.*.vec $dir/post.$x.vec || exit 1;
rm $dir/post.$x.*.vec;
echo "Re-adjusting priors based on computed posteriors"
$cmd $dir/log/adjust_priors.$x.log \
nnet-adjust-priors $dir/$x.mdl $dir/post.$x.vec $dir/$x.mdl || exit 1;
sleep 2
steps/nnet2/align.sh --nj $num_jobs_align --cmd "$align_cmd" --use-gpu $align_use_gpu \
--transform-dir "$transform_dir" --online-ivector-dir "$online_ivector_dir" \
--iter $x $data $lang $dir $dir/ali_$epoch || exit 1
steps/nnet2/relabel_egs2.sh --cmd "$cmd" --iter $x $dir/ali_$epoch \
$prev_egs_dir $cur_egs_dir || exit 1
if $cleanup && [[ $prev_egs_dir =~ $dir/egs* ]]; then
steps/nnet2/remove_egs.sh $prev_egs_dir
fi
fi
# Set off jobs doing some diagnostics, in the background.
# Use the egs dir from the previous iteration for the diagnostics
$cmd $dir/log/compute_prob_valid.$x.log \
nnet-compute-prob $dir/$x.mdl ark:$cur_egs_dir/valid_diagnostic.egs &
$cmd $dir/log/compute_prob_train.$x.log \
nnet-compute-prob $dir/$x.mdl ark:$cur_egs_dir/train_diagnostic.egs &
if [ $x -gt 0 ] && [ ! -f $dir/log/mix_up.$[$x-1].log ]; then
$cmd $dir/log/progress.$x.log \
nnet-show-progress --use-gpu=no $dir/$[$x-1].mdl $dir/$x.mdl \
ark:$cur_egs_dir/train_diagnostic.egs '&&' \
nnet-am-info $dir/$x.mdl &
fi
echo "Training neural net (pass $x)"
mdl=$dir/$x.mdl
if [ $x -eq 0 ]; then
# on iteration zero, use a smaller minibatch
# size and just one job: the model-averaging doesn't seem to be helpful
# when the model is changing too fast (i.e. it worsens the objective
# function), and the smaller minibatch size will help to keep
# the update stable.
this_minibatch_size=$[$minibatch_size/2];
do_average=false
else
this_minibatch_size=$minibatch_size
do_average=true
fi
rm $dir/.error 2>/dev/null
( # this sub-shell is so that when we "wait" below,
# we only wait for the training jobs that we just spawned,
# not the diagnostic jobs that we spawned above.
# We can't easily use a single parallel SGE job to do the main training,
# because the computation of which archive and which --frame option
# to use for each job is a little complex, so we spawn each one separately.
for n in $(seq $num_jobs_nnet); do
k=$[$x*$num_jobs_nnet + $n - 1]; # k is a zero-based index that we'll derive
# the other indexes from.
archive=$[($k%$num_archives)+1]; # work out the 1-based archive index.
frame=$[(($k/$num_archives)%$frames_per_eg)]; # work out the 0-based frame
# index; this increases more slowly than the archive index because the
# same archive with different frame indexes will give similar gradients,
# so we want to separate them in time.
$cmd $parallel_opts $dir/log/train.$x.$n.log \
nnet-train$parallel_suffix $parallel_train_opts \
--minibatch-size=$this_minibatch_size --srand=$x $dir/$x.mdl \
"ark,bg:nnet-copy-egs --frame=$frame ark:$cur_egs_dir/egs.$archive.ark ark:-|nnet-shuffle-egs --buffer-size=$shuffle_buffer_size --srand=$x ark:- ark:-|" \
$dir/$[$x+1].$n.mdl || touch $dir/.error &
done
wait
)
# the error message below is not that informative, but $cmd will
# have printed a more specific one.
[ -f $dir/.error ] && echo "$0: error on iteration $x of training" && exit 1;
nnets_list=
for n in `seq 1 $num_jobs_nnet`; do
nnets_list="$nnets_list $dir/$[$x+1].$n.mdl"
done
learning_rate=`perl -e '($x,$n,$i,$f)=@ARGV; print ($x >= $n ? $f : $i*exp($x*log($f/$i)/$n));' $[$x+1] $num_iters $initial_learning_rate $final_learning_rate`;
if $do_average; then
# average the output of the different jobs.
$cmd $dir/log/average.$x.log \
nnet-am-average $nnets_list - \| \
nnet-am-copy --learning-rate=$learning_rate - $dir/$[$x+1].mdl || exit 1;
else
# choose the best from the different jobs.
n=$(perl -e '($nj,$pat)=@ARGV; $best_n=1; $best_logprob=-1.0e+10; for ($n=1;$n<=$nj;$n++) {
$fn = sprintf($pat,$n); open(F, "<$fn") || die "Error opening log file $fn";
undef $logprob; while (<F>) { if (m/log-prob-per-frame=(\S+)/) { $logprob=$1; } }
close(F); if (defined $logprob && $logprob > $best_logprob) { $best_logprob=$logprob;
$best_n=$n; } } print "$best_n\n"; ' $num_jobs_nnet $dir/log/train.$x.%d.log) || exit 1;
[ -z "$n" ] && echo "Error getting best model" && exit 1;
$cmd $dir/log/select.$x.log \
nnet-am-copy --learning-rate=$learning_rate $dir/$[$x+1].$n.mdl $dir/$[$x+1].mdl || exit 1;
fi
if [ "$mix_up" -gt 0 ] && [ $x -eq $mix_up_iter ]; then
# mix up.
echo Mixing up from $num_leaves to $mix_up components
$cmd $dir/log/mix_up.$x.log \
nnet-am-mixup --min-count=10 --num-mixtures=$mix_up \
$dir/$[$x+1].mdl $dir/$[$x+1].mdl || exit 1;
fi
rm $nnets_list
[ ! -f $dir/$[$x+1].mdl ] && exit 1;
if [ -f $dir/$[$x-1].mdl ] && $cleanup && \
[ $[($x-1)%100] -ne 0 ] && [ $[$x-1] -lt $first_model_combine ]; then
rm $dir/$[$x-1].mdl
fi
fi
x=$[$x+1]
done
if [ $stage -le $num_iters ]; then
echo "Doing final combination to produce final.mdl"
# Now do combination.
nnets_list=()
# the if..else..fi statement below sets 'nnets_list'.
if [ $max_models_combine -lt $num_models_combine ]; then
# The number of models to combine is too large, e.g. > 20. In this case,
# each argument to nnet-combine-fast will be an average of multiple models.
cur_offset=0 # current offset from first_model_combine.
for n in $(seq $max_models_combine); do
next_offset=$[($n*$num_models_combine)/$max_models_combine]
sub_list=""
for o in $(seq $cur_offset $[$next_offset-1]); do
iter=$[$first_model_combine+$o]
mdl=$dir/$iter.mdl
[ ! -f $mdl ] && echo "Expected $mdl to exist" && exit 1;
sub_list="$sub_list $mdl"
done
nnets_list[$[$n-1]]="nnet-am-average $sub_list - |"
cur_offset=$next_offset
done
else
nnets_list=
for n in $(seq 0 $[num_models_combine-1]); do
iter=$[$first_model_combine+$n]
mdl=$dir/$iter.mdl
[ ! -f $mdl ] && echo "Expected $mdl to exist" && exit 1;
nnets_list[$n]=$mdl
done
fi
# Below, use --use-gpu=no to disable nnet-combine-fast from using a GPU, as
# if there are many models it can give out-of-memory error; set num-threads to 8
# to speed it up (this isn't ideal...)
num_egs=`nnet-copy-egs ark:$cur_egs_dir/combine.egs ark:/dev/null 2>&1 | tail -n 1 | awk '{print $NF}'`
mb=$[($num_egs+$combine_num_threads-1)/$combine_num_threads]
[ $mb -gt 512 ] && mb=512
# Setting --initial-model to a large value makes it initialize the combination
# with the average of all the models. It's important not to start with a
# single model, or, due to the invariance to scaling that these nonlinearities
# give us, we get zero diagonal entries in the fisher matrix that
# nnet-combine-fast uses for scaling, which after flooring and inversion, has
# the effect that the initial model chosen gets much higher learning rates
# than the others. This prevents the optimization from working well.
$cmd $combine_parallel_opts $dir/log/combine.log \
nnet-combine-fast --initial-model=100000 --num-lbfgs-iters=40 --use-gpu=no \
--num-threads=$combine_num_threads \
--verbose=3 --minibatch-size=$mb "${nnets_list[@]}" ark:$cur_egs_dir/combine.egs \
$dir/final.mdl || exit 1;
# Compute the probability of the final, combined model with
# the same subset we used for the previous compute_probs, as the
# different subsets will lead to different probs.
$cmd $dir/log/compute_prob_valid.final.log \
nnet-compute-prob $dir/final.mdl ark:$cur_egs_dir/valid_diagnostic.egs &
$cmd $dir/log/compute_prob_train.final.log \
nnet-compute-prob $dir/final.mdl ark:$cur_egs_dir/train_diagnostic.egs &
fi
if [ $stage -le $[$num_iters+1] ]; then
echo "Getting average posterior for purposes of adjusting the priors."
# Note: this just uses CPUs, using a smallish subset of data.
rm $dir/post.$x.*.vec 2>/dev/null
$cmd JOB=1:$num_jobs_compute_prior $dir/log/get_post.$x.JOB.log \
nnet-copy-egs --frame=random --srand=JOB ark:$cur_egs_dir/egs.1.ark ark:- \| \
nnet-subset-egs --srand=JOB --n=$prior_subset_size ark:- ark:- \| \
nnet-compute-from-egs "nnet-to-raw-nnet $dir/final.mdl -|" ark:- ark:- \| \
matrix-sum-rows ark:- ark:- \| vector-sum ark:- $dir/post.$x.JOB.vec || exit 1;
sleep 3; # make sure there is time for $dir/post.$x.*.vec to appear.
$cmd $dir/log/vector_sum.$x.log \
vector-sum $dir/post.$x.*.vec $dir/post.$x.vec || exit 1;
rm $dir/post.$x.*.vec;
echo "Re-adjusting priors based on computed posteriors"
$cmd $dir/log/adjust_priors.final.log \
nnet-adjust-priors $dir/final.mdl $dir/post.$x.vec $dir/final.mdl || exit 1;
fi
if [ ! -f $dir/final.mdl ]; then
echo "$0: $dir/final.mdl does not exist."
# we don't want to clean up if the training didn't succeed.
exit 1;
fi
sleep 2
echo Done
if $cleanup; then
echo Cleaning up data
if [[ $cur_egs_dir =~ $dir/egs* ]]; then
steps/nnet2/remove_egs.sh $cur_egs_dir
fi
echo Removing most of the models
for x in `seq 0 $num_iters`; do
if [ $[$x%100] -ne 0 ] && [ $x -ne $num_iters ] && [ -f $dir/$x.mdl ]; then
# delete all but every 100th model; don't delete the ones which combine to form the final model.
rm $dir/$x.mdl
fi
done
fi