add recipe and fix bugs

15 files changed, 662 insertions, 143 deletions

diff --git a/nerv/Makefile b/nerv/Makefile
index 7921bd9..68465a1 100644
--- a/nerv/Makefile
+++ b/nerv/Makefile
@@ -44,7 +44,7 @@ LUA_LIBS := matrix/init.lua io/init.lua init.lua \
 			layer/elem_mul.lua layer/lstm.lua layer/lstm_gate.lua layer/dropout.lua layer/gru.lua \
 			layer/graph.lua layer/rnn.lua layer/duplicate.lua layer/identity.lua \
 			nn/init.lua nn/layer_repo.lua nn/param_repo.lua nn/network.lua \
-			io/sgd_buffer.lua
+			io/sgd_buffer.lua io/seq_buffer.lua
 
 INCLUDE := -I $(LUA_INCDIR) -DLUA_USE_APICHECK
 CUDA_INCLUDE := -I $(CUDA_BASE)/include/
diff --git a/nerv/examples/network_debug/config.lua b/nerv/examples/network_debug/config.lua
new file mode 100644
index 0000000..e20d5a9
--- /dev/null
+++ b/nerv/examples/network_debug/config.lua
@@ -0,0 +1,62 @@
+function get_global_conf()
+    local global_conf = {
+        lrate = 0.15,
+        wcost = 1e-5,
+        momentum = 0,
+        clip = 5,
+        cumat_type = nerv.CuMatrixFloat,
+        mmat_type = nerv.MMatrixFloat,
+        vocab_size = 10000,
+        nn_act_default = 0,
+        hidden_size = 300,
+        layer_num = 1,
+        chunk_size = 15,
+        batch_size = 20,
+        max_iter = 35,
+        param_random = function() return (math.random() / 5 - 0.1) end,
+        dropout_rate = 0.5,
+        timer = nerv.Timer(),
+        pr = nerv.ParamRepo(),
+    }
+    return global_conf
+end
+
+function get_layers(global_conf)
+    local pr = global_conf.pr
+    local layers = {
+        ['nerv.LSTMLayer'] = {},
+        ['nerv.DropoutLayer'] = {},
+        ['nerv.SelectLinearLayer'] = {
+            ['select'] = {dim_in = {1}, dim_out = {global_conf.hidden_size}, vocab = global_conf.vocab_size, pr = pr},
+        },
+        ['nerv.AffineLayer'] = {
+            output = {dim_in = {global_conf.hidden_size}, dim_out = {global_conf.vocab_size}, pr = pr}
+        },
+        ['nerv.SoftmaxCELayer'] = {
+            softmax = {dim_in = {global_conf.vocab_size, global_conf.vocab_size}, dim_out = {1}, compressed = true},
+        },
+    }
+    for i = 1, global_conf.layer_num do
+        layers['nerv.LSTMLayer']['lstm' .. i] = {dim_in = {global_conf.hidden_size}, dim_out = {global_conf.hidden_size}, pr = pr}
+        layers['nerv.DropoutLayer']['dropout' .. i] = {dim_in = {global_conf.hidden_size}, dim_out = {global_conf.hidden_size}}
+    end
+    return layers
+end
+
+function get_connections(global_conf)
+    local connections = {
+        {'<input>[1]', 'select[1]', 0},
+        {'select[1]', 'lstm1[1]', 0},
+        {'dropout' .. global_conf.layer_num .. '[1]', 'output[1]', 0},
+        {'output[1]', 'softmax[1]', 0},
+        {'<input>[2]', 'softmax[2]', 0},
+        {'softmax[1]', '<output>[1]', 0},
+    }
+    for i = 1, global_conf.layer_num do
+        table.insert(connections, {'lstm' .. i .. '[1]', 'dropout' .. i .. '[1]', 0})
+        if i < 1 then
+            table.insert(connections, {'dropout' .. (i - 1) .. '[1]', 'lstm' .. i .. '[1]', 0})
+        end
+    end
+    return connections
+end
diff --git a/nerv/examples/network_debug/main.lua b/nerv/examples/network_debug/main.lua
new file mode 100644
index 0000000..790c404
--- /dev/null
+++ b/nerv/examples/network_debug/main.lua
@@ -0,0 +1,45 @@
+nerv.include('reader.lua')
+nerv.include('timer.lua')
+nerv.include('config.lua')
+nerv.include(arg[1])
+
+local global_conf = get_global_conf()
+local timer = global_conf.timer
+
+timer:tic('IO')
+
+local data_path = 'examples/lmptb/PTBdata/'
+local train_reader = nerv.Reader(data_path .. 'vocab', data_path .. 'ptb.train.txt.adds')
+local val_reader = nerv.Reader(data_path .. 'vocab', data_path .. 'ptb.valid.txt.adds')
+
+local train_data = train_reader:get_all_batch(global_conf)
+local val_data = val_reader:get_all_batch(global_conf)
+
+local layers = get_layers(global_conf)
+local connections = get_connections(global_conf)
+
+local NN = nerv.NN(global_conf, train_data, val_data, layers, connections)
+
+timer:toc('IO')
+timer:check('IO')
+io.flush()
+
+timer:tic('global')
+local best_cv = 1e10
+for i = 1, global_conf.max_iter do
+    timer:tic('Epoch' .. i)
+    local train_ppl, val_ppl = NN:epoch()
+    if val_ppl < best_cv then
+        best_cv = val_ppl
+    else
+        global_conf.lrate = global_conf.lrate / 2.0
+    end
+    nerv.printf('Epoch %d: %f %f %f\n', i, global_conf.lrate, train_ppl, val_ppl)
+    timer:toc('Epoch' .. i)
+    timer:check('Epoch' .. i)
+    io.flush()
+end
+timer:toc('global')
+timer:check('global')
+timer:check('network')
+timer:check('gc')
diff --git a/nerv/examples/network_debug/network.lua b/nerv/examples/network_debug/network.lua
new file mode 100644
index 0000000..5518e27
--- /dev/null
+++ b/nerv/examples/network_debug/network.lua
@@ -0,0 +1,110 @@
+nerv.include('select_linear.lua')
+
+local nn = nerv.class('nerv.NN')
+
+function nn:__init(global_conf, train_data, val_data, layers, connections)
+    self.gconf = global_conf
+    self.network = self:get_network(layers, connections)
+    self.train_data = self:get_data(train_data)
+    self.val_data = self:get_data(val_data)
+end
+
+function nn:get_network(layers, connections)
+    local layer_repo = nerv.LayerRepo(layers, self.gconf.pr, self.gconf)
+    local graph = nerv.GraphLayer('graph', self.gconf, 
+        {dim_in = {1, self.gconf.vocab_size}, dim_out = {1}, 
+        layer_repo = layer_repo, connections = connections})
+    local network = nerv.Network('network', self.gconf, 
+        {network = graph, clip = self.gconf.clip})
+    network:init(self.gconf.batch_size, self.gconf.chunk_size)
+    return network
+end
+
+function nn:get_data(data)
+    local err_output = {}
+    local softmax_output = {}
+    local output = {}
+    for i = 1, self.gconf.chunk_size do
+        err_output[i] = self.gconf.cumat_type(self.gconf.batch_size, 1)
+        softmax_output[i] = self.gconf.cumat_type(self.gconf.batch_size, self.gconf.vocab_size)
+        output[i] = self.gconf.cumat_type(self.gconf.batch_size, 1)
+    end
+    local ret = {}
+    for i = 1, #data do
+        ret[i] = {}
+        ret[i].input = {}
+        ret[i].output = {}
+        ret[i].err_input = {}
+        ret[i].err_output = {}
+        for t = 1, self.gconf.chunk_size do
+            ret[i].input[t] = {}
+            ret[i].output[t] = {}
+            ret[i].err_input[t] = {}
+            ret[i].err_output[t] = {}
+            ret[i].input[t][1] = data[i].input[t]
+            ret[i].input[t][2] = data[i].output[t]
+            ret[i].output[t][1] = output[t]
+            local err_input = self.gconf.mmat_type(self.gconf.batch_size, 1)
+            for j = 1, self.gconf.batch_size do
+                if t <= data[i].seq_len[j] then
+                    err_input[j - 1][0] = 1
+                else
+                    err_input[j - 1][0] = 0
+                end
+            end
+            ret[i].err_input[t][1] = self.gconf.cumat_type.new_from_host(err_input)
+            ret[i].err_output[t][1] = err_output[t]
+            ret[i].err_output[t][2] = softmax_output[t]
+        end
+        ret[i].seq_length = data[i].seq_len
+        ret[i].new_seq = {}
+        for j = 1, self.gconf.batch_size do
+            if data[i].seq_start[j] then
+                table.insert(ret[i].new_seq, j)
+            end
+        end
+    end
+    return ret
+end
+
+function nn:process(data, do_train)
+    local timer = self.gconf.timer
+    local total_err = 0
+    local total_frame = 0
+    self.network:epoch_init()
+    for id = 1, #data do
+        data[id].do_train = do_train
+        timer:tic('network')
+        self.network:mini_batch_init(data[id])
+        self.network:propagate()
+        timer:toc('network')
+        for t = 1, self.gconf.chunk_size do
+            local tmp = data[id].output[t][1]:new_to_host()
+            for i = 1, self.gconf.batch_size do
+                if t <= data[id].seq_length[i] then
+                    total_err = total_err + math.log10(math.exp(tmp[i - 1][0]))
+                    total_frame = total_frame + 1
+                end
+            end
+        end
+        if do_train then
+            timer:tic('network')
+            self.network:back_propagate()
+            self.network:update()
+            timer:toc('network')
+        end
+        timer:tic('gc')
+        collectgarbage('collect')
+        timer:toc('gc')
+    end
+    return math.pow(10, - total_err / total_frame)
+end
+
+function nn:epoch()
+    local train_error = self:process(self.train_data, true)
+    local tmp = self.gconf.dropout_rate
+    self.gconf.dropout_rate = 0
+    local val_error = self:process(self.val_data, false)
+    self.gconf.dropout_rate = tmp
+    return train_error, val_error
+end
diff --git a/nerv/examples/network_debug/reader.lua b/nerv/examples/network_debug/reader.lua
new file mode 100644
index 0000000..d2624d3
--- /dev/null
+++ b/nerv/examples/network_debug/reader.lua
@@ -0,0 +1,113 @@
+local Reader = nerv.class('nerv.Reader')
+
+function Reader:__init(vocab_file, input_file)
+    self:get_vocab(vocab_file)
+    self:get_seq(input_file)
+end
+
+function Reader:get_vocab(vocab_file)
+    local f = io.open(vocab_file, 'r')
+    local id = 0
+    self.vocab = {}
+    while true do
+        local word = f:read()
+        if word == nil then
+            break
+        end
+        self.vocab[word] = id
+        id = id + 1
+    end
+    self.size = id
+end
+
+function Reader:split(s, t)
+    local ret = {}
+    for x in (s .. t):gmatch('(.-)' .. t) do
+        table.insert(ret, x)
+    end
+    return ret
+end
+
+function Reader:get_seq(input_file)
+    local f = io.open(input_file, 'r')
+    self.seq = {}
+    while true do
+        local seq = f:read()
+        if seq == nil then
+            break
+        end
+        seq = self:split(seq, ' ')
+        local tmp = {}
+        for i = 1, #seq do
+            if seq[i] ~= '' then
+                table.insert(tmp, self.vocab[seq[i]])
+            end
+        end
+        table.insert(self.seq, tmp)
+    end
+end
+
+function Reader:get_in_out(id, pos)
+    return self.seq[id][pos], self.seq[id][pos + 1], pos + 1 == #self.seq[id]
+end
+
+function Reader:get_all_batch(global_conf)
+    local data = {}
+    local pos = {}
+    local offset = 1
+    for i = 1, global_conf.batch_size do
+        pos[i] = nil
+    end
+    while true do
+    --for i = 1, 100 do
+        local input = {}
+        local output = {}
+        for i = 1, global_conf.chunk_size do
+            input[i] = global_conf.mmat_type(global_conf.batch_size, 1)
+            input[i]:fill(global_conf.nn_act_default)
+            output[i] = global_conf.mmat_type(global_conf.batch_size, 1)
+            output[i]:fill(global_conf.nn_act_default)
+        end
+        local seq_start = {}
+        local seq_end = {}
+        local seq_len = {}
+        for i = 1, global_conf.batch_size do
+            seq_start[i] = false
+            seq_end[i] = false
+            seq_len[i] = 0
+        end
+        local has_new = false
+        for i = 1, global_conf.batch_size do
+            if pos[i] == nil then
+                if offset < #self.seq then
+                    seq_start[i] = true
+                    pos[i] = {offset, 1}
+                    offset = offset + 1
+                end
+            end
+            if pos[i] ~= nil then
+                has_new = true
+                for j = 1, global_conf.chunk_size do
+                    local final
+                    input[j][i-1][0], output[j][i-1][0], final = self:get_in_out(pos[i][1], pos[i][2])
+                    seq_len[i] = j
+                    if final then
+                        seq_end[i] = true
+                        pos[i] = nil
+                        break
+                    end
+                    pos[i][2] = pos[i][2] + 1
+                end
+            end
+        end
+        if not has_new then
+            break
+        end
+        for i = 1, global_conf.chunk_size do
+            input[i] = global_conf.cumat_type.new_from_host(input[i])
+            output[i] = global_conf.cumat_type.new_from_host(output[i])
+        end
+        table.insert(data, {input = input, output = output, seq_start = seq_start, seq_end = seq_end, seq_len = seq_len})
+    end
+    return data
+end
diff --git a/nerv/examples/network_debug/select_linear.lua b/nerv/examples/network_debug/select_linear.lua
new file mode 100644
index 0000000..91beedf
--- /dev/null
+++ b/nerv/examples/network_debug/select_linear.lua
@@ -0,0 +1,59 @@
+local SL = nerv.class('nerv.SelectLinearLayer', 'nerv.Layer')
+
+--id: string
+--global_conf: table
+--layer_conf: table
+--Get Parameters
+function SL:__init(id, global_conf, layer_conf)
+    nerv.Layer.__init(self, id, global_conf, layer_conf)
+
+    self.vocab = layer_conf.vocab
+    self.ltp = self:find_param("ltp", layer_conf, global_conf, nerv.LinearTransParam, {self.vocab, self.dim_out[1]}) --layer_conf.ltp
+ 
+    self:check_dim_len(1, 1)
+end
+
+--Check parameter 
+function SL:init(batch_size)
+    if (self.dim_in[1] ~= 1) then --one word id 
+        nerv.error("mismatching dimensions of ltp and input")
+    end
+    if (self.dim_out[1] ~= self.ltp.trans:ncol()) then
+        nerv.error("mismatching dimensions of bp and output")
+    end
+    
+    self.batch_size = bath_size
+    self.ltp:train_init()
+end
+
+function SL:update(bp_err, input, output)
+    --use this to produce reproducable result, don't forget to set the dropout to zero!
+    --for i = 1, input[1]:nrow(), 1 do
+    --    local word_vec = self.ltp.trans[input[1][i - 1][0]]
+    --    word_vec:add(word_vec, bp_err[1][i - 1], 1, - self.gconf.lrate / self.gconf.batch_size)
+    --end 
+    
+    --I tried the update_select_rows kernel which uses atomicAdd, but it generates unreproducable result
+    self.ltp.trans:update_select_rows_by_colidx(bp_err[1], input[1], - self.gconf.lrate / self.gconf.batch_size, 0)
+    self.ltp.trans:add(self.ltp.trans, self.ltp.trans, 1.0, - self.gconf.lrate * self.gconf.wcost)
+end
+
+function SL:propagate(input, output)
+    --for i = 0, input[1]:ncol() - 1, 1 do
+    --    if (input[1][0][i] > 0) then
+    --        output[1][i]:copy_fromd(self.ltp.trans[input[1][0][i]])
+    --    else
+    --        output[1][i]:fill(0)
+    --    end
+    --end
+    output[1]:copy_rows_fromd_by_colidx(self.ltp.trans, input[1])
+end
+
+function SL:back_propagate(bp_err, next_bp_err, input, output)
+    --input is compressed, do nothing
+end
+
+function SL:get_params()
+    local paramRepo = nerv.ParamRepo({self.ltp})
+    return paramRepo
+end
diff --git a/nerv/examples/network_debug/timer.lua b/nerv/examples/network_debug/timer.lua
new file mode 100644
index 0000000..2c54ca8
--- /dev/null
+++ b/nerv/examples/network_debug/timer.lua
@@ -0,0 +1,33 @@
+local Timer = nerv.class("nerv.Timer")
+
+function Timer:__init()
+    self.last = {}
+    self.rec = {}
+end
+
+function Timer:tic(item)
+    self.last[item] = os.clock()
+end
+
+function Timer:toc(item)
+    if (self.last[item] == nil) then
+        nerv.error("item not there")
+    end
+    if (self.rec[item] == nil) then
+        self.rec[item] = 0
+    end
+    self.rec[item] = self.rec[item] + os.clock() - self.last[item]
+end
+
+function Timer:check(item)
+    if self.rec[item]==nil then
+        nerv.error('item not there')
+    end
+    nerv.printf('"%s" lasts for %f secs.\n',item,self.rec[item])
+end
+
+function Timer:flush()
+    for key, value in pairs(self.rec) do
+        self.rec[key] = nil
+    end
+end
diff --git a/nerv/examples/network_debug/tnn.lua b/nerv/examples/network_debug/tnn.lua
new file mode 100644
index 0000000..bf9f118
--- /dev/null
+++ b/nerv/examples/network_debug/tnn.lua
@@ -0,0 +1,136 @@
+nerv.include('select_linear.lua')
+
+local reader = nerv.class('nerv.TNNReader')
+
+function reader:__init(global_conf, data)
+    self.gconf = global_conf
+    self.offset = 0
+    self.data = data
+end
+
+function reader:get_batch(feeds)
+    self.offset = self.offset + 1
+    if self.offset > #self.data then
+        return false
+    end
+    for i = 1, self.gconf.chunk_size do
+        feeds.inputs_m[i][1]:copy_from(self.data[self.offset].input[i])
+        feeds.inputs_m[i][2]:copy_from(self.data[self.offset].output[i]:decompress(self.gconf.vocab_size))
+    end
+    feeds.flags_now = self.data[self.offset].flags
+    feeds.flagsPack_now = self.data[self.offset].flagsPack
+    return true
+end
+
+function reader:has_data(t, i)
+    return t <= self.data[self.offset].seq_len[i]
+end
+
+function reader:get_err_input()
+    return self.data[self.offset].err_input
+end
+
+local nn = nerv.class('nerv.NN')
+
+function nn:__init(global_conf, train_data, val_data, layers, connections)
+    self.gconf = global_conf
+    self.tnn = self:get_tnn(layers, connections)
+    self.train_data = self:get_data(train_data)
+    self.val_data = self:get_data(val_data)
+end
+
+function nn:get_tnn(layers, connections)
+    self.gconf.dropout_rate = 0
+    local layer_repo = nerv.LayerRepo(layers, self.gconf.pr, self.gconf)
+    local tnn = nerv.TNN('TNN', self.gconf, {dim_in = {1, self.gconf.vocab_size}, 
+        dim_out = {1}, sub_layers = layer_repo, connections = connections, 
+        clip = self.gconf.clip})
+    tnn:init(self.gconf.batch_size, self.gconf.chunk_size)
+    return tnn
+end
+
+function nn:get_data(data)
+    local ret = {}
+    for i = 1, #data do
+        ret[i] = {}
+        ret[i].input = data[i].input
+        ret[i].output = data[i].output
+        ret[i].flags = {}
+        ret[i].err_input = {}
+        for t = 1, self.gconf.chunk_size do
+            ret[i].flags[t] = {}
+            local err_input = self.gconf.mmat_type(self.gconf.batch_size, 1)
+            for j = 1, self.gconf.batch_size do
+                if t <= data[i].seq_len[j] then
+                    ret[i].flags[t][j] = nerv.TNN.FC.SEQ_NORM
+                    err_input[j - 1][0] = 1
+                else
+                    ret[i].flags[t][j] = 0
+                    err_input[j - 1][0] = 0
+                end
+            end
+            ret[i].err_input[t] = self.gconf.cumat_type.new_from_host(err_input)
+        end
+        for j = 1, self.gconf.batch_size do
+            if data[i].seq_start[j] then
+                ret[i].flags[1][j] = bit.bor(ret[i].flags[1][j], nerv.TNN.FC.SEQ_START)
+            end
+            if data[i].seq_end[j] then
+                local t = data[i].seq_len[j]
+                ret[i].flags[t][j] = bit.bor(ret[i].flags[t][j], nerv.TNN.FC.SEQ_END)
+            end
+        end
+        ret[i].flagsPack = {}
+        for t = 1, self.gconf.chunk_size do
+            ret[i].flagsPack[t] = 0
+            for j = 1, self.gconf.batch_size do
+                ret[i].flagsPack[t] = bit.bor(ret[i].flagsPack[t], ret[i].flags[t][j])
+            end
+        end
+        ret[i].seq_len = data[i].seq_len
+    end
+    return ret
+end
+
+function nn:process(data, do_train)
+    local total_err = 0
+    local total_frame = 0
+    local reader = nerv.TNNReader(self.gconf, data)
+    while true do
+        local r, _ = self.tnn:getfeed_from_reader(reader)
+        if not r then
+            break
+        end
+        if do_train then
+            self.gconf.dropout_rate = self.gconf.dropout
+        else
+            self.gconf.dropout_rate = 0
+        end
+        self.tnn:net_propagate()
+        for t = 1, self.gconf.chunk_size do
+            local tmp = self.tnn.outputs_m[t][1]:new_to_host()
+            for i = 1, self.gconf.batch_size do
+                if reader:has_data(t, i) then
+                    total_err = total_err + math.log10(math.exp(tmp[i - 1][0]))
+                    total_frame = total_frame + 1
+                end
+            end
+        end
+        if do_train then
+            local err_input = reader:get_err_input()
+            for i = 1, self.gconf.chunk_size do
+                self.tnn.err_inputs_m[i][1]:copy_from(err_input[i])
+            end
+            self.tnn:net_backpropagate(false)
+            self.tnn:net_backpropagate(true)
+        end
+        collectgarbage('collect')
+    end
+    return math.pow(10, - total_err / total_frame)
+end
+
+function nn:epoch()
+    local train_error = self:process(self.train_data, true)
+    local val_error = self:process(self.val_data, false)
+    return train_error, val_error
+end
diff --git a/nerv/io/init.lua b/nerv/io/init.lua
index eb2e3e5..c36d850 100644
--- a/nerv/io/init.lua
+++ b/nerv/io/init.lua
@@ -52,8 +52,9 @@ function DataBuffer:__init(global_conf, buffer_conf)
     nerv.error_method_not_implemented()
 end
 
-function DataBuffer:get_batch()
+function DataBuffer:get_data()
     nerv.error_method_not_implemented()
 end
 
 nerv.include('sgd_buffer.lua')
+nerv.include('seq_buffer.lua')
diff --git a/nerv/io/seq_buffer.lua b/nerv/io/seq_buffer.lua
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/nerv/io/seq_buffer.lua
diff --git a/nerv/layer/dropout.lua b/nerv/layer/dropout.lua
index 1a379c9..39a8963 100644
--- a/nerv/layer/dropout.lua
+++ b/nerv/layer/dropout.lua
@@ -2,8 +2,7 @@ local DropoutLayer = nerv.class("nerv.DropoutLayer", "nerv.Layer")
 
 function DropoutLayer:__init(id, global_conf, layer_conf)
     nerv.Layer.__init(self, id, global_conf, layer_conf)
-    self.rate = layer_conf.dropout_rate or global_conf.dropout_rate
-    if self.rate == nil then
+    if self.gconf.dropout_rate == nil then
         nerv.warning("[DropoutLayer:propagate] dropout rate is not set")
     end
     self:check_dim_len(1, 1) -- two inputs: nn output and label
@@ -41,12 +40,12 @@ function DropoutLayer:propagate(input, output, t)
     if t == nil then
         t = 1
     end
-    if self.rate then
+    if self.gconf.dropout_rate ~= 0 then
         self.mask[t]:rand_uniform()
         -- since we will lose a portion of the actvations, we multiply the
         -- activations by 1 / (1 - rate) to compensate
-        self.mask[t]:thres_mask(self.mask[t], self.rate,
-                                0, 1 / (1.0 - self.rate))
+        self.mask[t]:thres_mask(self.mask[t], self.gconf.dropout_rate,
+                                0, 1 / (1.0 - self.gconf.dropout_rate))
         output[1]:mul_elem(input[1], self.mask[t])
     else
         output[1]:copy_fromd(input[1])
@@ -61,7 +60,7 @@ function DropoutLayer:back_propagate(bp_err, next_bp_err, input, output, t)
     if t == nil then
         t = 1
     end
-    if self.rate then
+    if self.gconf.dropout_rate then
         next_bp_err[1]:mul_elem(bp_err[1], self.mask[t])
     else
         next_bp_err[1]:copy_fromd(bp_err[1])
diff --git a/nerv/layer/graph.lua b/nerv/layer/graph.lua
index 5f42fca..68d5f51 100644
--- a/nerv/layer/graph.lua
+++ b/nerv/layer/graph.lua
@@ -112,7 +112,7 @@ function GraphLayer:graph_init(layer_repo, connections)
             end
             for i = 1, #ref.dim_out do
                 if ref.outputs[i] == nil then
-                   nerv.error('dangling output port %d os layer %s', i, id)
+                   nerv.error('dangling output port %d of layer %s', i, id)
                 end
             end
         end
diff --git a/nerv/layer/lstm.lua b/nerv/layer/lstm.lua
index 641d5dc..5dbcc20 100644
--- a/nerv/layer/lstm.lua
+++ b/nerv/layer/lstm.lua
@@ -1,144 +1,85 @@
-local LSTMLayer = nerv.class('nerv.LSTMLayer', 'nerv.Layer')
+local LSTMLayer = nerv.class('nerv.LSTMLayer', 'nerv.GraphLayer')
 
 function LSTMLayer:__init(id, global_conf, layer_conf)
-    -- input1:x
-    -- input2:h
-    -- input3:c
     nerv.Layer.__init(self, id, global_conf, layer_conf)
-    -- prepare a DAGLayer to hold the lstm structure
+    self:check_dim_len(1, 1)
+
+    local din = layer_conf.dim_in[1]
+    local dout = layer_conf.dim_out[1]
+
     local pr = layer_conf.pr
     if pr == nil then
         pr = nerv.ParamRepo({}, self.loc_type)
     end
-    
-    local function ap(str)
-        return self.id .. '.' .. str
-    end
-    local din1, din2, din3 = self.dim_in[1], self.dim_in[2], self.dim_in[3]
-    local dout1, dout2, dout3 = self.dim_out[1], self.dim_out[2], self.dim_out[3]
-    local layers = {
-        ["nerv.CombinerLayer"] = {
-            [ap("inputXDup")] = {dim_in = {din1},
-                                      dim_out = {din1, din1, din1, din1},
-                                      lambda = {1}},
 
-            [ap("inputHDup")] = {dim_in = {din2},
-                                      dim_out = {din2, din2, din2, din2},
-                                      lambda = {1}},
-
-            [ap("inputCDup")] = {dim_in = {din3},
-                                      dim_out = {din3, din3, din3},
-                                      lambda = {1}},
-
-            [ap("mainCDup")] = {dim_in = {din3, din3},
-                                     dim_out = {din3, din3, din3},
-                                     lambda = {1, 1}},
+    local layers = {
+        ['nerv.CombinerLayer'] = {
+            mainCombine = {dim_in = {dout, dout}, dim_out = {dout}, lambda = {1, 1}},
         },
-        ["nerv.AffineLayer"] = {
-            [ap("mainAffineL")] = {dim_in = {din1, din2},
-                                        dim_out = {dout1},
-                                        pr = pr},
+        ['nerv.DuplicateLayer'] = {
+            inputDup = {dim_in = {din}, dim_out = {din, din, din, din}},
+            outputDup = {dim_in = {dout}, dim_out = {dout, dout, dout, dout, dout}},
+            cellDup = {dim_in = {dout}, dim_out = {dout, dout, dout, dout, dout}},
         },
-        ["nerv.TanhLayer"] = {
-            [ap("mainTanhL")] = {dim_in = {dout1}, dim_out = {dout1}},
-            [ap("outputTanhL")] = {dim_in = {dout1}, dim_out = {dout1}},
+        ['nerv.AffineLayer'] = {
+            mainAffine = {dim_in = {din, dout}, dim_out = {dout}, pr = pr},
         },
-        ["nerv.LSTMGateLayer"] = {
-            [ap("forgetGateL")] = {dim_in = {din1, din2, din3},
-                                        dim_out = {din3}, pr = pr},
-            [ap("inputGateL")] = {dim_in = {din1, din2, din3},
-                                        dim_out = {din3}, pr = pr},
-            [ap("outputGateL")] = {dim_in = {din1, din2, din3},
-                                        dim_out = {din3}, pr = pr},
-
+        ['nerv.TanhLayer'] = {
+            mainTanh = {dim_in = {dout}, dim_out = {dout}},
+            outputTanh = {dim_in = {dout}, dim_out = {dout}},
         },
-        ["nerv.ElemMulLayer"] = {
-            [ap("inputGMulL")] = {dim_in = {din3, din3},
-                                        dim_out = {din3}},
-            [ap("forgetGMulL")] = {dim_in = {din3, din3},
-                                        dim_out = {din3}},
-            [ap("outputGMulL")] = {dim_in = {din3, din3},
-                                        dim_out = {din3}},
+        ['nerv.LSTMGateLayer'] = {
+            forgetGate = {dim_in = {din, dout, dout}, dim_out = {dout}, pr = pr},
+            inputGate = {dim_in = {din, dout, dout}, dim_out = {dout}, pr = pr},
+            outputGate = {dim_in = {din, dout, dout}, dim_out = {dout}, pr = pr},
+        },
+        ['nerv.ElemMulLayer'] = {
+            inputGateMul = {dim_in = {dout, dout}, dim_out = {dout}},
+            forgetGateMul = {dim_in = {dout, dout}, dim_out = {dout}},
+            outputGateMul = {dim_in = {dout, dout}, dim_out = {dout}},
         },
     }
     
-    self.lrepo = nerv.LayerRepo(layers, pr, global_conf)
-
     local connections = {
-        ["<input>[1]"] = ap("inputXDup[1]"),
-        ["<input>[2]"] = ap("inputHDup[1]"),
-        ["<input>[3]"] = ap("inputCDup[1]"),
-
-        [ap("inputXDup[1]")] = ap("mainAffineL[1]"),
-        [ap("inputHDup[1]")] = ap("mainAffineL[2]"),
-        [ap("mainAffineL[1]")] = ap("mainTanhL[1]"),
-
-        [ap("inputXDup[2]")] = ap("inputGateL[1]"),
-        [ap("inputHDup[2]")] = ap("inputGateL[2]"),
-        [ap("inputCDup[1]")] = ap("inputGateL[3]"),
-        
-        [ap("inputXDup[3]")] = ap("forgetGateL[1]"),
-        [ap("inputHDup[3]")] = ap("forgetGateL[2]"),
-        [ap("inputCDup[2]")] = ap("forgetGateL[3]"),
-
-        [ap("mainTanhL[1]")] = ap("inputGMulL[1]"),
-        [ap("inputGateL[1]")] = ap("inputGMulL[2]"),
-        
-        [ap("inputCDup[3]")] = ap("forgetGMulL[1]"),
-        [ap("forgetGateL[1]")] = ap("forgetGMulL[2]"),
-
-        [ap("inputGMulL[1]")] = ap("mainCDup[1]"),
-        [ap("forgetGMulL[1]")] = ap("mainCDup[2]"),
-
-        [ap("inputXDup[4]")] = ap("outputGateL[1]"),
-        [ap("inputHDup[4]")] = ap("outputGateL[2]"),
-        [ap("mainCDup[3]")] = ap("outputGateL[3]"),
-
-        [ap("mainCDup[2]")] = "<output>[2]",
-        [ap("mainCDup[1]")] = ap("outputTanhL[1]"),
-        
-        [ap("outputTanhL[1]")] = ap("outputGMulL[1]"),
-        [ap("outputGateL[1]")] = ap("outputGMulL[2]"),
-
-        [ap("outputGMulL[1]")] = "<output>[1]",
+        -- lstm input
+        {'<input>[1]', 'inputDup[1]', 0},
+
+        -- input gate
+        {'inputDup[1]', 'inputGate[1]', 0},
+        {'outputDup[1]', 'inputGate[2]', 1},
+        {'cellDup[1]', 'inputGate[3]', 1},
+
+        -- forget gate
+        {'inputDup[2]', 'forgetGate[1]', 0},
+        {'outputDup[2]', 'forgetGate[2]', 1},
+        {'cellDup[2]', 'forgetGate[3]', 1},
+
+        -- lstm cell
+        {'forgetGate[1]', 'forgetGateMul[1]', 0},
+        {'cellDup[3]', 'forgetGateMul[2]', 1},
+        {'inputDup[3]', 'mainAffine[1]', 0},
+        {'outputDup[3]', 'mainAffine[2]', 1},
+        {'mainAffine[1]', 'mainTanh[1]', 0},
+        {'inputGate[1]', 'inputGateMul[1]', 0},
+        {'mainTanh[1]', 'inputGateMul[2]', 0},
+        {'inputGateMul[1]', 'mainCombine[1]', 0},
+        {'forgetGateMul[1]', 'mainCombine[2]', 0},
+        {'mainCombine[1]', 'cellDup[1]', 0},
+
+        -- forget gate
+        {'inputDup[4]', 'outputGate[1]', 0},
+        {'outputDup[4]', 'outputGate[2]', 1},
+        {'cellDup[4]', 'outputGate[3]', 0},
+
+        -- lstm output
+        {'cellDup[5]', 'outputTanh[1]', 0},
+        {'outputGate[1]', 'outputGateMul[1]', 0},
+        {'outputTanh[1]', 'outputGateMul[2]', 0},
+        {'outputGateMul[1]', 'outputDup[1]', 0},
+        {'outputDup[5]', '<output>[1]', 0},
     }
-    self.dag = nerv.DAGLayer(self.id, global_conf,
-                                {dim_in = self.dim_in,
-                                 dim_out = self.dim_out,
-                                 sub_layers = self.lrepo,
-                                 connections = connections})
-    
-    self:check_dim_len(3, 2) -- x, h, c and h, c
-end
-
-function LSTMLayer:bind_params()
-    local pr = layer_conf.pr
-    if pr == nil then
-        pr = nerv.ParamRepo({}, self.loc_type)
-    end
-    self.lrepo:rebind(pr)
-end
-
-function LSTMLayer:init(batch_size, chunk_size)
-    self.dag:init(batch_size, chunk_size)
-end
-
-function LSTMLayer:batch_resize(batch_size, chunk_size)
-    self.dag:batch_resize(batch_size, chunk_size)
-end
-
-function LSTMLayer:update(bp_err, input, output, t)
-    self.dag:update(bp_err, input, output, t)
-end
-
-function LSTMLayer:propagate(input, output, t)
-    self.dag:propagate(input, output, t)
-end
-
-function LSTMLayer:back_propagate(bp_err, next_bp_err, input, output, t)
-    self.dag:back_propagate(bp_err, next_bp_err, input, output, t)
-end
 
-function LSTMLayer:get_params()
-    return self.dag:get_params()
+    self:add_prefix(layers, connections)
+    local layer_repo = nerv.LayerRepo(layers, pr, global_conf)
+    self:graph_init(layer_repo, connections)
 end
diff --git a/nerv/layer/rnn.lua b/nerv/layer/rnn.lua
index e59cf5b..0b5ccaa 100644
--- a/nerv/layer/rnn.lua
+++ b/nerv/layer/rnn.lua
@@ -4,6 +4,10 @@ function RNNLayer:__init(id, global_conf, layer_conf)
     nerv.Layer.__init(self, id, global_conf, layer_conf)
     self:check_dim_len(1, 1)
 
+    if layer_conf.activation == nil then
+        layer_conf.activation = 'nerv.SigmoidLayer'
+    end
+
     local din = layer_conf.dim_in[1]
     local dout = layer_conf.dim_out[1]
 
@@ -16,20 +20,20 @@ function RNNLayer:__init(id, global_conf, layer_conf)
         ['nerv.AffineLayer'] = {
             main = {dim_in = {din, dout}, dim_out = {dout}, pr = pr},
         },
-        ['nerv.SigmoidLayer'] = {
-            sigmoid = {dim_in = {dout}, dim_out = {dout}},
+        [layers.activation] = {
+            activation = {dim_in = {dout}, dim_out = {dout}},
         },
         ['nerv.DuplicateLayer'] = {
-            dup = {dim_in = {dout}, dim_out = {dout, dout}},
-        }
+            duplicate = {dim_in = {dout}, dim_out = {dout, dout}},
+        },
     }
 
     local connections = {
         {'<input>[1]', 'main[1]', 0},
-        {'main[1]', 'sigmoid[1]', 0},
-        {'sigmoid[1]', 'dup[1]', 0},
-        {'dup[1]', 'main[2]', 1},
-        {'dup[2]', '<output>[1]', 0},
+        {'main[1]', 'activation[1]', 0},
+        {'activation[1]', 'duplicate[1]', 0},
+        {'duplicate[1]', 'main[2]', 1},
+        {'duplicate[2]', '<output>[1]', 0},
     }
 
     self:add_prefix(layers, connections)
diff --git a/nerv/matrix/init.lua b/nerv/matrix/init.lua
index cf85004..722c780 100644
--- a/nerv/matrix/init.lua
+++ b/nerv/matrix/init.lua
@@ -40,7 +40,8 @@ end
 --- Assign each element in a matrix using the value returned by a callback `gen`.
 -- @param gen the callback used to generated the values in the matrix, to which
 -- the indices of row and column will be passed (e.g., `gen(i, j)`)
-function nerv.Matrix:generate(gen)
+
+function nerv.Matrix:_generate(gen)
     if (self:dim() == 2) then
         for i = 0, self:nrow() - 1 do
             local row = self[i]
@@ -55,6 +56,21 @@ function nerv.Matrix:generate(gen)
     end
 end
 
+function nerv.Matrix:generate(gen)
+    local tmp
+    if nerv.is_type(self, 'nerv.CuMatrixFloat') then
+        tmp = nerv.MMatrixFloat(self:nrow(), self:ncol())
+    elseif nerv.is_type(self, 'nerv.CuMatrixDouble') then
+        tmp = nerv.MMatrixDouble(self:nrow(), self:ncol())
+    else
+        tmp = self
+    end
+    tmp:_generate(gen)
+    if nerv.is_type(self, 'nerv.CuMatrix') then
+        self:copy_fromh(tmp)
+    end
+end
+
 --- Create a fresh new matrix of the same matrix type (as `self`).
 -- @param nrow optional, the number of rows in the created matrix if specified,
 -- otherwise `self:nrow()` will be used