network init complete

7 files changed, 367 insertions, 29 deletions

diff --git a/nerv/Makefile b/nerv/Makefile
index c9c3e42..0a2aa86 100644
--- a/nerv/Makefile
+++ b/nerv/Makefile
@@ -34,7 +34,7 @@ LUA_LIBS := matrix/init.lua io/init.lua init.lua \
 			layer/init.lua layer/affine.lua layer/sigmoid.lua layer/tanh.lua layer/softmax_ce.lua layer/softmax.lua \
 			layer/window.lua layer/bias.lua layer/combiner.lua layer/mse.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/graph.lua layer/rnn.lua layer/duplicate.lua\
 			nn/init.lua nn/layer_repo.lua nn/param_repo.lua nn/layer_dag.lua nn/network.lua \
 			io/sgd_buffer.lua \
 			tnn/init.lua tnn/sutil.lua tnn/tnn.lua
diff --git a/nerv/layer/duplicate.lua b/nerv/layer/duplicate.lua
new file mode 100644
index 0000000..58758e8
--- /dev/null
+++ b/nerv/layer/duplicate.lua
@@ -0,0 +1,40 @@
+local DuplicateLayer = nerv.class('nerv.DuplicateLayer', 'nerv.Layer')
+
+function DuplicateLayer:__init(id, global_conf, layer_conf)
+    self.id = id
+    self.dim_in = layer_conf.dim_in
+    self.dim_out = layer_conf.dim_out
+    self.gconf = global_conf
+    self:check_dim_len(1, -1)
+    if #self.dim_out < 1 then
+        nerv.error('no output specified')
+    end
+    for i = 1, #self.dim_out do
+        if self.dim_out[i] ~= self.dim_in[1] then
+            nerv.error('mismatching dimensions of outputs')
+        end
+    end
+end
+
+function DuplicateLayer:init(batch_size)
+end
+
+function DuplicateLayer:batch_resize(batch_size)
+end
+
+function DuplicateLayer:update(bp_err, input, output)
+end
+
+function DuplicateLayer:propagate(input, output)
+    for i = 1, #self.dim_out do
+        output[i]:copy_from(input[1])
+        -- FIXME: use reference copy to speed up
+    end
+end
+
+function DuplicateLayer:back_propagate(bp_err, next_bp_err, input, output)
+    next_bp_err:copy_from(bp_err[1])
+    for i = 2, #self.dim_out do
+        next_bp_err:add(next_bp_err, bp_err[i], 1.0, 1.0)
+    end
+end
diff --git a/nerv/layer/graph.lua b/nerv/layer/graph.lua
index 36a9672..d72d849 100644
--- a/nerv/layer/graph.lua
+++ b/nerv/layer/graph.lua
@@ -64,6 +64,9 @@ function GraphLayer:graph_init(layer_repo, connections)
         local id_to, port_to = parse_id(to)
         local ref_from = self:discover(id_from, layer_repo)
         local ref_to = self:discover(id_to, layer_repo)
+        if ref_from.outputs[port_from] ~= nil then
+            nerv.error('%s has already been attached', from)
+        end
         if ref_to.inputs[port_to] ~= nil then
             nerv.error('%s has already been attached', to)
         end
diff --git a/nerv/layer/init.lua b/nerv/layer/init.lua
index 5e3395c..6f26d4d 100644
--- a/nerv/layer/init.lua
+++ b/nerv/layer/init.lua
@@ -125,6 +125,7 @@ nerv.include('lstm_gate.lua')
 nerv.include('dropout.lua')
 nerv.include('gru.lua')
 nerv.include('rnn.lua')
+nerv.include('duplicate.lua')
 
 -- The following lines are for backward compatibility, and will be removed in
 -- the future. The use of these names are deprecated.
diff --git a/nerv/layer/rnn.lua b/nerv/layer/rnn.lua
index 8816891..806ac58 100644
--- a/nerv/layer/rnn.lua
+++ b/nerv/layer/rnn.lua
@@ -22,6 +22,9 @@ function RNNLayer:__init(id, global_conf, layer_conf)
         ['nerv.SigmoidLayer'] = {
             sigmoid = {dim_in = {dout}, dim_out = {dout}},
         },
+        ['nerv.DuplicateLayer'] = {
+            dup = {dim_in = {dout}, dim_out = {dout, dout}},
+        }
     }
 
     local layer_repo = nerv.LayerRepo(layers, pr, global_conf)
@@ -29,8 +32,9 @@ function RNNLayer:__init(id, global_conf, layer_conf)
     local connections = {
         {'<input>[1]', 'main[1]', 0},
         {'main[1]', 'sigmoid[1]', 0},
-        {'sigmoid[1]', 'main[2]', 1},
-        {'sigmoid[1]', '<output>[1]', 0},
+        {'sigmoid[1]', 'dup[1]', 0},
+        {'dup[1]', 'main[2]', 1},
+        {'dup[2]', '<output>[1]', 0},
     }
 
     self:graph_init(layer_repo, connections)
diff --git a/nerv/main.lua b/nerv/main.lua
index 0633e87..5cb7d07 100644
--- a/nerv/main.lua
+++ b/nerv/main.lua
@@ -17,6 +17,12 @@ local layer_repo = nerv.LayerRepo(
         ['nerv.SigmoidLayer'] = {
             sigmoid = {dim_in = {23}, dim_out = {23}},
         },
+        ['nerv.SoftmaxLayer'] = {
+            softmax = {dim_in = {79}, dim_out = {79}},
+        },
+        ['nerv.DuplicateLayer'] = {
+            dup = {dim_in = {79}, dim_out = {79, 79}},
+        },
     }, nerv.ParamRepo(), global_conf)
 
 local connections = {
@@ -24,10 +30,14 @@ local connections = {
     {'input[1]', 'sigmoid[1]', 0},
     {'sigmoid[1]', 'rnn[1]', 0},
     {'rnn[1]', 'output[1]', 0},
-    {'output[1]', 'output[2]', 1},
-    {'output[1]', '<output>[1]', 0},
+    {'output[1]', 'dup[1]', 0},
+    {'dup[1]', 'output[2]', -1},
+    {'dup[2]', 'softmax[1]', 0},
+    {'softmax[1]', '<output>[1]', 0},
 }
 
-local graph = nerv.GraphLayer('network', global_conf, {dim_in = {20}, dim_out = {79}, layer_repo = layer_repo, connections = connections})
+local graph = nerv.GraphLayer('graph', global_conf, {dim_in = {20}, dim_out = {79}, layer_repo = layer_repo, connections = connections})
+
+local network = nerv.Network('network', global_conf, {network = graph})
 
-local network = nerv.Network(graph)
+network:init(2,5)
diff --git a/nerv/nn/network.lua b/nerv/nn/network.lua
index 6cee08b..01290e7 100644
--- a/nerv/nn/network.lua
+++ b/nerv/nn/network.lua
@@ -1,15 +1,47 @@
 local network = nerv.class('nerv.Network')
 
-function network:__init(graph)
+function network:__init(id, global_conf, network_conf)
+    self.id = id
+    self.dim_in = network_conf.network.dim_in
+    self.dim_out = network_conf.network.dim_out
+    self.gconf = global_conf
+    if self.gconf.use_cpu then
+        self.mat_type = self.gconf.mmat_type
+    else
+        self.mat_type = self.gconf.cumat_type
+    end
+    self.clip = network_conf.clip
+    self.nn_act_default = network_conf.nn_act_default
+    if self.nn_act_default == nil then
+        self.nn_act_default = 0
+    end
     self.layers = {}
-    self.socket = self:compile(graph)
+    self.input_conn = {}
+    self.output_conn = {}
+    self.socket = self:compile(network_conf.network)
+    for i = 1, #self.dim_in do
+        local edge = self.socket.inputs[i]
+        local id, port, time = edge[1], edge[2], edge[3]
+        if self.input_conn[id][port] ~= nil then
+            nerv.error('duplicate edge')
+        end
+        self.input_conn[id][port] = {0, i, time}
+    end
+    for i = 1, #self.dim_out do
+        local edge = self.socket.outputs[i]
+        local id, port, time = edge[1], edge[2], edge[3]
+        if self.output_conn[id][port] ~= nil then
+            nerv.error('duplicate edge')
+        end
+        self.output_conn[id][port] = {0, i, time}
+    end
+    self.delay = 0
     for i = 1, #self.layers do
-        print(self.layers[i].layer.id)
-        local _, dim_out = self.layers[i].layer:get_dim()
-        for j = 1, #dim_out do
-            for k = 1, #self.layers[i].connections[j] do
-                local connections = self.layers[i].connections[j][k]
-                print(i, connections[1], connections[2], connections[3])
+        local dim_in, _ = self.layers[i]:get_dim()
+        for j = 1, #dim_in do
+            local time = self.input_conn[i][j][3]
+            if math.abs(time) > self.delay then
+                self.delay = math.abs(time)
             end
         end
     end
@@ -18,15 +50,16 @@ end
 function network:compile(layer)
     local socket = {inputs = {}, outputs = {}}
     if not nerv.is_type(layer, 'nerv.GraphLayer') then
-        table.insert(self.layers, {layer = layer, connections = {}})
+        table.insert(self.layers, layer)
         local id = #self.layers
+        self.input_conn[id] = {}
+        self.output_conn[id] = {}
         local dim_in, dim_out = layer:get_dim()
         for i = 1, #dim_in do
-            socket.inputs[i] = {{id, i, 0}}
+            socket.inputs[i] = {id, i, 0}
         end
         for i = 1, #dim_out do
             socket.outputs[i] = {id, i, 0}
-            self.layers[id].connections[i] = {}
         end
     else
         local sublayer_socket = {}
@@ -35,34 +68,281 @@ function network:compile(layer)
                sublayer_socket[sublayer.id] = self:compile(sublayer.layer)
             end
         end
-        local dim_in, _ = layer:get_dim()
-        for i = 1, #dim_in do
-            socket.inputs[i] = {}
-        end
         for _, edge in pairs(layer.connections) do
             -- id = 0 means <input> or <output>
             local id_from, port_from = edge[1], edge[2]
             local id_to, port_to = edge[3], edge[4]
             local time = edge[5]
             if id_from == 0 then
-                for _, input in pairs(sublayer_socket[id_to].inputs[port_to]) do
-                    local id, port, t = input[1], input[2], input[3] + time
-                    table.insert(socket.inputs[port_from], {id, port, t})
+                if socket.inputs[port_from] ~= nil then
+                    nerv.error('duplicate input socket')
                 end
+                local input = sublayer_socket[id_to].inputs[port_to]
+                local id, port, t = input[1], input[2], input[3] + time
+                socket.inputs[port_from] = {id, port, t}
             else
                 local output = sublayer_socket[id_from].outputs[port_from]
                 local id, port, t = output[1], output[2], output[3] + time
                 if id_to == 0 then
+                    if socket.outputs[port_to] ~= nil then
+                        nerv.error('duplicate output socket')
+                    end
                     socket.outputs[port_to] = {id, port, t}
                 else
-                    local connections = self.layers[id].connections[port]
-                    for _, input in pairs(sublayer_socket[id_to].inputs[port_to]) do
-                        local id1, port1, t1 = input[1], input[2], input[3]
-                        table.insert(connections, {id1, port1, t + t1})
+                    local input = sublayer_socket[id_to].inputs[port_to]
+                    local id1, port1, t1 = input[1], input[2], input[3]
+                    if self.input_conn[id1][port1] ~= nil or self.output_conn[id][port] ~= nil then
+                        nerv.error('duplicate edge')
                     end
+                    self.input_conn[id1][port1] = {id, port, t + t1}
+                    self.output_conn[id][port] = {id1, port1, t + t1}
                 end
             end
         end
     end
     return socket
 end
+
+function network:init(batch_size, chunk_size)
+    self.batch_size = batch_size
+    self.chunk_size = chunk_size
+
+    self:topsort()
+    
+    self:make_initial_store()
+    collectgarbage('collect')
+end
+
+function network:topsort()
+    nerv.info('Network topology sort')
+    local degree = {}
+    for t = 1, self.chunk_size do
+        degree[t] = {}
+        for i = 1, #self.layers do  
+            degree[t][i] = 0
+        end
+    end
+
+    for t = 1, self.chunk_size do
+        for i = 1, #self.layers do
+            local _, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_out do
+                if self.output_conn[i][j] ~= nil then
+                    local edge = self.output_conn[i][j]
+                    local id, _, time = edge[1], edge[2], edge[3] + t
+                    if time >= 1 and time <= self.chunk_size and id ~= 0 then
+                        degree[time][id] = degree[time][id] + 1
+                    end
+                end
+            end
+        end
+    end
+
+    self.queue = {}
+    local l = 1
+    local r = 0
+    for t = 1, self.chunk_size do
+        for i = 1, #self.layers do
+            if degree[t][i] == 0 then
+                r = r + 1
+                self.queue[r] = {chunk = t, id = i}
+            end
+        end
+    end
+    while l<=r do
+        local t, i = self.queue[l].chunk, self.queue[l].id
+        l = l + 1
+        local _, dim_out = self.layers[i]:get_dim()
+        for j = 1, #dim_out do
+            if self.output_conn[i][j] ~= nil then
+                local edge = self.output_conn[i][j]
+                local id, _, time = edge[1], edge[2], edge[3] + t
+                if time >= 1 and time <= self.chunk_size and id ~= 0 then
+                    degree[time][id] = degree[time][id] - 1
+                    if degree[time][id] == 0 then
+                        r = r + 1
+                        self.queue[r] = {chunk = time, id = id}
+                    end
+                end
+            end
+        end
+    end
+
+    if r ~= self.chunk_size * #self.layers then
+        nerv.error('loop detected')
+    end
+end
+
+function network:make_initial_store()
+    nerv.info('Network initing storage')
+
+    -- allocate memory
+    local memory = {}
+    local err_memory = {}
+    for t = 1 - self.delay, self.chunk_size + self.delay do
+        memory[t] = {}
+        err_memory[t] = {}
+        for i = 1, #self.layers do
+            memory[t][i] = {}
+            err_memory[t][i] = {}
+            local dim_in, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_in do
+                err_memory[t][i][j] = self.mat_type(self.batch_size, dim_in[j])
+                err_memory[t][i][j]:fill(0)
+            end
+            for j = 1, #dim_out do
+                memory[t][i][j] = self.mat_type(self.batch_size, dim_out[j])
+                memory[t][i][j]:fill(self.nn_act_default)
+            end
+        end
+        -- memory[t][0] stores network input
+        memory[t][0] = {}
+        for j = 1, #self.dim_in do
+            memory[t][0][j] = self.mat_type(self.batch_size, self.dim_in[j])
+            memory[t][0][j]:fill(self.nn_act_default)
+        end
+        -- err_memory[t][0] stores network err_input
+        err_memory[t][0] = {}
+        for j = 1, #self.dim_out do
+            err_memory[t][0][j] = self.mat_type(self.batch_size, self.dim_out[j])
+            err_memory[t][0][j]:fill(0)
+        end
+    end
+
+    -- connect memory and reference 
+    self.input = {}
+    self.output = {}
+    self.err_input = {}
+    self.err_output = {}
+    for t = 1, self.chunk_size do
+        self.input[t] = {}
+        self.output[t] = {}
+        self.err_input[t] = {}
+        self.err_output[t] = {}
+        for i = 1, #self.layers do
+            self.input[t][i] = {}
+            self.output[t][i] = {}
+            self.err_input[t][i] = {}
+            self.err_output[t][i] = {}
+            local dim_in, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_in do
+                local edge = self.input_conn[i][j]
+                local id, port, time = edge[1], edge[2], edge[3]
+                if id ~= 0 or t - time < 1 or t - time > self.chunk_size then
+                    self.input[t][i][j] = memory[t - time][id][port]
+                end
+                if id ~= 0 then
+                    self.err_output[t][i][j] = err_memory[t][i][j]
+                end
+            end
+            for j = 1, #dim_out do
+                local edge = self.output_conn[i][j]
+                local id, port, time = edge[1], edge[2], edge[3]
+                if id ~= 0 then
+                    self.output[t][i][j] = memory[t][i][j]
+                end
+                if id ~= 0 or t + time < 1 or t + time > self.chunk_size then
+                    self.err_input[t][i][j] = err_memory[t + time][id][port]
+                end
+            end
+        end
+    end
+
+    -- check dangling reference
+    for t = 1, self.chunk_size do
+        for i = 1, #self.dim_in do
+            local edge = self.socket.inputs[i]
+            local id, port, time = edge[1], edge[2], edge[3]
+            if t + time >= 1 and t + time <= self.chunk_size then
+                if self.input[t + time][id][port] ~= nil then
+                    nerv.error('input reference not nil')
+                end
+                self.input[t + time][id][port] = true      -- just a place holder
+                if self.err_output[t + time][id][port] ~= nil then
+                    nerv.error('err_output reference not nil')
+                end
+                self.err_output[t + time][id][port] = true -- just a place holder
+            end
+        end
+        for i = 1, #self.dim_out do
+            local edge = self.socket.outputs[i]
+            local id, port, time = edge[1], edge[2], edge[3]
+            if t - time >= 1 and t - time <= self.chunk_size then
+                if self.output[t - time][id][port] ~= nil then
+                    nerv.error('output reference not nil')
+                end
+                self.output[t - time][id][port] = true     -- just a place holder
+                if self.err_input[t - time][id][port] ~= nil then
+                    nerv.error('err_output reference not nil')
+                end
+                self.err_input[t - time][id][port] = true  -- just a place holder
+            end
+        end
+    end
+    for t = 1, self.chunk_size do
+        for i = 1, #self.layers do
+            local dim_in, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_in do
+                if self.input[t][i][j] == nil then
+                    nerv.error('input reference dangling')
+                end
+                if self.err_output[t][i][j] == nil then
+                    nerv.error('err_output reference dangling')
+                end
+            end
+            for j = 1, #dim_out do
+                if self.output[t][i][j] == nil then
+                    nerv.error('output reference dangling')
+                end
+                if self.err_input[t][i][j] == nil then
+                    nerv.error('err_input reference dangling')
+                end
+            end
+        end
+    end
+
+    -- allocate reference for legacy of previous mini-batch
+    self.legacy = {}
+    for t = 1 - self.delay, 0 do
+        self.legacy[t] = {}
+        for i = 1, #self.layers do
+            self.legacy[t][i] = {}
+            local _, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_out do
+                self.legacy[t][i][j] = memory[t][i][j]
+            end
+        end
+    end
+end
+
+function network:mini_batch_init(information)
+    self.info = information
+    self.max_chunk = 0
+    for i = 1, self.batch_size do
+        if self.info.seq_length[i] > self.max_chunk then
+            self.max_chunk = self.info.seq_length[i]
+        end
+    end
+    for t = 1 - self.delay, 0 do
+        for i = 1, #self.layers do
+            local _, dim_out = self.layers[i]:get_dim()
+            for j = 1, #dim_out do
+                self.output[t][i][j]:copy_from(self.output[t + self.chunk_size][i][j])
+            end
+        end
+    end
+    for t = self.max_chunk + 1, self.max_chunk + self.delay do
+        if t > self.chunk_size then
+            break
+        end
+        for i = 1, #self.layers do
+            local dim_in, _ = self.layers[i]:get_dim()
+            for j = 1, #dim_in do
+                self.err_output[t][i][j]:fill(0)
+            end
+        end
+    end
+end
+
+function network:propagate(input, output)
+end