Merge ../Marian

src/chainable.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <vector>
 #include <memory>
 
@@ -29,6 +50,12 @@ struct Chainable {
     };
 };
 
+// XXX Marcin, is ChainableStack the most appropriate name?
+//     AFAIK, this is never used as a FILO data structure.
+//     If so, perhaps "Tape" or "ChainLinks" or "ChainableList" might be more apropos?
+//
+//     Naumann (2012) uses "tape" to refer to this data structure.
+//     -- The Art of Differentiating Computer Programs: An Introduction to Algorithmic Differentiation, Naumann (2012)
 typedef std::vector<Chainable<Tensor>*> ChainableStack;
 typedef std::shared_ptr<ChainableStack> ChainableStackPtr;    
 typedef std::shared_ptr<Chainable<Tensor>> ChainPtr;

src/compile_time_crc32.h

@@ -1,5 +1,27 @@
 #pragma once
-  
+
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+
 static constexpr uint32_t crc_table[256] = {
     0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f,
 	0xe963a535, 0x9e6495a3,	0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,

src/definitions.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <vector>
 #include <string>
 #include <functional>

src/exception.cpp

@@ -1,5 +1,26 @@
 #include "exception.h"
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #ifdef __GXX_RTTI
 #include <typeinfo>
 #endif

src/exception.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <sstream>
 #include <exception>
 #include <limits>

src/expression_graph.cu

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <sstream>
 #include "expression_graph.h"
 

src/expression_graph.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <map>
 
 #include "definitions.h"
@@ -9,7 +30,10 @@
 
 namespace marian {
 
+// Forward declaration of ExpressionGraph class; this enables it to be used in the following typedef of ExpressionGraphPtr
 class ExpressionGraph;
+
+/** @brief A pointer to an expression graph. */
 typedef ExpressionGraph* ExpressionGraphPtr;
 
 class Expr {
@@ -36,15 +60,43 @@ class Expr {
     ChainPtr pimpl_;
 };
 
+/**
+ * @brief Represents a computation graph of expressions, over which algorithmic differentiation may be performed.
+ */
 class ExpressionGraph {
   public:
+
+    /** @brief Constructs a new expression graph */
     ExpressionGraph() : stack_(new ChainableStack) {}
-    
+  
+    /**
+     * @brief Performs backpropogation on this expression graph.
+     *
+     * Backpropogation is implemented by performing first the forward pass
+     *    and then the backward pass of algorithmic differentiation (AD) on the nodes of the graph.
+     *
+     * @param batchSize       XXX Marcin, could you provide a description of this param?
+     */
     void backprop(int batchSize) {
       forward(batchSize);
       backward();
     }
-    
+  
+    /**
+     * @brief Perform the forward pass of algorithmic differentiation (AD) on this graph.
+     *
+     * This pass traverses the nodes of this graph in the order they were created;
+     *    as each node is traversed, its <code>allocate()</code> method is called.
+     * 
+     * Once allocation is complete for all nodes, this pass again traverses the nodes, in creation order;
+     *    as each node is traversed, its <code>forward()</code> method is called.
+     *
+     * After this method has successfully completed, 
+     *    it is guaranteed that all node allocation has been completed,
+     *    and that all forward pass computations have been performed.
+     *
+     * @param batchSize       XXX Marcin, could you provide a description of this param?
+     */
     void forward(int batchSize) {
       for(auto&& v : *stack_) {
         v->allocate(batchSize);
@@ -52,7 +104,19 @@ class ExpressionGraph {
       for(auto&& v : *stack_)
         v->forward();    
     }
-    
+
+    /**
+     * @brief Perform the backward pass of algorithmic differentiation (AD) on this graph.
+     *
+     * This pass traverses the nodes of this graph in reverse of the order they were created;
+     *    as each node is traversed, its <code>set_zero_adjoint()</code> method is called.
+     *
+     * Once this has been performed for all nodes, this pass again traverses the nodes, again in reverse creation order;
+     *    as each node is traversed, its <code>backward()</code> method is called.
+     *
+     * After this method has successfully completed,
+     *    and that all backward pass computations have been performed.
+     */
     void backward() {
       for(auto&& v : *stack_)
         v->set_zero_adjoint();
@@ -62,7 +126,14 @@ class ExpressionGraph {
       for(It it = stack_->rbegin(); it != stack_->rend(); ++it)
         (*it)->backward();
     }
-    
+
+    /**
+     * @brief Returns a string representing this expression graph in <code>graphviz</code> notation.
+     *
+     * This string can be used by <code>graphviz</code> tools to visualize the expression graph.
+     *
+     * @return a string representing this expression graph in <code>graphviz</code> notation
+     */
     std::string graphviz() {
       std::stringstream ss;
       ss << "digraph ExpressionGraph {" << std::endl;
@@ -76,69 +147,165 @@ class ExpressionGraph {
     }
     
     /*********************************************************/
-    
+
+    /**
+     * @brief Constructs a new node representing an input in an expression graph.
+     *
+     * This method records the input node in a list of input nodes,
+     *    but does not attach the new input node to any existing expression graph.
+     *
+     * @param args           XXX Marcin, what are args here?
+     *
+     * @return a newly constructed input node
+     */
     template <typename ...Args>
     inline Expr input(Args ...args) {
       Expr e(this, new InputNode(args...));
       inputs_.emplace_back(e);
       return e;
     }
-    
+
+    /**
+     * @brief Constructs a new node representing a parameter in an expression graph.
+     *
+     * This method records the parameter node in a list of parameter nodes,
+     *    but does not attach the new parameter node to any existing expression graph.
+     *
+     * @param args           XXX Marcin, what are args here?
+     *
+     * @return a newly constructed parameter node
+     */
     template <typename ...Args>
     inline Expr param(Args ...args) {
       Expr e(this, new ParamNode(args...));
       params_.emplace_back(e);
       return e;
     }
-    
+
+    /**
+     * @brief Constructs a new node representing a constant in an expression graph.
+     *
+     * This method does not attach the new constant node to any existing expression graph.
+     *
+     * @param args           XXX Marcin, what are args here?
+     *
+     * @return a newly constructed constant node
+     */
     template <typename ...Args>
     inline Expr constant(Args ...args) {
       return Expr(this, new ConstantNode(args...));
     }
-    
+
+    /**
+     * @brief Constructs a new node representing a constant (with value 1) in an expression graph.
+     *
+     * This method does not attach the new constant node to any existing expression graph.
+     *
+     * @param args           XXX Marcin, what are args here?
+     *
+     * @return a newly constructed constant node
+     */
     template <typename ...Args>
     inline Expr ones(Args ...args) {
       return Expr(this, new ConstantNode(keywords::value=1, args...));
     }
-    
+
+    /**
+     * @brief Constructs a new node representing a constant (with value 0) in an expression graph.
+     *
+     * This method does not attach the new constant node to any existing expression graph.
+     *
+     * @param args           XXX Marcin, what are args here?
+     *
+     * @return a newly constructed constant node
+     */
     template <typename ...Args>
     inline Expr zeroes(Args ...args) {
       return Expr(this, new ConstantNode(keywords::value=0, args...));
     }
     
     /*********************************************************/
-        
+
+    /**
+     * @brief Returns a pointer to the list of items contained in this graph.
+     *
+     * The items in the list will be in the order they were created.
+     *
+     * @return a pointer to the list of items contained in this graph
+     */
     ChainableStackPtr stack() {
       return stack_;
     }
-    
+
+    /**
+     * @brief Returns the first item in the list with the specified name, if such an item exists.
+     *
+     * If no item with the specified name is found in the graph, this method throws an exception.
+     *
+     * @param name Name of the desired expression node
+     *
+     * @return the first item in the list with the specified name, if such an item exists
+     */
     Expr& operator[](const std::string& name) {
       auto it = named_.find(name);
       UTIL_THROW_IF2(it == named_.end(), "No such named node in graph: " << name);
       return it->second;  
     }
 
+    /**
+     * @brief Determines whether the graph contains a node with a specified name.
+     *
+     * @param name Name of the desired expression node
+     *
+     * @return <code>true</code> if the graph contains a node with a specified name,
+     *         <code>false</code> otherwise
+     */
     bool has_node(const std::string& name) const {
       return named_.count(name) > 0;
     }
-    
+
+    /**
+     * @brief Inserts an expression node with a specified name into the expression graph.
+     *
+     * @param e an expression node
+     * @param name name of the expression node
+     *
+     * @return the expression node that was added to the expression graph
+     */
     void add_named_node(Expr e, const std::string& name) {
       named_.emplace(name, e);
     }
-    
+
+    /**
+     * @brief Gets the list of all input nodes of this expression graph
+     *
+     * @return the list of all input nodes of this expression graph
+     */
     std::vector<Expr>& inputs() {
       return inputs_;
     }
-    
+
+    /**
+     * @brief Gets the list of all parameter nodes of this expression graph
+     *
+     * @return the list of all parameter nodes of this expression graph
+     */
     std::vector<Expr>& params() {
       return params_;
     }
     
   private:
+
+    /** @brief Pointer to the list of nodes */
     ChainableStackPtr stack_;
-    
+
+    /** @brief Maps from name to expression node. */
     std::map<std::string, Expr> named_;
+
+    /** @brief List of all parameter nodes of this expression graph. */
     std::vector<Expr> params_;
+
+    /** @brief List of all input nodes of this expression graph. */
     std::vector<Expr> inputs_;
 };
 

src/expression_operators.cu

@@ -1,3 +1,23 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
 
 #include "expression_operators.h"
 #include "node_operators.h"

src/expression_operators.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "expression_graph.h"
 
 namespace marian {

src/keywords.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <typeinfo>
 #include <typeindex>
 #include <unordered_map>
@@ -125,4 +146,4 @@ namespace keywords {
   name ## _k name(#name);
 }
 
-}
+}

src/marian.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "definitions.h"
 #include "expression_graph.h"
 #include "param_initializers.h"

src/mnist.h

@@ -1,5 +1,26 @@
 //#pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <string>
 #include <iostream>
 #include <fstream>

src/node.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "keywords.h"
 #include "tensor.h"
 #include "chainable.h"

src/node_operators.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "node.h"
 #include "tensor_operators.h"
 

src/npz_converter.cpp

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "npz_converter.h"
 
 
@@ -17,6 +38,7 @@ void NpzConverter::Destruct() {
   destructed_ = true;
 }
 
+/** TODO: Marcin, what does this function do? Why isn't it a method? */
 mblas::Matrix NpzConverter::operator[](const std::string& key) const {
   typedef blaze::CustomMatrix<float, blaze::unaligned,
     blaze::unpadded, blaze::rowMajor> BlazeWrapper;

src/npz_converter.h

@@ -1,31 +1,110 @@
 #pragma once
 
-#include "cnpy/cnpy.h"
-#include "tensor.h"
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
 
+#include "cnpy/cnpy.h"
+#include "tensor.h" //XXX Marcin, is this include actually needed? It appears to not be used.
+
+/**
+ * @brief Loads model data stored in a npz file.
+ *
+ * Use of this class enables such data to later be stored in standard Marian data structures.
+ *
+ * Note: this class makes use of the 3rd-party class <code>npy</code>.
+ */
 class NpzConverter {
+
+  // Private inner classes of the NpzConverter class
   private:
+
+    /**
+     * Wraps npy data such that the underlying matrix shape and
+     *    matrix data are made accessible.
+     */
     class NpyMatrixWrapper {
+
       public:
+
+        /**
+         * Constructs a wrapper around an underlying npy data structure,
+         *    enabling the underlying data to be accessed as a matrix.
+         *
+         * @param npy the underlying data
+         */
         NpyMatrixWrapper(const cnpy::NpyArray& npy)
         : npy_(npy) {}
 
+        /**
+         * Returns the total number of elements in the underlying matrix.
+         *
+         * @return the total number of elements in the underlying matrix
+         */
         size_t size() const {
           return size1() * size2();
         }
 
+        /**
+         * Returns a pointer to the raw data that underlies the matrix.
+         *
+         * @return a pointer to the raw data that underlies the matrix
+         */
         float* data() const {
           return (float*)npy_.data;
         }
 
+        /**
+         * Given the index (i, j) of a matrix element,
+         *   this operator returns the float value from the underlying npz data
+         *   that is stored in the matrix.
+         *
+         * XXX: Marcin, is the following correct? Or do I have the row/column labels swapped?
+         *
+         * @param i Index of a column in the matrix
+         * @param j Index of a row in the matrix
+         *
+         * @return the float value stored at column i, row j of the matrix
+         */
         float operator()(size_t i, size_t j) const {
           return ((float*)npy_.data)[i * size2() + j];
         }
 
+        /**
+         * Returns the number of columns in the matrix.
+         *
+         * XXX: Marcin, is this following correct? Or do I have the row/column labels swapped?
+         *
+         * @return the number of columns in the matrix
+         */
         size_t size1() const {
           return npy_.shape[0];
         }
 
+        /**
+         * Returns the number of rows in the matrix.
+         *
+         * XXX: Marcin, is this following correct? Or do I have the row/column labels swapped?
+         *
+         * @return the number of rows in the matrix
+         */
         size_t size2() const {
           if(npy_.shape.size() == 1)
             return 1;
@@ -34,25 +113,50 @@ class NpzConverter {
         }
 
       private:
-        const cnpy::NpyArray& npy_;
-    };
 
+        /** Instance of the underlying (3rd party) data structure. */
+        const cnpy::NpyArray& npy_;
+
+    }; // End of NpyMatrixWrapper class
+
+  // Public methods of the NpzConverter class
   public:
+
+    /**
+     * Constructs an object that reads npz data from a file.
+     *
+     * @param file Path to file containing npz data
+     */
     NpzConverter(const std::string& file)
       : model_(cnpy::npz_load(file)),
         destructed_(false) {
       }
 
+    /**
+     * Destructs the model that underlies this NpzConverter object,
+     *    if that data has not already been destructed.
+     */
     ~NpzConverter() {
       if(!destructed_)
         model_.destruct();
     }
 
+    /**
+     * Destructs the model that underlies this NpzConverter object,
+     *    and marks that data as having been destructed.
+     */
     void Destruct() {
       model_.destruct();
       destructed_ = true;
     }
 
+    /**
+     * Loads data corresponding to a search key into the provided vector.
+     *
+     * @param key Search key                                    XXX Marcin, what type of thing is "key"? What are we searching for here?
+     * @param data Container into which data will be loaded     XXX Lane, is there a way in Doxygen to mark and inout variable?
+     * @param shape Shape object into which the number of rows and columns of the vectors will be stored
+     */
     void Load(const std::string& key, std::vector<float>& data, marian::Shape& shape) const {
       auto it = model_.find(key);
       if(it != model_.end()) {
@@ -71,7 +175,13 @@ class NpzConverter {
       }
     }
 
+  // Private member data of the NpzConverter class
   private:
+
+    /** Underlying npz data */
     cnpy::npz_t model_;
+
+    /** Indicates whether the underlying data has been destructed. */
     bool destructed_;
-};
+
+}; // End of NpzConverter class

src/optimizers.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <map>
 #include <boost/any.hpp>
 #include "tensor_operators.h"

src/param_initializers.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <random>
 #include <algorithm>
 #include <iterator>

src/tensor.cu

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <fstream>
 #include "tensor.h"
 

src/tensor.h

@@ -1,21 +1,25 @@
 #pragma once
-/* Copyright (C) 
- * 2016 - MLAMU & friends
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- * 
- */
+
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
 
 #include <cublas_v2.h>
 #include <thrust/device_vector.h>

src/tensor_operators.cu

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "tensor_operators.h"
 
 using namespace std;

src/tensor_operators.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "tensor.h"
 
 namespace marian {

src/test.cu

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <fstream>
 #include "marian.h"
 #include "mnist.h"

src/thrust_functions.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <cmath>
 #include <cublas_v2.h>   
 #include <thrust/device_vector.h>
@@ -108,4 +129,4 @@ namespace thrust
       }
     }
   }
-}
+}

src/validate_encoder_decoder.cu

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include "marian.h"
 #include "mnist.h"
 #include "vocab.h"

src/validate_mnist_batch.cu

@@ -1,3 +1,23 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
 
 #include "marian.h"
 #include "mnist.h"

src/vocab.cpp

@@ -1,3 +1,24 @@
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <limits>
 #include "vocab.h"
 

src/vocab.h

@@ -1,5 +1,26 @@
 #pragma once
 
+// This file is part of the Marian toolkit.
+// Marian is copyright (c) 2016 Marcin Junczys-Dowmunt.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
 #include <unordered_map>
 #include <string>
 #include <vector>