Merge remote-tracking branch 'upstream/master'

14 files changed, 145 insertions, 62 deletions

diff --git a/README.md b/README.md
index be8e5b0..8c21bd9 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ cd nerv
 git clone https://github.com/Nerv-SJTU/nerv-speech.git speech
 git submodule init && git submodule update
 make
+make speech
 ```
 The `git submodule` command is for the __luajit__ repository inside __Nerv__.  
 Now, you can try to run some example scripts.  
diff --git a/nerv/examples/swb_baseline.lua b/nerv/examples/swb_baseline.lua
index bbc6467..8015884 100644
--- a/nerv/examples/swb_baseline.lua
+++ b/nerv/examples/swb_baseline.lua
@@ -173,7 +173,8 @@ function make_buffer(readers)
         {
             buffer_size = gconf.buffer_size,
             randomize = gconf.randomize,
-            readers = readers
+            readers = readers,
+            use_gpu = true
         })
 end
 
diff --git a/nerv/io/sgd_buffer.lua b/nerv/io/sgd_buffer.lua
index f9d281c..74c4934 100644
--- a/nerv/io/sgd_buffer.lua
+++ b/nerv/io/sgd_buffer.lua
@@ -5,8 +5,22 @@ function SGDBuffer:__init(global_conf, buffer_conf)
     self.buffer_size = math.floor(buffer_conf.buffer_size /
                                 global_conf.batch_size) * global_conf.batch_size
     self.randomize = buffer_conf.randomize
-    if self.randomize == nil then
-        self.randomize = false
+    self.consume = buffer_conf.consume
+    local cumat_type = global_conf.cumat_type
+    if buffer_conf.use_gpu then
+        self.mat_type = cumat_type
+        self.copy_rows_from_by_idx = cumat_type.copy_rows_fromd_by_idx
+        self.copy_from = cumat_type.copy_fromd
+        self.copy_from_reader = cumat_type.copy_fromh
+        self.perm_gen = function (x)
+            return cumat_type.new_from_host(nerv.MMatrixFloat.perm_gen(x))
+        end
+    else
+        self.mat_type = global_conf.mmat_type
+        self.copy_rows_from_by_idx = cumat_type.copy_rows_fromh_by_idx
+        self.copy_from = cumat_type.copy_fromh
+        self.perm_gen = nerv.MMatrixFloat.perm_gen
+        self.copy_from_reader = self.mat_type.copy_from
     end
     self.head = 0
     self.tail = 0
@@ -14,7 +28,7 @@ function SGDBuffer:__init(global_conf, buffer_conf)
     for i, reader_spec in ipairs(buffer_conf.readers) do
         local buffs = {}
         for id, width in pairs(reader_spec.data) do
-            buffs[id] = {data = global_conf.mmat_type(self.buffer_size, width),
+            buffs[id] = {data = self.mat_type(self.buffer_size, width),
                         leftover = nil,
                         width = width}
         end
@@ -41,7 +55,7 @@ function SGDBuffer:saturate()
                 buff.data:copy_from(buff.leftover, 0, lrow)
                 buff.leftover = nil
             end
-            nerv.printf("buffer leftover: %d\n", lrow)
+            nerv.info("buffer leftover: %d\n", lrow)
             reader.tail = lrow
             reader.has_leftover = false
         end
@@ -65,21 +79,21 @@ function SGDBuffer:saturate()
                     if d == nil then
                         nerv.error("reader does not provide data for %s", id)
                     end
-                    buff.leftover = self.gconf.mmat_type(drow - remain,
-                                                        buff.width)
-                    buff.leftover:copy_from(d, remain, drow)
+                    buff.leftover = self.mat_type(drow - remain,
+                                                  buff.width)
+                    self.copy_from_reader(buff.leftover, d, remain, drow)
                 end
                 drow = remain
                 reader.has_leftover = true
             end
             for id, buff in pairs(reader.buffs) do
-                buff.data:copy_from(data[id], 0, drow, reader.tail)
+                self.copy_from_reader(buff.data, data[id], 0, drow, reader.tail)
             end
             reader.tail = reader.tail + drow
         end
         self.tail = math.min(self.tail, reader.tail)
     end
-    self.rand_map = nerv.MMatrixInt.perm_gen(self.tail) -- generate shuffled index
+    self.rand_map = self.perm_gen(self.tail) -- generate shuffled index
     collectgarbage("collect")
     return self.tail >= self.gconf.batch_size
 end
@@ -88,26 +102,30 @@ function SGDBuffer:get_data()
     local batch_size = self.gconf.batch_size
     if self.head >= self.tail then -- buffer is empty
         local t = os.clock()
-        if not self:saturate() then
+        if (not self:saturate()) and (not self.consume) then
             return nil -- the remaining data cannot build a batch
         end
+        if self.tail == self.head then
+            return nil -- nothing left
+        end
         nerv.info("%.3fs to fill the buffer", os.clock() - t)
     end
-    if self.head + batch_size > self.tail then
+    if self.head + batch_size > self.tail and (not self.consume) then
         return nil -- the remaining data cannot build a batch
     end
+    actual_batch_size = math.min(batch_size, self.tail - self.head)
     local res = {}
     for i, reader in ipairs(self.readers) do
         for id, buff in pairs(reader.buffs) do
-            local batch = self.gconf.cumat_type(batch_size, buff.width)
+            local batch = self.gconf.cumat_type(actual_batch_size, buff.width)
             if self.randomize then
-                batch:copy_rows_fromh_by_idx(buff.data, self.rand_map, self.head)
+                self.copy_rows_from_by_idx(batch, buff.data, self.rand_map, self.head)
             else
-                batch:copy_fromh(buff.data, self.head, self.head + batch_size)
+                self.copy_from(batch, buff.data, self.head, self.head + actual_batch_size)
             end
             res[id] = batch
         end
     end
-    self.head = self.head + batch_size
+    self.head = self.head + actual_batch_size
     return res
 end
diff --git a/nerv/lib/matrix/cukernel.h b/nerv/lib/matrix/cukernel.h
index 7bb4c2c..2126c6f 100644
--- a/nerv/lib/matrix/cukernel.h
+++ b/nerv/lib/matrix/cukernel.h
@@ -18,4 +18,6 @@ void cudak_(cuda_rearrange_frm)(const Matrix *a, Matrix *b, int step);
 void cudak_(cuda_scale_rows_by_row)(const Matrix *a, Matrix *b);
 void cudak_(cuda_scale_rows_by_col)(const Matrix *a, Matrix *b);
 void cudak_(cuda_decompress)(const Matrix *a, Matrix *b);
+void cudak_(cuda_copy_rows_by_idx)(const Matrix *a, Matrix *b,
+                                    const Matrix *idx, int b_begin);
 #endif
diff --git a/nerv/lib/matrix/cumatrix.c b/nerv/lib/matrix/cumatrix.c
index aa81bfc..ff1168d 100644
--- a/nerv/lib/matrix/cumatrix.c
+++ b/nerv/lib/matrix/cumatrix.c
@@ -49,6 +49,7 @@ void nerv_cumatrix_init() {
 #define NERV_CUBLAS_(NAME) cublasS##NAME
 #define MATRIX_CUMATRIX_HOST_TNAME nerv_matrix_host_float_tname
 #include "generic/cumatrix.c"
+
 #undef NERV_CUBLAS_
 #undef cudak_
 #undef nerv_matrix_
diff --git a/nerv/lib/matrix/cumatrix.h b/nerv/lib/matrix/cumatrix.h
index 9f71507..e6def66 100644
--- a/nerv/lib/matrix/cumatrix.h
+++ b/nerv/lib/matrix/cumatrix.h
@@ -1,5 +1,6 @@
 #ifndef NERV_CUMATRIX_H
 #define NERV_CUMATRIX_H
+#include "matrix.h"
 void nerv_cumatrix_print_profile();
 void nerv_cumatrix_clear_profile();
 void nerv_cumatrix_init();
diff --git a/nerv/lib/matrix/generic/cukernel.cu b/nerv/lib/matrix/generic/cukernel.cu
index e337798..08feb59 100644
--- a/nerv/lib/matrix/generic/cukernel.cu
+++ b/nerv/lib/matrix/generic/cukernel.cu
@@ -284,6 +284,15 @@ __global__ void cudak_(gen_col_idx)(MATRIX_ELEM *b,
     b[j + i * stride] = j;
 }
 
+__global__ void cudak_(copy_rows_by_idx)(const MATRIX_ELEM *a, MATRIX_ELEM *b,
+                                    const MATRIX_ELEM *idx, int b_begin,
+                                    int nrow, int ncol, int stride) {
+    int j = blockIdx.x * blockDim.x + threadIdx.x;
+    int i = blockIdx.y * blockDim.y + threadIdx.y;
+    if (i >= nrow || j >= ncol) return;
+    b[j + i * stride] = a[j + lrintf(idx[i]) * stride];
+}
+
 extern "C" {
 #include "../cukernel.h"
     void cudak_(cuda_log_elem)(const Matrix *a, Matrix *b) {
@@ -589,5 +598,16 @@ extern "C" {
              b->stride / sizeof(MATRIX_ELEM));
         cudaStreamSynchronize(0);
     }
+
+    void cudak_(cuda_copy_rows_by_idx)(const Matrix *a, Matrix *b,
+                                        const Matrix *idx, int b_begin) {
+        dim3 threadsPerBlock(CUDA_THREADS_NN, 1);
+        dim3 numBlocks(CEIL_DIV(b->ncol, threadsPerBlock.x), b->nrow);
+        cudak_(copy_rows_by_idx)<<<numBlocks, threadsPerBlock>>> \
+            (MATRIX_ELEM_PTR(a), MATRIX_ELEM_PTR(b),
+            MATRIX_ELEM_PTR(idx) + b_begin,
+             b_begin, b->nrow, b->ncol, b->stride / sizeof(MATRIX_ELEM));
+        cudaStreamSynchronize(0);
+    }
 }
 #endif
diff --git a/nerv/lib/matrix/generic/cumatrix.c b/nerv/lib/matrix/generic/cumatrix.c
index 2cb3563..770e503 100644
--- a/nerv/lib/matrix/generic/cumatrix.c
+++ b/nerv/lib/matrix/generic/cumatrix.c
@@ -315,7 +315,7 @@ void nerv_matrix_(copy_rows_fromh_by_idx)(Matrix *a, const Matrix *b,
     long nrow = a->nrow;
     if (!(0 <= b_begin && b_begin + nrow <= idx->ncol))
         NERV_EXIT_STATUS(status, MAT_INVALID_COPY_INTERVAL, 0);
-    long *idx_ptr = idx->data.i;
+    float *idx_ptr = idx->data.f;
     int i;
     if (idx->nrow != 1)
         NERV_EXIT_STATUS(status, MAT_IDX_VECTOR_EXP, 0);
@@ -325,7 +325,7 @@ void nerv_matrix_(copy_rows_fromh_by_idx)(Matrix *a, const Matrix *b,
     cudaStream_t *streams = (cudaStream_t*)malloc(sizeof(cudaStream_t) * nrow);
     for (i = 0; i < nrow; i++)
     {
-        int src_row = idx_ptr[b_begin + i];
+        int src_row = (int)idx_ptr[b_begin + i];
         if (!(0 <= src_row && src_row < b->nrow))
             NERV_EXIT_STATUS(status, MAT_INVALID_IDX, 0);
         CUDA_SAFE_CALL(cudaStreamCreate(streams + i), status);
@@ -344,6 +344,21 @@ void nerv_matrix_(copy_rows_fromh_by_idx)(Matrix *a, const Matrix *b,
     NERV_SET_STATUS(status, NERV_NORMAL, 0);
 }
 
+void nerv_matrix_(copy_rows_fromd_by_idx)(Matrix *a, const Matrix *b,
+                            const Matrix *idx, int b_begin, Status *status) {
+    long nrow = a->nrow;
+    if (!(0 <= b_begin && b_begin + nrow <= idx->ncol))
+        NERV_EXIT_STATUS(status, MAT_INVALID_COPY_INTERVAL, 0);
+    if (idx->nrow != 1)
+        NERV_EXIT_STATUS(status, MAT_IDX_VECTOR_EXP, 0);
+    if (a->ncol != b->ncol)
+        NERV_EXIT_STATUS(status, MAT_MISMATCH_DIM, 0);
+    PROFILE_START
+    cudak_(cuda_copy_rows_by_idx)(b, a, idx, b_begin);
+    PROFILE_STOP
+    NERV_SET_STATUS(status, NERV_NORMAL, 0);
+}
+
 void nerv_matrix_(expand_frm)(Matrix *a, const Matrix *b,
                             int context, Status *status) {
     if (a->nrow != b->nrow)
diff --git a/nerv/lib/matrix/generic/cumatrix.h b/nerv/lib/matrix/generic/cumatrix.h
index 3f1f8a3..04e8c5a 100644
--- a/nerv/lib/matrix/generic/cumatrix.h
+++ b/nerv/lib/matrix/generic/cumatrix.h
@@ -40,6 +40,8 @@ void nerv_matrix_(log_elem)(Matrix *b, const Matrix *a, Status *status);
 Matrix *nerv_matrix_(decompress)(const Matrix *a, int orig_col, Status *status);
 void nerv_matrix_(copy_rows_fromh_by_idx)(Matrix *a, const Matrix *b,
                             const Matrix *idx, int b_begin, Status *status);
+void nerv_matrix_(copy_rows_fromd_by_idx)(Matrix *a, const Matrix *b,
+                            const Matrix *idx, int b_begin, Status *status);
 
 void nerv_matrix_(expand_frm)(Matrix *a, const Matrix *b,
                             int context, Status *status);
diff --git a/nerv/lib/matrix/mmatrix.c b/nerv/lib/matrix/mmatrix.c
index 94f1ea8..b8157eb 100644
--- a/nerv/lib/matrix/mmatrix.c
+++ b/nerv/lib/matrix/mmatrix.c
@@ -7,6 +7,25 @@
 #define nerv_matrix_(NAME) nerv_matrix_host_float_##NAME
 #include "generic/matrix.h"
 #include "generic/mmatrix.c"
+
+Matrix *nerv_matrix_(perm_gen)(int ncol, Status *status) {
+    int i;
+    Matrix *self = nerv_matrix_(create)(1, ncol, status);
+    if (status->err_code != NERV_NORMAL)
+        return NULL;
+    float *prow = self->data.f;
+    for (i = 0; i < ncol; i++)
+        prow[i] = i;
+    for (i = ncol - 1; i >= 0; i--)
+    {
+        size_t j = rand() % (i + 1);
+        float tmp = prow[i];
+        prow[i] = prow[j];
+        prow[j] = tmp;
+    }
+    return self;
+}
+
 #undef nerv_matrix_
 #undef host_matrix_
 #undef MATRIX_USE_FLOAT
@@ -33,21 +52,3 @@
 #define host_matrix_(NAME) host_matrix_int_##NAME
 #define nerv_matrix_(NAME) nerv_matrix_host_int_##NAME
 #include "generic/mmatrix.c"
-
-Matrix *nerv_matrix_(perm_gen)(int ncol, Status *status) {
-    int i;
-    Matrix *self = nerv_matrix_(create)(1, ncol, status);
-    if (status->err_code != NERV_NORMAL)
-        return NULL;
-    long *prow = self->data.i;
-    for (i = 0; i < ncol; i++)
-        prow[i] = i;
-    for (i = ncol - 1; i >= 0; i--)
-    {
-        size_t j = rand() % (i + 1);
-        long tmp = prow[i];
-        prow[i] = prow[j];
-        prow[j] = tmp;
-    }
-    return self;
-}
diff --git a/nerv/lib/matrix/mmatrix.h b/nerv/lib/matrix/mmatrix.h
index df91e4c..31e7984 100644
--- a/nerv/lib/matrix/mmatrix.h
+++ b/nerv/lib/matrix/mmatrix.h
@@ -1,4 +1,5 @@
 #ifndef NERV_MMATRIX_H
 #define NERV_MMATRIX_H
-Matrix *nerv_matrix_(perm_gen)(int ncol, Status *status);
+#include "matrix.h"
+Matrix *nerv_matrix_host_float_perm_gen(int ncol, Status *status);
 #endif
diff --git a/nerv/matrix/generic/cumatrix.c b/nerv/matrix/generic/cumatrix.c
index ab7f7c4..08cb4c2 100644
--- a/nerv/matrix/generic/cumatrix.c
+++ b/nerv/matrix/generic/cumatrix.c
@@ -228,12 +228,12 @@ static int nerv_matrix_(lua_decompress)(lua_State *L) {
     return 1;
 }
 
-extern const char *nerv_matrix_host_int_tname;
+extern const char *nerv_matrix_host_float_tname;
 static int nerv_matrix_(lua_copy_rows_fromh_by_idx)(lua_State *L) {
     Status status;
     Matrix *a = luaT_checkudata(L, 1, nerv_matrix_(tname));
     const Matrix *b = luaT_checkudata(L, 2, MATRIX_CUMATRIX_HOST_TNAME);
-    const Matrix *idx = luaT_checkudata(L, 3, nerv_matrix_host_int_tname);
+    const Matrix *idx = luaT_checkudata(L, 3, nerv_matrix_host_float_tname);
     long nrow = a->nrow;
     int b_begin = lua_gettop(L) > 3 ? luaL_checkinteger(L, 4) : 0;
     nerv_matrix_(copy_rows_fromh_by_idx)(a, b, idx, b_begin, &status);
@@ -241,6 +241,18 @@ static int nerv_matrix_(lua_copy_rows_fromh_by_idx)(lua_State *L) {
     return 0;
 }
 
+static int nerv_matrix_(lua_copy_rows_fromd_by_idx)(lua_State *L) {
+    Status status;
+    Matrix *a = luaT_checkudata(L, 1, nerv_matrix_(tname));
+    const Matrix *b = luaT_checkudata(L, 2, nerv_matrix_(tname));
+    const Matrix *idx = luaT_checkudata(L, 3, nerv_matrix_(tname));
+    long nrow = a->nrow;
+    int b_begin = lua_gettop(L) > 3 ? luaL_checkinteger(L, 4) : 0;
+    nerv_matrix_(copy_rows_fromd_by_idx)(a, b, idx, b_begin, &status);
+    NERV_LUA_CHECK_STATUS(L, status);
+    return 0;
+}
+
 static int nerv_matrix_(lua_expand_frm)(lua_State *L) {
     Status status;
     Matrix *a = luaT_checkudata(L, 1, nerv_matrix_(tname));
@@ -290,6 +302,8 @@ static const luaL_Reg nerv_matrix_(extra_methods)[] = {
     /* in-place calc */
     {"copy_fromh", nerv_matrix_(lua_copy_fromh)},
     {"copy_fromd", nerv_matrix_(lua_copy_fromd)},
+    /* alias for copy_fromd */
+    {"copy_from", nerv_matrix_(lua_copy_fromd)},
     {"copy_toh", nerv_matrix_(lua_copy_toh)},
     {"add", nerv_matrix_(lua_add)},
     {"mul", nerv_matrix_(lua_mul)},
@@ -302,6 +316,7 @@ static const luaL_Reg nerv_matrix_(extra_methods)[] = {
     {"mul_elem", nerv_matrix_(lua_mul_elem)},
     {"log_elem", nerv_matrix_(lua_log_elem)},
     {"copy_rows_fromh_by_idx", nerv_matrix_(lua_copy_rows_fromh_by_idx)},
+    {"copy_rows_fromd_by_idx", nerv_matrix_(lua_copy_rows_fromd_by_idx)},
     {"expand_frm", nerv_matrix_(lua_expand_frm)},
     {"rearrange_frm", nerv_matrix_(lua_rearrange_frm)},
     {"scale_rows_by_row", nerv_matrix_(lua_scale_rows_by_row)},
@@ -311,6 +326,9 @@ static const luaL_Reg nerv_matrix_(extra_methods)[] = {
 
 static void cuda_matrix_(init)(lua_State *L) {
     luaN_append_methods(L, nerv_matrix_(extra_methods));
+#ifdef CUMATRIX_INIT
+    CUMATRIX_INIT(L);
+#endif
 }
 
 int nerv_matrix_(lua_get_elem)(lua_State *L) {
diff --git a/nerv/matrix/mmatrix.c b/nerv/matrix/mmatrix.c
index 5561572..961059c 100644
--- a/nerv/matrix/mmatrix.c
+++ b/nerv/matrix/mmatrix.c
@@ -16,7 +16,30 @@ void nerv_lua_mmatrix_init(lua_State *L) {
 #define host_matrix_(NAME) host_matrix_float_##NAME
 #define nerv_matrix_(NAME) nerv_matrix_host_float_##NAME
 const char *nerv_matrix_(tname) = "nerv.MMatrixFloat";
+#define MMATRIX_INIT(L) host_matrix_(init_extra)(L)
+
+static const luaL_Reg nerv_matrix_(extra_methods_int)[];
+static void host_matrix_(init_extra)(lua_State *L) {
+    luaN_append_methods(L, nerv_matrix_(extra_methods_int));
+}
+
 #include "generic/mmatrix.c"
+#include "../lib/matrix/mmatrix.h"
+
+static int nerv_matrix_(lua_perm_gen)(lua_State *L) {
+    Status status;
+    int i, ncol = luaL_checkinteger(L, 1);
+    Matrix *self = nerv_matrix_(perm_gen)(ncol, &status);
+    NERV_LUA_CHECK_STATUS(L, status);
+    luaT_pushudata(L, self, nerv_matrix_(tname));
+    return 1;
+}
+
+static const luaL_Reg nerv_matrix_(extra_methods_int)[] = {
+    {"perm_gen", nerv_matrix_(lua_perm_gen)},
+    {NULL, NULL}
+};
+
 #undef nerv_matrix_
 #undef host_matrix_
 #undef MATRIX_USE_FLOAT
@@ -24,6 +47,7 @@ const char *nerv_matrix_(tname) = "nerv.MMatrixFloat";
 #undef MATRIX_ELEM_PTR
 #undef MATRIX_ELEM_FMT
 #undef MATRIX_ELEM_WRITE_FMT
+#undef MMATRIX_INIT
 
 #define NERV_GENERIC_MMATRIX
 #define MATRIX_USE_DOUBLE
@@ -44,26 +68,4 @@ const char *nerv_matrix_(tname) = "nerv.MMatrixDouble";
 #define host_matrix_(NAME) host_matrix_int_##NAME
 #define nerv_matrix_(NAME) nerv_matrix_host_int_##NAME
 const char *nerv_matrix_(tname) = "nerv.MMatrixInt";
-#define MMATRIX_INIT(L) host_matrix_(init_extra)(L)
-
-static const luaL_Reg nerv_matrix_(extra_methods_int)[];
-static void host_matrix_(init_extra)(lua_State *L) {
-    luaN_append_methods(L, nerv_matrix_(extra_methods_int));
-}
-
 #include "generic/mmatrix.c"
-#include "../lib/matrix/mmatrix.h"
-
-static int nerv_matrix_(lua_perm_gen)(lua_State *L) {
-    Status status;
-    int i, ncol = luaL_checkinteger(L, 1);
-    Matrix *self = nerv_matrix_(perm_gen)(ncol, &status);
-    NERV_LUA_CHECK_STATUS(L, status);
-    luaT_pushudata(L, self, nerv_matrix_(tname));
-    return 1;
-}
-
-static const luaL_Reg nerv_matrix_(extra_methods_int)[] = {
-    {"perm_gen", nerv_matrix_(lua_perm_gen)},
-    {NULL, NULL}
-};
diff --git a/nerv/nn/layer_dag.lua b/nerv/nn/layer_dag.lua
index 25297c2..f69d31c 100644
--- a/nerv/nn/layer_dag.lua
+++ b/nerv/nn/layer_dag.lua
@@ -266,7 +266,7 @@ function DAGLayer:get_intermediate(id, port_type)
     if id == "<input>" or id == "<output>" then
         nerv.error("an actual real layer id is expected")
     end
-    local layer = layers[id]
+    local layer = self.layers[id]
     if layer == nil then
         nerv.error("layer id %s not found", id)
     end