Merge pull request #23 from TurakhiaLab/transition_protein_sw

Implemented the protein local affine kernel with the switch that if enabled, it allows each PE to keep their own copy of the transition matrices.

CMakeLists.txt

@@ -164,7 +164,6 @@ add_executable(test_csim_local_two_piece_affine
     "kernels/local_two_piece_affine/kernel_local_two_piece_affine.cpp"
     ${COMMON_SRCS}) 
 
-
 add_executable(test_global_affine_real_data
     "testbench/test_csim_global_affine_real_data.cpp"
     "kernels/global_affine/kernel_global_affine.cpp"

include/PE.h

@@ -29,6 +29,9 @@ namespace PE
                   const input_char_block_t qry,
                   const input_char_block_t ref,
                   const Penalties penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+                  const type_t (&transitions)[PE_NUM][TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
                   tbp_vec_t &tbp);
 
     /**
@@ -47,6 +50,9 @@ namespace PE
         const input_char_block_t &qry,
         const input_char_block_t &ref,
         const Penalties penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+        const type_t (&transitions)[PE_NUM][TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
         wavefront_scores_inf_t &score,
         tbp_vec_t &tbp);
 
@@ -66,6 +72,9 @@ namespace PE
         const input_char_block_t qry,
         const input_char_block_t ref,
         const Penalties penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+        const type_t (&transitions)[PE_NUM][TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
         wavefront_scores_inf_t &score,
         tbp_vec_t &tbp);
 

include/align.h

@@ -254,6 +254,9 @@ namespace Align
 			const idx_t query_length,
 			const idx_t reference_length,
 			const Penalties &penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+			const type_t (&transitions)[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
 			idx_t &tb_i, idx_t &tb_j
 #ifndef NO_TRACEBACK
 			, tbr_t (&tb_out)[MAX_REFERENCE_LENGTH + MAX_QUERY_LENGTH]
@@ -286,6 +289,9 @@ namespace Align
 			idx_t global_query_length, idx_t query_length, idx_t reference_length,
 			const bool (&col_pred)[PE_NUM],
 			const Penalties &penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+			const type_t (&transitions)[PE_NUM][TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
 			ScorePack (&max)[PE_NUM]
 #ifndef NO_TRACEBACK
 			, tbp_t (&chunk_tbp_out)[PE_NUM][TBMEM_SIZE]
@@ -329,6 +335,9 @@ namespace Align
 			const idx_t query_length,
 			const idx_t reference_length,
 			const Penalties &penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+			const type_t (&transitions)[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
 			idx_t &tb_i, idx_t &tb_j
 #ifndef NO_TRACEBACK
 			, tbr_t (&tb_out)[MAX_REFERENCE_LENGTH + MAX_QUERY_LENGTH]
@@ -362,6 +371,9 @@ namespace Align
 			const bool (&col_pred)[PE_NUM],
 			const idx_t global_query_length, const idx_t local_query_length, const idx_t reference_length,
 			const Penalties &penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+			const type_t (&transitions)[PE_NUM][TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
 			ScorePack (&max)[PE_NUM] // write out so must pass by reference
 #ifndef NO_TRACEBACK
 			, tbp_t (&chunk_tbp_out)[PE_NUM][TBMEM_SIZE]

include/frontend.h

@@ -19,6 +19,9 @@ namespace ALIGN_TYPE
                      score_vec_t diag_prev,
                      score_vec_t left_prev,
                      const Penalties penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+                     const type_t transitions[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
                      score_vec_t &write_score,
                      tbp_t &write_traceback);
 

include/seq_align_multiple.h

@@ -24,7 +24,10 @@ extern "C" {
 		char_t (&references)[MAX_REFERENCE_LENGTH][N_BLOCKS],
 		idx_t (&query_lengths)[N_BLOCKS],
 		idx_t (&reference_lengths)[N_BLOCKS],
-		Penalties (&penalties)[N_BLOCKS],
+		const Penalties (&penalties)[N_BLOCKS],
+#ifdef LOCAL_TRANSITION_MATRIX
+		const type_t (&transitions)[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
 		idx_t (&tb_is)[N_BLOCKS], idx_t (&tb_js)[N_BLOCKS]
 #ifndef NO_TRACEBACK
 		, tbr_t (&tb_streams)[MAX_REFERENCE_LENGTH + MAX_QUERY_LENGTH][N_BLOCKS]

kernels/dtw/params.h

@@ -13,9 +13,10 @@
 #define PE_NUM 32
 #define LAYER_MAXIMIUM 0  // We need to indicate from which layer (main matrix) is the maximum score stored.
 
+#define BANDING RECTANGULAR
+
 typedef ap_fixed<32, 26> num_t;
 
-#define BANDING RECTANGULAR
 
 // Primitive Types
 struct char_t_st {
@@ -30,6 +31,7 @@ struct char_t_st {
 };
 
 typedef char_t_st char_t;  // Sequence Alphabet
+
 typedef ap_fixed<32,26> type_t;  // Scores Type <width, integer_width>
 typedef short idx_t;  // Indexing Type, could be much less than 32. ap_uint<8>
 typedef ap_uint<2> tbp_t;  // Traceback Pointer Type

kernels/global_linear/params.h

@@ -36,25 +36,6 @@ typedef ap_uint<2> tbp_t;  // Traceback Pointer Type
 #define DEBUG_OUTPUT_PATH "/home/[email protected]/DP-HLS-Debug/global_affine/"
 #define DEBUG_FILENAME "debug_kernel"
 
-struct ScorePack{  
-    type_t score;
-    idx_t row;
-    idx_t col;
-    idx_t p_col;
-    idx_t ck;
-    idx_t pe;
-
-	// Default Constructor
-    ScorePack() {
-        score = 0;
-        row = 0;
-        col = 0;
-        p_col = 0;
-        ck = 0;
-        pe = 0;
-    }
-};
-
 struct Penalties {
     type_t open;
     type_t extend;

kernels/local_affine/kernel_local_affine.cpp

@@ -13,9 +13,9 @@ void LocalAffine::PE::Compute(char_t local_query_val,
 // Define Traceback Pointer Navigation Direction
 
     const type_t insert_open = left_prev[1] + penalties.open + penalties.extend; // Insert open
-    const type_t insert_extend = left_prev[0] + penalties.open;                  // insert extend
+    const type_t insert_extend = left_prev[0] + penalties.extend;                  // insert extend
     const type_t delete_open = up_prev[1] + penalties.open + penalties.extend;   // delete open
-    const type_t delete_extend = up_prev[2] + penalties.open;                    // delete extend
+    const type_t delete_extend = up_prev[2] + penalties.extend;                    // delete extend
 
     bool insert_open_b = insert_open > insert_extend;
     bool delete_open_b = delete_open > delete_extend;

kernels/protein_local_affine/kernel_protein_local_affine.cpp

@@ -6,16 +6,19 @@ void ProteinLocalAffine::PE::Compute(char_t local_query_val,
                                score_vec_t diag_prev,
                                score_vec_t left_prev,
                                const Penalties penalties,
+#ifdef LOCAL_TRANSITION_MATRIX
+                               const type_t transitions[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
+#endif
                                score_vec_t &write_score,
                                tbp_t &write_traceback)
 {
 
 // Define Traceback Pointer Navigation Direction
 
-    const type_t insert_open = left_prev[1] + penalties.open + penalties.extend; // Insert open
-    const type_t insert_extend = left_prev[0] + penalties.open;                  // insert extend
-    const type_t delete_open = up_prev[1] + penalties.open + penalties.extend;   // delete open
-    const type_t delete_extend = up_prev[2] + penalties.open;                    // delete extend
+    const type_t insert_open = left_prev[1] + penalties.open; // Insert open
+    const type_t insert_extend = left_prev[0] + penalties.extend;                  // insert extend
+    const type_t delete_open = up_prev[1] + penalties.open;   // delete open
+    const type_t delete_extend = up_prev[2] + penalties.extend;                    // delete extend
 
     bool insert_open_b = insert_open > insert_extend;
     bool delete_open_b = delete_open > delete_extend;
@@ -24,8 +27,10 @@ void ProteinLocalAffine::PE::Compute(char_t local_query_val,
     tbp_t insert_tb = insert_open_b ? (tbp_t) 0 : TB_IMAT;
     tbp_t delete_tb = delete_open_b ? (tbp_t) 0 : TB_DMAT;
 
-
-    const type_t match = (local_query_val == local_reference_val) ? diag_prev[1] + penalties.match : diag_prev[1] + penalties.mismatch;
+    // transition SW
+    // std::cout << "accessing" << local_query_val.to_int() << "and" << local_reference_val.to_int()  << std::endl;
+    const type_t match = transitions[local_query_val][local_reference_val] + diag_prev[1];
+    // std::cout << "accessed" << std::endl;
 
     type_t max_value = write_score[0] > write_score[2] ? write_score[0] : write_score[2]; // compare between insertion and deletion
     max_value = max_value > match ? max_value : match;
@@ -68,16 +73,12 @@ void ProteinLocalAffine::InitializeScores(
     InitializeColumnScores:
     for (int i = 0; i < MAX_QUERY_LENGTH; i++)
     {
-        init_col_scr[i][0] = NINF;
-        init_col_scr[i][1] = 0.0;
-        init_col_scr[i][2] = 0.0;
+        init_col_scr[i] = {NINF, 0,0 };
     }
     InitializeRowScores:
     for (int i = 0; i < MAX_REFERENCE_LENGTH; i++)
     {
-        init_row_scr[i][0] = 0.0;
-        init_row_scr[i][1] = 0.0;
-        init_row_scr[i][2] = NINF;
+        init_row_scr[i] = {0, 0, NINF};
     }
 }
 

kernels/protein_local_affine/params.h

@@ -10,6 +10,11 @@
 
 #define BANDING RECTANGULAR
 
+#define LOCAL_TRANSITION_MATRIX
+#define TRANSITION_MATRIX_SIZE 20
+
+#define SCORED
+
 #define ALIGN_TYPE ProteinLocalAffine
 #define N_BLOCKS 1
 #define N_LAYERS 3
@@ -46,9 +51,6 @@ typedef ap_uint<4> tbp_t;  // Traceback Pointer Type
 struct Penalties {
     type_t open;
     type_t extend;
-    type_t mismatch;
-    type_t match;
-    type_t linear_gap;
 };
 
 enum TB_STATE {

kernels/sdtw/kernel_sdtw.cpp

@@ -35,6 +35,7 @@ void SDTW::PE::Compute(char_t local_query_val,
     // The RTL code uses left and diagonal is because possible the query and reference is transposed. 
     // find max from diagonal and left
     write_score[0] = (diag_prev[0] < up_prev[0] ? diag_prev[0] : up_prev[0]) + abs(local_query_val - local_reference_val);
+
 }
 
 void SDTW::UpdatePEMaximum(

kernels/sdtw/params.h

@@ -18,7 +18,7 @@
  */
 
 #define MAX_QUERY_LENGTH 500  // This is read length in SF
-#define MAX_REFERENCE_LENGTH 1000  // This is Reference length in SF. 
+#define MAX_REFERENCE_LENGTH 60000  // This is Reference length in SF. 
 
 // The default PE_NUM is 100. 
 

some notes

@@ -12,4 +12,7 @@
 /usr/lib64/libOpenCL.so
 /usr/lib64/libOpenCL.so.1
 /usr/lib64/libOpenCL.so.1.0.0
-(base) [centos@ip-172-31-21-210 DP-HLS]$ 
+(base) [centos@ip-172-31-21-210 DP-HLS]$ 
+
+Kernel   Aligned Query    : MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALV
+Kernel   Aligned Reference: ___________________________________________________________________________________MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYV_RCTYDADL_IDTQAQV