Correcting Viterbi Algorithm

cosim_scaling.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+python /home/centos/workspace/DP-HLS/py-hls/auto_cosim.py --config /home/centos/workspace/DP-HLS/compile_configs/scaling_global_linear/global_linear_scaling_pe.json --simulate True
+python /home/centos/workspace/DP-HLS/py-hls/auto_cosim.py --config /home/centos/workspace/DP-HLS/compile_configs/scaling_global_linear/global_linear_scaling_blocks.json --simulate True
+python /home/centos/workspace/DP-HLS/py-hls/auto_cosim.py --config /home/centos/workspace/DP-HLS/compile_configs/scaling_global_dtw/global_dtw_scaling_pes.json --simulate True
+python /home/centos/workspace/DP-HLS/py-hls/auto_cosim.py --config /home/centos/workspace/DP-HLS/compile_configs/scaling_global_dtw/global_dtw_scaling_blocks.json --simulate True

further_throughput_1.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+python /home/centos/workspace/DP-HLS/py-hls/parallel_compile.py --config /home/centos/workspace/DP-HLS/compile_configs/global_two_piece_affine/two_piece_affine_common_config_max.json --compile True --num_workers 1 --all True
+python /home/centos/workspace/DP-HLS/py-hls/parallel_compile.py --config /home/centos/workspace/DP-HLS/compile_configs/global_affine/global_affine_common_config.json --compile True --num_workers 1 --all True
+python /home/centos/workspace/DP-HLS/py-hls/parallel_compile.py --config /home/centos/workspace/DP-HLS/compile_configs/local_linear/local_linear_common_configs.json --compile True --num_workers 1 --all True

further_throughput_2.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+python /home/centos/workspace/DP-HLS/py-hls/parallel_compile.py --config /home/centos/workspace/DP-HLS/compile_configs/overlap_suffix_prefix/overlap_suffix_prefix_config.json --compile True --num_workers 1 --all True
+python /home/centos/workspace/DP-HLS/py-hls/parallel_compile.py --config /home/centos/workspace/DP-HLS/compile_configs/semiglobal_short_long/local_linear_common_configs.json --compile True --num_workers 1 --all True

include/solution_viterbi.h

@@ -89,6 +89,7 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
             double del_up;
             double ins_left;
             double main_diag, main_up, main_left;
+            double ins_diag, del_diag;
 
             if (i == 0 && j == 0)
             {
@@ -97,10 +98,10 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
                 main_left = initial_col[0][1];
 
                 ins_left = initial_col[0][0];
-                // ins_diag = 0;
+                ins_diag = 0;
 
                 del_up = initial_row[0][2];
-                // del_diag = 0;
+                del_diag = 0;
             }
             else if (i == 0 && j > 0)  // In first row, not column
             {
@@ -109,10 +110,10 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
                 main_left = score_mat[1][i][j - 1];
 
                 ins_left = score_mat[0][0][j - 1];
-                // ins_diag = initial_row[j - 1][0];
+                ins_diag = initial_row[j - 1][0];
 
                 del_up = initial_row[j][2];
-                // del_diag = initial_row[j - 1][2];
+                del_diag = initial_row[j - 1][2];
             }
             else if (i > 0 && j == 0)
             {
@@ -121,10 +122,10 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
                 main_left = initial_col[i][1];
 
                 ins_left = initial_col[i][0];
-                // ins_diag = initial_col[i - 1][0];
+                ins_diag = initial_col[i - 1][0];
 
                 del_up = score_mat[2][i - 1][j];
-                // del_diag = initial_col[i - 1][2];
+                del_diag = initial_col[i - 1][2];
             }
             else
             {
@@ -133,10 +134,10 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
                 main_left = score_mat[1][i][j - 1];
 
                 ins_left = score_mat[0][i][j - 1];
-                // ins_diag = score_mat[0][i-1][j-1];
+                ins_diag = score_mat[0][i-1][j-1];
 
                 del_up = score_mat[2][i - 1][j];
-                // del_diag = score_mat[2][i-1][j-1];
+                del_diag = score_mat[2][i-1][j-1];
             }
 
             double del_write, ins_write, main_write;           // values write to the score matrix
@@ -152,8 +153,8 @@ void viterbi_solution(std::string query, std::string reference, PENALTY_T &penal
             del_write = penalties.transition[4][HostUtils::Sequence::base_to_num(reference[j])] + (del_open_b ? del_open : del_extend);
 
             double main_match = penalties.log_1_m_2_lambda + main_diag;
-            double main_ins = penalties.log_mu + ins_left;
-            double main_del = penalties.log_mu + del_up;
+            double main_ins = penalties.log_mu + ins_diag;
+            double main_del = penalties.log_mu + del_diag;
 
             double main_max = main_match;
             main_max = main_max > main_ins ? main_max : main_ins;

kernels/viterbi/kernel_viterbi.cpp

@@ -1,5 +1,9 @@
 #include "frontend.h"
 
+#ifdef CMAKEDEBUG
+
+#endif
+
 void Viterbi::PE::Compute(char_t local_query_val,
                                char_t local_reference_val,
                                score_vec_t up_prev,
@@ -49,24 +53,24 @@ void Viterbi::PE::Compute(char_t local_query_val,
 #endif
 
     const type_t match_M = penalties.log_1_m_2_lambda + diag_prev[1];
-    const type_t match_I = penalties.log_mu + left_prev[0];
-    const type_t match_D = penalties.log_mu + up_prev[2];
+    const type_t match_I = penalties.log_mu + diag_prev[0];
+    const type_t match_D = penalties.log_mu + diag_prev[2];
 
 #ifdef CMAKEDEBUG
     auto diag_prev_s = diag_prev[1].to_float();
     auto local_query_val_s = local_query_val.to_int();
     auto local_reference_val_s = local_reference_val.to_int();
 #endif
 
-    type_t max_val = match_M;
-    tbp_t dir_tb = TB_DIAG;
-
     type_t transition_score = penalties.transition[local_query_val][local_reference_val];
 
 #ifdef CMAKEDEBUG
     auto write_score_1_s = write_score[1].to_float();
 #endif
 
+    type_t max_val = match_M;
+    tbp_t dir_tb = TB_DIAG;
+
     // Set traceback pointer based on the direction of the maximum score.
     if (max_val < match_I)
     { // Insert Case
@@ -129,49 +133,50 @@ void Viterbi::InitializeMaxScores(ScorePack (&max)[PE_NUM], idx_t qry_len, idx_t
 
 void Viterbi::Traceback::StateMapping(tbp_t tbp, TB_STATE &state, tbr_t &navigation)
 {
+#ifdef CMAKEDEBUG
+    std::cout << state << " ";
+#endif
 
     if (state == TB_STATE::MM)
     {
         if (tbp(1, 0) == TB_DIAG)
         {
-            navigation = AL_MMI;
+
         }
         else if (tbp(1, 0) == TB_UP)
         {
             state = TB_STATE::DEL;
-            navigation = AL_NULL;
         }
         else if (tbp(1, 0) == TB_LEFT)
         {
             state = TB_STATE::INS;
-            navigation = AL_NULL;
+
         } else {
             navigation = AL_END;
         }
+        navigation = AL_MMI;
     }
     else if (state == TB_STATE::DEL)
     {
         if ((bool)tbp[3])
-        { // deletion extending
-            // states remains the same.
-            // printf("delete extend");
+        { 
+            state = TB_STATE::MM; // set the state back to MM
         }
         else
         {                         // deletion closing
-            state = TB_STATE::MM; // set the state back to MM
+
         }
         navigation = AL_DEL;
     }
     else if (state == TB_STATE::INS)
     {
         if ((bool)tbp[2])
-        { // insertion extending
-            // states remains the same.
-            // ("delete extend");
+        { 
+            state = TB_STATE::MM; // set the state back to MM
         }
         else
         {                         // insertion closing
-            state = TB_STATE::MM; // set the state back to MM
+
         }
         navigation = AL_INS;
     }

kernels/viterbi/params.h

@@ -5,8 +5,8 @@
 #include <hls_vector.h>
 #include <ap_int.h>
 
-#define MAX_QUERY_LENGTH 64
-#define MAX_REFERENCE_LENGTH 64
+#define MAX_QUERY_LENGTH 256
+#define MAX_REFERENCE_LENGTH 256
 #define N_BLOCKS 1
 #define PE_NUM 8
 
@@ -28,7 +28,6 @@ typedef ap_uint<4> tbp_t;  // Traceback Pointer Type
 
 // Legacy Debugger Configuration
 #define DEBUG_OUTPUT_PATH "/home/[email protected]/DP-HLS-Debug/global_affine/"
-#define DEBUG_FILENAME "debug_kernel"
 
 // Define Traceback Pointer Navigation Direction
 #define TB_PH (tbp_t) 0b0000

testbench/test_csim_viterbi.cpp

@@ -25,29 +25,32 @@ struct Penalties_sol {
     double log_1_m_mu;
     double transition[5][5];
 };
-/*
-Query    : TTACTATTAATGCAAATGCACCTGATGGACGTATCGCAAATGCGTAACTCCCTCCGGTGTAACTAATAAAAGACTCTACGATAAAGGAACTACAGCGGGAACCGTCCGCTCTTTCGCGGATTCAGAGGCGCCACATGGGATCCAGGAAAAAGGTCAGGTAACGAGGAAAAATTTTGAAATTGGGAGATTCAGTTGTCTATGAAGCAAATGGCATAGCATCGTCCACATATACAATGAATC
-Reference: CCCTGGCAGTCTGCCCAAACTGCTAGCCCGATTATTTCGAAAGCTCACCCAGTGTCGGGGGATCGTTGAGGCAGCGCAACCAATTTGCAAATGTCGTAAAAACCTTAACACGGCTCTCCATAAGTGGTATGGTCCGGGTCCGGTATGCTGGACGGAGGCGGATGCACCCACGGTGGCACTACAACCCTGTTGGTTATATGGAGCTGATTAAAGGAGCGCACCATACAACCATCCCGACAGGGTCAGCCGCCTCG
-Solution Aligned Query    : ______________________________________________________________________________________________________________________________________________TTACTATTAATGCAAATGCACCTGATGGACGTATCGCAAATGCGTAACTCCCTCCGGTGTAACTAATAAAAGACTCTACGATAAAGGAACTACAGCGGGAACCGTCCGCTCTTTCGCGGATTCAGAGGCGCCACATGGGATCCAGGAAAAAGGTCAGGTAACGAGGAAAAATTTTGAAATTGGGAGATTCAGTTGTCTATGAAGCAAATGGCATAGCATCGTCCACATATACAATGAATC
-Solution Aligned Reference: CCCTGGCAGTCTGCCCAAACTGCTAGCCCGATTATTTCGAAAGCTCACCCAGTGTCGGGGGATCGTTGAGGCAGCGCAACCAATTTGCAAATGTCGTAAAAACCTTAACACGGCTCTCCATAAGTGGTATGGTCCGGGTCCGGT___A__________TGC___TG___GACGGA_______G_GC__________GGATGCACCCA________C_____GGTG___GCACTACA______AC_C___C_TGT_TG____GTTATA_TGGAGC__T_G__ATTA_A___A__GGA__GCGCACCA_______T___ACA_________ACCAT________CCCGACA_GGGTCA_GC______CGCCT_______CG___
-*/
 
-#define MU 0.4
-#define LAMBDA 0.4
+
+#define MU 0.6321
+#define LAMBDA 0.1353
 
 int main(){
-    // std::string query_string = "AGTCTG";     // CCGTAGACCCGAACTTCGCGGTACACCTTCTGAAACCGTCCCTAATCCGACGAGCGCCTTGAGAACG";
-    // std::string reference_string = "TGCCGAT";       // TGAGAACGTAGTCTAGGCGAATCGGCCCTTGTATATCGGGGCCGTAGACCCGAACTTCGCGGTACAC";
+    std::string query_string = "CCGTAGACCCGAACTTCGCGGTACACCTTCTGAAACCGTCCCTAATCCGACGAGCGCCTTGAGAACG";
+    std::string reference_string = "TGAGAACGTAGTCTAGGCGAATCGGCCCTTGTATATCGGGGCCGTAGACCCGAACTTCGCGGTACAC";
     char alphabet[4] = {'A', 'T', 'G', 'C'};
-    std::string query_string = Random::Sequence<4>(alphabet, INPUT_QUERY_LENGTH);
-    std::string reference_string = Random::Sequence<4>(alphabet, INPUT_REFERENCE_LENGTH);
+    // std::string query_string = Random::Sequence<4>(alphabet, INPUT_QUERY_LENGTH);
+    // std::string reference_string = Random::Sequence<4>(alphabet, INPUT_REFERENCE_LENGTH);
+
+    // float transition_[5][5] = {
+    //     {0.8, 0.3, 0.3, 0.3, 0.2},
+    //     {0.3, 0.8, 0.3, 0.3, 0.2},
+    //     {0.3, 0.3, 0.8, 0.3, 0.2},
+    //     {0.3, 0.3, 0.3, 0.8, 0.2},
+    //     {0.2, 0.2, 0.2, 0.2, 0.2}
+    // };
 
     float transition_[5][5] = {
-        {0.8, 0.3, 0.3, 0.3, 0.2},
-        {0.3, 0.8, 0.3, 0.3, 0.2},
-        {0.3, 0.3, 0.8, 0.3, 0.2},
-        {0.3, 0.3, 0.3, 0.8, 0.2},
-        {0.2, 0.2, 0.2, 0.2, 0.2}
+        {20.08, 0.1353, 0.1353, 0.1353, 0.3678},
+        {0.1353, 20.08, 0.1353, 0.1353, 0.3678},
+        {0.1353, 0.1353, 20.08, 0.1353, 0.3678},
+        {0.1353, 0.1353, 0.1353, 20.08, 0.3678},
+        {0.3678, 0.3678, 0.3678, 0.3678, 0.3678}
     };
 
     float log_transitions_[5][5];