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Current design causes II violation in banding kernel under 250MHz. Lo…
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…sen it to 200MHz resolve the issue.
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@ioeddk
ioeddk committed May 21, 2024
1 parent 1dd2dc5 commit 6259c85
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Showing 4 changed files with 41 additions and 36 deletions.
14 changes: 7 additions & 7 deletions kernels/banding_global_linear/params.h
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Expand Up @@ -4,20 +4,20 @@
#include <ap_fixed.h>
#include <hls_vector.h>

#define MAX_QUERY_LENGTH 16
#define MAX_REFERENCE_LENGTH 16
#define MAX_QUERY_LENGTH 256
#define MAX_REFERENCE_LENGTH 256

#define INPUT_QUERY_LENGTH 14
#define INPUT_REFERENCE_LENGTH 15
#define INPUT_QUERY_LENGTH 256
#define INPUT_REFERENCE_LENGTH 256

#define ALIGN_TYPE BandingGlobalLinear
#define N_BLOCKS 1
#define N_LAYERS 1
const int PE_NUM = 4;
const int PE_NUM = 5;
#define LAYER_MAXIMIUM 0 // We need to indicate from which layer (main matrix) is the maximum score stored.

#define BANDING FIXED
#define BANDWIDTH 3
#define BANDWIDTH 64

// Primitive Types
typedef ap_uint<2> char_t; // Sequence Alphabet
Expand All @@ -39,7 +39,7 @@ typedef ap_uint<2> tbp_t; // Traceback Pointer Type
#define TB_UP (tbp_t) 0b11

// Legacy Debugger Configuration
#define DEBUG_OUTPUT_FILE "/home/centos/workspace/banding/DP-HLS/banding_global_linear_out.txt"
#define DEBUG_OUTPUT_FILE "/home/centos/workspace/DP-HLS/banding_global_linear_out.txt"

struct Penalties {
type_t mismatch;
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54 changes: 27 additions & 27 deletions src/align.cpp
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Expand Up @@ -541,15 +541,15 @@ void Align::Fixed::AlignStatic(

#ifdef CMAKEDEBUG
// print l_lims and u_lims
std::cout << "Lower limits: ";
for (int j = 0; j < MAX_QUERY_LENGTH; j++) {
std::cout << l_lims[j] << " ";
}
std::cout << endl << "Upper limits: ";
for (int j = 0; j < MAX_QUERY_LENGTH; j++) {
std::cout << u_lims[j] << " ";
}
std::cout << endl;
// std::cout << "Lower limits: ";
// for (int j = 0; j < MAX_QUERY_LENGTH; j++) {
// std::cout << l_lims[j] << " ";
// }
// std::cout << endl << "Upper limits: ";
// for (int j = 0; j < MAX_QUERY_LENGTH; j++) {
// std::cout << u_lims[j] << " ";
// }
// std::cout << endl;
#endif

// Declare and initialize maximum scores.
Expand Down Expand Up @@ -656,17 +656,17 @@ void Align::Fixed::ChunkCompute(
){

#ifdef CMAKEDEBUG
std::cout << "Started Chunk: " << ck_idx << std::endl;
// print local l lim and local u lim
std::cout << "Local Lower limits: ";
for (int j = 0; j < PE_NUM; j++) {
std::cout << local_l_lim[j] << " ";
}
std::cout << endl << "Local Upper limits: ";
for (int j = 0; j < PE_NUM; j++) {
std::cout << local_u_lim[j] << " ";
}
std::cout << endl;
// std::cout << "Started Chunk: " << ck_idx << std::endl;
// // print local l lim and local u lim
// std::cout << "Local Lower limits: ";
// for (int j = 0; j < PE_NUM; j++) {
// std::cout << local_l_lim[j] << " ";
// }
// std::cout << endl << "Local Upper limits: ";
// for (int j = 0; j < PE_NUM; j++) {
// std::cout << local_u_lim[j] << " ";
// }
// std::cout << endl;
#endif

bool predicate[PE_NUM];
Expand All @@ -688,7 +688,7 @@ void Align::Fixed::ChunkCompute(
const idx_t chunk_end_col = local_u_lim[PE_NUM - 1];

// Set the upper left corner cell of the chunk, depending whether it's the first chunk.
dp_mem[0][0] = local_l_lim[0] > 0 ? init_row_scr[local_l_lim[0]-1] : init_col_scr[0];
dp_mem[0][0] = local_l_lim[0] > 0 ? init_row_scr[chunk_start_col-1] : init_col_scr[0];

Iterating_Wavefronts:
for (int i = chunk_start_col; i < chunk_end_col + PE_NUM; i++)
Expand All @@ -709,12 +709,12 @@ void Align::Fixed::ChunkCompute(
Align::Fixed::MapPredicate(local_l_lim, local_u_lim, i, col_pred, predicate);
#ifdef CMAKEDEBUG
// print predicate
std::cout << "Predicate: ";
for (int j = 0; j < PE_NUM; j++)
{
std::cout << predicate[j];
}
std::cout << endl;
// std::cout << "Predicate: ";
// for (int j = 0; j < PE_NUM; j++)
// {
// std::cout << predicate[j];
// }
// std::cout << endl;
#endif

// Align::ShiftReference(local_reference, reference, i, chunk_end_col);
Expand Down
3 changes: 2 additions & 1 deletion src/pe.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,7 @@ void PE::PEUnrollFixedSep(
for (int i = 0; i < PE_NUM; i++)
{
#pragma HLS unroll
// FIXME: I can probably fuse the predicate and feeding NINF logic here.
ALIGN_TYPE::PE::Compute(
qry[i],
ref[i],
Expand All @@ -108,6 +109,6 @@ void PE::PEUnrollFixedSep(
#endif
}
#ifdef CMAKEDEBUG
printf("\n");
// printf("\n");
#endif
}
6 changes: 5 additions & 1 deletion testbench/test_csim_banding_global_linear.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,9 @@
#include "solutions.h"
#include "debug.h"

#define INPUT_QUERY_LENGTH 256
#define INPUT_REFERENCE_LENGTH 256

using namespace std;

char tbp_to_char(tbp_t tbp){
Expand Down Expand Up @@ -201,10 +204,11 @@ int main(){

// print out the scores
// print_matrix<float, MAX_QUERY_LENGTH, MAX_REFERENCE_LENGTH>(scores_sol[k], "Solution Score Matrix, Layer: " + std::to_string(k));
#ifdef CMAKEDEBUG
fprint_matrix<float, MAX_QUERY_LENGTH, MAX_REFERENCE_LENGTH>(debug_file, sol_score_mat[0], query_string, reference_string, "Solution Score Matrix, Layer: " + std::to_string(0));
fprint_matrix<float, MAX_QUERY_LENGTH, MAX_REFERENCE_LENGTH>(debug_file, debuggers->scores_cpp[0], query_string, reference_string, "Kernel Score Matrix, Layer: " + std::to_string(0));
// print traceback pointer matrices
fprint_matrix<char, MAX_QUERY_LENGTH, MAX_REFERENCE_LENGTH>(debug_file, sol_tb_mat, "Solution Traceback Matrix, Layer: " + std::to_string(0));
#endif
return 0;
}

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