From 0708dd081c5352e065adacc47ed3ca4e04ed4db0 Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Wed, 27 Jul 2022 14:46:29 +0200 Subject: [PATCH 1/7] fix gitignore to remove vscode --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index edca7c8..6669343 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ **/out **/build +.vscode/* \ No newline at end of file From ed627243d70bb2c876c47f12c0faa6363df92124 Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Wed, 27 Jul 2022 14:48:51 +0200 Subject: [PATCH 2/7] added generate data script and binary --- .gitignore | 4 +++- Datasets/bin/generate_dataset | Bin 0 -> 30920 bytes Datasets/generatedata.sh | 15 +++++++++++++++ 3 files changed, 18 insertions(+), 1 deletion(-) create mode 100755 Datasets/bin/generate_dataset create mode 100755 Datasets/generatedata.sh diff --git a/.gitignore b/.gitignore index 6669343..c56ac81 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ **/out **/build -.vscode/* \ 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zc{9L9e~^a%y_vLsM8?>MlKR(f2E@rh`sS2W+7Qj=>+b_AxXc^h(Sh}HI@=S>%X{1l(AydXNJz|^8+0+AFHFrFY%g>NkH(Pk0HN6 z$jjVgW(JHs=PAd0U}pJ7Ausci6mGibNIhyS^74LM=AKmcLGqWQ9G|D7*Aw|6@7rZA z>&ISVepu}ffQp^RM*HRWFJxXR6jK|?cT!$nkA^{`Cd>Nea{!r_SR8Ia*%u*8-=>iA z@_B*G%TZ2;v|sYc954Sd`qqWS<#Pp@*KujRkIeQ9GV1|AeIn)M^9Pxq6pXTdYy0mI z^2-IEd`=BC-vb)4Nd0uF$PbZQ@4T(?a{$a{d5@5jd9J8mXtk}`-; zNMhPCo*T)(+i2yNxXeF-EZ#FRBo6N=`ku z%Fi1@zN$*+pC}z8)L7+L3?Uz^)&;IKCbsnTuNU%G|2;|%&~V(Y>AC!s^~?NsB4};k8maN|5Fu$+(s0Pb#*!7!>?{ dIy$l9D76HjwSJmz)5#y};NmQ95wM`_{{WX6#cluq literal 0 HcmV?d00001 diff --git a/Datasets/generatedata.sh b/Datasets/generatedata.sh new file mode 100755 index 0000000..7c93bf9 --- /dev/null +++ b/Datasets/generatedata.sh @@ -0,0 +1,15 @@ +#! /usr/bin/bash + +set -x + +seqLengths=("100" "1000" "5000" "10000" "20000" "25000" "50000" "100000") + +for seqLength in ${seqLengths[@]}; do + ./bin/generate_dataset --n 100000 -l $seqLength --e 0.01 --o ./const-seq/seq-l$seqLength-e1-100KPairs +done + +for seqLength in ${seqLengths[@]}; do + ./bin/generate_dataset --n 100000 -l $seqLength --e 0.05 --o ./const-seq/seq-l$seqLength-e5-100KPairs +done + +echo "finished generating data" From c803cfe470e9142db40838b1472ea4d9117809bc Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Wed, 27 Jul 2022 14:56:49 +0200 Subject: [PATCH 3/7] fix gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index c56ac81..2911001 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ **/out +**/dpu-out **/build .vscode/* Datasets/const-seq/* From 379b1d1e680eb55d45dbece161a779bb353aa77c Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Wed, 27 Jul 2022 15:30:52 +0200 Subject: [PATCH 4/7] in no backtrace mode, no need to allocate cigar --- WFA/DPU-MRAM/host/host.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/WFA/DPU-MRAM/host/host.c b/WFA/DPU-MRAM/host/host.c index 3d3526d..e04f572 100644 --- a/WFA/DPU-MRAM/host/host.c +++ b/WFA/DPU-MRAM/host/host.c @@ -338,13 +338,13 @@ int main(int argc, char *argv[]) for (i = 0; i < dpuParams[dpu].dpuNumReads; ++i) { fprintf(output_file, "%d, %d, \n", dpuResults[dpu][i].idx, dpuResults[dpu][i].score); + +#ifdef BACKTRACE edit_cigar_t cigar; cigar.score = dpuResults[dpu][i].score; cigar.max_operations = dpuResults[dpu][i].max_operations; cigar.begin_offset = dpuResults[dpu][i].begin_offset; cigar.end_offset = dpuResults[dpu][i].end_offset; - -#ifdef BACKTRACE cigar.operations = (char *)malloc(ROUND_UP_MULTIPLE_8(cigar.max_operations)); strncpy(cigar.operations, &(operations[i * 2 * READ_SIZE]), ROUND_UP_MULTIPLE_8(cigar.max_operations)); edit_cigar_print(&cigar, output_file); From ab83761790e78d448e834e28380d39667fad6269 Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Wed, 27 Jul 2022 15:38:23 +0200 Subject: [PATCH 5/7] fixed generatedata --- .gitignore | 3 ++- Datasets/generatedata.sh | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 2911001..4e1b0f4 100644 --- a/.gitignore +++ b/.gitignore @@ -3,4 +3,5 @@ **/build .vscode/* Datasets/const-seq/* -Datasets/var-seq/* \ No newline at end of file +Datasets/var-seq/* +Datasets/bin/* \ No newline at end of file diff --git a/Datasets/generatedata.sh b/Datasets/generatedata.sh index 7c93bf9..44336ee 100755 --- a/Datasets/generatedata.sh +++ b/Datasets/generatedata.sh @@ -1,5 +1,7 @@ #! /usr/bin/bash +# make sure Datasets/bin/generate_dataset exists (https://github.com/smarco/WFA) + set -x seqLengths=("100" "1000" "5000" "10000" "20000" "25000" "50000" "100000") From f4d934aea3ea52e5e4296ab3a981d533042787e6 Mon Sep 17 00:00:00 2001 From: Steven Yu Date: Wed, 27 Jul 2022 15:39:33 +0200 Subject: [PATCH 6/7] Delete Datasets/bin directory --- Datasets/bin/generate_dataset | Bin 30920 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100755 Datasets/bin/generate_dataset diff --git a/Datasets/bin/generate_dataset b/Datasets/bin/generate_dataset deleted file 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z>&ISVepu}ffQp^RM*HRWFJxXR6jK|?cT!$nkA^{`Cd>Nea{!r_SR8Ia*%u*8-=>iA z@_B*G%TZ2;v|sYc954Sd`qqWS<#Pp@*KujRkIeQ9GV1|AeIn)M^9Pxq6pXTdYy0mI z^2-IEd`=BC-vb)4Nd0uF$PbZQ@4T(?a{$a{d5@5jd9J8mXtk}`-; zNMhPCo*T)(+i2yNxXeF-EZ#FRBo6N=`ku z%Fi1@zN$*+pC}z8)L7+L3?Uz^)&;IKCbsnTuNU%G|2;|%&~V(Y>AC!s^~?NsB4};k8maN|5Fu$+(s0Pb#*!7!>?{ dIy$l9D76HjwSJmz)5#y};NmQ95wM`_{{WX6#cluq From 44e44bc72e7dfd9b568dd5f45cf669489f59cb91 Mon Sep 17 00:00:00 2001 From: stevenyuser Date: Thu, 11 Aug 2022 20:13:28 +0200 Subject: [PATCH 7/7] added wfa comments --- WFA/DPU-MRAM/dpu/wfa.c | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/WFA/DPU-MRAM/dpu/wfa.c b/WFA/DPU-MRAM/dpu/wfa.c index afe92f8..4e53e0c 100644 --- a/WFA/DPU-MRAM/dpu/wfa.c +++ b/WFA/DPU-MRAM/dpu/wfa.c @@ -140,16 +140,22 @@ void affine_wfa_reduce_wvs(wfa_component *wfa, awf_offset_t pattern_length, awf_ } } // insert new score +// change this function so it allocates using score % needed +// EDIT THIS FUNCTION!!!! wfa_component *allocate_new_score(dpu_alloc_wram_t *allocator, int score, int lo, int hi, int kernel, uint32_t *mramIdx, dpu_alloc_mram_t *dpu_alloc_mram) { int wv_len = hi - lo + 1; uint32_t cmpnt_size = 0; +// these two lines show that the size of the wfa_cmpnt is constant, but the size of the wfa cmpnt's offsets is not constant. wfa_component *wfa_cmpnt = (wfa_component *)allocate_new(allocator, sizeof(wfa_component)); awf_offset_t *offset_ptr = (awf_offset_t *)allocate_new(allocator, (wv_len * sizeof(awf_offset_t))); wfa_cmpnt->mwavefront = (awf_offset_t *)(offset_ptr - lo); cmpnt_size += ROUND_UP_MULTIPLE_8(wv_len * sizeof(awf_offset_t)); + // kernel = 3 means I and D + // kernel = 2 means I + // kernel = 1 means D if (kernel == 3 || kernel == 1) { @@ -281,6 +287,7 @@ wfa_component *affine_wfa_compute_next(int score, uint32_t *mramIdx, dpu_alloc_w int o_score = score - GAP_O - GAP_E; int e_score = score - GAP_E; +// edit here so it computes differently and loads mwaefront from score % something wfa_component *wfa_mismatch = (mismatch_score < 0 || mramIdx[mismatch_score] == 0) ? NULL : load_mwavefront_cmpnt_from_mram(alloc_obj, mramIdx[mismatch_score]); wfa_component *wfa_o_score = (o_score < 0 || mramIdx[o_score] == 0) ? NULL : load_mwavefront_cmpnt_from_mram(alloc_obj, mramIdx[o_score]); wfa_component *wfa_e_score = (e_score < 0 || mramIdx[e_score] == 0) ? NULL : load_idwavefront_cmpnt_from_mram(alloc_obj, mramIdx[e_score]);