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DNASequence
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Zengtudor 2024-09-20 10:39:14 +08:00
parent 37d12043d2
commit b3e037bf1b
2 changed files with 33 additions and 13 deletions
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41
README.md
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@ -69,23 +69,44 @@ xmake project -k vsxmake
> perf > perf
``` ```
Samples: 31K of event 'task-clock:ppp', Event count (approx.): 7866750000 31.88% test test [.] reverseComplement(char*, char*) [clone ._omp_fn.1]
Overhead Command Shared Object Symbol 10.27% test [unknown] [k] 0xffffffffc06abd30
90.39% test [unknown] [k] 0xffffffffa84435e1 7.32% test libgomp.so.1.0.0 [.] 0x0000000000024c6a
5.48% test test [.] reverseComplement(std::array<char, 50005ul>&, unsigned long) 4.39% test [unknown] [k] 0xffffffffa84435e1
1.58% test [unknown] [k] 0xffffffffc06abd30 3.32% test libgomp.so.1.0.0 [.] 0x0000000000024ab2
0.59% test [unknown] [k] 0xffffffffa83ab787 3.20% test [unknown] [k] 0xffffffffa8443ee5
0.51% test [unknown] [k] 0xffffffffa842aee0 2.35% test [unknown] [k] 0xffffffffa72d138b
2.30% test [unknown] [k] 0xffffffffa7309ed4
1.98% test [unknown] [k] 0xffffffffa7a5ba37
1.74% test [unknown] [k] 0xffffffffa760ecee
1.63% test test [.] reverseComplement(char*, char*) [clone ._omp_fn.0]
1.48% test [unknown] [k] 0xffffffffa83ab787
1.32% test [unknown] [k] 0xffffffffa842aee0
1.31% test [unknown] [k] 0xffffffffa766d76a
0.83% test [unknown] [k] 0xffffffffa7a5ad88
0.80% test libc.so.6 [.] __memset_evex_unaligned_erms
0.55% test [unknown] [k] 0xffffffffa766d747
0.47% test [unknown] [k] 0xffffffffa76c08f8
``` ```
> 800MB fastq DNA 序列处理性能展示 > 800MB fastq DNA 序列处理性能展示
``` ```
[Timer: All spent] Start timing
Open input file stream to value [input_file_stream] ok , from ["filteredReads.txt"] Open input file stream to value [input_file_stream] ok , from ["filteredReads.txt"]
Open output file stream to value [output_file_stream] ok , from ["reversedSequence.txt"] Open output file stream to value [output_file_stream] ok , from ["reversedSequence.txt"]
Undergoing transformation Chunk size :4294967296 bytes
[Timer: All spent] Stop timing , using 5960ms [Timer: All spent] Start timing
[Timer: chunk_id:[1]] Start timing
[Timer: read_chunk_id:[1]] Start timing
[Timer: read_chunk_id:[1]] Stop timing , used 1102ms
buf_len : 897963094
[Timer: calculate_chunk_id:[1]] Start timing
omp_get_num_threads() : 12
[Timer: calculate_chunk_id:[1]] Stop timing , used 463ms
[Timer: write_chunk_id:[1] , [Wrote bytes] start_pos : 897963094] Start timing
[Timer: write_chunk_id:[1] , [Wrote bytes] start_pos : 897963094] Stop timing , used 1287ms
[Timer: chunk_id:[1]] Stop timing , used 2854ms
[Timer: All spent] Stop timing , used 2855ms
``` ```
## 关于版权 ## 关于版权

5
xmake.lua
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@ -6,11 +6,10 @@ if is_mode("release")then
-- set_optimize("fastest") --上面和下面的二选一，--表示注释 -- set_optimize("fastest") --上面和下面的二选一，--表示注释
if is_plat("windows")then if is_plat("windows")then
-- 注意，下面是启用AVX512指令集矢量化加速，只有新2010年后的CPU支持，但是可以大大加快批量指令加速，可以试试将下面的--删除 -- 矢量化加速似乎没用
-- 但是似乎这个程序目前任然是IO密集型，性能差不多，目前注释掉了
-- add_cxxflags("/arch:AVX512") -- add_cxxflags("/arch:AVX512")
elseif is_plat("linux") or is_plat("mingw") or is_plat("clang")then elseif is_plat("linux") or is_plat("mingw") or is_plat("clang")then
-- 启用AVX512指令集矢量化加速，可能会导致无法在除了编译本程序的电脑上运行，出现兼容问题 -- 矢量化加速似乎没用
-- add_cxxflags("-march=native") -- add_cxxflags("-march=native")
end end
end end