shorter run time because of Crystal V1.2.1 Release
orangeSi opened this issue · 0 comments
orangeSi commented
Crystal lang had release V1.2.1 recently，so I tested fqcnt_cr1_klib.cr and bedcov_cr1_klib.cr(with nothing modify these two files) in my computer below showed:
For fqcnt: the run time of plain txt is from 1.5s to 0.9s！But the time of gzip file is still 9s. For bedcov: g2r cost 6.9s instead of 8.8s, r2g cost 10.8s instead of 14.8s!
Above shorter runtime maybe because of computer hardware difference OR Crystal version difference, so I rerun with biofast-bin-20200520-a7af6d8.tar.bz2 in my computer:
## fqcnt
$ hyperfine --warmup 3 ' ../biofast-bin-20200520-a7af6d8/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq'
Benchmark 1: ../biofast-bin-20200520-a7af6d8/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq
Time (mean ± σ): 891.0 ms ± 49.2 ms [User: 649.7 ms, System: 213.5 ms]
Range (min … max): 864.6 ms … 1028.0 ms 10 runs
$ hyperfine --warmup 3 ' ../biofast-bin-20200520-a7af6d8/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq.gz'
Benchmark 1: ../biofast-bin-20200520-a7af6d8/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq.gz
Time (mean ± σ): 8.938 s ± 0.042 s [User: 8.719 s, System: 0.096 s]
Range (min … max): 8.894 s … 9.041 s 10 runs
## bedcov
$ hyperfine --warmup 3 ' ../biofast-bin-20200520-a7af6d8/bedcov/bedcov_cr1_klib ex-rna.bed ex-anno.bed # g2r'
Benchmark 1: ../biofast-bin-20200520-a7af6d8/bedcov/bedcov_cr1_klib ex-rna.bed ex-anno.bed # g2r
Time (mean ± σ): 7.927 s ± 0.034 s [User: 7.272 s, System: 0.525 s]
Range (min … max): 7.878 s … 7.976 s 10 runs
$ hyperfine --warmup 3 ' ../biofast-bin-20200520-a7af6d8/bedcov/bedcov_cr1_klib ex-anno.bed ex-rna.bed # r2g'
Benchmark 1: ../biofast-bin-20200520-a7af6d8/bedcov/bedcov_cr1_klib ex-anno.bed ex-rna.bed # r2g
Time (mean ± σ): 17.731 s ± 0.069 s [User: 14.906 s, System: 2.579 s]
Range (min … max): 17.632 s … 17.810 s 10 runs
So with the latest Crystal V1.2.1(take the computer hardware difference into consideration):
For fqcnt, cost more a little time.
For bedcov, cost less a little time(especially for r2g).
Detail as below:
system and crystal version
$ lscpu|grep -E 'Model name|CPU family'
CPU family: 6
Model name: Intel(R) Xeon(R) Gold 6133 CPU @ 2.50GHz
$ cat /etc/os-release |grep PRETTY_NAME
PRETTY_NAME="Ubuntu 18.04.6 LTS"
$ crystal -v
Crystal 1.2.1 [4e6c0f26e] (2021-10-21)
LLVM: 10.0.0
$ git clone https://github.com/lh3/biofast.git
fqcnt with Crystal 1.2.1
$ crystal build fqcnt_cr1_klib.cr --release
$ ll biofast-data-v1/*fq
-rw-rw-r-- 1 ubuntu ubuntu 1396487030 Oct 23 10:50 biofast-data-v1/M_abscessus_HiSeq.fq
$ hyperfine --warmup 3 '~/biofast/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq'
Benchmark 1: ~/biofast/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq
Time (mean ± σ): 968.0 ms ± 8.0 ms [User: 743.2 ms, System: 206.8 ms]
Range (min … max): 960.7 ms … 981.4 ms 10 runs
# update LLVM from V10 to V12 and then recompile fqcnt_cr1_klib.cr
$ crystal_llvm12 build fqcnt_cr1_klib.cr -o fqcnt_cr1_klib_llvm12 --release
$ hyperfine --warmup 3 '~/biofast/fqcnt/fqcnt_cr1_klib_llvm12 biofast-data-v1/M_abscessus_HiSeq.fq'
Benchmark 1: ~/biofast/fqcnt/fqcnt_cr1_klib_llvm12 biofast-data-v1/M_abscessus_HiSeq.fq
Time (mean ± σ): 931.0 ms ± 6.0 ms [User: 716.9 ms, System: 197.2 ms]
Range (min … max): 923.5 ms … 940.3 ms 10 runs
$ gzip biofast-data-v1/M_abscessus_HiSeq.fq
$ ll -sh biofast-data-v1/*gz
465M -rw-r--r-- 1 ubuntu ubuntu 465M May 4 2020 biofast-data-v1/M_abscessus_HiSeq.fq.gz
$ hyperfine --warmup 3 '~/biofast/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq.gz'
Benchmark 1: ~/biofast/fqcnt/fqcnt_cr1_klib biofast-data-v1/M_abscessus_HiSeq.fq.gz
Time (mean ± σ): 9.100 s ± 0.068 s [User: 8.853 s, System: 0.107 s]
Range (min … max): 9.030 s … 9.259 s 10 runs
$ hyperfine --warmup 3 '~/biofast/fqcnt/fqcnt_cr1_klib_llvm12 biofast-data-v1/M_abscessus_HiSeq.fq.gz'
Benchmark 1: ~/biofast/fqcnt/fqcnt_cr1_klib_llvm12 biofast-data-v1/M_abscessus_HiSeq.fq.gz
Time (mean ± σ): 9.082 s ± 0.023 s [User: 8.848 s, System: 0.099 s]
Range (min … max): 9.046 s … 9.119 s 10 runs
bedcov with Crystal 1.2.1
$ hyperfine --warmup 3 './bedcov_cr1_klib ex-rna.bed ex-anno.bed # g2r'
Benchmark 1: ./bedcov_cr1_klib ex-rna.bed ex-anno.bed # g2r
Time (mean ± σ): 6.921 s ± 0.023 s [User: 6.587 s, System: 0.222 s]
Range (min … max): 6.887 s … 6.954 s 10 runs
$ hyperfine --warmup 3 './bedcov_cr1_klib_llvm12 ex-rna.bed ex-anno.bed # g2r'
Benchmark 1: ./bedcov_cr1_klib_llvm12 ex-rna.bed ex-anno.bed # g2r
Time (mean ± σ): 6.827 s ± 0.047 s [User: 6.501 s, System: 0.216 s]
Range (min … max): 6.756 s … 6.943 s 10 runs
$ hyperfine --warmup 3 './bedcov_cr1_klib ex-anno.bed ex-rna.bed # r2g'
Benchmark 1: ./bedcov_cr1_klib ex-anno.bed ex-rna.bed # r2g
Time (mean ± σ): 10.846 s ± 0.067 s [User: 10.524 s, System: 0.139 s]
Range (min … max): 10.739 s … 10.956 s 10 runs
$ hyperfine --warmup 3 './bedcov_cr1_klib_llvm12 ex-anno.bed ex-rna.bed # r2g'
Benchmark 1: ./bedcov_cr1_klib_llvm12 ex-anno.bed ex-rna.bed # r2g
Time (mean ± σ): 10.637 s ± 0.166 s [User: 10.339 s, System: 0.138 s]
Range (min … max): 10.498 s … 11.079 s 10 runs