bwa 线程数目对比对速度的影响

 

001、测试条件

 

(base) [b20223040323@admin1 batch_test]$ ls
SRR10083583_trim_1P.fastq.gz  SRR10083583_trim_2P.fastq.gz  template.slurm
(base) [b20223040323@admin1 batch_test]$ cat template.slurm
#!/bin/bash
#SBATCH   -J xxxx
#SBATCH   -p Cnode2
#SBATCH   -N 1
#SBATCH   -n xxxx
#SBATCH --cpus-per-task=1

STIME=`date +%s`
bwa mem -t xxxx -k 32 -M -R "@RG\tID:SRR1008358301\tSM:SRR1008358301\tPL:illumina\tLB:SRR1008358301\tPU:SRR1008358301" /public/home/b20223040323/003_goat_pan_second/003_goat_reference/GCF_001704415.2_ARS1.2_genomic.fna SRR10083583_trim_1P.fastq.gz SRR10083583_trim_2P.fastq.gz > xxxx.sam
let ETIME=`date +%s`-$STIME
echo thread xxxx Elapsed time: $ETIME s > xxxx.time
(base) [b20223040323@admin1 batch_test]$ for i in 4 16 32 64; do sed "s/xxxx/$i/g" template.slurm > $i.slurm; done
(base) [b20223040323@admin1 batch_test]$ ls
16.slurm  32.slurm  4.slurm  64.slurm  SRR10083583_trim_1P.fastq.gz  SRR10083583_trim_2P.fastq.gz  template.slurm
(base) [b20223040323@admin1 batch_test]$ find *.slurm | grep -v "template.slurm" | xargs -n 1 sbatch
Submitted batch job 396059
Submitted batch job 396060
Submitted batch job 396061
Submitted batch job 396062

 

 

002、测试结果

(base) [b20223040323@admin1 batch_test]$ cat 4.time 16.time 32.time 64.time     ## 查看运行时间
thread 4 Elapsed time: 10086 s
thread 16 Elapsed time: 1514 s
thread 32 Elapsed time: 744 s
thread 64 Elapsed time: 393 s

 

003、结论

线程数越多，运行速度越快。

。