From subsecret
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==Results== | ==Results== | ||
{| class="wikitable" | {| class="wikitable sortable" | ||
!Device | !Device | ||
!ARCH | !ARCH | ||
| Line 28: | Line 28: | ||
!OS | !OS | ||
!GCC | !GCC | ||
!1 thread walltime | !1 thread walltime (sec.) | ||
!4 thread walltime | !4 thread walltime (sec.) | ||
|- | |- | ||
|PC (i7-6700k@4.5 GHz) | |PC (i7-6700k@4.5 GHz) | ||
| Line 36: | Line 36: | ||
|Fedora 24 | |Fedora 24 | ||
|6.1.1 | |6.1.1 | ||
| 144.221 | |144.221 | ||
| 53.833 | |53.833 | ||
|- | |- | ||
|PC (i7-6700k@4.5 GHz) | |PC (i7-6700k@4.5 GHz) | ||
| Line 44: | Line 44: | ||
|Fedora 24 | |Fedora 24 | ||
|6.1.1 | |6.1.1 | ||
|77.836 | |77.836 | ||
|27.840 | |27.840 | ||
|- | |- | ||
|ODROID U2 | |ODROID U2 | ||
| Line 52: | Line 52: | ||
|Ubuntu 14.04.4 LTS | |Ubuntu 14.04.4 LTS | ||
|4.8.4 | |4.8.4 | ||
|939.300 | |939.300 | ||
|266.262 | |266.262 | ||
|- | |- | ||
|ODROID C2 | |ODROID C2 | ||
| Line 60: | Line 60: | ||
|Ubuntu 16.04 LTS | |Ubuntu 16.04 LTS | ||
|5.4.0 | |5.4.0 | ||
|797.158 | |797.158 | ||
|235.510 | |235.510 | ||
|- | |- | ||
|Raspberry Pi 3 | |Raspberry Pi 3 | ||
| Line 68: | Line 68: | ||
|Fedora 24 | |Fedora 24 | ||
|6.1.1 | |6.1.1 | ||
|1521.175 | |1521.175 | ||
|486.585 | |486.585 | ||
|- | |- | ||
|Raspberry Pi 3 | |Raspberry Pi 3 | ||
| Line 76: | Line 76: | ||
|Fedora 24 | |Fedora 24 | ||
|6.1.1 | |6.1.1 | ||
|2172.660 | |2172.660 | ||
|649.805 | |649.805 | ||
|- | |- | ||
|Raspberry Pi 3 | |Raspberry Pi 3 | ||
| Line 84: | Line 84: | ||
|Raspbian Jessie | |Raspbian Jessie | ||
|4.9.2 | |4.9.2 | ||
|1224.290 | |1224.290 | ||
|355.897 | |355.897 | ||
|} | |} | ||
Revision as of 14:03, 3 August 2016
BWA Benchmark
BWA is a tool for mapping reads against a genome. This is nice for doing a non-synthetic benchmark, as meaningful work is done, and IO, Memory and CPU is all used.
BWA Setup instructions
- Retrieve https://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
- Patch the Makefile:
- Add to DFLAGS: -std=gnu90 -D_NO_SSE2
- Compile BWA with command: make
- Patch the Makefile:
- Retrieve ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
- Retrieve https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m-trim.fastq.gz
- Run gunzip GCF_000005845.2_ASM584v2_genomic.fna.gz
- Run gunzip ecoli_ref-5m-trim.fastq.gz
- Run bwa index GCF_000005845.2_ASM584v2_genomic.fna
Running Benchmark
Benchmark command
- 1 thread
- bwa aln GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
- 4 threads
- bwa aln -t4 GCF_000005845.2_ASM584v2_genomic.fna ecoli_ref-5m-trim.fastq > /dev/null
Results
| Device | ARCH | Kernel | OS | GCC | 1 thread walltime (sec.) | 4 thread walltime (sec.) |
|---|---|---|---|---|---|---|
| PC (i7-6700k@4.5 GHz) | x86 | 4.6.4-301.fc24.x86_64 | Fedora 24 | 6.1.1 | 144.221 | 53.833 |
| PC (i7-6700k@4.5 GHz) | x64 | 4.6.4-301.fc24.x86_64 | Fedora 24 | 6.1.1 | 77.836 | 27.840 |
| ODROID U2 | armhf | 3.8.13.30 | Ubuntu 14.04.4 LTS | 4.8.4 | 939.300 | 266.262 |
| ODROID C2 | aarch64 | 3.14.65-73 | Ubuntu 16.04 LTS | 5.4.0 | 797.158 | 235.510 |
| Raspberry Pi 3 | aarch64 | 4.6.4-1-main | Fedora 24 | 6.1.1 | 1521.175 | 486.585 |
| Raspberry Pi 3 | armhf | 4.6.4-1-main | Fedora 24 | 6.1.1 | 2172.660 | 649.805 |
| Raspberry Pi 3 | armhf | 4.4.13-v7+ | Raspbian Jessie | 4.9.2 | 1224.290 | 355.897 |
