Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/coasterfreakde/dna-kmer-speed-test

DNA Kmer speed test in different languagues
https://github.com/coasterfreakde/dna-kmer-speed-test

coding differences speed test

Last synced: about 2 months ago
JSON representation

DNA Kmer speed test in different languagues

Host: GitHub
URL: https://github.com/coasterfreakde/dna-kmer-speed-test
Owner: CoasterFreakDE
License: mit
Created: 2022-11-28T11:40:15.000Z (about 2 years ago)
Default Branch: main
Last Pushed: 2024-05-16T09:35:55.000Z (7 months ago)
Last Synced: 2024-05-16T10:42:53.569Z (7 months ago)
Topics: coding, differences, speed, test
Language: C
Homepage: https://towardsdatascience.com/how-fast-is-c-compared-to-python-978f18f474c7
Size: 110 KB
Stars: 4
Watchers: 1
Forks: 6
Open Issues: 8
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        ![1_-ttbjLpp9HMrpWdzSPckZQ](https://user-images.githubusercontent.com/28011628/204269417-e3068e15-e3f7-4cb1-9528-6df97f61ae25.png)

# DNA-Kmer-Speed-Test

DNA Kmer speed test in different languagues

In order to understand the background of this test, visit the original article here: https://towardsdatascience.com/how-fast-is-c-compared-to-python-978f18f474c7

### How to run the test

1. Clone the repository

2. Install the dependencies

3. Run `make LENGTH=11 -s` to run the test with kmer length 11

4. Or use `make LENGTH=13 LANGUAGES="go c cpp rust" -s` to run the test with kmer length 13 and only for the languages go, c, cpp and rust

### Or run the test with docker

1. Clone the repository

2. Install docker

3. Build a docker image using `docker build -t kmers .`

4. Run and connect to the container with `docker run --rm -it kmers`

5. Start the test with `./generate.sh 1 10 >> data.txt`

6. Read the results with `cat data.txt`

### Kmer - Operation Amount

| Kmer | Generated      |

| ---- | -------------- |

| 11   | 4.194.304      |

| 12   | 16.777.216     |

| 13   | 67.108.864     |

| 14   | 268.435.456    |

| 15   | 1.073.741.824  |

| 16   | 4.294.967.296  |

| 17   | 17.179.869.184 |

# Test Results

##### Automated test results

You can find the automated test results at https://github.com/CoasterFreakDE/DNA-Kmer-Speed-Test/actions

Note that the results are not 100% accurate, because the test is run on a shared server with other processes running in the background.

## Comparison of the languages

| Language   | Kmer 11 | Kmer 12 | Kmer 13 | Kmer 14 | Kmer 15  | Kmer 16 | Kmer 17  | (Optional) Runtime Env / OS     |

| ---------- | ------- | ------- | ------- | ------- | -------- | ------- | -------- | ------------------------------- |

| C          | 3ms     | 12ms    | 45ms    | 181ms   | 753ms    | 2.887s  | 12.926s  | Win11 / i9-12900KF              |

| C++        | 3ms     | 11ms    | 55ms    | 309ms   | 1.062s   | 4.149s  | 15.784s  | Win11 / i9-12900KF              |

| Rust       | 5ms     | 23ms    | 94ms    | 365ms   | 1.195s   | 4.499s  | 17.949s  | Win11 / i9-12900KF              |

| Go         | 13ms    | 53ms    | 213ms   | 835ms   | 3.553s   | 12.429s | 49.861s  | Win11 / i9-12900KF              |

| Java       | 17ms    | 50ms    | 158ms   | 599ms   | 2.703s   | /       | /        | Win11 / i9-12900KF              |

| JavaScript | 58ms    | 225ms   | 894ms   | 3.467s  | 14.543s  | /       | /        | Win11 / i9-12900KF              |

| C#         | 98ms    | 333ms   | 1.207s  | 4.588s  | 18.205s  | 72.196s | 265.764s | Win11 / i9-12900KF              |

| Swift      | 184ms   | 765ms   | 3.034s  | 12.73s  | 49.86s   | /       | /        | Win11 / i5-12400F               |

| Mojo       | 319ms   | 1.289s  | 5.090s  | 20.944s | 83.584s  | /       | /        | Win11 / i9-12900KF (WSL Ubuntu) |

| Erlang     | 375ms   | 1.607s  | 6.397s  | 25.117s | 105.529s | /       | /        | Win11 / i9-12900KF              |

| php        | 561ms   | 2.164s  | 8.892s  | 35.038s | 140.391s | /       | /        | Win11 / i9-12900KF              |

| Perl       | 643ms   | 2.568s  | 10.182s | 41.137s | 169.598s | /       | /        | Win11 / i9-12900KF              |

| Python     | 2.266s  | 8.850s  | 35.374s | 99.665s | 414.169s | /       | /        | Win11 / i9-12900KF              |

## Splitting the results into languages

### C

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.003s   | Win11 / i9-12900KF          |

| 12   | 0.012s   | Win11 / i9-12900KF          |

| 13   | 0.045s   | Win11 / i9-12900KF          |

| 14   | 0.181s   | Win11 / i9-12900KF          |

| 15   | 0.753s   | Win11 / i9-12900KF          |

| 16   | 2.887s   | Win11 / i9-12900KF          |

| 17   | 13.926s  | Win11 / i9-12900KF          |

### C++

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.003s   | Win11 / i9-12900KF          |

| 12   | 0.011s   | Win11 / i9-12900KF          |

| 13   | 0.055s   | Win11 / i9-12900KF          |

| 14   | 0.309s   | Win11 / i9-12900KF          |

| 15   | 1.062s   | Win11 / i9-12900KF          |

| 16   | 4.149s   | Win11 / i9-12900KF          |

| 17   | 15.784s  | Win11 / i9-12900KF          |

### C#

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.098s   | Win11 / i9-12900KF          |

| 12   | 0.333s   | Win11 / i9-12900KF          |

| 13   | 1,207s   | Win11 / i9-12900KF          |

| 14   | 4.588s   | Win11 / i9-12900KF          |

| 15   | 18.205s  | Win11 / i9-12900KF          |

| 16   | 72.196s  | Win11 / i9-12900KF          |

| 17   | 265.764s | Win11 / i9-12900KF          |

### Erlang

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.375s   | Win11 / i9-12900KF          |

| 12   | 1.607s   | Win11 / i9-12900KF          |

| 13   | 6.397s   | Win11 / i9-12900KF          |

| 14   | 25.117s  | Win11 / i9-12900KF          |

| 15   | 105.529s | Win11 / i9-12900KF          |

### Go

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.013s   | Win11 / i9-12900KF          |

| 12   | 0.053s   | Win11 / i9-12900KF          |

| 13   | 0.213s   | Win11 / i9-12900KF          |

| 14   | 0.835s   | Win11 / i9-12900KF          |

| 15   | 3.553s   | Win11 / i9-12900KF          |

| 16   | 12.429s  | Win11 / i9-12900KF          |

| 17   | 49.861s  | Win11 / i9-12900KF          |

### Java

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.017s   | Win11 / i9-12900KF          |

| 12   | 0.050s   | Win11 / i9-12900KF          |

| 13   | 0.158s   | Win11 / i9-12900KF          |

| 14   | 0.599s   | Win11 / i9-12900KF          |

| 15   | 2.703s   | Win11 / i9-12900KF          |

### JavaScript

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.058s   | Win11 / i9-12900KF          |

| 12   | 0.225s   | Win11 / i9-12900KF          |

| 13   | 0.894s   | Win11 / i9-12900KF          |

| 14   | 3.467s   | Win11 / i9-12900KF          |

| 15   | 14.543s  | Win11 / i9-12900KF          |

### Perl

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.643s   | Win11 / i9-12900KF          |

| 12   | 2.568    | Win11 / i9-12900KF          |

| 13   | 10.182s  | Win11 / i9-12900KF          |

| 14   | 41.137s  | Win11 / i9-12900KF          |

| 15   | 169.598s | Win11 / i9-12900KF          |

### Python

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 2.266s   | Win11 / i9-12900KF          |

| 12   | 8.850s   | Win11 / i9-12900KF          |

| 13   | 35.374s  | Win11 / i9-12900KF          |

| 14   | 99.665s  | Win11 / i9-12900KF          |

| 15   | 414.169s | Win11 / i9-12900KF          |

### Mojo

| Kmer | Duration | (Optional) Runtime Env / OS     |

| ---- | -------- | ------------------------------- |

| 11   | 319ms    | Win11 / i9-12900KF (WSL Ubuntu) |

| 12   | 1.289s   | Win11 / i9-12900KF (WSL Ubuntu) |

| 13   | 5.090s   | Win11 / i9-12900KF (WSL Ubuntu) |

| 14   | 20.944s  | Win11 / i9-12900KF (WSL Ubuntu) |

| 15   | 83.584s  | Win11 / i9-12900KF (WSL Ubuntu) |

### Rust

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.005s   | Win11 / i9-12900KF          |

| 12   | 0.023s   | Win11 / i9-12900KF          |

| 13   | 0.094s   | Win11 / i9-12900KF          |

| 14   | 0.365s   | Win11 / i9-12900KF          |

| 15   | 1.195s   | Win11 / i9-12900KF          |

| 16   | 4.499s   | Win11 / i9-12900KF          |

| 17   | 17.949s  | Win11 / i9-12900KF          |

### php

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.561s   | Win11 / i9-12900KF          |

| 12   | 2.164s   | Win11 / i9-12900KF          |

| 13   | 8.892s   | Win11 / i9-12900KF          |

| 14   | 35.038s  | Win11 / i9-12900KF          |

| 15   | 140.391s | Win11 / i9-12900KF          |

### Swift

| Kmer | Duration | (Optional) Runtime Env / OS |

| ---- | -------- | --------------------------- |

| 11   | 0.184s   | Win11 / i5-12400F           |

| 12   | 0.765s   | Win11 / i5-12400F           |

| 13   | 3.034s   | Win11 / i5-12400F           |

| 14   | 12.73s   | Win11 / i5-12400F           |

| 15   | 49.86s   | Win11 / i5-12400F           |

# Now it's your turn!

Participate in this public repository with your favourite language