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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 23 hours ago
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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 (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-05-16T09:35:55.000Z (6 months ago)
- Last Synced: 2024-05-16T10:42:53.569Z (6 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
# 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!
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