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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

Correctness tests

  • Run all language correctness tests with make test TEST_LENGTH=5
  • Run one language correctness test with make test-lang LANGUAGE=python TEST_LENGTH=5
  • Run the first experimental language batch with make experimental LENGTH=8 -s
  • Run experimental correctness tests with make test-experimental TEST_LENGTH=5

The correctness tests validate that the generated k-mer count matches 4^k and that the output format contains a duration.

Current experimental language batch:

  • zig
  • nim
  • d
  • v
  • crystal
  • elixir

Experimental CI workflow:

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.

Quick tutorial: where to find CI results

  1. Open the GitHub Actions page: https://github.com/CoasterFreakDE/DNA-Kmer-Speed-Test/actions
  2. Choose a workflow:
  3. Open the latest run and click the correctness job (or speed-test job).
  4. Open a matrix entry (for example python, rust, java).
  5. Read the step logs:
    • Validate output for <lang> shows PASS / SKIP and parsed details for correctness tests.
    • The speed-test workflows write a Markdown table in the run Summary.
  6. For one combined file with all correctness matrix entries, open the latest run of Matrix Last Run Report and download the artifact matrix-results-run-<run_id>.

Tip: if you only want one language locally, run make test-lang LANGUAGE=python TEST_LENGTH=5.

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

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DNA Kmer speed test in different languagues

towardsdatascience.com/how-fast-is-c-compared-to-python-978f18f474c7

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test speed coding differences

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