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