Benchmarking Project

This project offers a straightforward method to benchmark computational performance across different machines using either a Docker container or Singularity.

Usage

Follow the instructions below to execute the benchmark on your computing nodes.

• On kimclust, you should use Singularity. On personal devices, it's recommended to use Docker.
• Replace <node-id> with the name of your machine. If you're using kimclust, please use one of the following:
  • kimclust35, kimclust36, kimclust37
  • kimclust50, kimclust51 (NA), kimclust52, kimclust53, kimclust54, kimclust55 (NA)
• Tip: You can check your node id by running hostname -s.
• On personal devices, you can use your own <node-id> to represent your device.
  • For instance, Apple-silicon, Apple-silicon-rosetta2.

Singularity

Preparation

1. Clone the repository from GitHub.
2. Convert the Docker image to a Singularity image: singularity pull docker://kuangda/simple-benchmark.

Running the R Test

1. Execute the Singularity container singularity exec simple-benchmark_latest.sif Rscript /benchmark.R <node-id> <sqlite-file> <debug-flg>.
   • By default Singularity bind your current working directory as a volume.

Example command for R:

singularity exec simple-benchmark_latest.sif Rscript simple-benchmark/benchmark.R $(hostname -s) /home/kuangda/simple-benchmark-test/benchmark_results.sqlite False

Running the C Test

Navigate to the test directory and compile the C code:

cd simple-benchmark-test/simple-benchmark
singularity exec simple-benchmark_latest.sif bash
Singularity> gcc -o benchmark benchmark.c -lm -lsqlite3

Then, execute the benchmark:

Singularity> ./benchmark $(hostname -s) /home/kuangda/simple-benchmark-test/benchmark_results.sqlite FALSE

Docker

Preparation

1. Clone the repository from GitHub.
2. Pull the Docker image from DockerHub: docker pull kuangda/simple-benchmark

Running the R Test

1. Execute the Docker container and mount your current working directory as a volume:

docker run --rm \
-v /Users/kuangda/Developer/1-projects/simple-benchmark:/simple-benchmark \
kuangda/simple-benchmark \
Rscript /benchmark.R <node_id> False

Running the C Test

docker run -it --rm \
-v /Users/kuangda/Developer/1-projects/simple-benchmark:/simple-benchmark \
kuangda/simple-benchmark \
bash

Singularity> cd /simple-benchmark
Singularity> gcc -o benchmark benchmark.c -lm -lsqlite3
Singularity> ./benchmark $(hostname -s) benchmark_results.sqlite FALSE

Output

The summary of the benchmark results will be printed in the terminal and also written to a SQLite file (benchmark_results.sqlite).