aaltoscienceit/fgci-benchmark repository overview

⁠docker-fgci-benchmark

This repository contains instructions on how to build a benchmark docker image for FGCI node evaluation.

⁠Before installation

Please verify that the hyperthreading is disabled from BIOS and that the system has a kernel version new enough to protect against Meltdown and Spectre⁠.

⁠Usage with Docker

1. Install Docker on your system.

2. Pull image from Docker Hub with

   sudo docker pull aaltoscienceit/fgci-benchmark:latest
   

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   or build the most recent image from GitHub

   sudo docker build -t aaltoscienceit/fgci-benchmark:latest github.com/AaltoScienceIT/docker-fgci-benchmark
   

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3. After this you should create a folder that is writable to every user. This is where the results will be stored. For example:

   mkdir /tmp/results
   chmod a+w /tmp/results
   

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4. Now you can run the benchmarks with:

   sudo docker run --hostname $(hostname)-benchmark --mount type=bind,source=/tmp/results,target=/results -it aaltoscienceit/fgci-benchmark:latest
   

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   Estimated runtime of the benchmarks is around 2 hours.

⁠Usage with Singularity

1. Install Singularity⁠ on your system.

2. Build image from Docker Hub with

   singularity build fgci-benchmark.simg docker://aaltoscienceit/fgci-benchmark:latest
   

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3. After this you should create a folder that is writable to every user. This is where the results will be stored. For example:

   mkdir /tmp/results
   chmod a+w /tmp/results
   

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4. Now you can run the benchmarks with:

   singularity run -B /tmp/results:/results fgci-benchmark.simg
   

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   Estimated runtime of the benchmarks is around 2 hours.

⁠Included benchmarks

⁠Multiple serial R jobs

This benchmark uses the command parallel to fill every CPU on the computer with R processes that solve group factor analysis using a package called GFA⁠. In total 200 different jobs are run.

⁠GROMACS with MPI

This benchmark runs GROMACS test A from PRACE's Unified European Applications Benchmark Suite⁠ using OpenMPI and all available cores.

⁠CP2K with MPI

This benchmark runs CP2K test A from PRACE's Unified European Applications Benchmark Suite⁠ using OpenMPI and all available cores.

⁠Analyzing results

All results are compared against a reference result run on a Dell PowerEdge C4130 machine with 2x14 core Xeon E5 2680 v4 2.40 GHz processors and 128 GB of DDR4-2400 memory.

Results are stored in /results as JSON files. There will also be output from running hardinfo, /proc/cpuinfo, GROMACS and CP2K. There are also histograms in /results/histograms.