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run-benchmark-biowulf.adoc

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Purpose:

Guidelines to run Keras DL model on Biowulf GPU nodes using singularity.

Setup:

Export the environment variable SINGULARITY_BINDPATH in your ~/.bashrc file.

export SINGULARITY_BINDPATH="/gpfs,/gs2,/gs3,/gs4,/gs5,/gs6,/spin1,/data,/scratch,/fdb,/lscratch"

This will automatically bind all the directories on Biowulf to the singularity image we use on Biowulf.

Clone the CANDLE benchmarks, and supervisor in your data directory:

candle_dir=/data/`whoami`/candle
mkdir $candle_dir
cd $candle_dir
git clone https://github.com/ECP-CANDLE/Benchmarks.git
git clone https://github.com/ECP-CANDLE/Supervisor.git

Run:

To run any of the benchmarks on GPU nodes interactively, get a GPU node interactively using:

sinteractive  --gres=gpu:k80:1 --mem=25G

once on the node run:

module load singularity
singularity exec --nv /data/classes/candle/candle-gpu.img <benchmark-python-script>

For example, to run P1B1, run:

singularity exec --nv /data/classes/candle/candle-gpu.img python /PATH/TO/Benchmarks/Pilot1/P1B1/p1b1_baseline_keras2.py

Interactive work:

singularity shell --nv /data/classes/candle/candle-gpu.img