run_training_experiments

#!/usr/bin/env bash

set -eu

IMG='docker.io/deepprojects/camelyon-cnns:tests'
OPTS='-u 1000:1000 --runtime=nvidia --device /dev/fuse --cap-add SYS_ADMIN --security-opt apparmor:unconfined --workdir=/home/cc/out'

# more information on merged.hf5: https://github.com/deep-projects/camelyon-experiments-v2
CMD='camelyon-cnns /home/cc/input/merged.hdf5'

# INPDIR_TYPE and INPDIR are set to run performance tests on a remote NFS share
# Change INPDIR_TYPE to SSD and INPDIR to an appropriate data location on your local SSD
INPDIR_TYPE="NFS"
#INPDIR_TYPE="SSD"
INPDIR="/remote_nfs/inputs"
#INPDIR="/local_ssd/inputs"
OUTDIR="/outputs"

docker pull ${IMG}

mkdir ${OUTDIR}
chmod 777 ${OUTDIR}

outdir="${OUTDIR}/${INPDIR_TYPE}"
mkdir ${outdir}
chmod 777 ${outdir}

for i in $(seq 1 9); do
    outdir_n="${outdir}/${i}"
    mkdir ${outdir_n}
    chmod 777 ${outdir_n}
    docker run ${OPTS} -e NVIDIA_VISIBLE_DEVICES=0 -v ${INPDIR}:/home/cc/input -v ${outdir_n}:/home/cc/out:rw ${IMG} ${CMD} --arch 1 --fast-hdf5 1 --mask-threshold 0.1 --epochs 8 --queue-size 1
done