bac_dev.job

#!/bin/bash
##SBATCH -p r630-hpc3
##SBATCH -w lewis4-r630-hpc3-node548
#SBATCH -p Gpu
#SBATCH -t 0-02:00  # time (days-hours:minutes)
#SBATCH --ntasks-per-node=10
#SBATCH --mem=100G
#SBATCH --output=/home/%u/log_bac_dev.job.%j
##SBATCH --mail-user=youremail@missouri.edu  # email address for notifications
##SBATCH --mail-type=END,FAIL  # which type of notifications to send
#SBATCH -J bac_dev

module load singularity

WORK_DIR=$(python -c 'import tempfile; print(tempfile.mkdtemp())')

mkdir -p -m 700 ${WORK_DIR}/run ${WORK_DIR}/tmp ${WORK_DIR}/var/lib/rstudio-server

HOME_R_DIR=${HOME}/R
R_DIR=/storage/hpc/data/${USER}/R
mkdir -p ${R_DIR}

HOME_MYDATA=$HOME/mydata
MYDATA=/storage/hpc/data/${USER}/mydata
mkdir -p ${MYDATA}

SITE_LIB=/storage/hpc/data/sw7v6/site-library

LOCAL_SHARE="/storage/hpc/data/${USER}/local_share"
mkdir -p ${LOCAL_SHARE}
RSTUDIO_SESSION="/storage/hpc/data/${USER}/logs/rstudio_${SLURM_JOB_ID}"
mkdir -p ${RSTUDIO_SESSION}

export SINGULARITYENV_RSTUDIO_SESSION_TIMEOUT=0

export SINGULARITYENV_USER=${USER}
export SINGULARITYENV_PASSWORD=$(openssl rand -base64 20)

readonly PORT=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')

cat 1>&2 <<END

#*** Credit: Sarayut (Nine) Winuthayanon, https://www.linkedin.com/in/winuthayanons/ ***#

How to Run RStudio Server on the Slurm Cluster: 

1. Execute either of the following commands in your local computer terminal:

    ssh -N -L ${PORT}:${HOSTNAME}:${PORT} ${SINGULARITYENV_USER}@lewis.rnet.missouri.edu

    ssh -N -L ${PORT}:${HOSTNAME}:${PORT} ${SINGULARITYENV_USER}@lewis42.rnet.missouri.edu

    ssh -N -L ${PORT}:${HOSTNAME}:${PORT} ${SINGULARITYENV_USER}@lewis4-dtn.rnet.missouri.edu

    ssh -N -L ${PORT}:${HOSTNAME}:${PORT} ${SINGULARITYENV_USER}@lewis4-dtn1.rnet.missouri.edu

2. In your browser, visit 

    http://localhost:${PORT}

3. Log in with these credentials:

    User: ${SINGULARITYENV_USER}
    Password: ${SINGULARITYENV_PASSWORD}

4. Check job status on login node:

        sacct

    # To find jobs were issued from May 2023:

        sacct -S 2023-05-01

To terminate the job:
1. Exit RStudio (top-right power button)
2. On the login node:

    scancel -f ${SLURM_JOB_ID}

END

SIF_FILE=/storage/hpc/group/ircf/software/singularity_bac_dev/bac_dev_20230525.sif

singularity exec -B ${SITE_LIB}:/usr/local/lib/R/site-library \
                    -B ${LOCAL_SHARE}:${HOME}/.local/share \
                    -B ${R_LIBS_USER}:${R_LIBS_USER} \
                    -B ${RSTUDIO_SESSION}:${HOME}/.local/share/rstudio \
                    -B ${MYDATA}:${HOME_MYDATA} \
                    -B ${R_DIR}:${HOME_R_DIR} \
                    -B ${WORK_DIR}/run:/run \
                    -B ${WORK_DIR}/tmp:/tmp \
                    -B ${WORK_DIR}/var/lib/rstudio-server:/var/lib/rstudio-server \
                    --writable-tmpfs \
                    --cleanenv ${SIF_FILE} \
            rserver --www-port=${PORT} \
                    --auth-none=0 \
                    --auth-pam-helper-path=pam-helper \
                    --auth-stay-signed-in-days=30 \
                    --auth-timeout-minutes=0 \
                    --server-user=${USER}

printf 'rserver exited' 1>&2