rstudio-server.job

rstudio-server.job

#!/bin/sh

#SBATCH --account=uwit
#SBATCH --partition=compute
#SBATCH --time=08:00:00

#SBATCH --signal=USR2
#SBATCH --ntasks=4
#SBATCH --mem=10G

#SBATCH --output=/mmfs1/home/%u/rstudio-server.job.%j

# Create temp directory for ephemeral content to bind-mount in the container
RSTUDIO_TMP=$(python -c 'import tempfile; print(tempfile.mkdtemp())')

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

cat > ${RSTUDIO_TMP}/database.conf <<END
provider=sqlite
directory=/var/lib/rstudio-server
END

# Set OMP_NUM_THREADS to prevent OpenBLAS (and any other OpenMP-enhanced
# libraries used by R) from spawning more threads than the number of processors
# allocated to the job.
#
# Set R_LIBS_USER to a path specific to rocker/rstudio to avoid conflicts with
# personal libraries from any R installation in the host environment

cat > ${RSTUDIO_TMP}/rsession.sh <<END
#!/bin/sh
export OMP_NUM_THREADS=${SLURM_JOB_CPUS_PER_NODE}
export R_LIBS_USER=$GSCRATCH/$USER/rocker-rstudio/4.0
exec rsession "\${@}"
END

chmod +x ${RSTUDIO_TMP}/rsession.sh

export SINGULARITY_BIND="/gscratch:/gscratch,${RSTUDIO_TMP}/run:/run,${RSTUDIO_TMP}/tmp:/tmp,${RSTUDIO_TMP}/database.conf:/etc/rstudio/database.conf,${RSTUDIO_TMP}/rsession.sh:/etc/rstudio/rsession.sh,${RSTUDIO_TMP}/var/lib/rstudio-server:/var/lib/rstudio-server"

# Do not suspend idle sessions.
# Alternative to setting session-timeout-minutes=0 in /etc/rstudio/rsession.conf
export SINGULARITYENV_RSTUDIO_SESSION_TIMEOUT=0

export SINGULARITYENV_USER=$(id -un)
export SINGULARITYENV_PASSWORD=$(openssl rand -base64 15)

# get unused socket per https://unix.stackexchange.com/a/132524
# tiny race condition between the python & singularity commands
readonly PORT=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')
cat 1>&2 <<END
1. SSH tunnel from your workstation using the following command:

   ssh -N -L 8787:${HOSTNAME}:${PORT} ${SINGULARITYENV_USER}@klone.hyak.uw.edu

   and point your web browser to http://localhost:8787

2. log in to RStudio Server using the following credentials:

   user: ${SINGULARITYENV_USER}
   password: ${SINGULARITYENV_PASSWORD}

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f ${SLURM_JOB_ID}
END

source /etc/bashrc
module load singularity
singularity exec --cleanenv $GSCRATCH/$USER/rstudio_4.1.0.sif \
    rserver --www-port ${PORT} \
            --auth-none=0 \
            --auth-pam-helper-path=pam-helper \
            --auth-stay-signed-in-days=30 \
            --auth-timeout-minutes=0 \
            --rsession-path=/etc/rstudio/rsession.sh
printf 'rserver exited' 1>&2