Running RStudio on CREATE

In order to run RStudio from the HPC nodes it is necessary to request a batch job and then create a tunnel to the running process.

Create a script to be submitted using sbatch

latestv2022.07.1_554

#!/bin/bash -l

#SBATCH --job-name=ops-rstudio
#SBATCH --partition=cpu
#SBATCH --ntasks=1
#SBATCH --mem=2G
#SBATCH --signal=USR2
#SBATCH --cpus-per-task=1

module load rstudio/v2023.03.0_386-gcc-10.3.0-r-4.2.2-python3+-chk-version

# get unused socket per https://unix.stackexchange.com/a/132524
export PASSWORD=$(openssl rand -base64 15)
readonly IPADDRESS=$(hostname -I | tr ' ' '\n' | grep '10.211.4.')
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:

   Linux and MacOS:
   ssh -NL 8787:${HOSTNAME}:${PORT} ${USER}@hpc.create.kcl.ac.uk

   Windows:
   ssh -m hmac-sha2-512 -NL 8787:${HOSTNAME}:${PORT} ${USER}@hpc.create.kcl.ac.uk

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

2. Login to RStudio Server using the following credentials:

   user: ${USER}
   password: ${PASSWORD}

When done using the 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

# Create custom database config
DBCONF=$TMPDIR/database.conf
if [ ! -e $DBCONF ]
then
printf "\nNOTE: creating $DBCONF database config file.\n\n"
echo "directory=$TMPDIR/var-rstudio-server" > $DBCONF
fi

rserver --server-user ${USER} --www-port ${PORT} --server-data-dir $TMPDIR/data-rstudio-server \
--secure-cookie-key-file $TMPDIR/data-rstudio-server/secure-cookie-key \
--database-config-file=$DBCONF --auth-none=0 \
--auth-pam-helper-path=pam-env-helper

printf 'RStudio Server exited' 1>&2

#!/bin/bash -l

#SBATCH --job-name=ops-rstudio
#SBATCH --partition=cpu
#SBATCH --ntasks=1
#SBATCH --mem=2G
#SBATCH --signal=USR2
#SBATCH --cpus-per-task=1

module load rstudio/v2022.07.1_554-gcc-10.3.0-r-4.1.3-python3+-chk-version

# get unused socket per https://unix.stackexchange.com/a/132524
export PASSWORD=$(openssl rand -base64 15)
readonly IPADDRESS=$(hostname -I | tr ' ' '\n' | grep '10.211.4.')
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:

   Linux and MacOS:
   ssh -NL 8787:${HOSTNAME}:${PORT} ${USER}@hpc.create.kcl.ac.uk

   Windows:
   ssh -m hmac-sha2-512 -NL 8787:${HOSTNAME}:${PORT} ${USER}@hpc.create.kcl.ac.uk

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

2. Login to RStudio Server using the following credentials:

   user: ${USER}
   password: ${PASSWORD}

When done using the 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

# Create custom database config
DBCONF=$TMPDIR/database.conf
if [ ! -e $DBCONF ]
then
printf "\nNOTE: creating $DBCONF database config file.\n\n"
echo "directory=$TMPDIR/var-rstudio-server" > $DBCONF
fi

rserver --server-user ${USER} --www-port ${PORT} --server-data-dir $TMPDIR/data-rstudio-server \
--secure-cookie-key-file $TMPDIR/data-rstudio-server/secure-cookie-key  --session-rpc-key-file \
$TMPDIR/data-rstudio-server/session-rpc-key --database-config-file=$DBCONF --auth-none=0 \
--auth-pam-helper-path=pam-env-helper

printf 'RStudio Server exited' 1>&2

Submit the script

k1234567@erc-hpc-login1:/scratch/users/k1234567$ sbatch ops-rstudio.sh

Connect to RStudio server using the output file details

Once the job has started an output file will be generated that will have the details and user credentials required for you to be able to login and connect.