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fix(rstudio): Resolve container errors and improve env handling #13

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fix(rstudio): Resolve container errors and improve env handling #13

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30 changes: 17 additions & 13 deletions rstudio.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,6 @@

#set -o xtrace

# Deactivate any active conda environment
if [[ -n "$CONDA_DEFAULT_ENV" ]]; then
conda deactivate
fi

# This may be required at some sites if the Apptainer configuration
# prevents SLURM from setting the appropriate memory cgroups ? See:
Expand Down Expand Up @@ -45,7 +41,7 @@ fi
export PASSWORD

# Use a shared cache location if unspecified
# export SINGULARITY_CACHEDIR=${SINGULARITY_CACHEDIR:-"/scratch/df22/andrewpe/singularity_cache"}
# export SINGULARITY_CACHEDIR=${SINGULARITY_CACHEDIR:-/scratch/df22/andrewpe/singularity_cache}

if [[ -z "${HOSTNAME}" ]]; then
_hostname=$(hostname)
Expand Down Expand Up @@ -75,7 +71,7 @@ function get_port {
}

# Make a dir name from the IMAGE
IMAGE_SLASHED=$(echo "${IMAGE}" | sed 's/:/\//g' | sed 's/\.\./__/g')
IMAGE_SLASHED=$(echo "${IMAGE}" | sed 's/:/\//g' | sed 's/\.\./__\//g')
R_DIRS="${HOME}/.rstudio-rocker/${IMAGE_SLASHED}/"
RSTUDIO_DOT_LOCAL="${R_DIRS}/.local/share/rstudio"
RSTUDIO_DOT_CONFIG="${R_DIRS}/.config/rstudio"
Expand Down Expand Up @@ -166,14 +162,20 @@ export LC_PAPER="C.UTF-8"
# shellcheck disable=SC2034
export LC_MEASUREMENT="C.UTF-8"

# Set RENV cache path to be inside the container and versioned.
# The destination of the bind mount for the renv cache is /home/rstudio/.local/share/renv
export RENV_PATHS_CACHE="/home/rstudio/.local/share/renv"

if [[ $HPC_ENV == 'm3' ]]; then
if [[ -n ${SLURM_JOB_ID} ]]; then
# For Strudel
echo '{"password":"'"${PASSWORD}"'", "port": '"${PORT}"'}' >"${HOME}/.rstudio-rocker/rserver-${SLURM_JOB_ID}.json"
fi
APPTAINERENV_PASSWORD="${PASSWORD}" \
SINGULARITYENV_PASSWORD="${PASSWORD}" \
${SINGULARITY_BIN} exec --bind "${RSTUDIO_HOME}:${HOME}/.rstudio" \
${SINGULARITY_BIN} exec --cleanenv \
--env "PASSWORD=${PASSWORD}" --env "USER=${USER}" --env "HOME=${HOME}" --env "LC_CTYPE=${LC_CTYPE}" --env "LC_TIME=${LC_TIME}" --env "LC_MONETARY=${LC_MONETARY}" --env "LC_MESSAGES=${LC_MESSAGES}" --env "LC_PAPER=${LC_PAPER}" --env "LC_MEASUREMENT=${LC_MEASUREMENT}" --env "HOSTNAME=${HOSTNAME}" --env "APPTAINER_BINDPATH=${APPTAINER_BINDPATH}" --env "SINGULARITY_BINDPATH=${SINGULARITY_BINDPATH}" --env "RENV_PATHS_CACHE=${RENV_PATHS_CACHE}" \
--bind "/etc/passwd:/etc/passwd:ro" \
--bind "/etc/group:/etc/group:ro" \
--bind "${RSTUDIO_HOME}:${HOME}/.rstudio" \
--bind "${RSTUDIO_TMP}:/tmp" \
--bind "${RSTUDIO_TMP}/var:/var/lib/rstudio-server" \
--bind "${RSTUDIO_TMP}/var/run:/var/run/rstudio-server" \
Expand All @@ -184,11 +186,13 @@ if [[ $HPC_ENV == 'm3' ]]; then
--writable-tmpfs \
"${IMAGE_LOCATION}" \
rserver --auth-none=1 --auth-pam-helper-path=pam-helper --www-port="${PORT}" --server-user="${USER}"
#--bind ${RSITELIB}:/usr/local/lib/R/site-library \
#--bind ${RSITELIB}:/usr/local/lib/R/site-library
else
APPTAINERENV_PASSWORD="${PASSWORD}" \
SINGULARITYENV_PASSWORD="${PASSWORD}" \
${SINGULARITY_BIN} exec --bind "${RSTUDIO_HOME}:${HOME}/.rstudio" \
${SINGULARITY_BIN} exec --cleanenv \
--env "PASSWORD=${PASSWORD}" --env "USER=${USER}" --env "HOME=${HOME}" --env "LC_CTYPE=${LC_CTYPE}" --env "LC_TIME=${LC_TIME}" --env "LC_MONETARY=${LC_MONETARY}" --env "LC_MESSAGES=${LC_MESSAGES}" --env "LC_PAPER=${LC_PAPER}" --env "LC_MEASUREMENT=${LC_MEASUREMENT}" --env "HOSTNAME=${HOSTNAME}" --env "APPTAINER_BINDPATH=${APPTAINER_BINDPATH}" --env "SINGULARITY_BINDPATH=${SINGULARITY_BINDPATH}" --env "RENV_PATHS_CACHE=${RENV_PATHS_CACHE}" \
--bind "/etc/passwd:/etc/passwd:ro" \
--bind "/etc/group:/etc/group:ro" \
--bind "${RSTUDIO_HOME}:${HOME}/.rstudio" \
--bind "${RSTUDIO_TMP}:/tmp" \
--bind "${RSTUDIO_TMP}/var:/var/lib/rstudio-server" \
--bind "${RSTUDIO_TMP}/var/run:/var/run/rstudio-server" \
Expand Down