use unix sockets rather than TCP ports. On Strudel2 setups, we alter …

m3/rocker-seurat_4.4.3-5.2.1.strudel.yaml.j2

@@ -14,7 +14,7 @@ instactions:
     paramscmd: cat ~/.rstudio-rocker/rserver-{jobid}.json
     client:
       cmd: null
-      redir: ""
+      redir: "{tunnelid}/"
     states:
       - RUNNING
   - name: View log

rstudio.sh

@@ -36,13 +36,6 @@ else
   IMAGE_LOCATION="docker://$IMAGE"
 fi
 
-PORT=${RSTUDIO_PORT:-8787}
-
-# Create a new password, or use whatever password is passed in the environment
-if [[ -z "$PASSWORD" ]]; then
-  PASSWORD=$(openssl rand -base64 15)
-fi
-export PASSWORD
 
 # Use a shared cache location if unspecified
 # export SINGULARITY_CACHEDIR=${SINGULARITY_CACHEDIR:-"/scratch/df22/andrewpe/singularity_cache"}
@@ -56,24 +49,12 @@ fi
 # Since we can't easily tell if we are in strudel2 we will actually check if we are in slurm (PBS should be the same)
 # Hardcode this to 'local' if you don't ever use an HPC cluster.
 if [[ -z "${SLURM_JOB_ID}" ]]; then
-    HPC_ENV="local"
+    HPC_ENV="shell"
 else
-    HPC_ENV="m3"
+    HPC_ENV="slurm"
 fi
 
 
-function get_port {
-    # lsof doesn't return open ports for system services, so we use netstat
-    # until ! lsof -i -P -n | grep -qc ':'${PORT}' (LISTEN)';
-
-    until ! netstat -ln | grep "  LISTEN  " | grep -iEo  ":[0-9]+" | cut -d: -f2 | grep -wqc "${PORT}";
-    do
-        ((PORT++))
-        echo "Checking port: ${PORT}"
-    done
-    echo "Got one !"
-}
-
 # Make a dir name from the IMAGE
 IMAGE_SLASHED=$(echo "${IMAGE}" | sed 's/:/\//g' | sed 's/\.\./__/g')
 R_DIRS="${HOME}/.rstudio-rocker/${IMAGE_SLASHED}/"
@@ -106,7 +87,7 @@ else
     _cachedir=${HOME}/.apptainer/cache/
 fi
 
-if [[ $HPC_ENV == "m3" ]]; then
+if [[ $HPC_ENV == "slurm" ]]; then
     BINDPATHS=("/fs02" "/fs03" "/fs04" "/scratch" "/scratch2" "/projects")
     SINGULARITY_BINDPATH=""
     for path in "${BINDPATHS[@]}"; do
@@ -127,35 +108,43 @@ echo "  Storing image in ${_cachedir}"
 # Test the image works, execute a no-op command
 ${SINGULARITY_BIN} exec "${IMAGE_LOCATION}" true
 
+get_socketid() {
+  if [[ -n "$SLURM_JOB_ID" ]]; then
+    SOCKETID="$SLURM_JOB_ID"
+  else
+    SOCKETID="rserver"
+  fi
+}
+
 echo
 echo "Finding an available port ..."
-get_port
+get_socketid
+SOCKET="/home/${USER}/.sock${SOCKETID}"
 
 LOCALPORT=${PORT}
 # LOCALPORT=8787
 PUBLIC_IP=$(curl --silent https://checkip.amazonaws.com)
 
 echo "On you local machine, open an SSH tunnel like:"
 # echo "  ssh -N -L ${LOCALPORT}:localhost:${PORT} ${USER}@m3-bio1.erc.monash.edu.au"
-echo "  ssh -N -L ${LOCALPORT}:localhost:${PORT} ${USER}@$(hostname -f)"
+echo "  ssh -N -L ${LOCALPORT}:${SOCKET} ${USER}@$(hostname -f)"
 echo "  or"
-echo "  ssh -N -L ${LOCALPORT}:localhost:${PORT} ${USER}@${PUBLIC_IP}"
+echo "  ssh -N -L ${LOCALPORT}:${SOCKET} ${USER}@${PUBLIC_IP}"
 
 # For smux/srun/sbatch jobs, route via the login node to a the compute node where rserver runs - not working for me
 # echo "  ssh -N -L ${LOCALPORT}:${HOSTNAME}:${PORT} ${USER}@m3.massive.org.au"
 echo
 echo "Point your web browser at http://localhost:${LOCALPORT}"
 echo
-echo "Login to RStudio with:"
-echo "  username: ${USER}"
-echo "  password: ${PASSWORD}"
-echo
 echo "Protip: You can choose your version of R from any of the tags listed here: https://hub.docker.com/r/rocker/rstudio/tags"
 echo "        and set the environment variable IMAGE, eg"
 echo "        IMAGE=rocker/rstudio:4.1.1 $(basename "$0")"
 echo
 echo "Starting RStudio Server (R version from image ${IMAGE})"
 
+
+
+
 # Set some locales to suppress warnings
 export LC_CTYPE="C.UTF-8"
 export LC_TIME="C.UTF-8"
@@ -166,10 +155,10 @@ export LC_PAPER="C.UTF-8"
 # shellcheck disable=SC2034
 export LC_MEASUREMENT="C.UTF-8"
 
-if [[ $HPC_ENV == 'm3' ]]; then
+if [[ $HPC_ENV == 'slurm' ]]; then
     if [[ -n ${SLURM_JOB_ID} ]]; then
       # For Strudel
-      echo '{"password":"'"${PASSWORD}"'", "port": '"${PORT}"'}' >"${HOME}/.rstudio-rocker/rserver-${SLURM_JOB_ID}.json"
+      echo '{"tunnelid":"s2rtid'${SOCKETID}'", "socket":"'${SOCKET}'"}'>"${HOME}/.rstudio-rocker/rserver-${SLURM_JOB_ID}.json"
     fi
     APPTAINERENV_PASSWORD="${PASSWORD}" \
     SINGULARITYENV_PASSWORD="${PASSWORD}" \
@@ -182,7 +171,7 @@ if [[ $HPC_ENV == 'm3' ]]; then
                      --bind "${RSTUDIO_DOT_CONFIG}:/home/rstudio/.config/rstudio" \
                      --bind "${R_LIBS_USER}:/home/rstudio/R" \
                      "${IMAGE_LOCATION}" \
-                     rserver --auth-none=1 --auth-pam-helper-path=pam-helper --www-port="${PORT}" --server-user="${USER}"
+                     rserver --auth-none=1 --www-socket="${SOCKET}" --server-user="${USER}" --www-root-path="s2rtid${SOCKETID}"
                      #--bind ${RSITELIB}:/usr/local/lib/R/site-library \
 else
     APPTAINERENV_PASSWORD="${PASSWORD}" \
@@ -196,7 +185,7 @@ else
                      --bind "${RSTUDIO_DOT_CONFIG}:/home/rstudio/.config/rstudio" \
                      --bind "${R_LIBS_USER}:/home/rstudio/R" \
                      "${IMAGE_LOCATION}" \
-                     rserver --auth-none=1 --auth-pam-helper-path=pam-helper --www-port="${PORT}" --server-user="${USER}"
+                     rserver --auth-none=1 --www-socket="${SOCKET}" --server-user="${USER}"
 fi
 
 printf 'rserver exited' 1>&2