[IA-4967] Update COS image (#4731)

Co-authored-by: LizBaldo <baldo@broadinstitute.org>
Co-authored-by: LizBaldo <LizBaldo@users.noreply.github.com>

http/src/main/resources/init-resources/gce-init.sh

@@ -218,11 +218,19 @@ mkdir -p ${DOCKER_COMPOSE_FILES_DIRECTORY}
 log 'Formatting and mounting persistent disk...'
 
 # Format and mount persistent disk
-# Fix this to `sdb`. We've never seen a device name that's not `sdb`,
-# Altho you some images, this cmd $(lsblk -o name,serial | grep 'user-disk' | awk '{print $1}')
-# can be used to find device name, this doesn't work for COS images
-USER_DISK_DEVICE_ID=$(lsblk -o name,serial | grep 'user-disk' | awk '{print $1}')
-DISK_DEVICE_ID=${USER_DISK_DEVICE_ID:-sdb}
+## The PD should be the only `sd` disk that is not mounted yet
+AllsdDisks=($(lsblk --nodeps --noheadings --output NAME --paths | grep -i "sd"))
+FreesdDisks=()
+for Disk in "${AllsdDisks[@]}"; do
+    Mounts="$(lsblk -no MOUNTPOINT "${Disk}")"
+    if [ -z "$Mounts" ]; then
+        echo "Found our unmounted persistent disk!"
+        FreesdDisks="${Disk}"
+    else
+        echo "Not our persistent disk!"
+    fi
+done
+DISK_DEVICE_ID=${FreesdDisks}
 
 ## Only format disk is it hasn't already been formatted
 if [ "$IS_GCE_FORMATTED" == "false" ] ; then
@@ -232,10 +240,10 @@ if [ "$IS_GCE_FORMATTED" == "false" ] ; then
   # Passing -F -F to mkfs.ext4 should force the tool to ignore the state of the partition.
   # Note that there should be two instances command-line switch (-F -F) to override this check
 
-  mkfs.ext4 -m 0 -E lazy_itable_init=0,lazy_journal_init=0,discard /dev/${DISK_DEVICE_ID} -F -F
+  mkfs.ext4 -m 0 -E lazy_itable_init=0,lazy_journal_init=0,discard ${DISK_DEVICE_ID} -F -F
 fi
 
-mount -t ext4 -O discard,defaults /dev/${DISK_DEVICE_ID} ${WORK_DIRECTORY}
+mount -t ext4 -O discard,defaults ${DISK_DEVICE_ID} ${WORK_DIRECTORY}
 
 # done persistent disk setup
 STEP_TIMINGS+=($(date +%s))
@@ -580,7 +588,7 @@ fi
 # If it's GCE, we resize the PD. Dataproc doesn't have PD
 if [ -f "/var/certs/jupyter-server.crt" ]; then
   echo "Resizing persistent disk attached to runtime $GOOGLE_PROJECT / $CLUSTER_NAME if disk size changed..."
-  resize2fs /dev/${DISK_DEVICE_ID}
+  resize2fs ${DISK_DEVICE_ID}
 fi
 
 # Remove any unneeded cached images to save disk space.

http/src/main/resources/init-resources/startup.sh

@@ -85,8 +85,19 @@ SERVER_CRT=$(proxyServerCrt)
 SERVER_KEY=$(proxyServerKey)
 ROOT_CA=$(rootCaPem)
 FILE=/var/certs/jupyter-server.crt
-USER_DISK_DEVICE_ID=$(lsblk -o name,serial | grep 'user-disk' | awk '{print $1}')
-DISK_DEVICE_ID=${USER_DISK_DEVICE_ID:-sdb}
+## The PD should be the only `sd` disk that is not mounted yet
+AllsdDisks=($(lsblk --nodeps --noheadings --output NAME --paths | grep -i "sd"))
+FreesdDisks=()
+for Disk in "${AllsdDisks[@]}"; do
+    Mounts="$(lsblk -no MOUNTPOINT "${Disk}")"
+    if [ -z "$Mounts" ]; then
+        echo "Found our unmounted persistent disk!"
+        FreesdDisks="${Disk}"
+    else
+        echo "Not our persistent disk!"
+    fi
+done
+DISK_DEVICE_ID=${FreesdDisks}
 JUPYTER_HOME=/etc/jupyter
 RSTUDIO_SCRIPTS=/etc/rstudio/scripts
 
@@ -119,9 +130,9 @@ then
     JUPYTER_DOCKER_COMPOSE=$(ls ${DOCKER_COMPOSE_FILES_DIRECTORY}/jupyter-docker*)
     export WORK_DIRECTORY='/mnt/disks/work'
 
-    fsck.ext4 -tvy /dev/${DISK_DEVICE_ID}
+    fsck.ext4 -tvy ${DISK_DEVICE_ID}
     mkdir -p /mnt/disks/work
-    mount -t ext4 -O discard,defaults /dev/${DISK_DEVICE_ID} ${WORK_DIRECTORY}
+    mount -t ext4 -O discard,defaults ${DISK_DEVICE_ID} ${WORK_DIRECTORY}
     chmod a+rwx /mnt/disks/work
 
     # (1/6/22) Restart Jupyter Container to reset `NOTEBOOKS_DIR` for existing runtimes. This code can probably be removed after a year
@@ -147,14 +158,12 @@ END
         ${DOCKER_COMPOSE} -f ${JUPYTER_DOCKER_COMPOSE} stop
         ${DOCKER_COMPOSE} -f ${JUPYTER_DOCKER_COMPOSE} rm -f
         ${DOCKER_COMPOSE} --env-file=/var/variables.env -f ${JUPYTER_DOCKER_COMPOSE} up -d
+
+        # the docker containers need to be restarted or the jupyter container
+        # will fail to start until the appropriate volume/device exists
+        docker restart $JUPYTER_SERVER_NAME
+        docker restart $WELDER_SERVER_NAME
 
-        if [ "${GPU_ENABLED}" == "true" ] ; then
-          # Containers will usually restart just fine. But when gpu is enabled,
-          # jupyter container will fail to start until the appropriate volume/device exists.
-          # Hence restart jupyter container here
-          docker restart jupyter-server
-          docker restart welder-server
-        fi
         # This line is only for migration (1/26/2022). Say you have an existing runtime where jupyter container's PD is mapped at $HOME/notebooks,
         # then all jupyter related files (.jupyter, .local) and things like bash history etc all lives under $HOME. The home diretory change will
         # make it so that next time this runtime starts up, PD will be mapped to $HOME, but this means that the previous files under $HOME (.jupyter, .local etc)
@@ -174,6 +183,16 @@ END
         docker cp /var/${JUPYTER_NOTEBOOK_FRONTEND_CONFIG} ${JUPYTER_SERVER_NAME}:${JUPYTER_HOME}/nbconfig/
     fi
 
+    if [ ! -z "$RSTUDIO_DOCKER_IMAGE" ] ; then
+        echo "Restarting Rstudio Container $GOOGLE_PROJECT / $CLUSTER_NAME..."
+
+        # the docker containers need to be restarted or the jupyter container
+        # will fail to start until the appropriate volume/device exists
+        docker restart $RSTUDIO_SERVER_NAME
+        docker restart $WELDER_SERVER_NAME
+
+    fi
+
     if [ "$UPDATE_WELDER" == "true" ] ; then
         echo "Upgrading welder..."
 
@@ -251,6 +270,7 @@ else
     fi
 fi
 
+
 function failScriptIfError() {
   if [ $EXIT_CODE -ne 0 ]; then
     echo "Fail to docker-compose start container ${EXIT_CODE}. Output is saved to ${START_USER_SCRIPT_OUTPUT_URI}"
@@ -396,5 +416,5 @@ fi
 # If it's GCE, we resize the PD. Dataproc doesn't have PD
 if [ -f "$FILE" ]; then
   echo "Resizing persistent disk attached to runtime $GOOGLE_PROJECT / $CLUSTER_NAME if disk size changed..."
-  resize2fs /dev/${DISK_DEVICE_ID}
+  resize2fs ${DISK_DEVICE_ID}
 fi

http/src/main/resources/reference.conf

@@ -111,7 +111,7 @@ dataproc {
 }
 
 gce {
-  customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-08-13-15-17-24"
+  customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-08-14-15-03-19"
   userDiskDeviceName = "user-disk"
   defaultScopes = [
     "https://www.googleapis.com/auth/userinfo.email",

jenkins/gce-custom-images/create_gce_image.sh

@@ -39,12 +39,13 @@ fi
 # Set this to the tag of the Daisy image you had pulled
 DAISY_IMAGE_TAG="release"
 
+
 # When updating, to find the resource path:
 #    1. run `gcloud compute images list --no-standard-images --project=cos-cloud | grep lts` to get the list of available container-optimized OS images
 #    2. select the image of interest, say, `cos-89-16108-403-22`
 #    3. run `gcloud compute images describe cos-89-16108-403-22 --project cos-cloud | grep selfLink`
 #    4. extract the segments starting with 'projects'
-BASE_IMAGE="projects/cos-cloud/global/images/cos-101-17162-463-16"
+BASE_IMAGE="projects/cos-cloud/global/images/cos-113-18244-85-64"
 
 if [[ "$VALIDATE_WORKFLOW" == "true" ]]; then
   DAISY_CONTAINER="gcr.io/compute-image-tools/daisy:${DAISY_IMAGE_TAG} -validate"
@@ -72,4 +73,4 @@ gcloud compute images add-iam-policy-binding \
 
 if ! [ -z "$OUTPUT_FILE_PATH" ]; then
   echo "projects/$GOOGLE_PROJECT/global/images/$OUTPUT_IMAGE_NAME" > $OUTPUT_FILE_PATH
-fi
+fi