diff --git a/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml b/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml index ddcd12f106..97146cdb4c 100644 --- a/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml +++ b/http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml @@ -19,12 +19,7 @@ services: volumes: # shared with welder - "/mnt/disks/work:${NOTEBOOKS_DIR}" - devices: - - /dev/fuse:/dev/fuse - cap_add: - - SYS_ADMIN - security_opt: - - apparmor:unconfined + - /mnt/disks/bucket:/usr/local/genomics restart: always environment: GOOGLE_PROJECT: "${GOOGLE_PROJECT}" diff --git a/http/src/main/resources/init-resources/jupyter-docker-compose.yaml b/http/src/main/resources/init-resources/jupyter-docker-compose.yaml index b3b3dd74da..80d36504cb 100644 --- a/http/src/main/resources/init-resources/jupyter-docker-compose.yaml +++ b/http/src/main/resources/init-resources/jupyter-docker-compose.yaml @@ -36,12 +36,7 @@ services: - /hadoop:/hadoop - /hadoop_gcs_connector_metadata_cache:/hadoop_gcs_connector_metadata_cache - /usr/local/share/google/dataproc:/usr/local/share/google/dataproc - devices: - - /dev/fuse:/dev/fuse - cap_add: - - SYS_ADMIN - security_opt: - - apparmor:unconfined + - /mnt/disks/bucket:/usr/local/genomics restart: always environment: GOOGLE_PROJECT: "${GOOGLE_PROJECT}" diff --git a/http/src/main/resources/init-resources/startup.sh b/http/src/main/resources/init-resources/startup.sh index 743abaa4c0..07d10e3767 100644 --- a/http/src/main/resources/init-resources/startup.sh +++ b/http/src/main/resources/init-resources/startup.sh @@ -123,6 +123,12 @@ then mount -t ext4 -O discard,defaults /dev/${DISK_DEVICE_ID} ${WORK_DIRECTORY} chmod a+rwx /mnt/disks/work + # Start gcsfuse as a sidecar + mkdir -p /mnt/disks/bucket + docker exec $JUPYTER_SERVER_NAME /bin/bash -c "mkdir /usr/local/genomics" + docker run -d --name gcsfuse-container --platform linux/amd64 --privileged --env BUCKET_NAME=genomics-public-data --device /dev/fuse --security-opt apparmor=unconfined -v /mnt/disks/bucket:/mnt/gcs-bucket:shared -v /mnt/disks/bucket:/mnt/gcs-data tarekmahmed/gcsfuse-container:latest + + # (1/6/22) Restart Jupyter Container to reset `NOTEBOOKS_DIR` for existing runtimes. This code can probably be removed after a year if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then echo "Restarting Jupyter Container $GOOGLE_PROJECT / $CLUSTER_NAME..."