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[Dont Merge] GCSFuse as a sidecar #4529

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[Dont Merge] GCSFuse as a sidecar #4529

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8e0da71
Try adding a device and sys admin capability to be able to mount a gc…
tarekmamdouh May 10, 2024
57810b5
add security-opt in docker-compose
tarekmamdouh May 15, 2024
8d50bcc
Try GCSFuse mounting as a side car
tarekmamdouh Jun 6, 2024
6c9d0a0
try shared mounting
tarekmamdouh Jun 7, 2024
9cd8153
No need to create the folder, it's already created
tarekmamdouh Jun 11, 2024
84fc382
Add gcsfuse in dataproc to experiment with
tarekmamdouh Jun 11, 2024
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8 changes: 8 additions & 0 deletions http/src/main/resources/init-resources/gce-init.sh
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Expand Up @@ -276,6 +276,14 @@ STEP_TIMINGS+=($(date +%s))

log 'Starting up the Jupyter...'


# Start gcsfuse as a sidecar
mkdir -p /mnt/disks/bucket
docker run -d --name gcsfuse-container --privileged -u root -e PIP_USER=false --env BUCKET_NAME=genomics-public-data --device /dev/fuse:/dev/fuse --security-opt apparmor=unconfined -v /mnt/disks/bucket:/mnt/gcs-bucket:shared tarekmahmed/gcsfuse-container:latest
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FYI, you likely want to use the --restart always option so that the volume get's mounted properly after pausing / resuming your runtime, see

leonardo/http/src/main/resources/init-resources/azure_vm_init_script.sh

Line 240 in a9a9c0f

docker run -d --restart always --network host --name listener \

# Use docker compose here
# $(DOCKER_COMPOSE) -f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename gcsfuse-docker-compose-gce.yaml` config


# Run docker-compose for each specified compose file.
# Note the `docker-compose pull` is retried to avoid intermittent network errors, but
# `docker-compose up` is not retried since if that fails, something is probably broken
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7 changes: 7 additions & 0 deletions http/src/main/resources/init-resources/init-actions.sh
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Expand Up @@ -304,6 +304,13 @@ END

log 'Starting up the Jupydocker...'

# Start gcsfuse as a sidecar
mkdir -p /mnt/disks/bucket
docker run -d --name gcsfuse-container --privileged -u root -e PIP_USER=false --env BUCKET_NAME=genomics-public-data --device /dev/fuse:/dev/fuse --security-opt apparmor=unconfined -v /mnt/disks/bucket:/mnt/gcs-bucket:shared tarekmahmed/gcsfuse-container:latest
# Use docker compose here
# $(DOCKER_COMPOSE) -f ${DOCKER_COMPOSE_FILES_DIRECTORY}/`basename gcsfuse-docker-compose-gce.yaml` config


# Run docker-compose for each specified compose file.
# Note the `docker-compose pull` is retried to avoid intermittent network errors, but
# `docker-compose up` is not retried.
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1 change: 1 addition & 0 deletions http/src/main/resources/init-resources/jupyter-docker-compose-gce.yaml
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Expand Up @@ -19,6 +19,7 @@ services:
volumes:
# shared with welder
- "/mnt/disks/work:${NOTEBOOKS_DIR}"
- /mnt/disks/bucket:/usr/local/genomics:shared
restart: always
environment:
GOOGLE_PROJECT: "${GOOGLE_PROJECT}"
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1 change: 1 addition & 0 deletions http/src/main/resources/init-resources/jupyter-docker-compose.yaml
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Expand Up @@ -36,6 +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
- /mnt/disks/bucket:/usr/local/genomics:shared
restart: always
environment:
GOOGLE_PROJECT: "${GOOGLE_PROJECT}"
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