8. Service Operations¶
In this section you can find the common operational activities related to keep the service available to our users.
8.1. Initial set-up¶
8.1.1. Notebooks VO¶
The resources used for the Notebooks deployments are managed with the
vo.notebooks.egi.eu VO. Operators of the service should join the VO, check
the entry at the operations portal
and at AppDB.
8.1.2. Clients installation¶
In order to manage the resources you will need these tools installed on your client machine:
egiclifor discovering sites and managing tokens,terraformto create the VMs at the providers,ansibleto configure the VMs and install kubernetes at the providers,terraform-inventoryto get the list of hosts to use from terraform.
8.1.3. Get the configuration repo¶
All the configuration of the notebooks is stored at a git repo available in
keybase. You’ll need to be part of the opslife team in keybase to access.
Start by cloning the repo:
$ git clone keybase://team/opslife/egi-notebooks
8.2. Kubernetes¶
We use terraform and ansible to build the cluster at one of the EGI Cloud
providers. If you are building the cluster for the first time, create a new
directory on your local git repository from the template, add it to the
repo, and get terraform ready:
$ cp -a template <new provider>
$ git add <new provider>
$ cd <new provider>/terraform
$ terraform init
Using the egicli you can get the list of projects and their ids
for a given site:
$ egicli endpoint projects --site CESGA
id Name enabled site
-------------------------------- ------------------- --------- ------
3a8e9d966e644405bf19b536adf7743d vo.access.egi.eu True CESGA
916506ac136741c28e4326975eef0bff vo.emso-eric.eu True CESGA
b1d2ef2cc2284c57bcde21cf4ab141e3 vo.nextgeoss.eu True CESGA
eb7ff20e603d471cb731bdb83a95a2b5 fedcloud.egi.eu True CESGA
fcaf23d103c1485694e7494a59ee5f09 vo.notebooks.egi.eu True CESGA
And with the project ID, you can obtain all the environment variables needed to interact with the OpenStack APIs of the site:
$ eval "$(egicli endpoint env --site CESGA --project-id fcaf23d103c1485694e7494a59ee5f09)"
Now you are ready to use the openstack or terraform at the site. The token obtained is valid for 1 hour, you can refresh it at any time with:
$ eval "$(egicli endpoint token --site CESGA --project-id fcaf23d103c1485694e7494a59ee5f09)"
First get the network IDs and pool to use for the site:
$ openstack network list
+--------------------------------------+-------------------------+--------------------------------------+
| ID | Name | Subnets |
+--------------------------------------+-------------------------+--------------------------------------+
| 1aaf20b6-47a1-47ef-972e-7b36872f678f | net-vo.notebooks.egi.eu | 6465a327-c261-4391-a0f5-d503cc2d43d3 |
| 6174db12-932f-4ee3-bb3e-7a0ca070d8f2 | public00 | 6af8c4f3-8e2e-405d-adea-c0b374c5bd99 |
+--------------------------------------+-------------------------+--------------------------------------+
In this case we will use public00 as the pool for public IPs and
1aaf20b6-47a1-47ef-972e-7b36872f678f as the network ID. Check with the provider
which is the right network to use. Use these values in the terraform.tfvars
file:
ip_pool = "public00"
net_id = "1aaf20b6-47a1-47ef-972e-7b36872f678f"
You may want to check the right flavors for your VMs and adapt other variables
in terraform.tfvars. To get a list of flavors you can use:
$ openstack flavor list
+--------------------------------------+----------------+-------+------+-----------+-------+-----------+
| ID | Name | RAM | Disk | Ephemeral | VCPUs | Is Public |
+--------------------------------------+----------------+-------+------+-----------+-------+-----------+
| 26d14547-96f2-4751-a686-f89a9f7cd9cc | cor4mem8hd40 | 8192 | 40 | 0 | 4 | True |
| 42eb9c81-e556-4b63-bc19-4c9fb735e344 | cor2mem2hd20 | 2048 | 20 | 0 | 2 | True |
| 4787d9fc-3923-4fc9-b770-30966fc3baee | cor4mem4hd40 | 4096 | 40 | 0 | 4 | True |
| 58586b06-7b9d-47af-b9d0-e16d49497d09 | cor24mem62hd60 | 63488 | 60 | 0 | 24 | True |
| 635c739a-692f-4890-b8fd-d50963bff00e | cor1mem1hd10 | 1024 | 10 | 0 | 1 | True |
| 6ba0080d-d71c-4aff-b6f9-b5a9484097f8 | small | 512 | 2 | 0 | 1 | True |
| 6e514065-9013-4ce1-908a-0dcc173125e4 | cor2mem4hd20 | 4096 | 20 | 0 | 2 | True |
| 85f66ce6-0b66-4889-a0bf-df8dc23ee540 | cor1mem2hd10 | 2048 | 10 | 0 | 1 | True |
| c4aa496b-4684-4a86-bd7f-3a67c04b1fa6 | cor24mem50hd50 | 51200 | 50 | 0 | 24 | True |
| edac68c3-50ea-42c2-ae1d-76b8beb306b5 | test-bigHD | 4096 | 237 | 0 | 2 | True |
+--------------------------------------+----------------+-------+------+-----------+-------+-----------+
Finally ensure your public ssh key is also listed in the cloud-init.yaml
file and then you are ready to deploy the cluster with:
$ terraform apply
Your VMs are up and running, it’s time to get kubernetes configured and running with ansible:
$ cd .. # you should be now in <new provider>
$ ANSIBLE_TRANSFORM_INVALID_GROUP_CHARS=silently TF_STATE=./terraform \
ansible-playbook --inventory-file=$(which terraform-inventory) \
playbooks/k8s.yaml
8.2.1. Interacting with the cluster¶
As the master will be on a private IP, you won’t be able to directly interact
with it, but you can still ssh into the VM using the ingress node as a gateway
host (you can get the different hosts with TF_STATE=./terraform terraform-inventory --inventory)
$ ssh -o ProxyCommand="ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -W %h:%p -q egi@<ingress ip>" \
-o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null egi@<master ip>
egi@k8s-master:~$ kubectl get nodes
NAME STATUS ROLES AGE VERSION
k8s-master Ready master 33m v1.15.7
k8s-nfs Ready <none> 16m v1.15.7
k8s-w-ingress Ready <none> 16m v1.15.7
egi@k8s-master:~$ helm list
NAME REVISION UPDATED STATUS CHART APP VERSION NAMESPACE
certs-man 2 Wed Jan 8 15:56:58 2020 DEPLOYED cert-manager-v0.11.0 v0.11.0 cert-manager
cluster-ingress 3 Wed Jan 8 15:56:53 2020 DEPLOYED nginx-ingress-1.7.0 0.24.1 kube-system
nfs-provisioner 3 Wed Jan 8 15:56:43 2020 DEPLOYED nfs-client-provisioner-1.2.8 3.1.0 kube-system
8.2.2. Modifying/Destroying the cluster¶
You should be able to change the number of workers in the cluster and re-apply terraform to start them and then execute the playbook to get them added to the cluster.
Any changes in the master, NFS or ingress VMs should be done carfully as those will probably break the configuration of the kubernetes cluster and of any application running on top.
Destroying the cluster can be done with a single command:
$ terraform destroy
8.3. Notebooks deployments¶
Once the k8s cluster is up and running, you can deploy a notebooks instance. For each deployment you should create a file in the deployments directory following the template provided:
$ cp deployments/hub.yaml.template deployments/hub.yaml
Each deployment will need a domain name pointing to your ingress host, you can create one at the FedCloud dynamic DNS service.
Then you will need to create an OpenID Connect client for EGI Check-in to authorise users
into the new deployment. You can create a client by going to the Check-in demo
OIDC clients management.
Use the following as redirect URL: https://<your host domain name>/hub/oauth_callback.
In the Access tab, add offline_access to the list of scopes. Save the
client and take note of the client ID and client secret for later.
Finally you will also need 3 different random strings generated with
openssl rand -hex 32 that will be used as secrets in the file describing
the deployment.
Go and edit the deployment description file to add this information (search for
# FIXME NEEDS INPUT in the file to quickly get there)
For deploying the notebooks instance we will also use ansible:
$ ANSIBLE_TRANSFORM_INVALID_GROUP_CHARS=silently TF_STATE=./terraform ansible-playbook \
--inventory-file=$(which terraform-inventory) playbooks/notebooks.yaml
The first deployment trial may fail due to a timeout caused by the downloading of the container images needed. You can retry after a while to re-deploy.
In the master you can check the status of your deployment (the name of the deployment will be the same as the name of your local deployment file):
$ helm status hub
LAST DEPLOYED: Thu Jan 9 08:14:49 2020
NAMESPACE: hub
STATUS: DEPLOYED
RESOURCES:
==> v1/ServiceAccount
NAME SECRETS AGE
hub 1 6m46s
user-scheduler 1 3m34s
==> v1/Service
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
hub ClusterIP 10.100.77.129 <none> 8081/TCP 6m46s
proxy-public NodePort 10.107.127.44 <none> 443:32083/TCP,80:30581/TCP 6m45s
proxy-api ClusterIP 10.103.195.6 <none> 8001/TCP 6m45s
==> v1/ConfigMap
NAME DATA AGE
hub-config 4 6m47s
user-scheduler 1 3m35s
==> v1/PersistentVolumeClaim
NAME STATUS VOLUME CAPACITY ACCESS MODES STORAGECLASS AGE
hub-db-dir Pending managed-nfs-storage 6m46s
==> v1/ClusterRole
NAME AGE
hub-user-scheduler-complementary 3m34s
==> v1/ClusterRoleBinding
NAME AGE
hub-user-scheduler-base 3m34s
hub-user-scheduler-complementary 3m34s
==> v1/RoleBinding
NAME AGE
hub 6m46s
==> v1/Pod(related)
NAME READY STATUS RESTARTS AGE
continuous-image-puller-flf5t 1/1 Running 0 3m34s
continuous-image-puller-scr49 1/1 Running 0 3m34s
hub-569596fc54-vjbms 0/1 Pending 0 3m30s
proxy-79fb6d57c5-nj8n2 1/1 Running 0 2m22s
user-scheduler-9685d654b-9zt5d 1/1 Running 0 3m30s
user-scheduler-9685d654b-k8v9p 1/1 Running 0 3m30s
==> v1/Secret
NAME TYPE DATA AGE
hub-secret Opaque 3 6m47s
==> v1/DaemonSet
NAME DESIRED CURRENT READY UP-TO-DATE AVAILABLE NODE SELECTOR AGE
continuous-image-puller 2 2 2 2 2 <none> 3m34s
==> v1/Deployment
NAME DESIRED CURRENT UP-TO-DATE AVAILABLE AGE
hub 1 1 1 0 6m45s
proxy 1 1 1 1 6m45s
user-scheduler 2 2 2 2 3m32s
==> v1/StatefulSet
NAME DESIRED CURRENT AGE
user-placeholder 0 0 6m44s
==> v1beta1/Ingress
NAME HOSTS ADDRESS PORTS AGE
jupyterhub notebooktest.fedcloud-tf.fedcloud.eu 80, 443 6m44s
==> v1beta1/PodDisruptionBudget
NAME MIN AVAILABLE MAX UNAVAILABLE ALLOWED DISRUPTIONS AGE
hub 1 N/A 0 6m48s
proxy 1 N/A 0 6m48s
user-placeholder 0 N/A 0 6m48s
user-scheduler 1 N/A 1 6m47s
==> v1/Role
NAME AGE
hub 6m46s
NOTES:
Thank you for installing JupyterHub!
Your release is named hub and installed into the namespace hub.
You can find if the hub and proxy is ready by doing:
kubectl --namespace=hub get pod
and watching for both those pods to be in status 'Running'.
You can find the public IP of the JupyterHub by doing:
kubectl --namespace=hub get svc proxy-public
It might take a few minutes for it to appear!
Note that this is still an alpha release! If you have questions, feel free to
1. Read the guide at https://z2jh.jupyter.org
2. Chat with us at https://gitter.im/jupyterhub/jupyterhub
3. File issues at https://github.com/jupyterhub/zero-to-jupyterhub-k8s/issues
8.3.1. Updating a deployment¶
Just edit the deployment description file and run ansible again. The helm will be upgraded at the cluster.