benjha / camicroscope_slate

caMicroscope deployment https://wolf.cci.emory.edu//camic_org/apps/landing/landing.html on SLATE

caMicroscope on Slate

• caMicroscope

https://wolf.cci.emory.edu//camic_org/apps/landing/landing.html

• OLCF's SLATE

https://docs.olcf.ornl.gov/services_and_applications/slate/overview.html#what-is-slate

Preliminaries

caMicroscope uses docker-compose to start its back-end and front-end services. Details about caMicroscope deployment is available in the next link:

https://github.com/camicroscope/Distro

This repository includes the caMicroscope v3.8.4 deployment process in Slate, a k8s cluster.

The caMicroscope service naming conventions follows those denoted in the next docker-compose specification:

https://github.com/camicroscope/Distro/blob/v3.8.4/caMicroscope.yml

Services' volumes are mounted in

/gpfs/alpine/proj-shared/gen150/caMicroscope 

Services: mongodb, iipimage, SlideLoader, caracal

• Login to Slate's Marble and activate GEN150-app subproject

oc login https://api.marble.ccs.ornl.gov
oc project gen150-app

MongoDB

ca-mongo

There are two caMicroscope services related to MongoDB, ca-mongo and ca-idx. ca-mongo hosts the database and ca-idx initialize it.

In terms of Slate, ca-mongo is an stateful set paired with a service so as to be accessible accross Slate nodes. From mongo-stateful-s.yaml note that ca-mongo creates the database in CA_MONGO_ROOT that points to

/gpfs/alpine/proj-shared/gen150/caMicroscope/mongodb

To create the ca-mongo service and stateful set use the next commands:

oc create -f mongo-service.yaml
oc create -f mongo-stateful-s.yaml

run oc describe service ca-mongo-service to get the IP address of the node that is running the pod of the stateful set:

Name:              ca-mongo-service
Namespace:         gen150-app
Labels:            app=ca-mongo
Annotations:       <none>
Selector:          app=ca-mongo
Type:              ClusterIP
IP:            --> 172.25.165.159 <---
Port:              ca-mongo-port-service  27017/TCP
TargetPort:        ca-mongo-port/TCP
Endpoints:         10.34.42.71:27017
Session Affinity:  None
Events:            <none>

in this case 172.25.165.159, will be used when initializing the mongodb tables. Note this service only exposes the IP Address within Slate.

ca-idx

ca-idx is a job that calls the configuration scripts available in

https://github.com/benjha/caMicroscope_SLATE/tree/main/Distro

These scripts where updated from caMicroscope's Distro repository to support Slate.

To create the ca-idx job use the next command:

oc create -f idx-job.yaml

From idx-job.yaml note CA_MICROSCOPE_DISTRO_ROOT and CA_MONGO_HOST environment variables. In particular, CA_MONGO_HOST should be set to 172.25.165.159 which is the IP address of ca-mongo-service.

IIPImage (ca-iip)

The Docker recipe from

https://github.com/benjha/iipImage/tree/v3.8.4_Slate

is used to build a Docker image of ca-iip on Slate using the next commmand:

oc new-build https://github.com/benjha/iipImage.git#v3.8.4_Slate

To create the ca-iip deployment use the next command:

oc create -f iip-deployment.yaml

From iip-deployment.yaml note log data from apache2 and iipsrv is stored in CA_IIP_ROOT that points to

/gpfs/alpine/gen150/proj-shared/caMicroscope/apache2

Apache2 and iipsrv ports are exposed by ca-iip service specification defined in iip-service.yaml. To create the service use the next command:

oc create -f iip-service.yaml

run oc describe service ca-iip-service to get the IP address of the node that is running the pod of the ca-iip deployment:

Name:              ca-iip-service
Namespace:         gen150-app
Labels:            app=ca-iip
Annotations:       <none>
Selector:          app=ca-iip
Type:              ClusterIP
IP:           -->  172.25.129.140  <--
Port:              iip-apache-service  80/TCP
TargetPort:        ca-iip-apache/TCP
Endpoints:         10.34.42.154:80
Port:              iip-port-service  8080/TCP
TargetPort:        ca-iip-port/TCP
Endpoints:         10.34.42.154:8080
Port:              iip-port-utils  8443/TCP
TargetPort:        ca-iip-utils/TCP
Endpoints:         10.34.42.154:8443
Session Affinity:  None
Events:            <none>

in this case 172.25.129.140, will be used for coordination. Note this service only exposes the IP Address within Slate.

SliderLoader (ca-load)

Caracal (ca-back)

The Docker recipe from

https://github.com/camicroscope/Caracal/blob/v3.8.4/Dockerfile

is used to build a Docker image of ca-back on Slate using the next command:

oc new-build https://github.com/camicroscope/caracal.git#v3.8.4 --build-arg "viewer=v3.8.4"

to verify that the caracal image is available on Slate type:

oc get imagestream

this is a sample of the output:

NAME           IMAGE REPOSITORY                                            TAGS              UPDATED
...
caracal        registry.apps.marble.ccs.ornl.gov/gen150-app/caracal                          
...

The back-deployment.yaml specification configures the ca-back deployment. Environment variables of the container are based on those defined in:

https://github.com/camicroscope/Distro/blob/v3.8.4/caMicroscope.yml

note DISABLE_SEC and ALLOW_PUBLIC are set to true given that Slate provides authentification services. Also note MONGO_URI is set to the IP address of ca-mongo-service and IIP_PATH is set to the IP address of ca-iip-service.