feat: nvidia nim for drug discovery

tutorials-and-examples/nvidia-nim/blueprints/README.md

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+### NVIDIA NIM Blueprints on GKE
+
+Here you will find the NVIDIA NIM Blueprints that can be provisioned to run on GKE. These are good for proof of concepts only.
+
+- [ ] [Generative Virtual Screening for Drug Discovery](./drugdiscovery/README.md) uses 3 NIMs
+  - AlphaFold2
+  - MolMIM
+  - DiffDock

tutorials-and-examples/nvidia-nim/blueprints/drugdiscovery/README.md

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+# Generative Virtual Screening for Drug Discovery on GKE
+
+This guide outlines the steps to deploy NVIDIA's NIM blueprint for [Generative Virtual screening for Drug Discovery](https://build.nvidia.com/nvidia/generative-virtual-screening-for-drug-discovery) on a Google Kubernetes Engine (GKE) cluster. Three NIMs - AlphaFold2, MolMIM & DiffDock are used to demonstrate Protein folding, molecular generation and protein docking.
+
+## Prerequisites
+
+* **GCloud SDK:** Ensure you have the Google Cloud SDK installed and configured.
+* **Project:**  A Google Cloud project with billing enabled.
+* **NGC API Key:** An API key from NVIDIA NGC.
+* **kubectl:**  kubectl command-line tool installed and configured.
+
+Clone the repo before proceeding further:
+`git clone https://github.com/GoogleCloudPlatform/ai-on-gke`
+`cd ai-on-gke/tutorials-and-examples/nvidia-nim/blueprints/drugdiscovery`
+
+## Deployment Steps
+
+1. **Set Project and Variables:**
+
+    ```bash
+
+    gcloud config set project "<GCP Project ID>"
+    export PROJECT_ID=$(gcloud config get project)
+    export CLUSTER_NAME="gke-nimbp-genscr"
+    export NODE_POOL_NAME="gke-nimbp-genscr-np"
+    export ZONE="<GCP zone>" #us-east5-b
+    export MACHINE_TYPE= "<GCP machine type>" #"a2-ultragpu-1g"
+    export ACCELERATOR_TYPE="<GPU Type>" #"nvidia-a100-80gb"
+    export ACCELERATOR_COUNT="1"
+    export NODE_POOL_NODES=3
+    export NGC_API_KEY="<NGC API Key>"
+
+    ```
+
+2. **Create GKE Cluster:** This creates the initial cluster with a default node pool for management tasks. GPU nodes will be added in the next step.
+
+    ```bash
+
+    gcloud container clusters create "${CLUSTER_NAME}" \
+      --project="${PROJECT_ID}" \
+      --num-nodes=1 --location="${ZONE}" \
+      --machine-type=e2-standard-16 \
+      --addons=GcpFilestoreCsiDriver
+  
+    ```
+
+3. **Create GPU Node Pool:** This creates a node pool with GPU machines optimized for BioNeMo workloads.
+
+    ```bash
+
+    gcloud container node-pools create "${NODE_POOL_NAME}" \
+        --cluster="${CLUSTER_NAME}" \
+        --location="${ZONE}" \
+        --node-locations="${ZONE}" \
+        --num-nodes="${NODE_POOL_NODES}" \
+        --machine-type="${MACHINE_TYPE}" \
+        --accelerator="type=${ACCELERATOR_TYPE},count=${ACCELERATOR_COUNT},gpu-driver-version=LATEST" \
+        --placement-type="COMPACT" \
+        --disk-type="pd-ssd" \
+        --disk-size="500GB"
+    
+    ```
+
+4. **Get Cluster Credentials:**
+
+    ```bash
+
+    gcloud container clusters get-credentials "${CLUSTER_NAME}" --location="${ZONE}"
+
+    ```
+
+5. **Set kubectl Alias (Optional):**
+
+    ```bash
+    
+    alias k=kubectl
+
+    ```
+
+6. **Create NGC Secret:** Creates the secret for pulling images from NVIDIA NGC.  **Important:** Replace the placeholder API key with your actual NGC API Key.
+
+    ```bash
+
+    k create secret docker-registry secret-nvcr \
+      --docker-username=\$oauthtoken \
+      --docker-password="${NGC_API_KEY}" \
+      --docker-server="nvcr.io"
+    
+    ```
+
+7. **Deploy BioNeMo Services:** Deploy AlphaFold2, MolMIM, and DiffDock.
+
+    ```bash
+
+    k create -f nim-storage-filestore.yaml
+    k create -f nim-bionemo-generative-virtual-screening.yaml 
+
+    ```
+
+8. **Port Forwarding (for local testing):**  These commands forward the service ports to your local machine for testing. Replace the pod names with the actual names of your deployed pods.
+
+    ```bash
+
+    POD_BIONEMO_ALPHAFOLD=$(k get pods -o go-template --template '{{range .items}}{{.metadata.name}}{{"\n"}}{{end}}' | grep '^alphafold2')
+    k port-forward pod/$POD_BIONEMO_ALPHAFOLD :8000
+
+    POD_BIONEMO_MOLMIM=$(k get pods -o go-template --template '{{range .items}}{{.metadata.name}}{{"\n"}}{{end}}' | grep '^molmim')
+    k port-forward pod/$POD_BIONEMO_MOLMIM :8000
+    
+    POD_BIONEMO_DIFFDOCK=$(k get pods -o go-template --template '{{range .items}}{{.metadata.name}}{{"\n"}}{{end}}' | grep '^diffdock')
+    k port-forward pod/$POD_BIONEMO_DIFFDOCK :8000
+  
+    ```
+
+9. **Test Deployments:**  Use `curl` or other tools to test the deployed services by sending requests to the forwarded ports.  Examples are provided in the `dev.sh` file.
+
+    ```bash
+  
+    # AlphaFold2
+    curl \
+    --max-time 900 \
+    -X POST \
+    -i \
+    "http://localhost:62921/protein-structure/alphafold2/predict-structure-from-sequence" \
+    -H 'accept: application/json' \
+    -H 'Content-Type: application/json' \
+    -d '{
+      "sequence": "MVPSAGQLALFALGIVLAACQALENSTSPLSADPPVAAAVVSHFNDCPDSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLLAVVAASQKKQAITALVVVSIVALAVLIITCVLIHCCQVRKHCEWCRALICRHEKPSALLKGRTACCHSETVV",
+      "databases": [
+        "small_bfd"
+      ]
+    }'
+  
+    ```
+
+    ```bash
+  
+    # MolMIM
+    curl -X POST \
+    -H 'Content-Type: application/json' \
+    -d '{
+      "smi": "CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C",
+      "num_molecules": 5,
+      "algorithm": "CMA-ES",
+      "property_name": "QED",
+      "min_similarity": 0.7,
+      "iterations": 10
+    }' \
+    "http://localhost:49530/generate"
+  
+    ```
+
+10. **Test end to end:**
+    Update the AF2_HOST, MOLMIM_HOST and DIFFDOCK_HOST variables with port numbers in `test-generative-virtual-screening.py` file.
+
+    ```bash
+
+    python3 -m venv venv
+    source venv/bin/activate
+    pip3 install requests
+    python3 test-generative-virtual-screening.py
+    deactivate
+
+    ```
+
+## Cleanup
+
+   To delete the cluster and all associated resources:
+
+   ```bash
+
+   k delete secret secret-nvcr
+   k delete -f nim-bionemo-generative-virtual-screening.yaml
+   k delete -f nim-storage-filestore.yaml
+   gcloud container clusters delete "${CLUSTER_NAME}" --location="${ZONE}"
+
+   ```

tutorials-and-examples/nvidia-nim/blueprints/drugdiscovery/nim-bionemo-generative-virtual-screening.yaml

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+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: alphafold2
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: alphafold2
+  template:
+    metadata:
+      labels:
+        app: alphafold2
+    spec:
+      containers:
+      - name: alphafold2
+        image: nvcr.io/nim/deepmind/alphafold2:2.1.0
+        securityContext:
+          runAsUser: 0
+        ports:
+        - containerPort: 8000
+        volumeMounts:
+        - name: alphafold2-cache
+          mountPath: /data
+        env:
+        - name: NGC_API_KEY
+          valueFrom:
+            secretKeyRef:
+              name: ngc-api-key  # Replace with your actual secret name
+              key: NGC_API_KEY
+        - name: NIM_CACHE_PATH
+          value: /data
+        - name: NIM_MODEL_ORG
+          value: nim
+        - name: NIM_MODEL_TEAM
+          value: deepmind
+        resources:
+          requests:
+            nvidia.com/gpu: 1
+          limits:
+            nvidia.com/gpu: 1
+      volumes:
+      - name: alphafold2-cache
+        persistentVolumeClaim:
+          claimName: nim-storage-filestore
+      imagePullSecrets:
+      - name: secret-nvcr
+
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: molmim
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: molmim
+  template:
+    metadata:
+      labels:
+        app: molmim
+    spec:
+      containers:
+      - name: molmim
+        image: nvcr.io/nim/nvidia/molmim:1.0.0
+        securityContext:
+          runAsUser: 0
+        ports:
+        - containerPort: 8000
+        volumeMounts:
+        - name: molmim-cache
+          mountPath: /data
+        env:
+        - name: NGC_API_KEY
+          valueFrom:
+            secretKeyRef:
+              name: ngc-api-key  # Replace with your actual secret name
+              key: NGC_API_KEY
+        - name: NIM_CACHE_PATH
+          value: /data
+        resources:
+          requests:
+            nvidia.com/gpu: 1
+          limits:
+            nvidia.com/gpu: 1
+      volumes:
+      - name: molmim-cache
+        persistentVolumeClaim:
+          claimName: nim-storage-filestore
+      imagePullSecrets:
+      - name: secret-nvcr
+
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: diffdock
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: diffdock
+  template:
+    metadata:
+      labels:
+        app: diffdock
+    spec:
+      containers:
+      - name: diffdock
+        image: nvcr.io/nim/mit/diffdock:2.0
+        securityContext:
+          runAsUser: 0
+        ports:
+        - containerPort: 8000
+        volumeMounts:
+        - name: diffdock-cache
+          mountPath: /data
+        env:
+        - name: NGC_API_KEY
+          valueFrom:
+            secretKeyRef:
+              name: ngc-api-key  # Replace with your actual secret name
+              key: NGC_API_KEY
+        - name: NVIDIA_VISIBLE_DEVICES
+          value: "0"  # Set the default value here
+        - name: NIM_CACHE_PATH
+          value: /data
+        resources:
+          requests:
+            nvidia.com/gpu: 1
+          limits:
+            nvidia.com/gpu: 1
+      imagePullSecrets:
+      - name: secret-nvcr
+      volumes:
+      - name: diffdock-cache
+        persistentVolumeClaim:
+          claimName: nim-storage-filestore
+
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: alphafold2-service
+spec:
+  selector:
+    app: alphafold2
+  ports:
+  - protocol: TCP
+    port: 8081
+    targetPort: 8000
+
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: diffdock-service
+spec:
+  selector:
+    app: diffdock
+  ports:
+  - protocol: TCP
+    port: 8082
+    targetPort: 8000
+
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: molmim-service
+spec:
+  selector:
+    app: molmim
+  ports:
+  - protocol: TCP
+    port: 8083
+    targetPort: 8000
+
+---
+# Create a Secret to hold the NGC API key
+apiVersion: v1
+kind: Secret
+metadata:
+  name: ngc-api-key
+type: Opaque
+stringData:
+  NGC_API_KEY: <NGC API Key>