microsoft · calufa · May 1, 2023 · May 2, 2023 · May 2, 2023 · May 2, 2023
diff --git a/README.md b/README.md
@@ -1,6 +1,10 @@
 # BioGPT
 This repository contains the implementation of [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9), by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 
+# Run BioGPT on Google Cloud Platform using Pulumi
+
+*To run BioGPT on Google Cloud Platform using Pulumi follow the instructions [here](https://github.com/calufa/BioGPT-Kubernetes-Pulumi-GCP/tree/main/infra).*
+
 
 # Requirements and Installation
 

diff --git a/infra/.gitignore b/infra/.gitignore
@@ -0,0 +1,3 @@
+gcp.json
+data
+Pulumi.dev.yaml
diff --git a/infra/.sample.env b/infra/.sample.env
@@ -0,0 +1,8 @@
+export NAME=biogpt
+export PROJECT={PROJECT} # <-- replace
+export REGION={REGION} # <-- replace
+export NODE_COUNT={NODE_COUNT} # <-- replace
+export MACHINE_TYPE={MACHINE_TYPE} # <-- replace
+export REPLICAS={REPLICAS} # <-- replace
+export PULUMI_CONFIG_PASSPHRASE={PULUMI_CONFIG_PASSPHRASE} # <-- replace
+export GOOGLE_APPLICATION_CREDENTIALS=./gcp.json
diff --git a/infra/Dockerfile b/infra/Dockerfile
@@ -0,0 +1,37 @@
+FROM pytorch/pytorch:1.12.0-cuda11.3-cudnn8-runtime
+
+RUN apt-get update && \
+	apt-get install -y \
+		git \
+		gcc \
+		build-essential \
+		wget
+
+WORKDIR /app
+
+# Install Fairseq
+RUN git clone https://github.com/pytorch/fairseq && \
+	cd fairseq && \
+	git checkout v0.12.0 && \
+	pip install . && \
+	python setup.py build_ext --inplace
+
+# Install Moses
+RUN git clone https://github.com/moses-smt/mosesdecoder.git
+ENV MOSES=/app/mosesdecoder
+
+# Install python dependencies
+RUN pip install \
+	sacremoses==0.0.53 \
+	scikit-learn==1.0.2 \
+	fastBPE==0.1.0 \
+	flask==2.2.4
+
+# Copy BioGPT into container
+COPY data data
+COPY server.py server.py
+COPY cmd.sh cmd.sh
+
+# Start server
+EXPOSE 80
+CMD ["bash", "cmd.sh"]
diff --git a/infra/Pulumi.yaml b/infra/Pulumi.yaml
@@ -0,0 +1,2 @@
+name: biogpt
+runtime: python
diff --git a/infra/__main__.py b/infra/__main__.py
@@ -0,0 +1,317 @@
+import pulumi
+from pulumi_gcp import projects, container, config
+from pulumi_docker import Image
+from pulumi_kubernetes import Provider
+from pulumi_kubernetes.core.v1 import Service
+from pulumi_kubernetes.apps.v1 import Deployment
+import google.auth
+from google.auth.transport.requests import Request
+from pulumi_kubernetes.apps.v1 import DaemonSet
+
+
+config = pulumi.Config()
+name = config.require("name")
+project = config.require("project")
+location = config.require("region")
+node_count = config.require_int("node_count")
+machine_type = config.require("machine_type")
+replicas = config.require_int("replicas")
+
+
+# Fetch access token from credentials
+def get_access_token():
+    scopes = ["https://www.googleapis.com/auth/cloud-platform"]
+    creds, _ = google.auth.default(scopes=scopes)
+
+    if not creds.token:
+        creds.refresh(Request())
+
+    return creds.token
+
+
+# Enable services
+container_api = projects.Service(
+    "container.googleapis.com",
+    service="container.googleapis.com",
+    project=project,
+)
+cloud_resource_manager_api = projects.Service(
+    "cloudresourcemanager.googleapis.com",
+    service="cloudresourcemanager.googleapis.com",
+    project=project,
+)
+
+# Build and push Docker image to container registry
+image = Image(
+    name,
+    image_name=f"gcr.io/{project}/{name}",
+    build={
+        "context": ".",
+        "platform": "linux/amd64",
+    },
+    registry={
+        "server": "gcr.io",
+        "username": "oauth2accesstoken",
+        "password": pulumi.Output.from_input(get_access_token()),
+    },
+    opts=pulumi.ResourceOptions(depends_on=[container_api, cloud_resource_manager_api]),
+)
+
+# Fetch GKE engine versions
+def get_engine_versions(digest):
+    return container.get_engine_versions(project=project, location=location)
+
+
+engine_versions = pulumi.Output.all([image.repo_digest]).apply(get_engine_versions)
+
+# Create Kubernetes cluster
+cluster = container.Cluster(
+    name,
+    project=project,
+    location=location,
+    initial_node_count=node_count,
+    min_master_version=engine_versions.latest_master_version,
+    node_version=engine_versions.latest_master_version,
+    node_config={
+        "machine_type": machine_type,
+        "oauth_scopes": [
+            "https://www.googleapis.com/auth/compute",
+            "https://www.googleapis.com/auth/devstorage.read_only",
+            "https://www.googleapis.com/auth/logging.write",
+            "https://www.googleapis.com/auth/monitoring",
+        ],
+        "image_type": "COS_CONTAINERD",
+        "guest_accelerator": [
+            {
+                "type": "nvidia-tesla-k80",
+                "count": 1,
+            }
+        ],
+    },
+    opts=pulumi.ResourceOptions(depends_on=[image]),
+)
+
+
+def generate_kubeconfig(name, endpoint, master_auth):
+    context = f"{project}_{location}_{name}"
+    return f"""apiVersion: v1
+clusters:
+- cluster:
+    certificate-authority-data: {master_auth['cluster_ca_certificate']}
+    server: https://{endpoint}
+  name: {context}
+contexts:
+- context:
+    cluster: {context}
+    user: {context}
+  name: {context}
+current-context: {context}
+kind: Config
+preferences: {{}}
+users:
+- name: {context}
+  user:
+    exec:
+      apiVersion: client.authentication.k8s.io/v1beta1
+      command: gke-gcloud-auth-plugin
+      installHint: Install gke-gcloud-auth-plugin for use with kubectl by following
+        https://cloud.google.com/blog/products/containers-kubernetes/kubectl-auth-changes-in-gke
+      provideClusterInfo: true
+"""
+
+
+kubeconfig = pulumi.Output.all(
+    cluster.name, cluster.endpoint, cluster.master_auth
+).apply(lambda args: generate_kubeconfig(*args))
+
+# Create a Kubernetes provider
+cluster_provider = Provider(name, kubeconfig=kubeconfig)
+
+# Deploy NVIDIA daemon set
+nvidia_gpu_device_plugin = DaemonSet(
+    "nvidia-gpu-device-plugin",
+    metadata={
+        "name": "nvidia-driver-installer",
+        "namespace": "kube-system",
+        "labels": {"k8s-app": "nvidia-driver-installer"},
+    },
+    spec={
+        "selector": {"matchLabels": {"k8s-app": "nvidia-driver-installer"}},
+        "updateStrategy": {"type": "RollingUpdate"},
+        "template": {
+            "metadata": {
+                "labels": {
+                    "name": "nvidia-driver-installer",
+                    "k8s-app": "nvidia-driver-installer",
+                }
+            },
+            "spec": {
+                "priorityClassName": "system-node-critical",
+                "affinity": {
+                    "nodeAffinity": {
+                        "requiredDuringSchedulingIgnoredDuringExecution": {
+                            "nodeSelectorTerms": [
+                                {
+                                    "matchExpressions": [
+                                        {
+                                            "key": "cloud.google.com/gke-accelerator",
+                                            "operator": "Exists",
+                                        },
+                                        {
+                                            "key": "cloud.google.com/gke-gpu-driver-version",
+                                            "operator": "DoesNotExist",
+                                        },
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                },
+                "tolerations": [{"operator": "Exists"}],
+                "hostNetwork": True,
+                "hostPID": True,
+                "volumes": [
+                    {"name": "dev", "hostPath": {"path": "/dev"}},
+                    {
+                        "name": "vulkan-icd-mount",
+                        "hostPath": {
+                            "path": "/home/kubernetes/bin/nvidia/vulkan/icd.d"
+                        },
+                    },
+                    {
+                        "name": "nvidia-install-dir-host",
+                        "hostPath": {"path": "/home/kubernetes/bin/nvidia"},
+                    },
+                    {"name": "root-mount", "hostPath": {"path": "/"}},
+                    {"name": "cos-tools", "hostPath": {"path": "/var/lib/cos-tools"}},
+                    {"name": "nvidia-config", "hostPath": {"path": "/etc/nvidia"}},
+                ],
+                "initContainers": [
+                    {
+                        "image": "cos-nvidia-installer:fixed",
+                        "imagePullPolicy": "Never",
+                        "name": "nvidia-driver-installer",
+                        "resources": {"requests": {"cpu": "150m"}},
+                        "securityContext": {"privileged": True},
+                        "env": [
+                            {
+                                "name": "NVIDIA_INSTALL_DIR_HOST",
+                                "value": "/home/kubernetes/bin/nvidia",
+                            },
+                            {
+                                "name": "NVIDIA_INSTALL_DIR_CONTAINER",
+                                "value": "/usr/local/nvidia",
+                            },
+                            {
+                                "name": "VULKAN_ICD_DIR_HOST",
+                                "value": "/home/kubernetes/bin/nvidia/vulkan/icd.d",
+                            },
+                            {
+                                "name": "VULKAN_ICD_DIR_CONTAINER",
+                                "value": "/etc/vulkan/icd.d",
+                            },
+                            {"name": "ROOT_MOUNT_DIR", "value": "/root"},
+                            {
+                                "name": "COS_TOOLS_DIR_HOST",
+                                "value": "/var/lib/cos-tools",
+                            },
+                            {
+                                "name": "COS_TOOLS_DIR_CONTAINER",
+                                "value": "/build/cos-tools",
+                            },
+                        ],
+                        "volumeMounts": [
+                            {
+                                "name": "nvidia-install-dir-host",
+                                "mountPath": "/usr/local/nvidia",
+                            },
+                            {
+                                "name": "vulkan-icd-mount",
+                                "mountPath": "/etc/vulkan/icd.d",
+                            },
+                            {"name": "dev", "mountPath": "/dev"},
+                            {"name": "root-mount", "mountPath": "/root"},
+                            {"name": "cos-tools", "mountPath": "/build/cos-tools"},
+                        ],
+                    },
+                    {
+                        "image": "gcr.io/gke-release/nvidia-partition-gpu@sha256:c54fd003948fac687c2a93a55ea6e4d47ffbd641278a9191e75e822fe72471c2",
+                        "name": "partition-gpus",
+                        "env": [
+                            {
+                                "name": "LD_LIBRARY_PATH",
+                                "value": "/usr/local/nvidia/lib64",
+                            }
+                        ],
+                        "resources": {"requests": {"cpu": "150m"}},
+                        "securityContext": {"privileged": True},
+                        "volumeMounts": [
+                            {
+                                "name": "nvidia-install-dir-host",
+                                "mountPath": "/usr/local/nvidia",
+                            },
+                            {"name": "dev", "mountPath": "/dev"},
+                            {"name": "nvidia-config", "mountPath": "/etc/nvidia"},
+                        ],
+                    },
+                ],
+                "containers": [
+                    {"image": "gcr.io/google-containers/pause:2.0", "name": "pause"}
+                ],
+            },
+        },
+    },
+    opts=pulumi.ResourceOptions(provider=cluster_provider),
+)
+
+# Create Kubernetes deployment
+deployment = Deployment(
+    name,
+    metadata={"name": name},
+    spec={
+        "strategy": {
+            "type": "Recreate",
+        },
+        "replicas": replicas,
+        "selector": {"matchLabels": {"app": name}},
+        "template": {
+            "metadata": {"labels": {"app": name}},
+            "spec": {
+                "containers": [
+                    {
+                        "name": name,
+                        "image": image.repo_digest,
+                        "resources": {"limits": {"nvidia.com/gpu": 1}},
+                        "ports": [{"containerPort": 80}],
+                    },
+                ],
+            },
+        },
+    },
+    opts=pulumi.ResourceOptions(
+        provider=cluster_provider, depends_on=[nvidia_gpu_device_plugin]
+    ),
+)
+
+# Create Kubernetes service to expose port 80
+service = Service(
+    name,
+    spec={
+        "type": "LoadBalancer",
+        "selector": {"app": name},
+        "ports": [
+            {
+                "protocol": "TCP",
+                "port": 80,
+                "targetPort": 80,
+            },
+        ],
+    },
+    opts=pulumi.ResourceOptions(provider=cluster_provider, depends_on=[deployment]),
+)
+
+# Export IP address of the LoadBalancer
+pulumi.export(
+    "load_balancer_ip",
+    service.status.apply(lambda status: status.load_balancer.ingress[0].ip),
+)
diff --git a/infra/cmd.sh b/infra/cmd.sh
@@ -0,0 +1,6 @@
+mkdir checkpoints
+cd checkpoints
+wget https://msramllasc.blob.core.windows.net/modelrelease/BioGPT/checkpoints/Pre-trained-BioGPT.tgz
+tar -zxvf Pre-trained-BioGPT.tgz
+cd ..
+python server.py
diff --git a/infra/destroy.sh b/infra/destroy.sh
@@ -0,0 +1,2 @@
+source .env
+pulumi destroy --yes --stack dev