Dariusz

Trawinski

July 19, 2022

January 26, 2023

Deploy AI Inference with OpenVINO™ and Kubernetes

Introduction

Model servers play a vital role in bringing AI models from development to production. Models are served via network endpoints which expose APIs to run predictions. These microservices abstract inference execution while providing scalability and efficient resource utilization.

In this blog, you will learn how to use key features of the OpenVINO™ Operator for Kubernetes. We will demonstrate how to deploy and use OpenVINO Model Server in two scenarios:

1. Serving a single model
2. Serving a pipeline of multiple models

Kubernetes provides an optimal environment for deploying model servers but managing these resources can be challenging in larger-scale deployments. Using our Operator for Kubernetes makes this easier.

Install via OperatorHub

The OpenVINO Operator can be installed in a Kubernetes cluster from the OperatorHub. Just search for OpenVINO and click the 'Install' button.

Serve a Single OpenVINO Model in Kubernetes

Create a new instance of OpenVINO Model Server by defining a custom resource called ModelServer using the provided CRD. All parameters are explained here.
In the sample below, a fully functional model server is deployed along with a ResNet-50 image classification model pulled from Google Cloud storage.

kubectl apply -f https://raw.githubusercontent.com/openvinotoolkit/operator/main/config/samples/intel_v1alpha1_ovms.y...

A successful deployment will create a service called ovms-sample.

kubectl get service
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
ovms-sample ClusterIP 10.98.164.11 <none> 8080/TCP,8081/TCP 5m30s

Now that the model is deployed and ready for requests, we can use the ovms-sample service with our Python client known as ovmsclient.

Send Inference Requests to the Service

The example below shows how to use the ovms-sample service inside the same Kubernetes cluster where it’s running. To create a client container, launch an interactive session to a pod with Python installed:

kubectl create deployment client-test --image=python:3.8.13 -- sleep infinity
kubectl exec -it $(kubectl get pod -o jsonpath="{.items[0].metadata.name}" -l app=client-test) -- bash

From inside the client container, we will connect to the model server API endpoints. A simple curl command lists the served models with their version and status:

curl http://ovms-sample:8081/v1/config
{
"resnet" : 
{
  "model_version_status": [
   {
    "version": "1",
    "state": "AVAILABLE",
    "status": {
    "error_code": "OK",
    "error_message": "OK"
   }
  }
 ]
}

Additional REST API calls are described in the documentation.

Now let’s use the ovmsclient Python library to process an inference request. Create a virtual environment and install the client with pip:

python3 -m venv /tmp/venv
source /tmp/venv/bin/activate
pip install ovmsclient

Download a sample image of a zebra:

curl https://raw.githubusercontent.com/openvinotoolkit/model_server/main/demos/common/static/images/zebra... -o /tmp/zebra.jpeg

The Python code below collects the model metadata using the ovmsclient library:

from ovmsclient import make_grpc_client
client = make_grpc_client("ovms-sample:8080")
model_metadata = client.get_model_metadata(model_name="resnet")
print(model_metadata)

The code above returns the following response:

{'model_version': 1, 'inputs': {'map/TensorArrayStack/TensorArrayGatherV3:0': {'shape': [-1, -1, -1, -1], 'dtype': 'DT_FLOAT'}}, 'outputs': {'softmax_tensor': {'shape': [-1, 1001], 'dtype': 'DT_FLOAT'}}}

Now create a simple Python script to classify the JPEG image of the zebra :

cat >> /tmp/predict.py <<EOL
from ovmsclient import make_grpc_client
import numpy as np
client = make_grpc_client("ovms-sample:8080")
with open("/tmp/zebra.jpeg", "rb") as f:
data = f.read()
inputs = {"map/TensorArrayStack/TensorArrayGatherV3:0": data}
results = client.predict(inputs=inputs, model_name="resnet")
print("Detected class:", np.argmax(results))
EOL

python /tmp/predict.py
Detected class: 341

The detected class from imagenet is 341, which represents `zebra`.

Serve a Multi-Model Pipeline

Now that we have run a simple example of serving a single model, let’s explore the more advanced scenario of a multi-model vehicle analysis pipeline. This pipeline leverages the Directed Acyclic Graph feature in OpenVINO Model Server.

The remaining steps in this demo require `mc` minio client binary and access to an S3-compatible bucket. See the quick start with MinIO for more information about setting up S3 storage in your cluster.

First, prepare all dependencies using the vehicle analysis pipeline example below:

git clone https://github.com/openvinotoolkit/model_server
cd model_server/demos/vehicle_analysis_pipeline/python
make

The command above downloads the required models and builds a custom library to run the pipeline, then places these files in the workspace directory. Copy these files to a shared S3-compatible storage accessible within the cluster (like MinIO). In the example below, the S3 server alias is mys3:

mc cp --recursive workspace/vehicle-detection-0202 mys3/models-repository/
mc cp --recursive workspace/vehicle-attributes-recognition-barrier-0042 mys3/models-repository/
mc ls -r mys3
43MiB models-repository/vehicle-attributes-recognition-barrier-0042/1/vehicle-attributes-recognition-barrier-0042.bin
118KiB models-repository/vehicle-attributes-recognition-barrier-0042/1/vehicle-attributes-recognition-barrier-0042.xml
7.1MiB models-repository/vehicle-detection-0202/1/vehicle-detection-0202.bin
331KiB models-repository/vehicle-detection-0202/1/vehicle-detection-0202.xml

To use the previously created model server config file in `workspace/config.json`, we need to adjust the paths to models and the custom node library. The commands below change the model paths to use our S3 bucket and the custom node library to `/config` directory which will be mounted as a Kubernetes configmap.

sed -i 's/\/workspace\/vehicle-detection-0202/s3:\/\/models-repository\/vehicle-detection-0202/g' workspace/config.json
sed -i 's/\/workspace\/vehicle-attributes-recognition-barrier-0042/s3:\/\/models-repository\/vehicle-attributes-recognition-barrier-0042/g' workspace/config.json
sed -i 's/workspace\/lib/config/g' workspace/config.json

Next, add both the config file and the custom name library to a Kubernetes config map:

kubectl create configmap ovms-pipeline --from-file=config.json=workspace/config.json \
--from-file=libcustom_node_model_zoo_intel_object_detection.so=workspace/lib/libcustom_node_model_zoo_intel_object_detection.so

Now we are ready to deploy the model server with the pipeline configuration. Use kubectl to apply the following ovms-pipeline.yaml configuration:

apiVersion: intel.com/v1alpha1
kind: ModelServer
metadata:
  name: ovms-pipeline
spec:
  image_name: openvino/model_server:latest
  deployment_parameters:
    replicas: 1
  models_settings:
    single_model_mode: false
    config_configmap_name: "ovms-pipeline"
  server_settings:
    file_system_poll_wait_seconds: 0
    log_level: "INFO"
  service_parameters:
    grpc_port: 8080
    rest_port: 8081
    service_type: ClusterIP
  models_repository:
storage_type: "s3"
    aws_access_key_id: minioadmin
    aws_secret_access_key: minioadmin
    aws_region: us-east-1
    s3_compat_api_endpoint: http://mys3.example.com:9000

kubectl apply -f ovms-pipeline.yaml

This creates the model serving service

kubectl get service
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
ovms-pipeline ClusterIP 10.99.53.175 <none> 8080/TCP,8081/TCP 26m

To test the pipeline, we can use the same client container as the previous example with a single model. From inside the client container shell, download a sample image to analyze:

curl https://raw.githubusercontent.com/openvinotoolkit/model_server/main/demos/common/static/images/cars/... -o /tmp/road1.jpg

cat >> /tmp/pipeline.py <<EOL
from ovmsclient import make_grpc_client
import numpy as np
client = make_grpc_client("ovms-pipeline:8080")
with open("/tmp/road1.jpg", "rb") as f:
data = f.read()
inputs = {"image": data}
results = client.predict(inputs=inputs, model_name="multiple_vehicle_recognition")
print("Returned outputs:",results.keys())
EOL

Run a prediction using the following command:

python /tmp/pipeline.py
Returned outputs: dict_keys(['colors', 'vehicle_coordinates', 'types', 'vehicle_images', 'confidence_levels'])

The sample code above returns a list of the pipeline outputs without data interpretation. More complete client code samples for vehicle analysis are available on GitHub.

Conclusion

OpenVINO Model Server makes it easy to deploy and manage inference as a service in Kubernetes environments. In this blog, we learned how to run predictions using the ovmsclient Python library with both a single model scenario and with multiple models using a DAG pipeline.

Learn more about the OpenVINO Operator: https://github.com/openvinotoolkit/operator

Check out our other model serving demos.

OpenVINO GenAI Serving (OGS) update

October 25, 2024

Authors: Xiake Sun, Su Yang, Tianmeng Chen, Tong Qiu

openvino.genai/samples/cpp/rag_sample at openvino_genai_serving · sammysun0711/openvino.genai (github.com)

OpenVINO GenAI Server (OGS) Update:

-Update LLM: stream generation, reset handle, multi-round chat, model cache config

-Support VLM

-Support Reranker for RAG sample

-Support BLIP image embedding for photo search with DB

-Support C++ GUI with imgui for photo search

Now we scale the text embedding to image embedding for RAG sample and support multi-Vector Retriever for RAG.

Multi-Vector Retriever for RAG on text: QA over Document
Multi-Vector Retriever for RAG on image: Photo search with DB retrieval

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Here is a photo search sample with image embedding.

Usage 2: Photo Search with DB retrieval

Steps:

1.use python client to create image vector DB (PostgreSQL)

2.use GUI to search image

Here is a sample image to demonstrate GUI usage on client platform. we search the bus photo with top 10 similar images from the 100 images which are embedded into Vector DB.

Usage 3: Chat with images via MiniCPM-V

Once we have created a multimodal vector DB through image embedding, we can further communicate with the image through VLM.

We integrate the C++ GenAI sample visual_language_chat with openbmb/MiniCPM-V-2_6.

Here is the demo image on client platform.

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OpenVINO GenAI Serving (OGS)

July 4, 2024

October 25, 2024

Authors: Fiona Zhao, Xiake Sun, Wenyi Zou, Su Yang, Tianmeng Chen

Model Server reference implementation based on OpenVINO GenAI Package for Edge/Client AI PC Use Case.

openvino.genai/samples/cpp/rag_sample at openvino_genai_serving · sammysun0711/openvino.genai (github.com)

Use Case 1: C++ RAG Sample that supports most popular models like LLaMA 2

This example showcases for Retrieval-Augmented Generation based on text-generation Large Language Models (LLMs): chatglm, LLaMA, Qwen and other models with the same signature and Bert model for embedding feature extraction. The sample fearures ov::genai::LLMPipeline and configures it for the chat scenario. There is also a Jupyter notebook which provides an example of LLM-powered RAG in Python.

Download and convert the model and tokenizers

The --upgrade-strategy eager option is needed to ensure optimum-intel is upgraded to the latest version.

python3 -m pip install --upgrade-strategy eager -r ../../requirements.txt
optimum-cli export openvino --trust-remote-code --model TinyLlama/TinyLlama-1.1B-Chat-v1.0 TinyLlama-1.1B-Chat-v1.0

Setup of PostgreSQL, Libpqxx and Pgvector

Langchain's document Loader and Spliter

Load: document_loaders is used to load document data.
Split: text_splitter breaks large Documents into smaller chunks. This is useful both for indexing data and for passing it in to a model, since large chunks are harder to search over and won’t in a model’s finite context window.

PostgreSQL

Download postgresql from enterprisedb.(postgresql-16.2-1-windows-x64.exe is tested)

Install PostgreSQL with postgresqltutorial.
Setup of PostgreSQL:
1. Open pgAdmin 4 from Windows Search Bar.
2. Click Browser (left side) > Servers > Postgre SQL 10.
3. Create the user postgres with password openvino (or your own setting)
4. Open SQL Shell from Windows Search Bar to check this setup. 'Enter' to set Server, Database, Port, Username as default and type Password.

Server [localhost]: 
Database [postgres]:
Port [5432]:
Username [postgres]:
Password for user postgres:

libpqxx

'Official' C++ client library (language binding), built on top of C library

Update the source code from https://github.com/jtv/libpqxx in deps\libpqxx

The pipeline connects with DB based on Libpqxx.

pgvector

Open-source vector similarity search for Postgres.

By default, pgvector performs exact nearest neighbor search, which provides perfect recall. It also supports approximate nearest neighbor search (HNSW), which trades some recall for speed.

For Windows, Ensure C++ support in Visual Studio 2022 is installed, then use nmake to build in Command Prompt for VS 2022(run as Administrator). Please follow with the pgvector

Enable the extension (do this once in each database where you want to use it), run SQL Shell from Windows Search Bar with "CREATE EXTENSION vector;".

Printing CREATE EXTENSION shows successful setup of Pgvector.

pgvector-cpp

pgvector support for C++ (supports libpqxx). The headers (pqxx.hpp, vector.hpp, halfvec.hpp) are copied into the local folder rag_sample\include. Our pipeline does the vector similarity search for the chunks embeddings in PostgreSQL, based on pgvector-cpp.

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Install OpenVINO, VS2022 and Build this pipeline

Download 2024.2 release from OpenVINO™ archives*. This OV built package is for C++ OpenVINO pipeline, no need to build the source code. Install latest Visual Studio 2022 Community for the C++ dependencies and LLM C++ pipeline editing.

Extract the zip file in any location and set the environment variables with dragging this setupvars.bat in the terminal Command Prompt. setupvars.ps1 is used for terminal PowerShell. <INSTALL_DIR> below refers to the extraction location. Run the following CMD in the terminal Command Prompt.

git submodule update --init
<INSTALL_DIR>\setupvars.bat
cd openvino.genai
cmake -S .\ -B .\build\ && cmake --build .\build\ --config Release -j8
cd .\build\samples\cpp\rag_sample\Release

Notice:

Install on Windows: Copy all the DLL files of PostgreSQL, OpenVINO and tbb and openvino-genai into the release folder. The SQL DLL files locate in the installed PostgreSQL path like "C:\Program Files\PostgreSQL\16\bin".
If cmake not installed in the terminal Command Prompt, please use the terminal Developer Command Prompt for VS 2022 instead.
The openvino tokenizer in the third party needs several minutes to build. Set 8 for -j option to specify the number of parallel jobs.
Once the cmake finishes, check rag_sample_client.exe and rag_sample_server.exe in the relative path .\build\samples\cpp\rag_sample\Release.
If Cmake completed without errors, but not find exe, please open the .\build\OpenVINOGenAI.sln in VS2022, and set the solution configuration as Release instead of Debug, then build the llm project within VS2022 again.

Run

Launch RAG Server

rag_sample_server.exe --llm_model_path TinyLlama-1.1B-Chat-v1.0 --llm_device CPU --embedding_model_path bge-large-zh-v1.5 --embedding_device CPU --db_connection "user=postgres host=localhost password=openvino port=5432 dbname=postgres"

Lanuch RAG Client

rag_sample_client.exe

Lanuch python Client

Use python client to send the message of DB init and send the document chunks to DB for embedding and storing.

python client_get_chunks_embeddings.py --docs test_document_README.md

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Creating AI Pipeline for Cell Image Analysis: Insights, Challenges, and CHO Use Case (Part 1 of 2, Intel Edge AI in the Realm of Biopharma and Drug Development)

April 23, 2024

June 5, 2024

In the ever-evolving landscape of biopharmaceutical technology and drug development, a recent effort in the field of Cell Analytics for Monoclonal Antibody Production has shed light on the crucial role of Edge AI Technology in navigating complex challenges of scaling and producing solutions.

In this 2-part blog series, we will explore the use of Intel Edge AI Technology in biopharma and drug development, addressing challenges and providing insights into the development of AI pipelines for cell segmentation and analysis.

Intel has been involved in this process with a variety of partners. One of Intel’s contributions to the cell image project centers around processing brightfield¹ images using an AI pipeline containing multiple deep learning models. The pipeline's purpose is to identify cells and other biological components and provide feedback on dynamic biological characteristics such as cell morphology, viability, and phenotypic changes, among others. Throughout this process, working on cell-AI projects usually brings a unique set of challenges to the forefront.

First, it is an interdisciplinary field and the knowledge gap between data scientists and biopharma experts requires more back-and-forth clear communications for planning and validity checks. Frequently when attempting to implement AI solutions in the laboratory, data scientists and bench scientists struggle to fully grasp the nature and needs of each other’s role. This lack of mutual understanding can also hinder the usability and scalability of an AI solution needing to be integrated into diverse lab environments.

The second challenge is instrument variability. Different plate reader² microscopes have different hardware, optics, and apertures which cause their produced images not to be consistent. This adds an extra layer of work to assess and address these inconsistencies along the way (like regular tracked calibration and adjustment). Additionally, equipment vendor-to-vendor differences, culture temperature, medium conditions, and genetic modifications can all affect the variability of data and the inherent transferability of the deep learning pipeline. This would drive the need to monitor the performance of DL models at the edge and cloud ML ops components.

The third challenge is obtaining peer-review labels because the process is based on supervised Machine Learning and obtaining clean accurate labels is very costly and time-consuming.

And the last challenge is about the model deployment. In most cases, cloud deployment is not an option due to data size and data privacy. Produced images from plate reader microscopes are huge and transferring data to the cloud and sending the results back would create high latency because a huge amount of data must be streamed (30Gb per hour). And more importantly, laboratories are usually not willing to share the data. Due to these two constraints, cloud deployments are not usually an option, and the pipeline must be deployed at the edge.

Now, let’s talk about a specific application of this technology: the CHO Cell Segmentation Use Case.

CHO Cell Segmentation Use Case

CHO cells, or Chinese Hamster Ovary cells, are a cornerstone in the production of complex protein molecules such as monoclonal antibodies, fusion proteins, hormones, and coagulation factors. Unlike stem cells or CAR-T cells, where the cells themselves are the therapeutic product, in CHO cells, it is the proteins they produce that are of paramount importance. Monitoring the health, viability, and production capability of these cells is a critical step in commercial protein production.

Traditionally, assessing the condition of CHO cells involves a multi-step process that is not only time-consuming but also requires the use of expensive reagents and chemicals. Depending on the process, the workflow can be something like below.

Culture cells

Fix cells – wash in expensive reagents to remove the culture medium.

Permeabilization – wash in more expensive chemicals to permeabilize the cell membrane (to stain for intercellular proteins).

Blocking – incubate cells in another expensive reagent to prevent binding of no specific antibodies.

Primary Antibody Incubation – antibody specifically to bind to a protein that is being produced.

Washing – removing unbound Primary Antibodies using more expensive chemicals.

Nuclear staining – use nuclear stain like DAPI to visualize cell nuclei then wash with the same chemicals from the washing step

Mounting – get ready to read in the microscope (plate reader¹)

Imaging – Stained cells …. count them up and determine the state in the protein production cycle and relative cell health (eventually they peter out and stop producing and the batch needs to be flushed. (Cell count, viability number, etc. are the output not the image)

From culturing to imaging, each step plays a vital role in ensuring the quality of the protein product. However, with the advent of AI and deep learning, there is an opportunity to streamline this workflow significantly. Using an AI pipeline including multiple Deep Learning models and data pre and post-processing, we can go from Step 1 directly to Step 9, removing the majority of the labor and latency in getting actionable results out of a staining workflow and bypassing expensive specialty chemicals requirement. Intel has put together a reference implementation for deploying said pipeline and inferencing of these images on the edge as part of the Cell Image project https://www.cellimage.ie/. OpenVINO Toolkit, OpenVINO Model Server, and AI Connect for Scientific Data are used in this design. Let’s briefly talk about each of these wonderful SW packages in part 2 of this article series. Stay tuned!

Conclusion

In conclusion, the integration of Intel Edge AI Technology into the biopharmaceutical sector represents a transformative step towards more efficient and scalable drug development processes. As we have seen in this first installment of our blog series, the deployment of AI pipelines for cell segmentation and analysis in monoclonal antibody production is not without its challenges. These include bridging the interdisciplinary knowledge gap, managing instrument variability, acquiring peer-reviewed labels, and overcoming the hurdles associated with model deployment.

Despite these challenges, the potential benefits of Edge AI in biopharma are substantial. By leveraging Intel's advanced AI technologies, we can significantly reduce the time and cost associated with traditional cell analysis methods, while also enhancing the accuracy and reliability of the results. The use of edge computing addresses the concerns of data size and privacy, allowing for real-time processing and analysis without the need for cloud transfer.

As we move forward in this blog series, we will delve deeper into the specifics of Intel's Edge AI solutions, including the OpenVINO toolkit, OpenVINO Model Server, and AI Connect for Scientific Data. We will explore how these tools are being applied in real-world scenarios to drive innovation and improve outcomes in the realm of biopharma and drug development in the next part of this series.

Reach out to Intel's Health and Life Sciences team at health.lifesciences@intel.com or learn more about what we do at https://www.intel.com/health.

We'd like to hear from you! Let us know in the comments or discuss – which AI use cases in health and life sciences do you think will have the greatest impact on global health?

If you enjoyed hearing from the Health and Life Sciences team and want to hear more, give this post a like and ensure you subscribe to get the latest updates from the team. 

About the Author

Nooshin Nabizadeh has Ph.D. in Electrical and Computer Engineering from the University of Miami and works at Intel Corporation as AI Solutions Architect. She enjoys photography, writing poetry, reading about psychology and philosophy, and optimizing solutions to run as fast as possible on a given piece of hardware. Connect with her on LinkedIn https://www.linkedin.com/in/nooshin-nabizadeh/ by mentioning this blog.

Brightfield microscopy is a widely used technique for observing the morphology of cells and tissues.

A plate reader is a laboratory instrument used to obtain images from samples in microtiter plates. The reader shines a specific calibrated frequency of light (UV, visible, fluorescence, etc.) through the samples in the wells of the plate. Plate reader microscopy data sets have inherent variability which drives the requirement of regular tracked calibration and adjustment.

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