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Pytorch (IRIS)

Running and IRIS dataset classifier through CUSTOM endpoints

Overview

This documentation shows Konduit-Serving can serve a custom model and include post-processing in the pipeline to give a direct output label understood by a human. Iris model is used in this example to deploy on the server as a classifier through custom endpoints.

Adding package to the classpath

First of all we need to add the main package to the classpath so that the notebook can load all the necessary libraries from Konduit-Serving into the Jupyter Notebook kernel.

Classpaths can be considered similar to site-packages in the python ecosystem where each library that's to be imported to your code is loaded from.

We package almost everything you need to get started with the konduit.jar package so you can just start working on the actual code, without having to care about any boilerplate configuration.

%classpath add jar ../../konduit.jar

Let's ensure the working directory is correct and list all the file available in the directory.

%%bash
echo "Current directory $(pwd)" && tree

You'll be able to view as the following.

Current directory /root/konduit/demos/1-pytorch-onnx-iris
.
├── dataset
│   └── iris.csv
├── iris.onnx
├── onnx-iris.ipynb
├── onnx.yaml
└── train.py

1 directory, 5 files

Main model script code

We're creating a Pytorch model from scratch here and then converting that into ONNX format.

%%bash
less train.py

You'll be able to browse the source code how the training takes places.

import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.metrics import accuracy_score, precision_score, recall_score

import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable


class Net(nn.Module):
    # define nn
    def __init__(self):
        super(Net, self).__init__()
        self.fc1 = nn.Linear(4, 100)
        self.fc2 = nn.Linear(100, 100)
        self.fc3 = nn.Linear(100, 3)
        self.softmax = nn.Softmax(dim=1)

    def forward(self, X):
        X = F.relu(self.fc1(X))
        X = self.fc2(X)
        X = self.fc3(X)
        X = self.softmax(X)

        return X


# load IRIS dataset
dataset = pd.read_csv('dataset/iris.csv')

# transform species to numerics
dataset.loc[dataset.species == 'Iris-setosa', 'species'] = 0
dataset.loc[dataset.species == 'Iris-versicolor', 'species'] = 1
dataset.loc[dataset.species == 'Iris-virginica', 'species'] = 2

train_X, test_X, train_y, test_y = train_test_split(dataset[dataset.columns[0:4]].values,
                                                    dataset.species.values, test_size=0.8)

# wrap up with Variable in pytorch
train_X = Variable(torch.Tensor(train_X).float())
test_X = Variable(torch.Tensor(test_X).float())
train_y = Variable(torch.Tensor(train_y).long())
test_y = Variable(torch.Tensor(test_y).long())

net = Net()

criterion = nn.CrossEntropyLoss()  # cross entropy loss

optimizer = torch.optim.SGD(net.parameters(), lr=0.01)

for epoch in range(1000):
    optimizer.zero_grad()
    out = net(train_X)
    loss = criterion(out, train_y)
    loss.backward()
    optimizer.step()

    if epoch % 100 == 0:
        print('number of epoch', epoch, 'loss', loss.item())

predict_out = net(test_X)
_, predict_y = torch.max(predict_out, 1)

print('prediction accuracy', accuracy_score(test_y.data, predict_y.data))

print('macro precision', precision_score(test_y.data, predict_y.data, average='macro'))
print('micro precision', precision_score(test_y.data, predict_y.data, average='micro'))
print('macro recall', recall_score(test_y.data, predict_y.data, average='macro'))
print('micro recall', recall_score(test_y.data, predict_y.data, average='micro'))

# Input to the model
x = torch.randn(1, 4, requires_grad=True)

# Export the model
torch.onnx.export(net,  # model being run
                  x,  # model input (or a tuple for multiple inputs)
                  "iris.onnx",  # where to save the model (can be a file or file-like object)
                  export_params=True,  # store the trained parameter weights inside the model file
                  opset_version=10,  # the ONNX version to export the model to
                  do_constant_folding=True,  # whether to execute constant folding for optimization
                  input_names=['input'],  # the model's input names
                  output_names=['output'],  # the model's output names
                  dynamic_axes={'input': {0: 'batch_size'},  # variable length axes
                                'output': {0: 'batch_size'}})

Viewing the configuration file

The configuration for the custom endpoint is as follow:

%%bash
less onnx.yaml

The output shows configurations in YAML, in which you can see two steps in the pipeline, serving a model and post-processing to make it directly understood by a human.

---
host: "localhost"
port: 0
protocol: "HTTP"
pipeline:
  steps:
  - '@type': "ONNX"
    modelUri: "iris.onnx"
    inputNames:
    - "input"
    outputNames:
    - "output"
  - '@type': "CLASSIFIER_OUTPUT"
    input_name: "output"
    labels:
      - Setosa
      - Versicolor
      - Virginica

Starting the server

konduit serve can be used together with ID's name (use any name) and configuration file to start the server.

%%bash
konduit serve -id onnx-iris -c onnx.yaml -rwm -b

You'll get the following message.

Starting konduit server...
Using classpath: /root/konduit/bin/../konduit.jar
INFO: Running command /root/miniconda/jre/bin/java -Dkonduit.logs.file.path=/root/.konduit-serving/command_logs/onnx-iris.log -Dlogback.configurationFile=/tmp/logback-run_command_80a3902b721c4c3f.xml -jar /root/konduit/bin/../konduit.jar run --instances 1 -s inference -c onnx.yaml -Dserving.id=onnx-iris
For server status, execute: 'konduit list'
For logs, execute: 'konduit logs onnx-iris'

To view the logs of the running server, use konduit logs commands.

%%bash
konduit logs onnx-iris -l 100

You'll be able to see the following from logging.

15:01:50.334 [main] INFO  a.k.s.c.l.command.KonduitRunCommand - Processing configuration: /root/konduit/demos/1-pytorch-onnx-iris/onnx.yaml
.
.
.

####################################################################
#                                                                  #
#    |  /   _ \   \ |  _ \  |  | _ _| __ __|    |  /     |  /      #
#    . <   (   | .  |  |  | |  |   |     |      . <      . <       #
#   _|\_\ \___/ _|\_| ___/ \__/  ___|   _|     _|\_\ _) _|\_\ _)   #
#                                                                  #
####################################################################

.
.
.
15:01:50.919 [vert.x-eventloop-thread-0] INFO  a.k.s.v.p.h.v.InferenceVerticleHttp - Inference HTTP server is listening on host: 'localhost'
15:01:50.919 [vert.x-eventloop-thread-0] INFO  a.k.s.v.p.h.v.InferenceVerticleHttp - Inference HTTP server started on port 35761 with 2 pipeline steps

Sending inputs

Now we can send our inputs through cURL for inference

%%bash
konduit predict onnx-iris "{\"input\":[[5.1,3.5,1.4,0.2]]}"

So, the server will print out the output with a label.

{
  "output" : [ [ 0.99312085, 0.0068791825, 6.1220806E-9 ] ],
  "prob" : 0.9931208491325378,
  "index" : 0,
  "label" : "Setosa"
}

Try once again with --input-type flag.

%%bash
konduit predict onnx-iris --input-type multipart "input=[[5.1,3.5,1.4,0.2]]"

You'll see the output of the prediction.

{
  "output" : [ [ 0.99312085, 0.0068791825, 6.1220806E-9 ] ],
  "prob" : 0.9931208491325378,
  "index" : 0,
  "label" : "Setosa"
}

Stopping the server

Now after we're done with the server, we can stop it through the konduit stop command

%%bash
konduit stop onnx-iris

You'll receive this once the server is terminated. 

Stopping konduit server 'onnx-iris'
Application 'onnx-iris' terminated with status 0

Let's take a look at the following example, where we are going to give an image input and doing pre-processing step before fetching it into the model.

PreviousONNXNextPytorch (MNIST)

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