nerd

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Version: v0.4.1 Latest Latest
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Published: Sep 27, 2021 License: BSD-3-Clause

README

nerd

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Welcome to the nerd repo! This service offers machine learning capabilities through a simple API, thus allowing other services to be smarter without requiring a huge effort.

Index

Quick Start

If you just want to try nerd out and see what it can do, here is a quick guide for running a test setup with containers:

  1. Start a nerd instance:

    Here we're going to run nerd using the filesystem to store its data and the REST API to send it updates. If you'd like a more performant setup, refer to the "Requirements" section for instructions on how to setup Redis, Elasticsearch, Kafka and Zookeeper instead.

    docker run -d --restart=unless-stopped -m 64m \
      --log-opt max-size=5m --log-driver=json-file \
      -p 5400:5400 \
      -e "LOG_LEVEL=INFO" \
      --name nerd qvantel/nerd:0.4.1
    
  2. Check that everything is up and running by going to http://localhost:5400 with your browser (if you see a welcome message, everything is good)

    Not seeing anything? You can check the nerd logs with docker logs --tail 100 nerd to see if there are any errors

  3. Train a network to detect forged banknotes:
    1. Download the dataset from the UCI ML repo here

      Credit: Dua, D. and Graff, C. (2019). UCI Machine Learning Repository [http://archive.ics.uci.edu/ml]. Irvine, CA: University of California, School of Information and Computer Science.

    2. Shuffle the points:
      sort -R -o shuffled-dataset.txt data_banknote_authentication.txt
      
    3. Load the test data using the built-in file collector:

      If you want, you can add variance,skewness,kurtosis,entropy,class to the beginning of shuffled-dataset.txt and use the -headers flag to properly label the values, otherwise names will be auto-generated

      1. On Linux (or WSL):
        docker run -it --rm \
          --add-host host.docker.internal:host-gateway \
          -v $PWD/shuffled-dataset.txt:/opt/docker/dataset \
          --entrypoint=/opt/docker/fcollect qvantel/nerd:0.4.1 \
            -batch 50 \
            -in 4 \
            -margin 0.4999999 \
            -sep "," \
            -series "banknote-forgery-detection" \
            -targets "http://host.docker.internal:5400" \
            dataset
        
      2. On MacOS:
        docker run -it --rm \
          -v $PWD/shuffled-dataset.txt:/opt/docker/dataset \
          --entrypoint=/opt/docker/fcollect qvantel/nerd:0.4.1 \
            -batch 50 \
            -in 4 \
            -margin 0.4999999 \
            -sep "," \
            -series "banknote-forgery-detection" \
            -targets "http://host.docker.internal:5400" \
            dataset
        
    4. Send a training request:

      If you opted to add the headers in the previous step, use ["variance","skewness","kurtosis","entropy"] as inputs and ["class"] as the output instead of the values bellow

      curl -XPOST -H "Content-Type: application/json" --data @- \
          localhost:5400/api/v1/nets <<EOF
      {
          "errMargin": 0.4999999,
          "inputs": ["value-0", "value-1", "value-2", "value-3"],
          "outputs": ["value-4"],
          "required": 1372,
          "seriesID": "banknote-forgery-detection"
      }
      EOF
      
    5. Check out the resulting net by going to http://localhost:5400/api/v1/series/banknote-forgery-detection/nets
  4. Use the network:
    1. With an authentic note (the output should be closer to 0 than 1)
      # (with headers) NET=banknote-forgery-detection-f6217c7e74da371fea775c5a0b11b5b36d9438ed-8d767bf5b72373d12f0efd4406677e9ed076f592-mlp
      NET=banknote-forgery-detection-8921e4a37dabacc06fec3318e908d9fe4eb75b46-7804b6fc74b5c0a74cc0820420fa0edf6b1a117c-mlp
      ENDPOINT=localhost:5400/api/v1/nets/$NET/evaluate
      
      curl -XPOST -H"Content-Type: application/json" --data @- \
          $ENDPOINT <<EOF
      {
          "value-0": 3.2403,
          "value-1": -3.7082,
          "value-2": 5.2804,
          "value-3": 0.41291
      }
      EOF
      
    2. With a forged note (the output should be closer to 1 than 0)
      curl -XPOST -H"Content-Type: application/json" --data @- \
          $ENDPOINT <<EOF
      {
          "value-0": -1.4377,
          "value-1": -1.432,
          "value-2": 2.1144,
          "value-3": 0.42067
      }
      EOF
      

Requirements

This service has the following dependencies:

Kafka

Even though nerd can be used without it (sending updates through the REST API), it's better to use a service like Kafka (maybe nats in the future) to decouple that interaction and benefit from built-in load balancing. When producing metrics updates, the series ID should be used by the partitioning strategy to reduce the chance of triggering training for the same series twice.

For testing, the following commands can be used to start Zookeeper and Kafka:

If running on Linux, include --add-host host.docker.internal:host-gateway in the Kafka docker run command (anywhere between docker run and the image)

docker run -d --restart=unless-stopped \
  --log-driver json-file \
  -p 2181:2181 \
  --name zookeeper zookeeper:3.6.2

docker run -d --restart=unless-stopped \
  --log-driver json-file \
  -p 7203:7203 -p 7204:7204 -p 9092:9092 \
  -e "KAFKA_LISTENERS=PLAINTEXT://:9092" \
  -e "KAFKA_ADVERTISED_LISTENERS=PLAINTEXT://host.docker.internal:9092" \
  -e "KAFKA_DEFAULT_REPLICATION_FACTOR=1" \
  -e "KAFKA_DELETE_TOPIC_ENABLE=true" \
  -e "KAFKA_ZOOKEEPER_CONNECT=host.docker.internal:2181" \
  -e "KAFKA_BROKER_ID=1" \
  -e "KAFKA_HEAP_OPTS=-Xmx4G -Xms4G" \
  -e "ZOOKEEPER_SESSION_TIMEOUT_MS=30000" \
  --name kafka wurstmeister/kafka:2.12-2.1.1
A Network Parameter Store

Currently, Redis (and the filesystem but that should only be used for testing).

When using Redis with Sentinel, the ML_STORE_PARAMS variable should be used (instead of SD_REDIS) like so:

  -e 'ML_STORE_PARAMS={"group": "<group-name>", "URLs": "<sen1-host>:<sen1-port>,...,<senN-host>:<senN-port>"}'

Where group contains the replica group name and URLs the comma-separated list of Sentinel instance host:port pairs.

For testing, the following command can be used to start up a Redis replica:

docker run -d \
  --log-driver json-file \
  -p 6379:6379 \
  --name redis redis:6.0.10-alpine3.13
A Point Store

Currently, Elasticsearch (and the filesystem but that should only be used for testing).

If Elasticsearch is used:

  • The action.auto_create_index setting must be set to .watches,.triggered_watches,.watcher-history-* otherwise it will create non optimal mappings increasing the storage impact.

  • Given how index refreshing works, the automatic training request for a series that gets a high number of metrics updates in a very short period of time (less than a second)(possible when the lag is momentarily high for example) might not get issued. To avoid this, it's recommended to include multiple points per update with a lower frequency rather than sending one update per point as it is extracted.

For testing, it is possible to get a working Elasticsearch instance quickly with the following command:

docker run -d \
  --log-driver json-file \
  -p 9200:9200 -p 9300:9300 \
  -e "discovery.type=single-node" \
  -e "action.auto_create_index=.watches,.triggered_watches,.watcher-history-*" \
  --name elasticsearch elasticsearch:7.10.1

Deployment

For a simple deployment, the following command can be used to start up a nerd instance that'll use Kafka, Redis and Elasticsearch (changing the ip:ports for those of the corresponding services in your setup):

If running on Linux, include --add-host host.docker.internal:host-gateway in the docker run command (anywhere between docker run and the image) if you're going to use it as is

docker run -d --restart=unless-stopped -m 64m \
  --log-opt max-size=5m --log-driver=json-file \
  -p 5400:5400 \
  -e "LOG_LEVEL=INFO" \
  -e "SD_ELASTICSEARCH=http://host.docker.internal:9200" \
  -e "SERIES_STORE_TYPE=elasticsearch" \
  -e "SD_KAFKA=host.docker.internal:9092" \
  -e "SD_REDIS=host.docker.internal:6379" \
  -e "ML_STORE_TYPE=redis" \
  --name nerd qvantel/nerd:0.4.1

You can find all available tags here

The following environment variables are available:

Variable Required Default Description
LOG_LEVEL NO INFO Application/root log level, supported values are TRACE, DEBUG, INFO, WARNING and ERROR
MARATHON_APP_DOCKER_IMAGE NO qvantel/nerd:$VERSION? Included in the artifact_id field of log messages, gets filled in automatically when ran through Marathon
SERVICE_NAME NO nerd Included in the service_name field of the log messages
SERVICE_5400_NAME NO $SERVICE_NAME Included in the service_name field of the log messages. If set, overrides whatever is defined in $SERVICE_NAME
ML_GENS NO 5 Number of cycles to run the genetic algorithm for in search of the optimal net params
ML_MIN_HLAYERS NO 1 Minimum starting number of hidden layers (the genetic algorithm can go down to 1)
ML_MAX_HLAYERS NO 5 Maximum starting number of hidden layers (the genetic algorithm can surpass it)
ML_MAX_EPOCH NO 1000 Maximum number of times the net should iterate over the training set if the tolerance is never met
ML_STORE_TYPE NO* file Storage adapter that should be used for keeping network parameters. Currently supported values are file (for testing) and redis
ML_STORE_PARAMS NO {"Path": "."} Settings for the net params storage adapter
SD_REDIS NO Redis replica host:port. Serves as a shortcut for filling in $ML_STORE_PARAMS when selecting the redis adapter
ML_TEST_SET NO 0.4 Fraction of the patterns provided to the training function that should be put aside for testing the accuracy of the net after training (0.4 is usually a good value)
ML_TOLERANCE NO 0.1 Mean squared error change rate at which the training should stop to avoid overfitting
ML_VARS NO 6 Number of different network configurations to evaluate in each generation of the genetic algorithm (4 minimum)
SERIES_FAIL_LIMIT NO 5 Number of subsequent processing failures in the consumer service at which the instance should crash (not used when running in "rest-only" mode)
SD_KAFKA NO* Comma separated list of Kafka broker host:port pairs. When empty, nerd will run in "rest-only" mode (only recommended for testing or when running in envs with very limited resources)
SERIES_KAFKA_GROUP NO nerd Consumer group ID that the instance should use (not used when running in "rest-only" mode)
SERIES_KAFKA_TOPIC NO nerd-events Topic from which metrics updates will be consumed (not used when running in "rest-only" mode)
SERIES_STORE_TYPE NO* file Storage adapter that should be used for storing time series. Currently supported values are file (for testing) and elasticsearch
SERIES_STORE_PARAMS NO {"Path": "."} Settings for the time series storage adapter
SERIES_STORE_PASS NO "" Password for the selected series store (if applicable)
SERIES_STORE_USER NO "" User for the selected series store (if applicable)
SD_ELASTICSEARCH NO Elasticsearch protocol://host:port. Serves as a shortcut for filling in $SERIES_STORE_PARAMS when selecting the elasticsearch adapter

* While not strictly required for operation, the default value should be overridden for anything other than testing and even then, not all testing should be done with those values

Use

Once the service has been deployed, it is possible to interact with it either through Kafka or the REST API.

Collectors

These are lightweight components that can be used to import data from other services into nerd. To facilitate their development, nerd exposes the github.com/qvantel/nerd/api/types and github.com/qvantel/nerd/pkg/producer modules which include the types used by the REST and Kafka interfaces as well as ready-made methods for producing messages to them.

File

At the time of writing, the only public collector is the one built into this project under the fcollect command, which imports datasets from plain text files. It can be accessed from the container (as seen in the "Quick Start" section) by changing the entrypoint to /opt/docker/fcollect like so (anything placed after the image will be passed to fcollect as an argument):

docker run -it --rm \
  -v $PWD/shuffled-dataset.txt:/opt/docker/dataset \
  --entrypoint=/opt/docker/fcollect \
  --name fcollect qvantel/nerd:0.4.1 -series "demo" -producer "kafka" -targets "host.docker.internal:9092" -sep "," dataset

Where the -series and -targets flags as well as the path to the dataset (full or relative to /opt/docker inside the container) are required. Additionally, the following flags can be used to change the behaviour of the tool:

Flag Type Default Description
-batch int 10 Maximum number of points to bundle in a single metrics update
-headers bool false If true, the first line will be used to name the values
-in int 1 Number of inputs, counted left to right, all others will be considered outputs
-margin float 0 Maximum difference between a prediction and the expected value for it to still be considered correct
-producer string "rest" What producer to use. Supported values are rest and kafka
-sep string " " String sequence that denotes the end of one field and the start of the next
-series string N/A ID of the series that these points belong to
-stage string "test" Category of the data, production for real world patterns, test for anything else
-targets string N/A Comma separated list of protocol://host:port for nerd instances when using rest, host:port of Kafka brokers when using kafka
-timeout duration 15s Maximum time to wait for the production of a message
-topic string "nerd-events" Where to produce the messages when using kafka
Metrics Updates

Metrics updates can be ingested through either the $SERIES_KAFKA_TOPIC topic in Kafka or the /api/v1/series/process endpoint. In both cases the message must conform to the Cloud Events v1 specification where the metadata fields should be filled in as follows:

Field Value
datacontenttype "application/json"
dataschema "github.com/qvantel/nerd/api/types/"
id (a unique string identifier for this event)
source (name of the service that generated the event)
specversion (cloud events spec version, should be "1.0")
subject (the entity that we are reporting about, it can be an environment name for example)
type "com.qvantel.nerd.metricsupdate"

Additionally, the data fields should be filled in like so:

Field Considerations
data.seriesID Should conform to [a-z][a-z0-9\._\-]+ and reference what that data can be used to predict. For example, if it's generic enough to predict storage impact in any env that uses that product stack, it should contain the stack version but not the env
data.errMargin Maximum difference between the expected and produced result to still be considered correct during testing. Currently, this margin will be applied to all outputs of networks generated automatically
data.labels Should include any labels that might be useful for filtering later. Note that subject and data.stage will be copied here automatically
data.points All points for the same series ID must contain the same attributes (doesn't matter if they are noted as inputs or outputs although within the same metrics update they do have to all be categorized in the same way)
data.stage Must be either production for production grade data (usually that which originates from real world usage) or test (for anything else). The message will not be processed if this field doesn't have a valid value

Example:

{
    "data": {
        "seriesID": "heart-of-gold-lightbulb-usage",
        "errMargin": 0.1,
        "labels": {
            "captain": "Zaphod Beeblebrox"
        },
        "points": [
            {
                "inputs": {
                    "humans": 2,
                    "robots": 1,
                    "aliens": 2
                },
                "outputs": {
                    "lightbulbs-on": 1500
                },
                "timestamp": 777808800
            }
        ],
        "stage": "test"
    },
    "datacontenttype": "application/json",
    "dataschema": "github.com/qvantel/nerd/api/types/",
    "id": "1",
    "source": "test-script",
    "specversion": "1.0",
    "subject": "heart-of-gold",
    "type": "com.qvantel.nerd.metricsupdate"
}
Manual Training

Even though the service will automatically schedule training when it has enough points of a series, it is still possible to manually trigger training from any preexisting series. To do this, just post a training request to the /api/v1/nets endpoint like so (where $URL contains the address of the nerd service):

curl -XPOST -H"Content-Type: application/json" --data @- \
    $URL/api/v1/nets <<EOF
{
    "errMargin": 0.4999999,
    "inputs": ["value-0", "value-1", "value-2", "value-3", "value-4", "value-5", "value-6", "value-7", "value-8"],
    "outputs": ["value-9", "value-10"],
    "required": 699,
    "seriesID": "testloadtestset"
}
EOF

Where, the fields contain the following information:

Field Description
errMargin Maximum difference between the expected and produced result to still be considered correct during testing
inputs Which of the series values should be used as inputs
outputs Which of the series values should be used as outputs
required Number of points from the series that should be used to train and test
seriesID ID of the series that should be used for training
Evaluating An Input

Once a net has been trained, it can be exploited through the /api/v1/nets/{id}/evaluate endpoint like so (where $URL contains the address of the nerd service and $ID the ID of the network):

NOTE: The network ID is different from that of the series it comes from, as multiple nets could be (and are) created from a single series. The nets for a given series can be found through the /api/v1/nets endpoint (by using the seriesID query param) or the /api/v1/series/{id}/nets endpoint.

curl -XPOST -H"Content-Type: application/json" --data @- \
    $URL/api/v1/nets/$ID/evaluate <<EOF
{
    "value-0": 5000,
    "value-1": 0.07,
    "value-2": 0.1,
    "value-3": 100,
    "value-4": 1,
    "value-5": 0.1,
    "value-6": 0.1,
    "value-7": 0.1,
    "value-8": 1000
}
EOF

Sample response:

{"value-9":0.16796547}
Listing Available Entities
  • Nets:
    • Endpoint: /api/v1/nets
    • Method: GET
    • Params:
      • offset: Offset to fetch, 0 by default
      • limit: How many networks to fetch, the service might return more in some cases, 10 by default, 50 maximum
      • seriesID: Filter by series ID (/api/v1/series/{id}/nets can be used to pass the ID as a path param instead)
    • Returns: A types.PagedRes object and a 200 if successful, a types.SimpleRes object and a 400 or 500 if not (depending on the error)
    • Sample response:
{
  "last": true,
  "next": 0,
  "results": [
    {
      "accuracy": 0.9908759,
      "activationFunc": "bipolar-sigmoid",
      "averages": {
        "class": 0.42718446,
        "entropy": -1.2009263,
        "kurtosis": 1.334538,
        "skewness": 2.1060672,
        "variance": 0.47604737
      },
      "deviations": {
        "class": 0.49497,
        "entropy": 2.1664677,
        "kurtosis": 4.235366,
        "skewness": 5.8205276,
        "variance": 2.8741868
      },
      "errMargin": 0.4999999,
      "hLayers": 1,
      "id": "banknote-forgery-detection-f6217c7e74da371fea775c5a0b11b5b36d9438ed-8d767bf5b72373d12f0efd4406677e9ed076f592-mlp",
      "inputs": [
        "entropy",
        "kurtosis",
        "skewness",
        "variance"
      ],
      "learningRate": 0.092,
      "outputs": [
        "class"
      ],
      "type": "mlp"
    }
  ]
}
  • Series:
    • Endpoint: /api/v1/series
    • Method: GET
    • Returns: An array of types.BriefSeries objects and a 200 if successful, a types.SimpleRes object and a 500 if not
    • Sample response:
[
  {
    "name": "banknote-forgery-detection",
    "count": 1372
  }
]
  • Points:
    • Endpoint: /api/v1/series/{id}/points
    • Method: GET
    • Params:
      • limit: How many points to fetch, 10 by default, 500 maximum
    • Returns: An array of pointstores.Point objects and a 200 if successful, a types.SimpleRes object and a 404 or 500 if not (depending on the error)
    • Sample response:
[
  {
    "@timestamp": 1612706310,
    "class": 0,
    "kurtosis": 2.0938,
    "entropy": 0.20085,
    "skewness": 2.599,
    "stage": "test",
    "subject": "dataset",
    "variance": 2.5367
  },
  {
    "@timestamp": 1612706309,
    "class": 0,
    "kurtosis": -2.4089,
    "entropy": -0.056479,
    "skewness": 5.5788,
    "stage": "test",
    "subject": "dataset",
    "variance": 5.7823
  }
]
Health
  • Startup probe:
    • Endpoint: /api/v1/health/startup
    • Method: GET
    • Returns: A types.SimpleRes object and a 200 if successful
    • Sample response:
{
  "result": "ok",
  "message": "The API is up"
}

Testing

NOTE: The tests automatically spin up Docker containers for dependencies like Elasticsearch and Redis so the host must have it installed and the user running them must have the necessary rights

  • Unit tests:

    go test -cover ./...
    
  • Functional tests:

    These can take a while as they build the nerd image from the Dockerfile

    go test -v --tags=functional github.com/qvantel/nerd/cmd
    

Directories

Path Synopsis
api
Package api contains the handlers and types that support nerd's REST API
Package api contains the handlers and types that support nerd's REST API
types
Package types contains most of the objects that the API reads or writes
Package types contains most of the objects that the API reads or writes
cmd
pkg
producer
Package producer exposes common logic that all Go collectors can use for producing nerd events
Package producer exposes common logic that all Go collectors can use for producing nerd events
internal
config
Package config centralizes the parsing of application configuration
Package config centralizes the parsing of application configuration
logger
Package logger includes extended JSON logging functionality
Package logger includes extended JSON logging functionality
nets
Package nets provides a standard interface for interacting with neural networks
Package nets provides a standard interface for interacting with neural networks
nets/paramstores
Package paramstores contains the implementation of all the supported storage adapters for the network parameters
Package paramstores contains the implementation of all the supported storage adapters for the network parameters
series
Package series contains the logic that manages the datasets used for machine learning
Package series contains the logic that manages the datasets used for machine learning
series/pointstores
Package pointstores contains the implementation of all the supported storage adapters for the series
Package pointstores contains the implementation of all the supported storage adapters for the series

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