Pytorchでhyperparmeter searchするための Docker-composeのセットアップ( MySQL )

目的: Optunaを分散環境で動かす, ついでにtensorbaordで可視化

完成したコードはここにあります。

手順

1. docker 及び docker-composeの準備
2. optunaのsimple exampleを書く

注意:mysqlのパスワードを直書きしたりしてるのでセキュリティ的によくないです

Dockerで環境構築

FROM pytorch/pytorch:1.1.0-cuda10.0-cudnn7.5-runtime
ARG PYTHON_VERSION=3.6

RUN apt-get update
RUN apt-get install -y wget
RUN apt-get -y install language-pack-ja-base language-pack-ja ibus-mozc

RUN update-locale LANG=ja_JP.UTF-8 LANGUAGE=ja_JP:ja
ENV LANG ja_JP.UTF-8
ENV LC_ALL ja_JP.UTF-8
ENV LC_CTYPE ja_JP.UTF-8

RUN pip install -U pip
RUN pip install numpy matplotlib bokeh holoviews pandas tqdm sklearn joblib nose pandas tabulate xgboost lightgbm optuna nose coverage
RUN pip install torch torchvision
# install tensorboardX to /tmp for hparams in tensorboardX
RUN pip install -e git+https://github.com/eisenjulian/tensorboardX.git@add-hparam-support#egg=tensorboardX --src /tmp
RUN pip install tensorflow==1.14.0
RUN pip install future moviepy

# mysqlclient
RUN apt-get install -y libssl-dev
RUN apt-get update
RUN apt-get install -y python3-dev libmysqlclient-dev
RUN pip install mysqlclient

可視化のためにtensorboardもいれた

docker-compose.yml

version: '2.3'

services:
  optuna_pytorch:
    build: ./
    container_name: "optuna_pytorch"
    working_dir: "/workspace"
    ports:
    - "6006:6006"
    - "8888:8888"
    #runtime: nvidia
    volumes:
    - .:/workspace
    tty: true

  db:
    image: mysql:5.7
    container_name: 'db'
    ports:
        - "3306:3306"
    volumes:
        # 初期データを投入するSQLが格納されているdir
        - ./db/mysql_init:/docker-entrypoint-initdb.d
        # 永続化するときにマウントするdir
        - ./db/mysql_data:/var/lib/mysql
    environment:
        MYSQL_ROOT_PASSWORD: root
        MYSQL_USER: root
        MYSQL_ALLOW_EMPTY_PASSWORD: 'yes'
        MYSQL_DATABASE: optuna

MYSQL_DATABASE: optuna　を用意しておくのがポイント (optuna_pytorchからはmysqlはdbというドメインで参照可能になっている)

optunaのコード

main.py

from torch.utils.data import DataLoader
from torchvision.datasets import MNIST
from torchvision import transforms
from torch.utils.data.dataset import Subset
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import optuna
from tensorboardX import SummaryWriter
#optuna.logging.disable_default_handler()

from tqdm import tqdm_notebook as tqdm

BATCHSIZE = 128

transform = transforms.Compose(
    [transforms.ToTensor(),
     transforms.Normalize((0.5,), (0.5,))])

train_set = MNIST(root='./data', train=True,
                  download=True, transform=transform)
subset1_indices = list(range(0,6000))
train_set = Subset(train_set, subset1_indices)

train_loader = DataLoader(train_set, batch_size=BATCHSIZE,
                          shuffle=True, num_workers=2)
subset2_indices = list(range(0,1000))
test_set = MNIST(root='./data', train=False,
                 download=True, transform=transform)
test_set = Subset(test_set, subset2_indices)
test_loader = DataLoader(test_set, batch_size=BATCHSIZE,
                         shuffle=False, num_workers=2)

classes = tuple(np.linspace(0, 9, 10, dtype=np.uint8))
h_params = {}
print('finish data load')
EPOCH = 10
writer = SummaryWriter()

class Net(nn.Module):
    def __init__(self, trial):
        super(Net, self).__init__()
        self.activation = get_activation(trial)
        self.conv1 = nn.Conv2d(1, 10, kernel_size=5)
        self.conv2 = nn.Conv2d(10, 20, kernel_size=5)
        self.conv1_drop = nn.Dropout2d(p=trial.suggest_uniform("dropout_prob", 0, 0.8))
        self.fc1 = nn.Linear(320, 50)
        self.fc2 = nn.Linear(50, 10)

    def forward(self, x):
        x = self.activation(F.max_pool2d(self.conv1(x), 2))
        x = self.activation(F.max_pool2d(self.conv1_drop(self.conv2(x)), 2))
        x = x.view(-1, 320)
        x = self.activation(self.fc1(x))
        x = F.dropout(x, training=self.training)
        x = self.fc2(x)
        return F.log_softmax(x, dim=1)


def train(model, device, train_loader, optimizer):
    model.train()
    for batch_idx, (data, target) in enumerate(train_loader):
        data, target = data.to(device), target.to(device)
        optimizer.zero_grad()
        output = model(data)
        loss = F.nll_loss(output, target)
        loss.backward()
        optimizer.step()


def test(model, device, test_loader):
    model.eval()
    correct = 0
    with torch.no_grad():
        for data, target in test_loader:
            data, target = data.to(device), target.to(device)
            output = model(data)
            pred = output.max(1, keepdim=True)[1]
            correct += pred.eq(target.view_as(pred)).sum().item()

    return 1 - correct / len(test_loader.dataset)

def get_optimizer(trial, model):
    optimizer_names = ['Adam', 'MomentumSGD']
    optimizer_name = trial.suggest_categorical('optimizer', optimizer_names)
    h_params['opt_name'] = optimizer_name
    weight_decay = trial.suggest_loguniform('weight_decay', 1e-10, 1e-3)
    if optimizer_name == optimizer_names[0]:
        adam_lr = trial.suggest_loguniform('adam_lr', 1e-5, 1e-1)
        h_params['adam_lr'] = adam_lr
        optimizer = optim.Adam(model.parameters(), lr=adam_lr, weight_decay=weight_decay)
    else:
        momentum_sgd_lr = trial.suggest_loguniform('momentum_sgd_lr', 1e-5, 1e-1)
        h_params['momentum_sgd_lr'] = momentum_sgd_lr
        optimizer = optim.SGD(model.parameters(), lr=momentum_sgd_lr,
                              momentum=0.9, weight_decay=weight_decay)
    return optimizer


def get_activation(trial):
    activation_names = ['ReLU', 'ELU']
    activation_name = trial.suggest_categorical('activation', activation_names)
    h_params['activation'] = activation_name
    if activation_name == activation_names[0]:
        activation = F.relu
    else:
        activation = F.elu
    return activation


def objective_wrapper(pbar):
    def objective(trial):
        global writer
        writer = SummaryWriter()
        device = "cuda" if torch.cuda.is_available() else "cpu"

        model = Net(trial).to(device)
        optimizer = get_optimizer(trial, model)
        writer.add_hparams_start(h_params)
        for step in range(EPOCH):
            train(model, device, train_loader, optimizer)
            error_rate = test(model, device, test_loader)
            writer.add_scalar('test/loss', error_rate, step)
            trial.report(error_rate, step)
            if trial.should_prune(step):
                pbar.update()
                raise optuna.structs.TrialPruned()

        pbar.update()
        writer.add_hparams_end()  # save hyper parameter
        return error_rate
    return objective



TRIAL_SIZE = 50
with tqdm(total=TRIAL_SIZE) as pbar:
    study = optuna.create_study(pruner=optuna.pruners.MedianPruner(), study_name='distributed-mysql', storage='mysql://root:root@db/optuna', load_if_exists=True)
    study.optimize(objective_wrapper(pbar), n_trials=TRIAL_SIZE, n_jobs=2)

print(study.best_params)
print(study.best_value)

df = study.trials_dataframe()
print(df.head)
df.to_csv('result.csv')

本質は

• optuna.create_study を作り
• trial.suggest_loguniform, trial.suggest_categorical　で探索の候補を決め
• study.optimize で探索を実行する

あたりである。
とくにcreate_studyはDBの指定とpruningのルールも指定するところなので重要
documentをみるとよい

枝刈りのルールも確認しておくと良いここ

使い方

run

# create env
docker-compose up -d
docker exec -it optuna_pytorch /bin/bash
# run
python main.py

# remove env
exit
docker-compose down

最適化の過程はmysqlに記録されるのでmysqlが参照できる場所でmain.pyを動かせば分散環境での最適化になる!

結果をtensorboardで確認

# on host
docker exec -it optuna_pytorch /bin/bassh
tensorboard --logdir runs

# access to http://localhost:6006/#hparams on browser

枝刈りが行われてるのがわかる

結果をmysqlから確認

# on host
# install mysql
brew install mysql

# check tables on Optuna db
mysql -h 127.0.0.1 --port 3306 -uroot -proot -D optuna -e 'show tables'

# check results on Optuna db
mysql -h 127.0.0.1 --port 3306 -uroot -proot -D optuna -e 'select * from trials'

結果の削除

mysql -h 127.0.0.1 --port 3306 -uroot -proot -D optuna -e 'drop database optuna'