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Merge branch 'master' of https://github.com/yandex/ClickHouse into CLICKHOUSE-2720

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This commit is contained in:
Ivan Blinkov 2018-05-31 16:37:46 +03:00
commit df9b783068
23 changed files with 942 additions and 43 deletions
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1
dbms/scripts/gen_benchmark_data/README.md Normal file
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Hits table generator based on LSTM neural network trained on real hits. You need to have weights for model or train model on real hits to generate data.

22
dbms/scripts/gen_benchmark_data/generate.py Normal file
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import argparse
from model import Model
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-n', type=int, default=100000,
help='number of objects to generate')
parser.add_argument('--output_file', type=str, default='out.tsv',
help='output file name')
parser.add_argument('--weights_path', type=str,
help='path to weights')
args = parser.parse_args()
if __name__ == '__main__':
if not args.weights_path:
raise Exception('please specify path to model weights with --weights_path')
gen = Model()
gen.generate(args.n, args.output_file, args.weights_path)

147
dbms/scripts/gen_benchmark_data/model.py Normal file
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import numpy as np
import os
import pickle
import tensorflow as tf
from random import sample
from keras.layers import Dense, Embedding
from tqdm import tqdm
RNN_NUM_UNITS = 256
EMB_SIZE = 32
MAX_LENGTH = 1049
with open('tokens', 'rb') as f:
tokens = pickle.load(f)
n_tokens = len(tokens)
token_to_id = {c: i for i, c in enumerate(tokens)}
def to_matrix(objects, max_len=None, pad=0, dtype='int32'):
max_len = max_len or max(map(len, objects))
matrix = np.zeros([len(objects), max_len], dtype) + pad
for i in range(len(objects)):
name_ix = list(map(token_to_id.get, objects[i]))
matrix[i, :len(name_ix)] = name_ix
return matrix.T
class Model:
def __init__(self, learning_rate=0.0001):
# an embedding layer that converts character ids into embeddings
self.embed_x = Embedding(n_tokens, EMB_SIZE)
get_h_next = Dense(1024, activation='relu')
# a dense layer that maps current hidden state
# to probabilities of characters [h_t+1]->P(x_t+1|h_t+1)
self.get_probas = Dense(n_tokens, activation='softmax')
self.input_sequence = tf.placeholder('int32', (MAX_LENGTH, None))
batch_size = tf.shape(self.input_sequence)[1]
self.gru_cell_first = tf.nn.rnn_cell.GRUCell(RNN_NUM_UNITS)
self.lstm_cell_second = tf.nn.rnn_cell.LSTMCell(RNN_NUM_UNITS)
h_prev_first = self.gru_cell_first.zero_state(batch_size, dtype=tf.float32)
h_prev_second = tf.nn.rnn_cell.LSTMStateTuple(
tf.zeros([batch_size, RNN_NUM_UNITS]), # initial cell state,
tf.zeros([batch_size, RNN_NUM_UNITS]) # initial hidden state
)
predicted_probas = []
for t in range(MAX_LENGTH):
x_t = self.input_sequence[t]
# convert character id into embedding
x_t_emb = self.embed_x(tf.reshape(x_t, [-1, 1]))[:, 0]
out_next_first, h_next_first = self.gru_cell_first(x_t_emb, h_prev_first)
h_prev_first = h_next_first
out_next_second, h_next_second = self.lstm_cell_second(out_next_first, h_prev_second)
h_prev_second = h_next_second
probas_next = self.get_probas(out_next_second)
predicted_probas.append(probas_next)
predicted_probas = tf.stack(predicted_probas)
predictions_matrix = tf.reshape(predicted_probas[:-1], [-1, len(tokens)])
answers_matrix = tf.one_hot(tf.reshape(self.input_sequence[1:], [-1]), n_tokens)
self.loss = tf.reduce_mean(tf.reduce_sum(
-answers_matrix * tf.log(tf.clip_by_value(predictions_matrix, 1e-7, 1.0)),
reduction_indices=[1]
))
optimizer = tf.train.AdamOptimizer(learning_rate)
gvs = optimizer.compute_gradients(self.loss)
capped_gvs = [(gr if gr is None else tf.clip_by_value(gr, -1., 1.), var) for gr, var in gvs]
self.optimize = optimizer.apply_gradients(capped_gvs)
self.sess = tf.Session()
self.sess.run(tf.global_variables_initializer())
self.saver = tf.train.Saver()
def train(self, train_data_path, save_dir, num_iters, batch_size=64, restore_from=False):
history = []
if restore_from:
with open(restore_from + '_history') as f:
history = pickle.load(f)
self.saver.restore(self.sess, restore_from)
with open(train_data_path, 'r') as f:
train_data = f.readlines()
train_data = filter(lambda a: len(a) < MAX_LENGTH, train_data)
for i in tqdm(range(num_iters)):
batch = to_matrix(
map(lambda a: '\n' + a.rstrip('\n'), sample(train_data, batch_size)),
max_len=MAX_LENGTH
)
loss_i, _ = self.sess.run([self.loss, self.optimize], {self.input_sequence: batch})
history.append(loss_i)
if len(history) % 2000 == 0:
self.saver.save(self.sess, os.path.join(save_dir, '{}_iters'.format(len(history))))
self.saver.save(self.sess, os.path.join(save_dir, '{}_iters'.format(len(history))))
with open(os.path.join(save_dir, '{}_iters_history'.format(len(history)))) as f:
pickle.dump(history, f)
def generate(self, num_objects, output_file, weights_path):
self.saver.restore(self.sess, weights_path)
batch_size = num_objects
x_t = tf.placeholder('int32', (None, batch_size))
h_t_first = tf.Variable(tf.zeros([batch_size, RNN_NUM_UNITS]))
h_t_second = tf.nn.rnn_cell.LSTMStateTuple(
tf.Variable(tf.zeros([batch_size, RNN_NUM_UNITS])),
tf.Variable(tf.zeros([batch_size, RNN_NUM_UNITS]))
)
x_t_emb = self.embed_x(tf.reshape(x_t, [-1, 1]))[:, 0]
first_out_next, next_h_first = self.gru_cell_first(x_t_emb, h_t_first)
second_out_next, next_h_second = self.lstm_cell_second(first_out_next, h_t_second)
next_probs = self.get_probas(second_out_next)
x_sequence = np.zeros(shape=(1, batch_size), dtype=int) + token_to_id['\n']
self.sess.run(
[tf.assign(h_t_first, h_t_first.initial_value),
tf.assign(h_t_second[0], h_t_second[0].initial_value),
tf.assign(h_t_second[1], h_t_second[1].initial_value)]
)
for i in tqdm(range(MAX_LENGTH - 1)):
x_probs, _, _, _ = self.sess.run(
[next_probs,
tf.assign(h_t_second[0], next_h_second[0]),
tf.assign(h_t_second[1], next_h_second[1]),
tf.assign(h_t_first, next_h_first)],
{x_t: [x_sequence[-1, :]]}
)
next_char = [np.random.choice(n_tokens, p=x_probs[i]) for i in range(batch_size)]
if sum(next_char) == 0:
break
x_sequence = np.append(x_sequence, [next_char], axis=0)
with open(output_file, 'w') as f:
f.writelines([''.join([tokens[ix] for ix in x_sequence.T[k]]) + '\n' for k in range(batch_size)])

3
dbms/scripts/gen_benchmark_data/requirements.txt Normal file
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Keras==2.0.6
numpy
tensorflow-gpu==1.4.0

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dbms/scripts/gen_benchmark_data/tokens Normal file
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26
dbms/scripts/gen_benchmark_data/train.py Normal file
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import argparse
from model import Model
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--n_iter', type=int, default=10000,
help='number of iterations')
parser.add_argument('--save_dir', type=str, default='save',
help='dir for saving weights')
parser.add_argument('--data_path', type=str,
help='path to train data')
parser.add_argument('--learning_rate', type=int, default=0.0001,
help='learning rate')
parser.add_argument('--batch_size', type=int, default=64,
help='batch size')
parser.add_argument('--restore_from', type=str,
help='path to train saved weights')
args = parser.parse_args()
if __name__ == '__main__':
if not args.data_path:
raise Exception('please specify path to train data with --data_path')
gen = Model(args.learning_rate)
gen.train(args.data_path, args.save_dir, args.n_iter, args.batch_size, args.restore_from)

6
dbms/src/Interpreters/Context.cpp
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@ -1732,6 +1732,11 @@ void Context::setFormatSchemaPath(const String & path)
shared->format_schema_path = path;
}
Context::getSampleBlockCacheType & Context::getSampleBlockCache() const
{
return getQueryContext().get_sample_block_cache;
}
std::shared_ptr<ActionLocksManager> Context::getActionLocksManager()
{
auto lock = getLock();
@ -1742,7 +1747,6 @@ std::shared_ptr<ActionLocksManager> Context::getActionLocksManager()
return shared->action_locks_manager;
}
SessionCleaner::~SessionCleaner()
{
try

5
dbms/src/Interpreters/Context.h
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@ -10,6 +10,7 @@
#include <common/MultiVersion.h>
#include <Core/Types.h>
#include <Core/NamesAndTypes.h>
#include <Core/Block.h>
#include <Interpreters/Settings.h>
#include <Interpreters/ClientInfo.h>
#include <IO/CompressionSettings.h>
@ -398,6 +399,10 @@ public:
/// User name and session identifier. Named sessions are local to users.
using SessionKey = std::pair<String, String>;
using getSampleBlockCacheType = std::unordered_map<std::string, Block>;
mutable Context::getSampleBlockCacheType get_sample_block_cache;
getSampleBlockCacheType & getSampleBlockCache() const;
private:
/** Check if the current client has access to the specified database.
* If access is denied, throw an exception.

12
dbms/src/Interpreters/InterpreterSelectWithUnionQuery.cpp
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@ -9,7 +9,7 @@
#include <DataTypes/getLeastSupertype.h>
#include <Columns/ColumnConst.h>
#include <Common/typeid_cast.h>
#include <Parsers/queryToString.h>
namespace DB
{
@ -157,7 +157,15 @@ Block InterpreterSelectWithUnionQuery::getSampleBlock(
const ASTPtr & query_ptr,
const Context & context)
{
return InterpreterSelectWithUnionQuery(query_ptr, context).getSampleBlock();
auto & cache = context.getSampleBlockCache();
/// Using query string because query_ptr changes for every internal SELECT
auto key = queryToString(query_ptr);
if (cache.find(key) != cache.end())
{
return cache[key];
}
return cache[key] = InterpreterSelectWithUnionQuery(query_ptr, context).getSampleBlock();
}

4
dbms/src/Interpreters/executeQuery.cpp
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@ -109,8 +109,6 @@ static void onExceptionBeforeStart(const String & query, Context & context, time
bool log_queries = context.getSettingsRef().log_queries;
/// Log the start of query execution into the table if necessary.
if (log_queries)
{
QueryLogElement elem;
elem.type = QueryLogElement::EXCEPTION_BEFORE_START;
@ -126,9 +124,9 @@ static void onExceptionBeforeStart(const String & query, Context & context, time
setExceptionStackTrace(elem);
logException(context, elem);
if (log_queries)
if (auto query_log = context.getQueryLog())
query_log->add(elem);
}
}

2
dbms/tests/queries/0_stateless/00632_get_sample_block_cache.reference Normal file
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@ -0,0 +1,2 @@
Still alive
65535

174
dbms/tests/queries/0_stateless/00632_get_sample_block_cache.sql Normal file
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File diff suppressed because one or more lines are too long

12
docker/builder/Dockerfile
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@ -1,11 +1,11 @@
FROM ubuntu:17.10
FROM ubuntu:18.04
RUN apt-get update -y && \
apt-get install -y \
cmake pkg-config gcc-7 g++-7 \
liblld-5.0-dev libclang-5.0-dev \
libssl-dev libicu-dev libreadline-dev libmysqlclient-dev unixodbc-dev
# For tests: bash expect python python-lxml python-termcolor curl perl sudo tzdata
env DEBIAN_FRONTEND=noninteractive apt-get install -y \
cmake ninja-build ccache pkg-config gcc g++ \
liblld-6.0-dev libclang-6.0-dev \
libssl-dev libicu-dev libreadline-dev libmysqlclient-dev unixodbc-dev \
bash expect python python-lxml python-termcolor python-requests curl perl sudo tzdata
ADD build.sh /
RUN chmod +x /build.sh

5
docker/builder/Makefile
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@ -1,5 +1,6 @@
build:
docker run --network=host --rm --workdir /server --volume $(realpath ../..):/server -it yandex/clickhouse-builder
build: image
mkdir -p $(HOME)/.ccache
docker run --network=host --rm --workdir /server --volume $(realpath ../..):/server --mount=type=bind,source=$(HOME)/.ccache,destination=/ccache -e CCACHE_DIR=/ccache -it yandex/clickhouse-builder
pull:
docker pull yandex/clickhouse-builder

7
docker/builder/build.sh
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@ -1,7 +1,8 @@
#!/bin/bash
#ccache -s
mkdir -p /server/build_docker
cd /server/build_docker
cmake /server -D ENABLE_TESTS=0
make -j $(nproc || grep -c ^processor /proc/cpuinfo)
#ctest -V -j $(nproc || grep -c ^processor /proc/cpuinfo)
cmake -G Ninja /server -DENABLE_TESTS=1
cmake --build .
env TEST_OPT="--skip long compile $TEST_OPT" ctest -V -j $(nproc || grep -c ^processor /proc/cpuinfo)

4
docker/client/Dockerfile
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@ -1,4 +1,4 @@
FROM ubuntu:17.10
FROM ubuntu:18.04
ARG repository="deb http://repo.yandex.ru/clickhouse/deb/stable/ main/"
ARG version=\*
@ -9,7 +9,7 @@ RUN apt-get update && \
apt-key adv --keyserver keyserver.ubuntu.com --recv E0C56BD4 && \
echo $repository | tee /etc/apt/sources.list.d/clickhouse.list && \
apt-get update && \
apt-get install --allow-unauthenticated -y clickhouse-client=$version locales tzdata && \
env DEBIAN_FRONTEND=noninteractive apt-get install --allow-unauthenticated -y clickhouse-client=$version locales tzdata && \
rm -rf /var/lib/apt/lists/* /var/cache/debconf && \
apt-get clean

4
docker/server/Dockerfile
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@ -1,4 +1,4 @@
FROM ubuntu:17.10
FROM ubuntu:18.04
ARG repository="deb http://repo.yandex.ru/clickhouse/deb/stable/ main/"
ARG version=\*
@ -9,7 +9,7 @@ RUN apt-get update && \
apt-key adv --keyserver keyserver.ubuntu.com --recv E0C56BD4 && \
echo $repository | tee /etc/apt/sources.list.d/clickhouse.list && \
apt-get update && \
apt-get install --allow-unauthenticated -y "clickhouse-server=$version" libgcc-7-dev && \
env DEBIAN_FRONTEND=noninteractive apt-get install --allow-unauthenticated -y "clickhouse-server=$version" libgcc-7-dev && \
rm -rf /var/lib/apt/lists/* /var/cache/debconf && \
apt-get clean

7
docker/test/Dockerfile
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@ -1,4 +1,4 @@
FROM ubuntu:17.10
FROM ubuntu:18.04
ARG repository="deb http://repo.yandex.ru/clickhouse/deb/stable/ main/"
ARG version=\*
@ -9,11 +9,8 @@ RUN apt-get update && \
apt-key adv --keyserver keyserver.ubuntu.com --recv E0C56BD4 && \
echo $repository | tee /etc/apt/sources.list.d/clickhouse.list && \
apt-get update && \
apt-get install --allow-unauthenticated -y clickhouse-test && \
env DEBIAN_FRONTEND=noninteractive apt-get install --allow-unauthenticated -y clickhouse-test && \
rm -rf /var/lib/apt/lists/* /var/cache/debconf && \
apt-get clean
# clickhouse-test bug: it doesn't start without server config, remove after release 1.1.54372 :
RUN mkdir -p /etc/clickhouse-server && echo "<y></y>" > /etc/clickhouse-server/config.xml
ENTRYPOINT ["/usr/bin/clickhouse-test"]

2
docs/en/interfaces/third-party_client_libraries.md
View File

@ -38,5 +38,7 @@ There are libraries for working with ClickHouse for:
- [clickhouse_ecto](https://github.com/appodeal/clickhouse_ecto)
- Java
- [clickhouse-client-java](https://github.com/VirtusAI/clickhouse-client-java)
- Nim
- [nim-clickhouse](https://github.com/leonardoce/nim-clickhouse)
We have not tested these libraries. They are listed in random order.

2
docs/ru/interfaces/third-party_client_libraries.md
View File

@ -38,3 +38,5 @@
- [clickhouse_ecto](https://github.com/appodeal/clickhouse_ecto)
- Java
- [clickhouse-client-java](https://github.com/VirtusAI/clickhouse-client-java)
- Nim
- [nim-clickhouse](https://github.com/leonardoce/nim-clickhouse)

2
release
View File

@ -53,7 +53,7 @@ do
shift
elif [[ $1 == '--fast' ]]; then
# Wrong but fast pbuilder mode: create base package with all depends
EXTRAPACKAGES="$EXTRAPACKAGES debhelper cmake ninja-build gcc-7 g++-7 libc6-dev libmariadbclient-dev libicu-dev libltdl-dev libreadline-dev libssl-dev unixodbc-dev psmisc bash expect python python-lxml python-termcolor curl perl sudo openssl"
EXTRAPACKAGES="$EXTRAPACKAGES debhelper cmake ninja-build gcc-7 g++-7 libc6-dev libmariadbclient-dev libicu-dev libltdl-dev libreadline-dev libssl-dev unixodbc-dev psmisc bash expect python python-lxml python-termcolor python-requests curl perl sudo openssl"
shift
else
echo "Unknown option $1"

2
utils/build/build_debian.sh
View File

@ -11,7 +11,7 @@ sudo apt install -y git bash cmake gcc-7 g++-7 libicu-dev libreadline-dev libmys
#sudo apt install -y libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-thread-dev zlib1g-dev liblz4-dev libdouble-conversion-dev libzstd-dev libre2-dev libsparsehash-dev librdkafka-dev libcapnp-dev libpoco-dev libsparsehash-dev libgoogle-perftools-dev libunwind-dev googletest libcctz-dev
# install testing only stuff if you want:
sudo apt install -y python python-lxml python-termcolor curl perl
sudo apt install -y python python-lxml python-termcolor python-requests curl perl
# Checkout ClickHouse sources
git clone --recursive https://github.com/yandex/ClickHouse.git

2
utils/build/build_freebsd.sh
View File

@ -22,7 +22,7 @@
sudo pkg install devel/git devel/cmake shells/bash devel/icu devel/libltdl databases/unixODBC devel/google-perftools devel/libdouble-conversion archivers/zstd archivers/liblz4 devel/sparsehash devel/re2
# install testing only stuff if you want:
sudo pkg install lang/python devel/py-lxml devel/py-termcolor ftp/curl perl5
sudo pkg install lang/python devel/py-lxml devel/py-termcolor www/py-requests ftp/curl perl5
# If you want ODBC support: Check UNIXODBC option:
# make -C /usr/ports/devel/poco config reinstall