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arangodb/arangod/Pregel/GraphStore.cpp

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////////////////////////////////////////////////////////////////////////////////
/// DISCLAIMER
///
/// Copyright 2016 ArangoDB GmbH, Cologne, Germany
///
/// Licensed under the Apache License, Version 2.0 (the "License");
/// you may not use this file except in compliance with the License.
/// You may obtain a copy of the License at
///
/// http://www.apache.org/licenses/LICENSE-2.0
///
/// Unless required by applicable law or agreed to in writing, software
/// distributed under the License is distributed on an "AS IS" BASIS,
/// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
/// See the License for the specific language governing permissions and
/// limitations under the License.
///
/// Copyright holder is ArangoDB GmbH, Cologne, Germany
///
/// @author Simon Grätzer
////////////////////////////////////////////////////////////////////////////////
#include "GraphStore.h"
#include <algorithm>
#include "Basics/Common.h"
#include "Basics/MutexLocker.h"
#include "Cluster/ClusterInfo.h"
#include "Pregel/CommonFormats.h"
#include "Pregel/PregelFeature.h"
#include "Pregel/ThreadPool.h"
#include "Pregel/Utils.h"
#include "Pregel/WorkerConfig.h"
#include "Utils/CollectionNameResolver.h"
#include "Utils/UserTransaction.h"
#include "Utils/OperationCursor.h"
#include "Utils/OperationOptions.h"
#include "Transaction/StandaloneContext.h"
#include "Transaction/Methods.h"
#include "VocBase/EdgeCollectionInfo.h"
#include "VocBase/LogicalCollection.h"
#include "VocBase/ticks.h"
#include "VocBase/vocbase.h"
using namespace arangodb;
using namespace arangodb::pregel;
template <typename V, typename E>
GraphStore<V, E>::GraphStore(TRI_vocbase_t* vb, GraphFormat<V, E>* graphFormat)
: _vocbaseGuard(vb),
_graphFormat(graphFormat),
_localVerticeCount(0),
_localEdgeCount(0),
_runningThreads(0) {}
template <typename V, typename E>
GraphStore<V, E>::~GraphStore() {
_destroyed = true;
usleep(25 * 1000);
}
template <typename V, typename E>
std::map<ShardID, uint64_t> GraphStore<V, E>::_allocateMemory() {
double t = TRI_microtime();
std::unique_ptr<transaction::Methods> countTrx(_createTransaction());
std::map<ShardID, uint64_t> shardSizes;
// Allocating some memory
uint64_t count = 0;
for (auto const& shard : _config->localVertexShardIDs()) {
OperationResult opResult = countTrx->count(shard, true);
if (opResult.failed() || _destroyed) {
THROW_ARANGO_EXCEPTION(TRI_ERROR_BAD_PARAMETER);
}
shardSizes[shard] = opResult.slice().getUInt();
count += opResult.slice().getUInt();
}
_index.resize(count);
if (_graphFormat->estimatedVertexSize() > 0) {
_vertexData.resize(count);
}
count = 0;
for (auto const& shard : _config->localEdgeShardIDs()) {
OperationResult opResult = countTrx->count(shard, true);
if (opResult.failed() || _destroyed) {
THROW_ARANGO_EXCEPTION(TRI_ERROR_BAD_PARAMETER);
}
shardSizes[shard] = opResult.slice().getUInt();
count += opResult.slice().getUInt();
}
_edges.resize(count);
if (countTrx->commit() != TRI_ERROR_NO_ERROR) {
LOG_TOPIC(WARN, Logger::PREGEL)
<< "Pregel worker: Failed to commit on a read transaction";
}
LOG_TOPIC(INFO, Logger::PREGEL) << "Allocating memory took "
<< TRI_microtime() - t << "s";
return shardSizes;
}
template <typename V, typename E>
void GraphStore<V, E>::loadShards(WorkerConfig* config,
std::function<void()> callback) {
_config = config;
std::map<ShardID, uint64_t> shardSizes(_allocateMemory());
ThreadPool* pool = PregelFeature::instance()->threadPool();
uint64_t vertexOffset = 0, edgeOffset = 0;
// Contains the shards located on this db server in the right order
std::map<CollectionID, std::vector<ShardID>> const& vertexCollMap =
_config->vertexCollectionShards();
std::map<CollectionID, std::vector<ShardID>> const& edgeCollMap =
_config->edgeCollectionShards();
_runningThreads = config->localVertexShardIDs().size();
LOG_TOPIC(INFO, Logger::PREGEL) << "Using " << _runningThreads
<< " threads to load data";
for (auto const& pair : vertexCollMap) {
std::vector<ShardID> const& vertexShards = pair.second;
for (size_t i = 0; i < vertexShards.size(); i++) {
// we might have already loaded these shards
if (_loadedShards.find(vertexShards[i]) != _loadedShards.end()) {
continue;
}
ShardID const& vertexShard(vertexShards[i]);
uint64_t nextEdgeOffset = edgeOffset;
std::vector<ShardID> edgeLookups;
// distributeshardslike should cause the edges for a vertex to be
// in the same shard index. x in vertexShard2 => E(x) in edgeShard2
for (auto const& pair2 : edgeCollMap) {
std::vector<ShardID> const& edgeShards = pair2.second;
if (vertexShards.size() != edgeShards.size()) {
THROW_ARANGO_EXCEPTION_MESSAGE(
TRI_ERROR_BAD_PARAMETER,
"Collections need to have the same number of shards");
}
edgeLookups.push_back(edgeShards[i]);
nextEdgeOffset += shardSizes[edgeShards[i]];
}
_loadedShards.insert(vertexShard);
pool->enqueue([this, &vertexShard, edgeLookups, vertexOffset, edgeOffset,
callback] {
_loadVertices(vertexShard, edgeLookups, vertexOffset, edgeOffset);
{
MUTEX_LOCKER(guard, _threadMutex);
_runningThreads--;
if (_runningThreads == 0) {
if (_localEdgeCount < _edges.size()) {
_edges.resize(_localEdgeCount);
}
callback();
}
}
});
// update to next offset
vertexOffset += shardSizes[vertexShard];
edgeOffset = nextEdgeOffset;
}
}
}
template <typename V, typename E>
void GraphStore<V, E>::loadDocument(WorkerConfig* config,
std::string const& documentID) {
PregelID _id = config->documentIdToPregel(documentID);
if (config->isLocalVertexShard(_id.shard)) {
loadDocument(config, _id.shard, _id.key);
}
}
template <typename V, typename E>
void GraphStore<V, E>::loadDocument(WorkerConfig* config,
prgl_shard_t sourceShard,
std::string const& _key) {
_config = config;
std::unique_ptr<transaction::Methods> trx(_createTransaction());
ShardID const& vertexShard = _config->globalShardIDs()[sourceShard];
VPackBuilder builder;
builder.openObject();
builder.add(StaticStrings::KeyString, VPackValue(_key));
builder.close();
OperationOptions options;
options.ignoreRevs = false;
TRI_voc_cid_t cid = trx->addCollectionAtRuntime(vertexShard);
trx->pinData(cid); // will throw when it fails
OperationResult opResult =
trx->document(vertexShard, builder.slice(), options);
if (!opResult.successful()) {
THROW_ARANGO_EXCEPTION(opResult.code);
}
std::string documentId = trx->extractIdString(opResult.slice());
_index.emplace_back(sourceShard, _key);
_localVerticeCount++;
VertexEntry& entry = _index.back();
if (_graphFormat->estimatedVertexSize() > 0) {
entry._vertexDataOffset = _vertexData.size();
entry._edgeDataOffset = _edges.size();
// allocate space
_vertexData.push_back(V());
V& data = _vertexData.back();
_graphFormat->copyVertexData(documentId, opResult.slice(), &data,
sizeof(V));
}
// load edges
std::map<CollectionID, std::vector<ShardID>> const& vertexMap =
_config->vertexCollectionShards();
std::map<CollectionID, std::vector<ShardID>> const& edgeMap =
_config->edgeCollectionShards();
for (auto const& pair : vertexMap) {
std::vector<ShardID> const& vertexShards = pair.second;
auto it = std::find(vertexShards.begin(), vertexShards.end(), vertexShard);
if (it != vertexShards.end()) {
size_t pos = (size_t)(it - vertexShards.begin());
for (auto const& pair2 : edgeMap) {
std::vector<ShardID> const& edgeShards = pair2.second;
_loadEdges(trx.get(), edgeShards[pos], entry, documentId);
}
break;
}
}
if (trx->commit() != TRI_ERROR_NO_ERROR) {
LOG_TOPIC(WARN, Logger::PREGEL)
<< "Pregel worker: Failed to commit on a read transaction";
}
}
template <typename V, typename E>
RangeIterator<VertexEntry> GraphStore<V, E>::vertexIterator() {
return vertexIterator(0, _index.size());
}
template <typename V, typename E>
RangeIterator<VertexEntry> GraphStore<V, E>::vertexIterator(size_t start,
size_t end) {
return RangeIterator<VertexEntry>(_index, start, end);
}
template <typename V, typename E>
V* GraphStore<V, E>::mutableVertexData(VertexEntry const* entry) {
return _vertexData.data() + entry->_vertexDataOffset;
}
template <typename V, typename E>
void GraphStore<V, E>::replaceVertexData(VertexEntry const* entry, void* data,
size_t size) {
// if (size <= entry->_vertexDataOffset)
void* ptr = _vertexData.data() + entry->_vertexDataOffset;
memcpy(ptr, data, size);
LOG_TOPIC(WARN, Logger::PREGEL)
<< "Don't use this function with varying sizes";
}
template <typename V, typename E>
RangeIterator<Edge<E>> GraphStore<V, E>::edgeIterator(
VertexEntry const* entry) {
size_t end = entry->_edgeDataOffset + entry->_edgeCount;
return RangeIterator<Edge<E>>(_edges, entry->_edgeDataOffset, end);
}
template <typename V, typename E>
std::unique_ptr<transaction::Methods> GraphStore<V, E>::_createTransaction() {
double lockTimeout = transaction::Methods::DefaultLockTimeout;
auto ctx = transaction::StandaloneContext::Create(_vocbaseGuard.vocbase());
std::unique_ptr<transaction::Methods> trx(
new UserTransaction(ctx, {}, {}, {}, lockTimeout, false, true));
int res = trx->begin();
if (res != TRI_ERROR_NO_ERROR) {
THROW_ARANGO_EXCEPTION(res);
}
return trx;
}
template <typename V, typename E>
void GraphStore<V, E>::_loadVertices(ShardID const& vertexShard,
std::vector<ShardID> const& edgeShards,
uint64_t vertexOffset,
uint64_t edgeOffset) {
uint64_t originalVertexOffset = vertexOffset;
std::unique_ptr<transaction::Methods> trx(_createTransaction());
TRI_voc_cid_t cid = trx->addCollectionAtRuntime(vertexShard);
trx->pinData(cid); // will throw when it fails
prgl_shard_t sourceShard = (prgl_shard_t)_config->shardId(vertexShard);
ManagedDocumentResult mmdr;
std::unique_ptr<OperationCursor> cursor = trx->indexScan(
vertexShard, transaction::Methods::CursorType::ALL,
&mmdr, 0, UINT64_MAX, 1000, false);
if (cursor->failed()) {
THROW_ARANGO_EXCEPTION_FORMAT(cursor->code, "while looking up shard '%s'",
vertexShard.c_str());
}
// tell the formatter the number of docs we are about to load
LogicalCollection* collection = cursor->collection();
uint64_t number = collection->numberDocuments();
_graphFormat->willLoadVertices(number);
auto cb = [&](DocumentIdentifierToken const& token) {
if (collection->readDocument(trx.get(), token, mmdr)) {
VPackSlice document(mmdr.vpack());
if (document.isExternal()) {
document = document.resolveExternal();
}
VertexEntry& ventry = _index[vertexOffset];
ventry._shard = sourceShard;
ventry._key = document.get(StaticStrings::KeyString).copyString();
ventry._edgeDataOffset = edgeOffset;
// load vertex data
std::string documentId = trx->extractIdString(document);
if (_graphFormat->estimatedVertexSize() > 0) {
ventry._vertexDataOffset = vertexOffset;
V* ptr = _vertexData.data() + vertexOffset;
_graphFormat->copyVertexData(documentId, document, ptr, sizeof(V));
}
// load edges
for (ShardID const& it : edgeShards) {
_loadEdges(trx.get(), it, ventry, documentId);
}
vertexOffset++;
edgeOffset += ventry._edgeCount;
}
};
while (cursor->getMore(cb, 1000)) {
if (_destroyed) {
LOG_TOPIC(WARN, Logger::PREGEL) << "Aborted loading graph";
break;
}
}
// Add all new vertices
_localVerticeCount += (vertexOffset - originalVertexOffset);
if (trx->commit() != TRI_ERROR_NO_ERROR) {
LOG_TOPIC(WARN, Logger::PREGEL)
<< "Pregel worker: Failed to commit on a read transaction";
}
}
template <typename V, typename E>
void GraphStore<V, E>::_loadEdges(transaction::Methods* trx, ShardID const& edgeShard,
VertexEntry& vertexEntry,
std::string const& documentID) {
// offset into the edge store, edgeCount is 0 initally
size_t offset = vertexEntry._edgeDataOffset + vertexEntry._edgeCount;
size_t originalOffset = offset;
traverser::EdgeCollectionInfo info(trx, edgeShard, TRI_EDGE_OUT,
StaticStrings::FromString, 0);
ManagedDocumentResult mmdr;
std::unique_ptr<OperationCursor> cursor = info.getEdges(documentID, &mmdr);
if (cursor->failed()) {
THROW_ARANGO_EXCEPTION_FORMAT(cursor->code,
"while looking up edges '%s' from %s",
documentID.c_str(), edgeShard.c_str());
}
LogicalCollection* collection = cursor->collection();
auto cb = [&](DocumentIdentifierToken const& token) {
if (collection->readDocument(trx, token, mmdr)) {
VPackSlice document(mmdr.vpack());
if (document.isExternal()) {
document = document.resolveExternal();
}
// LOG_TOPIC(INFO, Logger::PREGEL) << "Loaded Edge: " <<
// document.toJson();
std::string toValue = document.get(StaticStrings::ToString).copyString();
std::size_t pos = toValue.find('/');
std::string collectionName = toValue.substr(0, pos);
// If this is called from loadDocument we didn't preallocate the vector
if (_edges.size() <= offset) {
if (!_config->lazyLoading()) {
LOG_TOPIC(ERR, Logger::PREGEL) << "WTF";
}
_edges.push_back(Edge<E>());
}
Edge<E>& edge(_edges[offset]);
edge._toKey = toValue.substr(pos + 1, toValue.length() - pos - 1);
auto collInfo = Utils::resolveCollection(
_config->database(), collectionName, _config->collectionPlanIdMap());
if (collInfo) {
// resolve the shard of the target vertex.
ShardID responsibleShard;
Utils::resolveShard(collInfo.get(), StaticStrings::KeyString,
edge._toKey, responsibleShard);
prgl_shard_t sourceShard = (prgl_shard_t)_config->shardId(edgeShard);
edge._targetShard = (prgl_shard_t)_config->shardId(responsibleShard);
_graphFormat->copyEdgeData(document, edge.data(), sizeof(E));
if (sourceShard == (prgl_shard_t)-1 ||
edge._targetShard == (prgl_shard_t)-1) {
return;
}
offset++;
}
}
};
while (cursor->getMore(cb, 1000)) {
}
// Add up all added elements
size_t added = offset - originalOffset;
vertexEntry._edgeCount += added;
_localEdgeCount += added;
}
/// Loops over the array starting a new transaction for different shards
/// Should not dead-lock unless we have to wait really long for other threads
template <typename V, typename E>
void GraphStore<V, E>::_storeVertices(std::vector<ShardID> const& globalShards,
RangeIterator<VertexEntry>& it) {
// transaction on one shard
std::unique_ptr<UserTransaction> trx;
prgl_shard_t currentShard = (prgl_shard_t)-1;
int res = TRI_ERROR_NO_ERROR;
// loop over vertices
while (it != it.end()) {
if (it->shard() != currentShard) {
if (trx) {
res = trx->finish(res);
if (res != TRI_ERROR_NO_ERROR) {
THROW_ARANGO_EXCEPTION(res);
}
}
currentShard = it->shard();
ShardID const& shard = globalShards[currentShard];
double timeout = transaction::Methods::DefaultLockTimeout;
trx.reset(new UserTransaction(transaction::StandaloneContext::Create(_vocbaseGuard.vocbase()), {},
{shard}, {}, timeout, false, false));
res = trx->begin();
if (res != TRI_ERROR_NO_ERROR) {
THROW_ARANGO_EXCEPTION(res);
}
}
transaction::BuilderLeaser b(trx.get());
b->openArray();
size_t buffer = 0;
while (it != it.end() && buffer < 1000) {
if (it->shard() != currentShard) {
break;
}
V* data = _vertexData.data() + it->_vertexDataOffset;
b->openObject();
b->add(StaticStrings::KeyString, VPackValue(it->key()));
// bool store =
_graphFormat->buildVertexDocument(*(b.get()), data, sizeof(V));
b->close();
++it;
++buffer;
}
b->close();
ShardID const& shard = globalShards[currentShard];
OperationOptions options;
OperationResult result = trx->update(shard, b->slice(), options);
if (result.code != TRI_ERROR_NO_ERROR) {
THROW_ARANGO_EXCEPTION(result.code);
}
}
if (trx) {
res = trx->finish(res);
if (res != TRI_ERROR_NO_ERROR) {
THROW_ARANGO_EXCEPTION(res);
}
}
}
template <typename V, typename E>
void GraphStore<V, E>::storeResults(WorkerConfig const& state) {
double now = TRI_microtime();
// for (auto const& shard : state.localEdgeShardIDs()) {
// writeColls.push_back(shard);
//}
std::atomic<size_t> tCount(0);
size_t total = _index.size();
size_t delta = _index.size() / state.localVertexShardIDs().size();
if (delta < 1000) {
delta = _index.size();
}
size_t start = 0, end = delta;
do {
tCount++;
ThreadPool* pool = PregelFeature::instance()->threadPool();
pool->enqueue([this, start, end, &state, &tCount] {
try {
RangeIterator<VertexEntry> it = vertexIterator(start, end);
_storeVertices(state.globalShardIDs(), it);
} catch (...) {
LOG_TOPIC(ERR, Logger::PREGEL) << "Storing vertex data failed";
}
tCount--;
});
start = end;
end = end + delta;
if (total < end + delta) { // swallow the rest
end = total;
}
} while (start != end);
while (tCount > 0 && !_destroyed) {
usleep(25 * 1000); // 25ms
}
LOG_TOPIC(INFO, Logger::PREGEL) << "Storing data took "
<< (TRI_microtime() - now) << "s";
}
template class arangodb::pregel::GraphStore<int64_t, int64_t>;
template class arangodb::pregel::GraphStore<float, float>;
template class arangodb::pregel::GraphStore<double, float>;
template class arangodb::pregel::GraphStore<double, double>;
// specific algo combos
template class arangodb::pregel::GraphStore<SCCValue, int8_t>;
template class arangodb::pregel::GraphStore<ECValue, int8_t>;
template class arangodb::pregel::GraphStore<HITSValue, int8_t>;
template class arangodb::pregel::GraphStore<DMIDValue, float>;
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