Merge pull request BVLC#3731 from lukeyeager/lmdb-map-full

dynamically set LMDB map size (double when full)

examples/cifar10/convert_cifar_data.cpp

@@ -91,6 +91,8 @@ void convert_dataset(const string& input_folder, const string& output_folder,
 }
 
 int main(int argc, char** argv) {
+  FLAGS_alsologtostderr = 1;
+
   if (argc != 4) {
     printf("This script converts the CIFAR dataset to the leveldb format used\n"
            "by caffe to perform classification.\n"

examples/mnist/convert_mnist_data.cpp

@@ -22,12 +22,15 @@
 #include <fstream>  // NOLINT(readability/streams)
 #include <string>
 
+#include "boost/scoped_ptr.hpp"
 #include "caffe/proto/caffe.pb.h"
+#include "caffe/util/db.hpp"
 #include "caffe/util/format.hpp"
 
 #if defined(USE_LEVELDB) && defined(USE_LMDB)
 
 using namespace caffe;  // NOLINT(build/namespaces)
+using boost::scoped_ptr;
 using std::string;
 
 DEFINE_string(backend, "lmdb", "The backend for storing the result");
@@ -67,43 +70,10 @@ void convert_dataset(const char* image_filename, const char* label_filename,
   image_file.read(reinterpret_cast<char*>(&cols), 4);
   cols = swap_endian(cols);
 
-  // lmdb
-  MDB_env *mdb_env;
-  MDB_dbi mdb_dbi;
-  MDB_val mdb_key, mdb_data;
-  MDB_txn *mdb_txn;
-  // leveldb
-  leveldb::DB* db;
-  leveldb::Options options;
-  options.error_if_exists = true;
-  options.create_if_missing = true;
-  options.write_buffer_size = 268435456;
-  leveldb::WriteBatch* batch = NULL;
-
-  // Open db
-  if (db_backend == "leveldb") {  // leveldb
-    LOG(INFO) << "Opening leveldb " << db_path;
-    leveldb::Status status = leveldb::DB::Open(
-        options, db_path, &db);
-    CHECK(status.ok()) << "Failed to open leveldb " << db_path
-        << ". Is it already existing?";
-    batch = new leveldb::WriteBatch();
-  } else if (db_backend == "lmdb") {  // lmdb
-    LOG(INFO) << "Opening lmdb " << db_path;
-    CHECK_EQ(mkdir(db_path, 0744), 0)
-        << "mkdir " << db_path << "failed";
-    CHECK_EQ(mdb_env_create(&mdb_env), MDB_SUCCESS) << "mdb_env_create failed";
-    CHECK_EQ(mdb_env_set_mapsize(mdb_env, 1099511627776), MDB_SUCCESS)  // 1TB
-        << "mdb_env_set_mapsize failed";
-    CHECK_EQ(mdb_env_open(mdb_env, db_path, 0, 0664), MDB_SUCCESS)
-        << "mdb_env_open failed";
-    CHECK_EQ(mdb_txn_begin(mdb_env, NULL, 0, &mdb_txn), MDB_SUCCESS)
-        << "mdb_txn_begin failed";
-    CHECK_EQ(mdb_open(mdb_txn, NULL, 0, &mdb_dbi), MDB_SUCCESS)
-        << "mdb_open failed. Does the lmdb already exist? ";
-  } else {
-    LOG(FATAL) << "Unknown db backend " << db_backend;
-  }
+
+  scoped_ptr<db::DB> db(db::GetDB(db_backend));
+  db->Open(db_path, db::NEW);
+  scoped_ptr<db::Transaction> txn(db->NewTransaction());
 
   // Storing to db
   char label;
@@ -125,59 +95,28 @@ void convert_dataset(const char* image_filename, const char* label_filename,
     string key_str = caffe::format_int(item_id, 8);
     datum.SerializeToString(&value);
 
-    // Put in db
-    if (db_backend == "leveldb") {  // leveldb
-      batch->Put(key_str, value);
-    } else if (db_backend == "lmdb") {  // lmdb
-      mdb_data.mv_size = value.size();
-      mdb_data.mv_data = reinterpret_cast<void*>(&value[0]);
-      mdb_key.mv_size = key_str.size();
-      mdb_key.mv_data = reinterpret_cast<void*>(&key_str[0]);
-      CHECK_EQ(mdb_put(mdb_txn, mdb_dbi, &mdb_key, &mdb_data, 0), MDB_SUCCESS)
-          << "mdb_put failed";
-    } else {
-      LOG(FATAL) << "Unknown db backend " << db_backend;
-    }
+    txn->Put(key_str, value);
 
     if (++count % 1000 == 0) {
-      // Commit txn
-      if (db_backend == "leveldb") {  // leveldb
-        db->Write(leveldb::WriteOptions(), batch);
-        delete batch;
-        batch = new leveldb::WriteBatch();
-      } else if (db_backend == "lmdb") {  // lmdb
-        CHECK_EQ(mdb_txn_commit(mdb_txn), MDB_SUCCESS)
-            << "mdb_txn_commit failed";
-        CHECK_EQ(mdb_txn_begin(mdb_env, NULL, 0, &mdb_txn), MDB_SUCCESS)
-            << "mdb_txn_begin failed";
-      } else {
-        LOG(FATAL) << "Unknown db backend " << db_backend;
-      }
+      txn->Commit();
     }
   }
   // write the last batch
   if (count % 1000 != 0) {
-    if (db_backend == "leveldb") {  // leveldb
-      db->Write(leveldb::WriteOptions(), batch);
-      delete batch;
-      delete db;
-    } else if (db_backend == "lmdb") {  // lmdb
-      CHECK_EQ(mdb_txn_commit(mdb_txn), MDB_SUCCESS) << "mdb_txn_commit failed";
-      mdb_close(mdb_env, mdb_dbi);
-      mdb_env_close(mdb_env);
-    } else {
-      LOG(FATAL) << "Unknown db backend " << db_backend;
-    }
-    LOG(ERROR) << "Processed " << count << " files.";
+      txn->Commit();
   }
+  LOG(INFO) << "Processed " << count << " files.";
   delete[] pixels;
+  db->Close();
 }
 
 int main(int argc, char** argv) {
 #ifndef GFLAGS_GFLAGS_H_
   namespace gflags = google;
 #endif
 
+  FLAGS_alsologtostderr = 1;
+
   gflags::SetUsageMessage("This script converts the MNIST dataset to\n"
         "the lmdb/leveldb format used by Caffe to load data.\n"
         "Usage:\n"

include/caffe/util/db_lmdb.hpp

@@ -3,6 +3,7 @@
 #define CAFFE_UTIL_DB_LMDB_HPP
 
 #include <string>
+#include <vector>
 
 #include "lmdb.h"
 
@@ -54,14 +55,16 @@ class LMDBCursor : public Cursor {
 
 class LMDBTransaction : public Transaction {
  public:
-  explicit LMDBTransaction(MDB_dbi* mdb_dbi, MDB_txn* mdb_txn)
-    : mdb_dbi_(mdb_dbi), mdb_txn_(mdb_txn) { }
+  explicit LMDBTransaction(MDB_env* mdb_env)
+    : mdb_env_(mdb_env) { }
   virtual void Put(const string& key, const string& value);
-  virtual void Commit() { MDB_CHECK(mdb_txn_commit(mdb_txn_)); }
+  virtual void Commit();
 
  private:
-  MDB_dbi* mdb_dbi_;
-  MDB_txn* mdb_txn_;
+  MDB_env* mdb_env_;
+  vector<string> keys, values;
+
+  void DoubleMapSize();
 
   DISABLE_COPY_AND_ASSIGN(LMDBTransaction);
 };

src/caffe/util/db_lmdb.cpp

@@ -7,11 +7,8 @@
 
 namespace caffe { namespace db {
 
-const size_t LMDB_MAP_SIZE = 1099511627776;  // 1 TB
-
 void LMDB::Open(const string& source, Mode mode) {
   MDB_CHECK(mdb_env_create(&mdb_env_));
-  MDB_CHECK(mdb_env_set_mapsize(mdb_env_, LMDB_MAP_SIZE));
   if (mode == NEW) {
     CHECK_EQ(mkdir(source.c_str(), 0744), 0) << "mkdir " << source << "failed";
   }
@@ -48,19 +45,61 @@ LMDBCursor* LMDB::NewCursor() {
 }
 
 LMDBTransaction* LMDB::NewTransaction() {
-  MDB_txn* mdb_txn;
-  MDB_CHECK(mdb_txn_begin(mdb_env_, NULL, 0, &mdb_txn));
-  MDB_CHECK(mdb_dbi_open(mdb_txn, NULL, 0, &mdb_dbi_));
-  return new LMDBTransaction(&mdb_dbi_, mdb_txn);
+  return new LMDBTransaction(mdb_env_);
 }
 
 void LMDBTransaction::Put(const string& key, const string& value) {
-  MDB_val mdb_key, mdb_value;
-  mdb_key.mv_data = const_cast<char*>(key.data());
-  mdb_key.mv_size = key.size();
-  mdb_value.mv_data = const_cast<char*>(value.data());
-  mdb_value.mv_size = value.size();
-  MDB_CHECK(mdb_put(mdb_txn_, *mdb_dbi_, &mdb_key, &mdb_value, 0));
+  keys.push_back(key);
+  values.push_back(value);
+}
+
+void LMDBTransaction::Commit() {
+  MDB_dbi mdb_dbi;
+  MDB_val mdb_key, mdb_data;
+  MDB_txn *mdb_txn;
+
+  // Initialize MDB variables
+  MDB_CHECK(mdb_txn_begin(mdb_env_, NULL, 0, &mdb_txn));
+  MDB_CHECK(mdb_dbi_open(mdb_txn, NULL, 0, &mdb_dbi));
+
+  bool out_of_memory = false;
+  for (int i = 0; i < keys.size(); i++) {
+    mdb_key.mv_size = keys[i].size();
+    mdb_key.mv_data = const_cast<char*>(keys[i].data());
+    mdb_data.mv_size = values[i].size();
+    mdb_data.mv_data = const_cast<char*>(values[i].data());
+
+    int put_rc = mdb_put(mdb_txn, mdb_dbi, &mdb_key, &mdb_data, 0);
+    if (put_rc == MDB_MAP_FULL) {
+      out_of_memory = true;
+      break;
+    } else {
+      // Failed for some other reason
+      MDB_CHECK(put_rc);
+    }
+  }
+
+  if (!out_of_memory) {
+    // Commit the transaction
+    MDB_CHECK(mdb_txn_commit(mdb_txn));
+    mdb_dbi_close(mdb_env_, mdb_dbi);
+    keys.clear();
+    values.clear();
+  } else {
+    // Double the map size and retry
+    mdb_txn_abort(mdb_txn);
+    mdb_dbi_close(mdb_env_, mdb_dbi);
+    DoubleMapSize();
+    Commit();
+  }
+}
+
+void LMDBTransaction::DoubleMapSize() {
+  struct MDB_envinfo current_info;
+  MDB_CHECK(mdb_env_info(mdb_env_, &current_info));
+  size_t new_size = current_info.me_mapsize * 2;
+  DLOG(INFO) << "Doubling LMDB map size to " << (new_size>>20) << "MB ...";
+  MDB_CHECK(mdb_env_set_mapsize(mdb_env_, new_size));
 }
 
 }  // namespace db