view audioDB.h @ 340:a6edbe97fddf

Added LSH_CORE_ARRAY structure for hashtables instead of linked lists. Maintained Backwards Compatibiliity with indexes build for linked list format. Added tests for indexing and merging. Tested backwards compatibility OK.\n\n The purpose of the LSH_CORE_ARRAY data structure is greater space efficiency and L1/2 cache usage. Essential for multiple indexes with multiple hashtables in RAM

#ifndef __AUDIODB_H_
#define __AUDIODB_H_

#include <stdio.h>
#include <stdlib.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <sys/mman.h>
#include <fcntl.h>
#include <string.h>
#include <iostream>
#include <fstream>
#include <set>
#include <string>
#include <math.h>
#include <sys/time.h>
#include <assert.h>
#include <float.h>
#include <signal.h>
#include <gsl/gsl_rng.h>

// includes for LSH indexing
#include "ReporterBase.h"
#include "lshlib.h"

// includes for web services
#include "soapH.h"
#include "cmdline.h"

#define MAXSTR 512

// Databse PRIMARY commands
#define COM_CREATE "--NEW"
#define COM_INSERT "--INSERT"
#define COM_BATCHINSERT "--BATCHINSERT"
#define COM_QUERY "--QUERY"
#define COM_STATUS "--STATUS"
#define COM_L2NORM "--L2NORM"
#define COM_POWER "--POWER"
#define COM_DUMP "--DUMP"
#define COM_SERVER "--SERVER"
#define COM_INDEX "--INDEX"
#define COM_SAMPLE "--SAMPLE"
#define COM_LISZT "--LISZT"

// parameters
#define COM_CLIENT "--client"
#define COM_DATABASE "--database"
#define COM_QTYPE "--qtype"
#define COM_SEQLEN "--sequencelength"
#define COM_SEQHOP "--sequencehop"
#define COM_POINTNN "--pointnn"
#define COM_RADIUS "--radius"
#define COM_TRACKNN "--resultlength"
#define COM_QPOINT "--qpoint"
#define COM_FEATURES "--features"
#define COM_QUERYKEY "--key"
#define COM_KEYLIST "--keyList"
#define COM_TIMES "--times"
#define COM_QUERYPOWER "--power"
#define COM_RELATIVE_THRESH "--relative-threshold"
#define COM_ABSOLUTE_THRESH "--absolute-threshold"
#define COM_EXHAUSTIVE "--exhaustive"
#define COM_LSH_EXACT "--lsh_exact"

// Because LSH returns NN with P(1)<1 we want to return exact
// points above this boundary. 
// Because we work in Radius^2 units,
// The sqrt of this number is the multiplier on the radius

#define O2_LSH_EXACT_MULT 9

#define O2_OLD_MAGIC ('O'|'2'<<8|'D'<<16|'B'<<24)
#define O2_MAGIC ('o'|'2'<<8|'d'<<16|'b'<<24)
#define O2_FORMAT_VERSION (4U)

#define O2_DEFAULT_POINTNN (10U)
#define O2_DEFAULT_TRACKNN  (10U)

//#define O2_DEFAULTDBSIZE (4000000000) // 4GB table size
#define O2_DEFAULTDBSIZE (2000000000) // 2GB table size

// Bit masks for packing (trackID,pointID) into 32-bit unsigned int
// This can be controlled at compile time
#define O2_DEFAULT_LSH_N_POINT_BITS 14

// Override the default point bit width for large database support
#ifndef LSH_N_POINT_BITS
#define LSH_N_POINT_BITS O2_DEFAULT_LSH_N_POINT_BITS
#endif

// LIMIT PARAMETERS
#define O2_DEFAULT_DATASIZE (1355U) // in MB
#define O2_DEFAULT_NTRACKS (20000U)
#define O2_DEFAULT_DATADIM (9U)
#define O2_REALTYPE (double)
#define O2_MAXFILES (1000000U)
#define O2_MAXFILESTR (256U)
#define O2_FILETABLE_ENTRY_SIZE (O2_MAXFILESTR)
#define O2_TRACKTABLE_ENTRY_SIZE (sizeof(unsigned))
#define O2_HEADERSIZE (sizeof(dbTableHeaderT))
#define O2_MEANNUMVECTORS (1000U)
#define O2_MAXDIM (2000U)
#define O2_MAXNN (1000000U)
#define O2_MAXSEQLEN (8000U)            // maximum feature vectors in a sequence
#define O2_MAXTRACKS (1000000U)           // maximum number of tracks
#define O2_MAXTRACKLEN (1<<LSH_N_POINT_BITS) // maximum shingles in a track
#define O2_MAXDOTPRODUCTMEMORY (sizeof(O2_REALTYPE)*O2_MAXSEQLEN*O2_MAXSEQLEN) // 512MB
#define O2_DISTANCE_TOLERANCE (1e-6)
#define O2_SERIAL_MAX_TRACKBATCH (1000000)
#define O2_LARGE_ADB_SIZE (O2_DEFAULT_DATASIZE+1) // datasize at which features are kept externally (in Mbytes)
#define O2_LARGE_ADB_NTRACKS (O2_DEFAULT_NTRACKS+1) // ntracks at which features are kept externally
#define O2_MAX_VECTORS ( O2_MEANNUMVECTORS * O2_MAXTRACKS )

// Flags
#define O2_FLAG_L2NORM (0x1U)
#define O2_FLAG_MINMAX (0x2U)
#define O2_FLAG_POWER (0x4U)
#define O2_FLAG_TIMES (0x20U)
#define O2_FLAG_LARGE_ADB (0x40U)
#define DISPLAY_FLAG(x) (x?"on":"off")

// Query types
#define O2_POINT_QUERY (0x4U)
#define O2_SEQUENCE_QUERY (0x8U)
#define O2_TRACK_QUERY (0x10U)
#define O2_N_SEQUENCE_QUERY (0x20U)
#define O2_ONE_TO_ONE_N_SEQUENCE_QUERY (0x40U)

// Error Codes
#define O2_ERR_KEYNOTFOUND (0xFFFFFF00)

// Macros
#define O2_ACTION(a) (strcmp(command,a)==0)

#define ALIGN_UP(x,w) ((x) + ((1<<w)-1) & ~((1<<w)-1))
#define ALIGN_DOWN(x,w) ((x) & ~((1<<w)-1))

#define ALIGN_PAGE_UP(x) ((x) + (getpagesize()-1) & ~(getpagesize()-1))
#define ALIGN_PAGE_DOWN(x) ((x) & ~(getpagesize()-1))

#define ENSURE_STRING(x) ((x) ? (x) : "")

#define CHECKED_MMAP(type, var, start, length) \
  { void *tmp = mmap(0, length, (PROT_READ | (forWrite ? PROT_WRITE : 0)), MAP_SHARED, dbfid, (start)); \
    if(tmp == (void *) -1) { \
      error("mmap error for db table", #var, "mmap"); \
    } \
    var = (type) tmp; \
  }

#define VERB_LOG(vv, ...) \
  if(verbosity > vv) { \
    fprintf(stderr, __VA_ARGS__); \
    fflush(stderr); \
  }

// We will only use this in a 32-bit address space
// So map the off_t down to 32-bits first
#define INSERT_FILETABLE_STRING(TABLE, STR) \
    strncpy(TABLE + dbH->numFiles*O2_FILETABLE_ENTRY_SIZE, STR, strlen(STR));

#define SAFE_DELETE(PTR) delete PTR; PTR=0;
#define SAFE_DELETE_ARRAY(PTR) delete[] PTR; PTR=0;

extern LSH* SERVER_LSH_INDEX_SINGLETON;
extern char* SERVER_ADB_ROOT;
extern char* SERVER_ADB_FEATURE_ROOT;

typedef struct dbTableHeader {
  uint32_t magic;
  uint32_t version;
  uint32_t numFiles;
  uint32_t dim;
  uint32_t flags;
  uint32_t headerSize;
  off_t length;
  off_t fileTableOffset;
  off_t trackTableOffset;
  off_t dataOffset;
  off_t l2normTableOffset;
  off_t timesTableOffset;
  off_t powerTableOffset;
  off_t dbSize;
} dbTableHeaderT, *dbTableHeaderPtr;


class PointPair{
 public:
  Uns32T trackID;
  Uns32T qpos;
  Uns32T spos;
  PointPair(Uns32T a, Uns32T b, Uns32T c);
};

bool operator<(const PointPair& a, const PointPair& b);

class audioDB{  
 private:
  gengetopt_args_info args_info;
  unsigned dim;
  const char *dbName;
  const char *inFile;
  const char *hostport;
  const char *key;
  const char* trackFileName;
  std::ifstream *trackFile;
  const char *command;
  const char *output;
  const char *timesFileName;
  std::ifstream *timesFile;
  const char *powerFileName;
  std::ifstream *powerFile;
  const char* adb_root;
  const char* adb_feature_root;

  int powerfd;
  int dbfid;
  int lshfid;
  bool forWrite;
  int infid;
  char* db;
  char* indata;
  struct stat statbuf;  
  dbTableHeaderPtr dbH;

  gsl_rng *rng;
  
  char* fileTable;
  unsigned* trackTable;
  off_t* trackOffsetTable;
  double* dataBuf;
  double* inBuf;
  double* l2normTable;
  double* timesTable;
  double* powerTable;

  char* featureFileNameTable;
  char* timesFileNameTable;
  char* powerFileNameTable;

  size_t fileTableLength;
  size_t trackTableLength;
  off_t dataBufLength;
  size_t timesTableLength;
  size_t powerTableLength;
  size_t l2normTableLength;

  // Flags and parameters
  unsigned verbosity;   // how much do we want to know?

  unsigned nsamples;

  //off_t size; // given size (for creation)
  unsigned datasize; // size in MB
  unsigned ntracks;
  unsigned datadim;

  unsigned queryType; // point queries default
  unsigned pointNN;   // how many point NNs ?
  unsigned trackNN;   // how many track NNs ?
  unsigned sequenceLength;
  unsigned sequenceHop;
  bool normalizedDistance;
  bool no_unit_norming;
  unsigned queryPoint;
  unsigned usingQueryPoint;
  unsigned usingTimes;
  unsigned usingPower;
  unsigned isClient;
  unsigned isServer;
  unsigned port;
  double timesTol;
  double radius;
  bool query_from_key;
  Uns32T query_from_key_index;
  bool use_absolute_threshold;
  double absolute_threshold;
  bool use_relative_threshold;
  double relative_threshold;
  
  ReporterBase* reporter;  // track/point reporter
  priority_queue<PointPair, std::vector<PointPair>, std::less<PointPair> >* exact_evaluation_queue;

  // Timers
  struct timeval tv1;
  struct timeval tv2;

  // LISZT parameters
  unsigned lisztOffset;
  unsigned lisztLength;

  // private methods
  void error(const char* a, const char* b = "", const char *sysFunc = 0);
  void sequence_sum(double *buffer, int length, int seqlen);
  void sequence_sqrt(double *buffer, int length, int seqlen);
  void sequence_average(double *buffer, int length, int seqlen);

  void initialize_arrays(int track, unsigned int numVectors, double *query, double *data_buffer, double **D, double **DD);
  void delete_arrays(int track, unsigned int numVectors, double **D, double **DD);
  void read_data(int trkfid, int track, double **data_buffer_p, size_t *data_buffer_size_p);
  void set_up_query(double **qp, double **vqp, double **qnp, double **vqnp, double **qpp, double **vqpp, double *mqdp, unsigned int *nvp);
  void set_up_query_from_key(double **qp, double **vqp, double **qnp, double **vqnp, double **qpp, double **vqpp, double *mqdp, unsigned *nvp, Uns32T queryIndex);
  void set_up_db(double **snp, double **vsnp, double **spp, double **vspp, double **mddp, unsigned int *dvp);
  void query_loop(const char* dbName, Uns32T queryIndex);
  void query_loop_points(double* query, double* qnPtr, double* qpPtr, double meanQdur, Uns32T numVectors);
  double dot_product_points(double* q, double* p, Uns32T  L);
  void initRNG();
  void initDBHeader(const char *dbName);
  void initInputFile(const char *inFile, bool loadData = true);
  void initTables(const char* dbName, const char* inFile = 0);
  void initTablesFromKey(const char* dbName, const Uns32T queryIndex);
  void unitNorm(double* X, unsigned d, unsigned n, double* qNorm);
  void unitNormAndInsertL2(double* X, unsigned dim, unsigned n, unsigned append);
  void insertTimeStamps(unsigned n, std::ifstream* timesFile, double* timesdata);
  void insertPowerData(unsigned n, int powerfd, double *powerdata);
  unsigned getKeyPos(char* key);
  void prefix_name(char** const name, const char* prefix);

 public:
  audioDB(const unsigned argc, char* const argv[]);
  audioDB(const unsigned argc, char* const argv[], adb__queryResponse *adbQueryResponse);
  audioDB(const unsigned argc, char* const argv[], adb__statusResponse *adbStatusResponse);
  audioDB(const unsigned argc, char* const argv[], adb__lisztResponse *adbLisztResponse);

  void cleanup();
  ~audioDB();
  int processArgs(const unsigned argc, char* const argv[]);
  void get_lock(int fd, bool exclusive);
  void release_lock(int fd);
  void create(const char* dbName);
  bool enough_per_file_space_free();
  bool enough_data_space_free(off_t size);
  void insert_data_vectors(off_t offset, void *buffer, size_t size);
  void insert(const char* dbName, const char* inFile);
  void batchinsert(const char* dbName, const char* inFile);
  void batchinsert_large_adb(const char* dbName, const char* inFile);
  void query(const char* dbName, const char* inFile, adb__queryResponse *adbQueryResponse=0);
  void status(const char* dbName, adb__statusResponse *adbStatusResponse=0);
  unsigned random_track(unsigned *propTable, unsigned total);
  void sample(const char *dbName);
  void l2norm(const char* dbName);
  void power_flag(const char *dbName);
  bool powers_acceptable(double p1, double p2);
  void dump(const char* dbName);
  void liszt(const char* dbName, unsigned offset, unsigned numLines, adb__lisztResponse* adbLisztResponse=0);

  // LSH indexing parameters and data structures
  LSH* lsh;
  bool lsh_in_core;     // load LSH tables for query into core (true) or keep on disk (false)
  bool lsh_use_u_functions;
  bool lsh_exact;      // flag to indicate use exact evaluation of points returned by LSH
  bool WS_load_index; // flag to indicate that we want to make a Web Services index memory resident
  double lsh_param_w; // Width of LSH hash-function bins
  Uns32T lsh_param_k; // Number of independent hash functions
  Uns32T lsh_param_m; // Combinatorial parameter for m(m-1)/2 hash tables
  Uns32T lsh_param_N; // Number of rows per hash table
  Uns32T lsh_param_b; // Batch size, in number of tracks, per indexing iteration
  Uns32T lsh_param_ncols; // Maximum number of collision in a hash-table row
  Uns32T lsh_n_point_bits; // How many bits to use to encode point ID within a track


  // LSH vector<> containers for one in-core copy of a set of feature vectors
  vector<float>::iterator vi; // feature vector iterator
  vector<vector<float> > *vv;  // one-track's worth data

  // LSH indexing and retrieval methods  
  void index_index_db(const char* dbName);
  void index_initialize(double**,double**,double**,double**,unsigned int*);
  void index_insert_tracks(Uns32T start_track, Uns32T end_track, double** fvpp, double** sNormpp,double** snPtrp, double** sPowerp, double** spPtrp);
  int index_insert_track(Uns32T trackID, double** fvpp, double** snpp, double** sppp);
  Uns32T index_insert_shingles(vector<vector<float> >*, Uns32T trackID, double* spp);
  void index_make_shingle(vector<vector<float> >*, Uns32T idx, double* fvp, Uns32T dim, Uns32T seqLen);
  int index_norm_shingles(vector<vector<float> >*, double* snp, double* spp);
  int index_query_loop(const char* dbName, Uns32T queryIndex);
  vector<vector<float> >* index_initialize_shingles(Uns32T sz);
  int index_init_query(const char* dbName);
  int index_exists(const char* dbName, double radius, Uns32T sequenceLength);
  char* index_get_name(const char*dbName, double radius, Uns32T sequenceLength);
  static void index_add_point_approximate(void* instance, Uns32T pointID, Uns32T qpos, float dist); // static point reporter callback method
  static void index_add_point_exact(void* instance, Uns32T pointID, Uns32T qpos, float dist); // static point reporter callback method
  static Uns32T index_to_trackID(Uns32T lshID, Uns32T nPntBits);  // Convert lsh point index to audioDB trackID
  static Uns32T index_to_trackPos(Uns32T lshID, Uns32T nPntBits); // Convert lsh point index to audioDB trackPos (spos)
  static Uns32T index_from_trackInfo(Uns32T trackID, Uns32T pntID, Uns32T nPntBits); // Convert audioDB trackID and trackPos to an lsh point index
  void initialize_exact_evalutation_queue();
  void index_insert_exact_evaluation_queue(Uns32T trackID, Uns32T qpos, Uns32T spos);
  LSH* index_allocate(char* indexName, bool load_hashTables);
  void init_track_aux_data(Uns32T trackID, double* fvp, double** sNormpp,double** snPtrp, double** sPowerp, double** spPtrp);
  
  // Web Services
  void startServer();
  void ws_status(const char*dbName, char* hostport);
  void ws_query(const char*dbName, const char *featureFileName, const char* hostport);
  void ws_query_by_key(const char*dbName, const char *trackKey, const char* featureFileName, const char* hostport);
  void ws_liszt(const char* dbName, char* hostport);

};

#define O2_AUDIODB_INITIALIZERS			\
  dim(0),					\
    dbName(0),					\
    inFile(0),					\
    key(0),					\
    trackFileName(0),				\
    trackFile(0),				\
    command(0),					\
    output(0),					\
    timesFileName(0),				\
    timesFile(0),				\
    powerFileName(0),				\
    powerFile(0),				\
    adb_root(0),                                \
    adb_feature_root(0),                        \
    powerfd(0),                                 \
    dbfid(0),					\
    lshfid(0),					\
    forWrite(false),				\
    infid(0),					\
    db(0),					\
    indata(0),					\
    dbH(0),					\
    rng(0),                                     \
    fileTable(0),				\
    trackTable(0),				\
    trackOffsetTable(0),                        \
    dataBuf(0),					\
    l2normTable(0),				\
    timesTable(0),				\
    powerTable(0),                              \
    featureFileNameTable(0),                    \
    timesFileNameTable(0),                      \
    powerFileNameTable(0),                      \
    fileTableLength(0),				\
    trackTableLength(0),			\
    dataBufLength(0),				\
    timesTableLength(0),			\
    powerTableLength(0),			\
    l2normTableLength(0),			\
    verbosity(1),				\
    nsamples(2000),                             \
    datasize(O2_DEFAULT_DATASIZE),              \
    ntracks(O2_DEFAULT_NTRACKS),                \
    datadim(O2_DEFAULT_DATADIM),                \
    queryType(O2_POINT_QUERY),			\
    pointNN(O2_DEFAULT_POINTNN),		\
    trackNN(O2_DEFAULT_TRACKNN),		\
    sequenceLength(16),				\
    sequenceHop(1),				\
    normalizedDistance(true),			\
    no_unit_norming(false),                     \
    queryPoint(0),				\
    usingQueryPoint(0),				\
    usingTimes(0),				\
    usingPower(0),				\
    isClient(0),				\
    isServer(0),				\
    port(0),					\
    timesTol(0.1),				\
    radius(0),					\
    query_from_key(false),                      \
    query_from_key_index(O2_ERR_KEYNOTFOUND),   \
    use_absolute_threshold(false),		\
    absolute_threshold(0.0),			\
    use_relative_threshold(false),		\
    relative_threshold(0.0),			\
    reporter(0),                                \
    exact_evaluation_queue(0),                  \
    lisztOffset(0),                             \
    lisztLength(0),                             \
    lsh(0),					\
    lsh_in_core(false),				\
    lsh_use_u_functions(false),                 \
    lsh_exact(false),                           \
    WS_load_index(false),                       \
    lsh_param_k(0),				\
    lsh_param_m(0),				\
    lsh_param_N(0),				\
    lsh_param_b(0),				\
    lsh_param_ncols(0),                         \
    lsh_n_point_bits(0),                        \
    vv(0)
#endif