int main(int argc, const char ** argv) {
print_copyright();
/* GraphChi initialization will read the command line
arguments and the configuration file. */
graphchi_init(argc, argv);
/* Metrics object for keeping track of performance counters
and other information. Currently required. */
metrics m("itemsim2rating2");
/* Basic arguments for application */
min_allowed_intersection = get_option_int("min_allowed_intersection", min_allowed_intersection);
debug = get_option_int("debug", 0);
parse_command_line_args();
std::string similarity = get_option_string("similarity", "");
if (similarity == "")
Rcpp::Rcerr<<"Missing similarity input file. Please specify one using the --similarity=filename command line flag" << std::endl;
undirected = get_option_int("undirected", 1);
Q = get_option_float("Q", Q);
K = get_option_int("K");
mytimer.start();
vec unused;
int nshards = convert_matrixmarket_and_item_similarity<edge_data>(training, similarity, 3, unused);
assert(M > 0 && N > 0);
//initialize data structure which saves a subset of the items (pivots) in memory
adjcontainer = new adjlist_container();
//array for marking which items are conected to the pivot items via users.
relevant_items = new bool[N];
/* Run */
ItemDistanceProgram program;
graphchi_engine<VertexDataType, edge_data> engine(training, nshards, true, m);
set_engine_flags(engine);
out_file = open_file((training + "-rec").c_str(), "w");
//run the program
engine.run(program, niters);
/* Report execution metrics */
if (!quiet)
metrics_report(m);
Rcpp::Rcout<<"Total item pairs compared: " << item_pairs_compared << " total written to file: " << written_pairs << std::endl;
if (zero_edges)
Rcpp::Rcout<<"Found: " << zero_edges<< " user edges with weight zero. Those are ignored." <<std::endl;
delete[] relevant_items;
fclose(out_file);
return 0;
}
static VARIABLE_IS_NOT_USED void metrics_report(metrics &m) {
std::string reporters = get_option_string("metrics.reporter", "console");
char * creps = (char*)reporters.c_str();
const char * delims = ",";
char * t = strtok(creps, delims);
while(t != NULL) {
std::string repname(t);
if (repname == "basic" || repname == "console") {
basic_reporter rep;
m.report(rep);
} else if (repname == "file") {
file_reporter rep(get_option_string("metrics.reporter.filename", "metrics.txt"));
m.report(rep);
} else if (repname == "html") {
html_reporter rep(get_option_string("metrics.reporter.htmlfile", "metrics.html"));
m.report(rep);
} else {
logstream(LOG_WARNING) << "Could not find metrics reporter with name [" << repname << "], ignoring." << std::endl;
}
t = strtok(NULL, delims);
}
}
int main(int argc, const char ** argv) {
print_copyright();
//* GraphChi initialization will read the command line arguments and the configuration file. */
graphchi_init(argc, argv);
/* Metrics object for keeping track of performance counters
and other information. Currently required. */
metrics m("sgd-inmemory-factors");
algorithm = get_option_string("algorithm", "global_mean");
if (algorithm == "global_mean")
algo = GLOBAL_MEAN;
else if (algorithm == "user_mean")
algo = USER_MEAN;
else if (algorithm == "item_mean")
algo = ITEM_MEAN;
else logstream(LOG_FATAL)<<"Unsupported algorithm name. Should be --algorithm=XX where XX is one of [global_mean,user_mean,item_mean] for example --algorithm=global_mean" << std::endl;
parse_command_line_args();
mytimer.start();
/* Preprocess data if needed, or discover preprocess files */
int nshards = convert_matrixmarket<float>(training, NULL, 0, 0, 3, TRAINING, false);
init_feature_vectors<std::vector<vertex_data> >(M+N, latent_factors_inmem, false);
rmse_vec = zeros(number_of_omp_threads());
print_config();
/* Run */
BaselineVerticesInMemProgram program;
graphchi_engine<VertexDataType, EdgeDataType> engine(training, nshards, false, m);
set_engine_flags(engine);
pengine = &engine;
engine.run(program, 1);
if (algo == USER_MEAN || algo == ITEM_MEAN)
output_baseline_result(training);
test_predictions(&baseline_predict);
/* Report execution metrics */
if (!quiet)
metrics_report(m);
return 0;
}
int convert_matrixmarket(std::string base_filename, size_t nodes = 0, size_t edges = 0, int tokens_per_row = 3, int type = TRAINING, int allow_square = true) {
// Note, code based on: http://math.nist.gov/MatrixMarket/mmio/c/example_read.c
FILE *f;
size_t nz;
/**
* Create sharder object
*/
int nshards;
if ((nshards = find_shards<als_edge_type>(base_filename, get_option_string("nshards", "auto")))) {
if (check_origfile_modification_earlier<als_edge_type>(base_filename, nshards)) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
read_global_mean(base_filename, type);
return nshards;
}
}
sharder<als_edge_type> sharderobj(base_filename);
sharderobj.start_preprocessing();
detect_matrix_size(base_filename, f, type == TRAINING?M:Me, type == TRAINING?N:Ne, nz, nodes, edges, type);
if (f == NULL){
if (type == TRAINING){
logstream(LOG_FATAL)<<"Failed to open training input file: " << base_filename << std::endl;
}
else if (type == VALIDATION){
logstream(LOG_INFO)<<"Validation file: " << base_filename << " is not found. " << std::endl;
return -1;
}
}
compute_matrix_size(nz, type);
uint I, J;
double val = 1.0;
bool active_edge = true;
int zero_entries = 0;
for (size_t i=0; i<nz; i++)
{
if (tokens_per_row == 3){
int rc = fscanf(f, "%u %u %lg\n", &I, &J, &val);
if (rc != 3)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
if (val == 0 && ! allow_zeros)
logstream(LOG_FATAL)<<"Encountered zero edge [ " << I << " " <<J << " 0] in line: " << i << " . Run with --allow_zeros=1 to ignore zero weights." << std::endl;
else if (val == 0){
zero_entries++;
continue;
}
}
else if (tokens_per_row == 2){
int rc = fscanf(f, "%u %u\n", &I, &J);
if (rc != 2)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
}
else assert(false);
if (I ==987654321 || J== 987654321) //hack - to be removed later
continue;
I-=(uint)input_file_offset; /* adjust from 1-based to 0-based */
J-=(uint)input_file_offset;
if (I >= M)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I+1 << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J+1 << " > " << N << " in line; " << i << std::endl;
if (minval != -1e100 && val < minval)
logstream(LOG_FATAL)<<"Found illegal rating value: " << val << " where min value is: " << minval << std::endl;
if (maxval != 1e100 && val > maxval)
logstream(LOG_FATAL)<<"Found illegal rating value: " << val << " where max value is: " << maxval << std::endl;
active_edge = decide_if_edge_is_active(i, type);
if (active_edge){
if (type == TRAINING)
globalMean += val;
else globalMean2 += val;
sharderobj.preprocessing_add_edge(I, (M==N && allow_square)?J:M + J, als_edge_type((float)val));
}
}
if (type == TRAINING){
uint toadd = 0;
if (implicitratingtype == IMPLICIT_RATING_RANDOM)
toadd = add_implicit_edges(implicitratingtype, sharderobj);
globalMean += implicitratingvalue * toadd;
L += toadd;
globalMean /= L;
logstream(LOG_INFO) << "Global mean is: " << globalMean << " Now creating shards." << std::endl;
}
else {
globalMean2 /= Le;
logstream(LOG_INFO) << "Global mean is: " << globalMean2 << " Now creating shards." << std::endl;
}
write_global_mean(base_filename, type);
sharderobj.end_preprocessing();
if (zero_entries)
logstream(LOG_WARNING)<<"Found " << zero_entries << " zero edges!" << std::endl;
fclose(f);
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
logstream(LOG_INFO) << "Successfully finished sharding for " << base_filename<< std::endl;
logstream(LOG_INFO) << "Created " << nshards << " shards." << std::endl;
return nshards;
}
int convert_matrixmarket_and_item_similarity(std::string base_filename, std::string similarity_file, int tokens_per_row, vec & degrees) {
FILE *f = NULL, *fsim = NULL;
size_t nz, nz_sim;
/**
* Create sharder object
*/
int nshards;
if ((nshards = find_shards<als_edge_type>(base_filename, get_option_string("nshards", "auto")))) {
if (check_origfile_modification_earlier<als_edge_type>(base_filename, nshards)) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
read_global_mean(base_filename, TRAINING);
return nshards;
}
}
sharder<als_edge_type> sharderobj(base_filename);
sharderobj.start_preprocessing();
detect_matrix_size(base_filename, f, M, N, nz);
if (f == NULL)
logstream(LOG_FATAL)<<"Failed to open training input file: " << base_filename << std::endl;
uint N_row = 0 ,N_col = 0;
detect_matrix_size(similarity_file, fsim, N_row, N_col, nz_sim);
if (fsim == NULL || nz_sim == 0)
logstream(LOG_FATAL)<<"Failed to open item similarity input file: " << similarity_file << std::endl;
if (N_row != N || N_col != N)
logstream(LOG_FATAL)<<"Wrong item similarity file matrix size: " << N_row <<" x " << N_col << " Instead of " << N << " x " << N << std::endl;
L=nz + nz_sim;
degrees.resize(M+N);
uint I, J;
double val = 1.0;
int zero_entries = 0;
unsigned int actual_edges = 0;
logstream(LOG_INFO) << "Starting to read matrix-market input. Matrix dimensions: "
<< M << " x " << N << ", non-zeros: " << nz << std::endl;
for (size_t i=0; i<nz; i++){
if (tokens_per_row == 3){
int rc = fscanf(f, "%u %u %lg\n", &I, &J, &val);
if (rc != 3)
logstream(LOG_FATAL)<<"Error when reading input file in line: " << i << std::endl;
if (val == 0 && ! allow_zeros)
logstream(LOG_FATAL)<<"Zero weight encountered at input file line: " << i << " . Run with --allow_zeros=1 to ignore zero weights." << std::endl;
else if (val == 0) { zero_entries++; continue; }
}
else if (tokens_per_row == 2){
int rc = fscanf(f, "%u %u\n", &I, &J);
if (rc != 2)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
}
else assert(false);
I-=input_file_offset; /* adjust from 1-based to 0-based */
J-=input_file_offset;
if (I >= M)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J << " > " << N << " in line; " << i << std::endl;
degrees[J+M]++;
degrees[I]++;
if (I< (uint)start_user || I >= (uint)end_user){
continue;
}
sharderobj.preprocessing_add_edge(I, M + J, als_edge_type((float)val, 0));
//std::cout<<"adding an edge: " <<I << " -> " << M+J << std::endl;
actual_edges++;
}
logstream(LOG_DEBUG)<<"Finished loading " << actual_edges << " ratings from file: " << base_filename << std::endl;
for (size_t i=0; i<nz_sim; i++){
if (tokens_per_row == 3){
int rc = fscanf(fsim, "%u %u %lg\n", &I, &J, &val);
if (rc != 3)
logstream(LOG_FATAL)<<"Error when reading input file: " << similarity_file << " line: " << i << std::endl;
}
else if (tokens_per_row == 2){
int rc = fscanf(fsim, "%u %u\n", &I, &J);
if (rc != 2)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
}
else assert(false);
I-=input_file_offset; /* adjust from 1-based to 0-based */
J-=input_file_offset;
if (I >= N)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J << " > " << N << " in line; " << i << std::endl;
if (I == J)
logstream(LOG_FATAL)<<"Item similarity to itself found for item " << I << " in line; " << i << std::endl;
//std::cout<<"Adding an edge between "<<M+I<< " : " << M+J << " " << (I<J) << " " << val << std::endl;
sharderobj.preprocessing_add_edge(M+I, M+J, als_edge_type(I < J? val: 0, I>J? val: 0));
actual_edges++;
}
L = actual_edges;
logstream(LOG_DEBUG)<<"Finished loading " << nz_sim << " ratings from file: " << similarity_file << std::endl;
write_global_mean(base_filename, TRAINING);
sharderobj.end_preprocessing();
if (zero_entries)
logstream(LOG_WARNING)<<"Found " << zero_entries << " edges with zero weight!" << std::endl;
fclose(f);
fclose(fsim);
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
logstream(LOG_INFO) << "Successfully finished sharding for " << base_filename << std::endl;
logstream(LOG_INFO) << "Created " << nshards << " shards." << std::endl;
return nshards;
}
int convert_matrixmarket4(std::string base_filename, bool add_time_edges = false, bool square = false, int type = TRAINING, int matlab_time_offset = 1) {
// Note, code based on: http://math.nist.gov/MatrixMarket/mmio/c/example_read.c
FILE *f = NULL;
size_t nz;
/**
* Create sharder object
*/
int nshards;
if ((nshards = find_shards<als_edge_type>(base_filename, get_option_string("nshards", "auto")))) {
if (check_origfile_modification_earlier<als_edge_type>(base_filename, nshards)) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
read_global_mean(base_filename, type);
}
if (type == TRAINING)
time_nodes_offset = M+N;
return nshards;
}
sharder<als_edge_type> sharderobj(base_filename);
sharderobj.start_preprocessing();
detect_matrix_size(base_filename, f, type == TRAINING? M:Me, type == TRAINING? N:Ne, nz);
if (f == NULL){
if (type == VALIDATION){
logstream(LOG_INFO)<< "Did not find validation file: " << base_filename << std::endl;
return -1;
}
else if (type == TRAINING)
logstream(LOG_FATAL)<<"Failed to open training input file: " << base_filename << std::endl;
}
if (type == TRAINING)
time_nodes_offset = M+N;
compute_matrix_size(nz, type);
uint I, J;
double val, time;
bool active_edge = true;
for (size_t i=0; i<nz; i++)
{
int rc = fscanf(f, "%d %d %lg %lg\n", &I, &J, &time, &val);
if (rc != 4)
logstream(LOG_FATAL)<<"Error when reading input file - line " << i << std::endl;
if (time < 0)
logstream(LOG_FATAL)<<"Time (third columns) should be >= 0 " << std::endl;
I-=input_file_offset; /* adjust from 1-based to 0-based */
J-=input_file_offset;
if (I >= M)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J << " > " << N << " in line; " << i << std::endl;
K = std::max((int)time, (int)K);
time -= matlab_time_offset;
if (time < 0 && add_time_edges)
logstream(LOG_FATAL)<<"Time bins should be >= " << matlab_time_offset << " in row " << i << std::endl;
//only for tensor ALS we add edges between user and time bin and also item and time bin
//time bins are numbered beteen M+N to M+N+K
if (!weighted_als)
time += time_nodes_offset;
//avoid self edges
if (square && I == J)
continue;
active_edge = decide_if_edge_is_active(i, type);
if (active_edge){
if (type == TRAINING)
globalMean += val;
else globalMean2 += val;
sharderobj.preprocessing_add_edge(I, (square? J : (M + J)), als_edge_type(val, time));
}
//in case of a tensor, add besides of the user-> movie edge also
//time -> user and time-> movie edges
if (add_time_edges){
sharderobj.preprocessing_add_edge((uint)time, I, als_edge_type(val, M+J));
sharderobj.preprocessing_add_edge((uint)time, M+J , als_edge_type(val, I));
}
}
if (type == TRAINING){
uint toadd = 0;
if (implicitratingtype == IMPLICIT_RATING_RANDOM)
toadd = add_implicit_edges4(implicitratingtype, sharderobj);
globalMean += implicitratingvalue * toadd;
L += toadd;
globalMean /= L;
logstream(LOG_INFO) << "Global mean is: " << globalMean << " time bins: " << K << " . Now creating shards." << std::endl;
}
else {
globalMean2 /= Le;
logstream(LOG_INFO) << "Global mean is: " << globalMean2 << " time bins: " << K << " . Now creating shards." << std::endl;
}
write_global_mean(base_filename, type);
sharderobj.end_preprocessing();
fclose(f);
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
return nshards;
}
void parse_parser_command_line_arges(){
fc.string_features = get_option_string("features", fc.default_feature_str);
csv = get_option_int("csv", 0);
if (csv)
ptokens = csv_tokens;
file_columns = get_option_int("file_columns", file_columns); //get the number of columns in the edge file
//input sanity checks
if (file_columns < 3)
logstream(LOG_FATAL)<<"You must have at least 3 columns in input file: [from] [to] [value] on each line"<<std::endl;
if (file_columns >= FEATURE_WIDTH)
logstream(LOG_FATAL)<<"file_columns exceeds the allowed storage limit - please increase FEATURE_WIDTH and recompile." << std::endl;
fc.from_pos = get_option_int("from_pos", fc.from_pos);
fc.to_pos = get_option_int("to_pos", fc.to_pos);
fc.val_pos = get_option_int("val_pos", fc.val_pos);
if (fc.from_pos >= file_columns || fc.to_pos >= file_columns || fc.val_pos >= file_columns)
logstream(LOG_FATAL)<<"Please note that column numbering of from_pos, to_pos and val_pos starts from zero and should be smaller than file_columns" << std::endl;
if (fc.from_pos == fc.to_pos || fc.from_pos == fc.val_pos || fc.to_pos == fc.val_pos)
logstream(LOG_FATAL)<<"from_pos, to_pos and val_pos should have different values" << std::endl;
if (fc.val_pos == -1)
logstream(LOG_FATAL)<<"you must specify a target column using --val_pos=XXX. Colmn index starts from 0." << std::endl;
has_header_titles = get_option_int("has_header_titles", has_header_titles);
limit_rating= get_option_int("limit_rating", 0);
//parse features (optional)
if (fc.string_features != ""){
char * pfeatures = strdup(fc.string_features.c_str());
char * pch = strtok(pfeatures, ptokens);
int node = atoi(pch);
if (node < 0 || node >= MAX_FEATURES+3)
logstream(LOG_FATAL)<<"Feature id using the --features=XX command should be non negative, starting from zero"<<std::endl;
if (node >= file_columns)
logstream(LOG_FATAL)<<"Feature id using the --feature=XX command should be < file_columns (counting starts from zero)" << std::endl;
if (node == fc.from_pos || node == fc.to_pos || node == fc.val_pos)
logstream(LOG_FATAL)<<"Feature id " << node << " can not be equal to --from_pos, --to_pos or --val_pos " << std::endl;
fc.feature_selection[node] = true;
fc.total_features++;
while ((pch = strtok(NULL, ptokens))!= NULL){
node = atoi(pch);
if (node < 0 || node >= MAX_FEATURES+3)
logstream(LOG_FATAL)<<"Feature id using the --features=XX command should be non negative, starting from zero"<<std::endl;
fc.feature_selection[node] = true;
fc.total_features++;
}
}
train_only = get_option_int("train_only", 0);
validation_only = get_option_int("validation_only", 0);
fc.node_id_maps.resize(2+fc.total_features);
real_features_string = get_option_string("real_features", real_features_string);
//parse real features (optional)
if (real_features_string != ""){
int i=0;
char * pfeatures = strdup(real_features_string.c_str());
char * pch = strtok(pfeatures, ptokens);
int node = atoi(pch);
if (node < 0 || node >= MAX_FEATURES+3)
logstream(LOG_FATAL)<<"Feature id using the --real_features=XX command should be non negative, starting from zero"<<std::endl;
if (node >= file_columns)
logstream(LOG_FATAL)<<"Feature id using the --real_feature=XX command should be < file_columns (counting starts from zero)" << std::endl;
if (node == fc.from_pos || node == fc.to_pos || node == fc.val_pos)
logstream(LOG_FATAL)<<"Feature id " << node << " can not be equal to --from_pos, --to_pos or --val_pos " << std::endl;
fc.real_features_indicators[node] = true;
fc.feature_positions[node] = i;
i++;
while ((pch = strtok(NULL, ptokens))!= NULL){
node = atoi(pch);
if (node < 0 || node >= MAX_FEATURES+3)
logstream(LOG_FATAL)<<"Feature id using the --real_features=XX command should be non negative, starting from zero"<<std::endl;
fc.real_features_indicators[node] = true;
fc.feature_positions[node] = i;
i++;
}
}
}
int convert_matrixmarket_N(std::string base_filename, bool square, int limit_rating = 0) {
// Note, code based on: http://math.nist.gov/MatrixMarket/mmio/c/example_read.c
FILE *f;
size_t nz;
int nshards;
if (validation_only && (nshards = find_shards<als_edge_type>(base_filename, get_option_string("nshards", "auto")))) {
if (check_origfile_modification_earlier<als_edge_type>(base_filename, nshards)) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
FILE * infile = fopen((base_filename + ".gm").c_str(), "r");
int node_id_maps_size = 0;
assert( fscanf(infile, "%d\n%d\n%ld\n%d\n%lf\n%d\n%d\n%d\n", &M, &N, &L, &fc.total_features, &globalMean, &node_id_maps_size, &latent_factors_inmem_size,&num_feature_bins_size) ==8);
assert(node_id_maps_size >= 0);
assert(latent_factors_inmem_size >=M+N);
fclose(infile);
fc.node_id_maps.resize(node_id_maps_size);
for (int i=0; i < (int)fc.node_id_maps.size(); i++){
char buf[256];
sprintf(buf, "%s.map.%d", training.c_str(), i);
load_map_from_txt_file(fc.node_id_maps[i].string2nodeid, buf, 2);
assert(fc.node_id_maps[i].string2nodeid.size() > 0);
}
logstream(LOG_INFO)<<"Finished loading " << node_id_maps_size << " maps. "<<std::endl;
return nshards;
}
}
/**
* Create sharder object
*/
sharder<als_edge_type> sharderobj(base_filename);
sharderobj.start_preprocessing();
detect_matrix_size(base_filename, f, M, N, nz, 0, 0, 0);
if (f == NULL)
logstream(LOG_FATAL) << "Could not open file: " << base_filename << ", error: " << strerror(errno) << std::endl;
if (M == 0 && N == 0)
logstream(LOG_FATAL)<<"Failed to detect matrix size. Please prepare a file named: " << base_filename << ":info with matrix market header, as explained here: http://bickson.blogspot.co.il/2012/12/collaborative-filtering-3rd-generation_14.html " << std::endl;
logstream(LOG_INFO) << "Starting to read matrix-market input. Matrix dimensions: " << M << " x " << N << ", non-zeros: " << nz << std::endl;
if (has_header_titles){
char * linebuf = NULL;
size_t linesize;
char linebuf_debug[1024];
/* READ LINE */
int rc = getline(&linebuf, &linesize, f);
if (rc == -1)
logstream(LOG_FATAL)<<"Error header line " << " [ " << linebuf_debug << " ] " << std::endl;
strncpy(linebuf_debug, linebuf, 1024);
char *pch = strtok(linebuf,ptokens);
if (pch == NULL)
logstream(LOG_FATAL)<<"Error header line " << " [ " << linebuf_debug << " ] " << std::endl;
header_titles.push_back(std::string(pch));
while (pch != NULL){
pch = strtok(NULL, ptokens);
if (pch == NULL)
break;
header_titles.push_back(pch);
}
}
compute_matrix_size(nz, TRAINING);
uint I, J;
int val_array_len = std::max(1, fc.total_features);
assert(val_array_len < FEATURE_WIDTH);
std::vector<float> valarray; valarray.resize(val_array_len);
float val = 0.0f;
if (limit_rating > 0 && limit_rating < (int)nz)
nz = limit_rating;
char linebuf_debug[1024];
for (size_t i=0; i<nz; i++)
{
if (!read_line(f, base_filename, i,I, J, val, valarray, TRAINING, linebuf_debug))
logstream(LOG_FATAL)<<"Failed to read line: " <<i<< " in file: " << base_filename << std::endl;
if (I>= M || J >= N || I < 0 || J < 0){
if (i == 0)
logstream(LOG_FATAL)<<"Failed to parse first line, there are too many tokens. Did you forget the --has_header_titles=1 flag when file has string column headers? [ " << linebuf_debug << " ] " << " I : " << I << " J: " << J << std::endl;
else
logstream(LOG_FATAL)<<"Problem parsing input line number: " << i <<" in file: " << base_filename << ". Can not add edge from " << I << " to J " << J <<
" since matrix size is: " << M <<"x" <<N<< " [ original line: " << linebuf_debug << " ] . You probaably need to increase matrix size in the matrix market header." << std::endl;
}
bool active_edge = decide_if_edge_is_active(i, TRAINING);
if (active_edge){
//calc stats
globalMean += val;
sharderobj.preprocessing_add_edge(I, square?J:M+J, als_edge_type(val, &valarray[0], val_array_len));
}
}
sharderobj.end_preprocessing();
//calc stats
assert(L > 0);
//assert(globalMean != 0);
if (globalMean == 0)
logstream(LOG_WARNING)<<"Found global mean of the data to be zero (val_pos). Please verify this is correct." << std::endl;
globalMean /= L;
logstream(LOG_INFO)<<"Computed global mean is: " << globalMean << std::endl;
inputGlobalMean = globalMean;
fclose(f);
if (fc.hash_strings){
for (int i=0; i< fc.total_features+2; i++){
if (fc.node_id_maps[i].string2nodeid.size() == 0)
logstream(LOG_FATAL)<<"Failed sanity check for feature number : " << i << " no values find in data " << std::endl;
}
}
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
return nshards;
}
int main(int argc, const char ** argv) {
print_copyright();
/* GraphChi initialization will read the command line
arguments and the configuration file. */
graphchi_init(argc, argv);
/* Metrics object for keeping track of performance counters
and other information. Currently required. */
metrics m("itemsim2rating2");
/* Basic arguments for application */
min_allowed_intersection = get_option_int("min_allowed_intersection", min_allowed_intersection);
debug = get_option_int("debug", 0);
parse_command_line_args();
std::string similarity = get_option_string("similarity", "");
if (similarity == "")
logstream(LOG_FATAL)<<"Missing similarity input file. Please specify one using the --similarity=filename command line flag" << std::endl;
undirected = get_option_int("undirected", 0);
mytimer.start();
int nshards = convert_matrixmarket_and_item_similarity<edge_data>(training, similarity, 3, °rees);
assert(M > 0 && N > 0);
prob_sim_normalization_constant = (double)L / (double)(M*N-L);
//initialize data structure which saves a subset of the items (pivots) in memory
adjcontainer = new adjlist_container();
//array for marking which items are conected to the pivot items via users.
relevant_items = new bool[N];
/* Run */
ItemDistanceProgram program;
graphchi_engine<VertexDataType, edge_data> engine(training, nshards, true, m);
set_engine_flags(engine);
//open output files as the number of operating threads
out_files.resize(number_of_omp_threads());
for (uint i=0; i< out_files.size(); i++){
char buf[256];
sprintf(buf, "%s-rec.out%d", training.c_str(), i);
out_files[i] = open_file(buf, "w");
}
K = get_option_int("K");
assert(K > 0);
//run the program
engine.run(program, niters);
for (uint i=0; i< out_files.size(); i++)
fclose(out_files[i]);
delete[] relevant_items;
/* Report execution metrics */
if (!quiet)
metrics_report(m);
std::cout<<"Total item pairs compared: " << item_pairs_compared << " total written to file: " << sum(written_pairs) << std::endl;
logstream(LOG_INFO)<<"Going to sort and merge output files " << std::endl;
std::string dname= dirname(strdup(argv[0]));
system(("bash " + dname + "/topk.sh " + std::string(basename(strdup((training+"-rec").c_str())))).c_str());
return 0;
}
int convert_matrixmarket4(std::string base_filename, bool add_time_edges = false, bool square = false) {
// Note, code based on: http://math.nist.gov/MatrixMarket/mmio/c/example_read.c
int ret_code;
MM_typecode matcode;
FILE *f;
size_t nz;
/**
* Create sharder object
*/
int nshards;
if ((nshards = find_shards<als_edge_type>(base_filename, get_option_string("nshards", "auto")))) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
FILE * inf = fopen((base_filename + ".gm").c_str(), "r");
int rc = fscanf(inf,"%d\n%d\n%ld\n%lg\n%d\n",&M, &N, &L, &globalMean, &K);
if (rc != 5)
logstream(LOG_FATAL)<<"Failed to read global mean from file" << base_filename << ".gm" << std::endl;
fclose(inf);
if (K <= 0)
logstream(LOG_FATAL)<<"Incorrect number of time bins K in .gm file " << base_filename << ".gm" << std::endl;
logstream(LOG_INFO) << "Read matrix of size " << M << " x " << N << " Global mean is: " << globalMean << " time bins: " << K << " Now creating shards." << std::endl;
return nshards;
}
sharder<als_edge_type> sharderobj(base_filename);
sharderobj.start_preprocessing();
if ((f = fopen(base_filename.c_str(), "r")) == NULL) {
logstream(LOG_FATAL) << "Could not open file: " << base_filename << ", error: " << strerror(errno) << std::endl;
}
if (mm_read_banner(f, &matcode) != 0)
logstream(LOG_FATAL) << "Could not process Matrix Market banner. File: " << base_filename << std::endl;
/* This is how one can screen matrix types if their application */
/* only supports a subset of the Matrix Market data types. */
if (mm_is_complex(matcode) || !mm_is_sparse(matcode))
logstream(LOG_FATAL) << "Sorry, this application does not support complex values and requires a sparse matrix." << std::endl;
/* find out size of sparse matrix .... */
if ((ret_code = mm_read_mtx_crd_size(f, &M, &N, &nz)) !=0) {
logstream(LOG_FATAL) << "Failed reading matrix size: error=" << ret_code << std::endl;
}
logstream(LOG_INFO) << "Starting to read matrix-market input. Matrix dimensions: "
<< M << " x " << N << ", non-zeros: " << nz << std::endl;
uint I, J;
double val, time;
if (!sharderobj.preprocessed_file_exists()) {
for (size_t i=0; i<nz; i++)
{
int rc = fscanf(f, "%d %d %lg %lg\n", &I, &J, &time, &val);
if (rc != 4)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
if (time < 0)
logstream(LOG_FATAL)<<"Time (third columns) should be >= 0 " << std::endl;
I--; /* adjust from 1-based to 0-based */
J--;
if (I >= M)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J << " > " << N << " in line; " << i << std::endl;
K = std::max((int)time, (int)K);
//avoid self edges
if (square && I == J)
continue;
globalMean += val;
L++;
sharderobj.preprocessing_add_edge(I, (square? J : (M + J)), als_edge_type(val, time+M+N));
//in case of a tensor, add besides of the user-> movie edge also
//time -> user and time-> movie edges
if (add_time_edges){
sharderobj.preprocessing_add_edge((uint)time + M + N, I, als_edge_type(val, M+J));
sharderobj.preprocessing_add_edge((uint)time + M + N, M+J , als_edge_type(val, I));
}
}
uint toadd = 0;
if (implicitratingtype == IMPLICIT_RATING_RANDOM)
toadd = add_implicit_edges4(implicitratingtype, sharderobj);
globalMean += implicitratingvalue * toadd;
L += toadd;
sharderobj.end_preprocessing();
globalMean /= L;
logstream(LOG_INFO) << "Global mean is: " << globalMean << " time bins: " << K << " . Now creating shards." << std::endl;
FILE * outf = fopen((base_filename + ".gm").c_str(), "w");
fprintf(outf, "%d\n%d\n%ld\n%lg\n%d\n", M, N, L, globalMean, K);
fclose(outf);
} else {
logstream(LOG_INFO) << "Matrix already preprocessed, just run sharder." << std::endl;
}
fclose(f);
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
return nshards;
}
int convert_matrixmarket(std::string base_filename, SharderPreprocessor<als_edge_type> * preprocessor = NULL) {
// Note, code based on: http://math.nist.gov/MatrixMarket/mmio/c/example_read.c
int ret_code;
MM_typecode matcode;
FILE *f;
size_t nz;
std::string suffix = "";
if (preprocessor != NULL) {
suffix = preprocessor->getSuffix();
}
/**
* Create sharder object
*/
int nshards;
if ((nshards = find_shards<als_edge_type>(base_filename+ suffix, get_option_string("nshards", "auto")))) {
logstream(LOG_INFO) << "File " << base_filename << " was already preprocessed, won't do it again. " << std::endl;
FILE * inf = fopen((base_filename + ".gm").c_str(), "r");
int rc = fscanf(inf,"%d\n%d\n%ld\n%lg\n%d\n",&M, &N, &L, &globalMean, &K);
if (rc != 5)
logstream(LOG_FATAL)<<"Failed to read global mean from file" << base_filename+ suffix << ".gm" << std::endl;
fclose(inf);
logstream(LOG_INFO) << "Opened matrix size: " <<M << " x " << N << " Global mean is: " << globalMean << " time bins: " << K << " Now creating shards." << std::endl;
return nshards;
}
sharder<als_edge_type> sharderobj(base_filename + suffix);
sharderobj.start_preprocessing();
if ((f = fopen(base_filename.c_str(), "r")) == NULL) {
logstream(LOG_FATAL) << "Could not open file: " << base_filename << ", error: " << strerror(errno) << std::endl;
}
if (mm_read_banner(f, &matcode) != 0)
logstream(LOG_FATAL) << "Could not process Matrix Market banner. File: " << base_filename << std::endl;
/* This is how one can screen matrix types if their application */
/* only supports a subset of the Matrix Market data types. */
if (mm_is_complex(matcode) || !mm_is_sparse(matcode))
logstream(LOG_FATAL) << "Sorry, this application does not support complex values and requires a sparse matrix." << std::endl;
/* find out size of sparse matrix .... */
if ((ret_code = mm_read_mtx_crd_size(f, &M, &N, &nz)) !=0) {
logstream(LOG_FATAL) << "Failed reading matrix size: error=" << ret_code << std::endl;
}
L=nz;
logstream(LOG_INFO) << "Starting to read matrix-market input. Matrix dimensions: "
<< M << " x " << N << ", non-zeros: " << nz << std::endl;
uint I, J;
double val;
if (!sharderobj.preprocessed_file_exists()) {
for (size_t i=0; i<nz; i++)
{
int rc = fscanf(f, "%d %d %lg\n", &I, &J, &val);
if (rc != 3)
logstream(LOG_FATAL)<<"Error when reading input file: " << i << std::endl;
I--; /* adjust from 1-based to 0-based */
J--;
if (I >= M)
logstream(LOG_FATAL)<<"Row index larger than the matrix row size " << I << " > " << M << " in line: " << i << std::endl;
if (J >= N)
logstream(LOG_FATAL)<<"Col index larger than the matrix col size " << J << " > " << N << " in line; " << i << std::endl;
globalMean += val;
sharderobj.preprocessing_add_edge(I, M + J, als_edge_type((float)val));
}
uint toadd = 0;
if (implicitratingtype == IMPLICIT_RATING_RANDOM)
toadd = add_implicit_edges(implicitratingtype, sharderobj);
globalMean += implicitratingvalue * toadd;
L += toadd;
sharderobj.end_preprocessing();
globalMean /= L;
logstream(LOG_INFO) << "Global mean is: " << globalMean << " Now creating shards." << std::endl;
if (preprocessor != NULL) {
preprocessor->reprocess(sharderobj.preprocessed_name(), base_filename);
}
FILE * outf = fopen((base_filename + ".gm").c_str(), "w");
fprintf(outf, "%d\n%d\n%ld\n%lg\n%d\n", M, N, L, globalMean, K);
fclose(outf);
} else {
logstream(LOG_INFO) << "Matrix already preprocessed, just run sharder." << std::endl;
}
fclose(f);
logstream(LOG_INFO) << "Now creating shards." << std::endl;
// Shard with a specified number of shards, or determine automatically if not defined
nshards = sharderobj.execute_sharding(get_option_string("nshards", "auto"));
logstream(LOG_INFO) << "Successfully finished sharding for " << base_filename + suffix << std::endl;
logstream(LOG_INFO) << "Created " << nshards << " shards." << std::endl;
return nshards;
}
void run_functional_unweighted_semisynchronous(std::string filename, int niters, metrics &_m) {
FunctionalProgramProxySemisync<KERNEL> program;
/* Process input file - if not already preprocessed */
int nshards
= convert_if_notexists<typename FunctionalProgramProxySemisync<KERNEL>::EdgeDataType>(filename, get_option_string("nshards", "auto"));
functional_engine<typename FunctionalProgramProxySemisync<KERNEL>::VertexDataType,
typename FunctionalProgramProxySemisync<KERNEL>::EdgeDataType,
typename FunctionalProgramProxySemisync<KERNEL>::fvertex_t >
engine(filename, nshards, false, _m);
engine.set_modifies_inedges(false); // Important
engine.set_modifies_outedges(true); // Important
engine.run(program, niters);
}
void run_functional_unweighted_synchronous(std::string filename, int niters, metrics &_m) {
FunctionalProgramProxyBulkSync<KERNEL> program;
int nshards
= convert_if_notexists<typename FunctionalProgramProxyBulkSync<KERNEL>::EdgeDataType>(filename, get_option_string("nshards", "auto"));
functional_engine<typename FunctionalProgramProxyBulkSync<KERNEL>::VertexDataType,
typename FunctionalProgramProxyBulkSync<KERNEL>::EdgeDataType,
typename FunctionalProgramProxyBulkSync<KERNEL>::fvertex_t >
engine(filename, nshards, false, _m);
engine.set_modifies_inedges(false); // Important
engine.set_modifies_outedges(true); // Important
engine.set_enable_deterministic_parallelism(false); // Bulk synchronous does not need consistency.
engine.run(program, niters);
}
int main(int argc, const char ** argv) {
print_copyright();
/* GraphChi initialization will read the command line
arguments and the configuration file. */
graphchi_init(argc, argv);
/* Metrics object for keeping track of performance counters
and other information. Currently required. */
metrics m("label_propagation");
contexts_file = get_option_string("contexts");
nouns_file = get_option_string("nouns");
pos_seeds = get_option_string("pos_seeds");
neg_seeds = get_option_string("neg_seeds");
parse_command_line_args();
load_map_from_txt_file(contexts.string2nodeid, contexts_file, 1);
load_map_from_txt_file(nouns.string2nodeid, nouns_file, 1);
//load graph (adj matrix) from file
int nshards = convert_matrixmarket<EdgeDataType>(training, 0, 0, 3, TRAINING, true);
init_feature_vectors<std::vector<vertex_data> >(M+N, latent_factors_inmem);
load_seeds_from_txt_file(nouns.string2nodeid, pos_seeds, false);
load_seeds_from_txt_file(nouns.string2nodeid, neg_seeds, true);
#pragma omp parallel for
for (int i=0; i< (int)M; i++){
//normalize seed probabilities to sum up to one
if (latent_factors_inmem[i].seed){
if (sum(latent_factors_inmem[i].pvec) != 0)
latent_factors_inmem[i].pvec /= sum(latent_factors_inmem[i].pvec);
continue;
}
//other nodes get random label probabilities
for (int j=0; j< D; j++)
latent_factors_inmem[i].pvec[j] = drand48();
}
/* load initial state from disk (optional) */
if (load_factors_from_file){
load_matrix_market_matrix(training + "_U.mm", 0, D);
}
/* Run */
COEMVerticesInMemProgram program;
graphchi_engine<VertexDataType, EdgeDataType> engine(training, nshards, false, m);
set_engine_flags(engine);
pengine = &engine;
engine.run(program, niters);
/* Output latent factor matrices in matrix-market format */
output_coem_result(training);
/* Report execution metrics */
if (!quiet)
metrics_report(m);
return 0;
}
/* ---------------------------------------------------------------------- */
int
spread_row_to_solution (struct spread_row *heading, struct spread_row *units,
struct spread_row *data, struct defaults defaults)
/* ---------------------------------------------------------------------- */
{
int i, j, n, l, next_keyword_save;
int n_user, n_user_end;
int default_pe, alk;
int count_isotopes;
int max_mass_balance, count_mass_balance;
char *ptr, *ptr1;
char *description;
char token[MAX_LENGTH], token1[MAX_LENGTH];
char string[2 * MAX_LENGTH];
LDBLE dummy;
int return_value, opt;
char *next_char;
const char *opt_list[] = {
"temp", /* 0 */
"temperature", /* 1 */
"dens", /* 2 */
"density", /* 3 */
"units", /* 4 */
"redox", /* 5 */
"ph", /* 6 */
"pe", /* 7 */
"unit", /* 8 */
"isotope", /* 9 */
"water", /* 10 */
"description", /* 11 */
"desc", /* 12 */
"descriptor" /* 13 */
};
int count_opt_list = 14;
/*
* look for solution number
*/
n_user = -1;
n_user_end = -1;
description = string_duplicate ("");
for (i = 0; i < heading->count; i++)
{
if (strcmp_nocase (heading->char_vector[i], "number") == 0)
{
break;
}
}
if (i == heading->count || data->type_vector[i] == EMPTY
|| data->count <= i)
{
n_user = -1;
#ifdef SKIP
for (i = 0; i < count_solution; i++)
{
if (n_user <= solution[i]->n_user)
{
n_user = solution[i]->n_user + 1;
}
}
#endif
}
else if (data->type_vector[i] == STRING)
{
input_error++;
sprintf (error_string,
"Expected solution number or number range in 'number' column, found: %s.",
data->char_vector[i]);
error_msg (error_string, CONTINUE);
}
else
{
strcpy (string, "solution_s ");
strcat (string, data->char_vector[i]);
ptr = string;
description = (char *) free_check_null (description);
next_keyword_save = next_keyword;
next_keyword = 42;
read_number_description (ptr, &n_user, &n_user_end, &description);
next_keyword = next_keyword_save;
}
/*
* set up solution
*/
if (n_user >= 0 && solution_bsearch (n_user, &n, FALSE) != NULL)
{
solution_free (solution[n]);
}
else
{
n = count_solution++;
if (count_solution >= max_solution)
{
space ((void **) ((void *) &(solution)), count_solution, &max_solution,
sizeof (struct solution *));
}
}
solution[n] = solution_alloc ();
solution[n]->n_user = n_user;
solution[n]->n_user_end = n_user_end;
if (use.solution_in == FALSE)
{
use.solution_in = TRUE;
use.n_solution_user = n_user;
}
max_mass_balance = MAX_MASS_BALANCE;
/*
* Set default ph, temp, density, pe, units
*/
solution[n]->description = description;
solution[n]->tc = defaults.temp;
solution[n]->ph = defaults.ph;
solution[n]->density = defaults.density;
solution[n]->solution_pe = defaults.pe;
solution[n]->mass_water = defaults.water;
solution[n]->ah2o = 1.0;
solution[n]->mu = 1e-7;
solution[n]->cb = 0.0;
default_pe = 0;
solution[n]->units = defaults.units;
solution[n]->totals[0].description = NULL;
count_mass_balance = 0;
count_isotopes = 0;
default_pe = pe_data_store (&(solution[n]->pe), defaults.redox);
/*
* Read concentration data
*/
return_value = UNKNOWN;
for (i = 0; i < heading->count; i++)
{
if (strcmp_nocase (heading->char_vector[i], "number") == 0)
continue;
if (strcmp_nocase (heading->char_vector[i], "uncertainty") == 0)
continue;
if (strcmp_nocase (heading->char_vector[i], "uncertainties") == 0)
continue;
if (strcmp_nocase (heading->char_vector[i], "isotope_uncertainty") == 0)
continue;
/*
* Copy in element name
*/
if (heading->type_vector[i] == EMPTY)
continue;
strcpy (string, heading->char_vector[i]);
strcat (string, " ");
/*
* Copy in concentration data
*/
if (i >= data->count || data->type_vector[i] == EMPTY)
continue;
strcat (string, data->char_vector[i]);
strcat (string, " ");
/*
* Copy in concentration data
*/
if (units != NULL && i < units->count && units->type_vector[i] != EMPTY)
{
strcat (string, units->char_vector[i]);
}
/*
* Parse string just like read_solution input
*/
next_char = string;
opt = get_option_string (opt_list, count_opt_list, &next_char);
if (opt == OPTION_DEFAULT && heading->type_vector[i] == NUMBER)
{
opt = 9;
}
switch (opt)
{
case OPTION_EOF: /* end of file */
return_value = EOF;
break;
case OPTION_KEYWORD: /* keyword */
return_value = KEYWORD;
break;
case OPTION_ERROR:
input_error++;
error_msg ("Unknown input in SOLUTION keyword.", CONTINUE);
error_msg (line_save, CONTINUE);
break;
case 0: /* temperature */
case 1:
sscanf (next_char, SCANFORMAT, &(solution[n]->tc));
break;
case 2: /* density */
case 3:
sscanf (next_char, SCANFORMAT, &(solution[n]->density));
break;
case 4: /* units */
case 8: /* unit */
if (copy_token (token, &next_char, &l) == EMPTY)
break;
if (check_units (token, FALSE, FALSE, solution[n]->units, TRUE) == OK)
{
solution[n]->units = string_hsave (token);
}
else
{
input_error++;
}
break;
case 5: /* redox */
if (copy_token (token, &next_char, &l) == EMPTY)
break;
if (parse_couple (token) == OK)
{
default_pe = pe_data_store (&(solution[n]->pe), token);
}
else
{
input_error++;
}
break;
case 6: /* ph */
next_char = string;
if (read_conc (n, count_mass_balance, next_char) == ERROR)
{
input_error++;
break;
}
solution[n]->ph = solution[n]->totals[count_mass_balance].input_conc;
if (solution[n]->totals[count_mass_balance].equation_name == NULL)
{
break;
}
solution[n]->totals[count_mass_balance].description =
string_hsave ("H(1)");
count_mass_balance++;
break;
case 7: /* pe */
next_char = string;
if (read_conc (n, count_mass_balance, next_char) == ERROR)
{
input_error++;
break;
}
solution[n]->solution_pe =
solution[n]->totals[count_mass_balance].input_conc;
if (solution[n]->totals[count_mass_balance].equation_name == NULL)
{
break;
}
solution[n]->totals[count_mass_balance].description =
string_hsave ("E");
count_mass_balance++;
break;
case 9: /* isotope */
next_char = string;
if (copy_token (token, &next_char, &l) != DIGIT)
{
input_error++;
sprintf (error_string, "Expected isotope name to"
" begin with an isotopic number.");
error_msg (error_string, CONTINUE);
continue;
}
solution[n]->isotopes =
(struct isotope *) PHRQ_realloc (solution[n]->isotopes,
(size_t) (count_isotopes +
1) *
sizeof (struct isotope));
if (solution[n]->isotopes == NULL)
malloc_error ();
/* read and save element name */
ptr1 = token;
get_num (&ptr1,
&(solution[n]->isotopes[count_isotopes].isotope_number));
if (ptr1[0] == '\0' || isupper ((int) ptr1[0]) == FALSE)
{
error_msg ("Expecting element name.", CONTINUE);
error_msg (line_save, CONTINUE);
input_error++;
return (ERROR);
}
solution[n]->isotopes[count_isotopes].elt_name = string_hsave (ptr1);
/* read and store isotope ratio */
if (copy_token (token, &next_char, &l) != DIGIT)
{
input_error++;
sprintf (error_string, "Expected numeric value for isotope ratio.");
error_msg (error_string, CONTINUE);
continue;
}
sscanf (token, SCANFORMAT,
&(solution[n]->isotopes[count_isotopes].ratio));
/* read and store isotope ratio uncertainty */
/* first choice is next column */
if ((i + 1) < heading->count &&
(strcmp_nocase (heading->char_vector[i + 1], "uncertainty") == 0 ||
strcmp_nocase (heading->char_vector[i + 1],
"isotope_uncertainty") == 0
|| strcmp_nocase (heading->char_vector[i + 1],
"uncertainties") == 0) && (i + 1) < data->count
&& data->type_vector[i + 1] == NUMBER)
{
solution[n]->isotopes[count_isotopes].ratio_uncertainty =
data->d_vector[i + 1];
}
else
{
next_char = string;
copy_token (token, &next_char, &l);
for (j = 0; j < defaults.count_iso; j++)
{
if (strcmp (token, defaults.iso[j].name) == 0)
{
solution[n]->isotopes[count_isotopes].ratio_uncertainty =
defaults.iso[j].uncertainty;
break;
}
}
if (j == defaults.count_iso)
{
solution[n]->isotopes[count_isotopes].ratio_uncertainty = NAN;
}
}
count_isotopes++;
break;
case 10: /* water */
j = copy_token (token, &next_char, &l);
if (j == EMPTY)
{
solution[n]->mass_water = 1.0;
}
else if (j != DIGIT)
{
input_error++;
sprintf (error_string,
"Expected numeric value for mass of water in solution.");
error_msg (error_string, CONTINUE);
}
else
{
sscanf (token, SCANFORMAT, &dummy);
solution[n]->mass_water = (LDBLE) dummy;
}
break;
case 11: /* description */
case 12: /* desc */
case 13: /* descriptor */
solution[n]->description =
(char *) free_check_null (solution[n]->description);
solution[n]->description = string_duplicate (next_char);
break;
case OPTION_DEFAULT:
/*
* Read concentration
*/
next_char = string;
if (copy_token (token, &next_char, &l) == LOWER)
continue;
next_char = string;
if (read_conc (n, count_mass_balance, next_char) == ERROR)
{
#ifdef SKIP
input_error++;
break;
#endif
}
count_mass_balance++;
break;
}
if (count_mass_balance + 1 >= max_mass_balance)
{
space ((void **) ((void *) &(solution[n]->totals)), count_mass_balance + 1,
&max_mass_balance, sizeof (struct conc));
}
if (return_value == EOF || return_value == KEYWORD)
break;
}
/*
* Sort totals by description
*/
qsort (solution[n]->totals,
(size_t) count_mass_balance,
(size_t) sizeof (struct conc), conc_compare);
/*
* fix up default units and default pe
*/
for (i = 0; i < count_mass_balance; i++)
{
strcpy (token, solution[n]->totals[i].description);
str_tolower (token);
if (solution[n]->totals[i].units == NULL)
{
solution[n]->totals[i].units = solution[n]->units;
}
else
{
alk = FALSE;
if (strstr (token, "alk") == token)
alk = TRUE;
strcpy (token1, solution[n]->totals[i].units);
if (check_units (token1, alk, TRUE, solution[n]->units, TRUE) == ERROR)
{
input_error++;
}
else
{
solution[n]->totals[i].units = string_hsave (token1);
}
}
if (solution[n]->totals[i].n_pe < 0)
{
solution[n]->totals[i].n_pe = default_pe;
}
}
solution[n]->default_pe = default_pe;
/*
* Mark end of solution
*/
solution[n]->totals[count_mass_balance].description = NULL;
solution[n]->count_isotopes = count_isotopes;
if (count_isotopes > 0)
{
qsort (solution[n]->isotopes,
(size_t) count_isotopes,
(size_t) sizeof (struct isotope), isotope_compare);
}
else
{
solution[n]->isotopes =
(struct isotope *) free_check_null (solution[n]->isotopes);
}
return (return_value);
}
int main(int argc, const char ** argv) {
mytimer.start();
print_copyright();
/* GraphChi initialization will read the command line
arguments and the configuration file. */
graphchi_init(argc, argv);
/* Metrics object for keeping track of performance counters
and other information. Currently required. */
metrics m("rating2");
knn_sample_percent = get_option_float("knn_sample_percent", 1.0);
if (knn_sample_percent <= 0 || knn_sample_percent > 1)
logstream(LOG_FATAL)<<"Sample percente should be in the range (0, 1] " << std::endl;
num_ratings = get_option_int("num_ratings", 10);
if (num_ratings <= 0)
logstream(LOG_FATAL)<<"num_ratings, the number of recomended items for each user, should be >=1 " << std::endl;
debug = get_option_int("debug", 0);
tokens_per_row = get_option_int("tokens_per_row", tokens_per_row);
std::string algorithm = get_option_string("algorithm");
/* Basic arguments for RBM algorithm */
rbm_bins = get_option_int("rbm_bins", rbm_bins);
rbm_scaling = get_option_float("rbm_scaling", rbm_scaling);
if (algorithm == "svdpp" || algorithm == "svd++")
algo = SVDPP;
else if (algorithm == "biassgd")
algo = BIASSGD;
else if (algorithm == "rbm")
algo = RBM;
else logstream(LOG_FATAL)<<"--algorithm should be svd++ or biassgd or rbm"<<std::endl;
parse_command_line_args();
/* Preprocess data if needed, or discover preprocess files */
int nshards = 0;
if (tokens_per_row == 3)
nshards = convert_matrixmarket<edge_data>(training, 0, 0, 3, TRAINING, false);
else if (tokens_per_row == 4)
nshards = convert_matrixmarket4<edge_data4>(training);
else logstream(LOG_FATAL)<<"--tokens_per_row should be either 3 or 4" << std::endl;
assert(M > 0 && N > 0);
latent_factors_inmem.resize(M+N); // Initialize in-memory vertices.
//initialize data structure to hold the matrix read from file
if (algo == RBM){
#pragma omp parallel for
for (uint i=0; i< M+N; i++){
if (i < M){
latent_factors_inmem[i].pvec = zeros(D*3);
}
else {
latent_factors_inmem[i].pvec = zeros(rbm_bins + rbm_bins * D);
}
}
}
read_factors(training);
if ((uint)num_ratings > N){
logstream(LOG_WARNING)<<"num_ratings is too big - setting it to: " << N << std::endl;
num_ratings = N;
}
srand(time(NULL));
/* Run */
if (tokens_per_row == 3){
RatingVerticesInMemProgram<VertexDataType, EdgeDataType> program;
graphchi_engine<VertexDataType, EdgeDataType> engine(training, nshards, false, m);
set_engine_flags(engine);
engine.run(program, 1);
}
else if (tokens_per_row == 4){
RatingVerticesInMemProgram<VertexDataType, edge_data4> program;
graphchi_engine<VertexDataType, edge_data4> engine(training, nshards, false, m);
set_engine_flags(engine);
engine.run(program, 1);
}
/* Output latent factor matrices in matrix-market format */
output_knn_result(training);
rating_stats();
if (users_without_ratings > 0)
logstream(LOG_WARNING)<<"Found " << users_without_ratings << " without ratings. For those users no items are recommended (item id 0)" << std::endl;
if (users_no_ratings > 0)
logstream(LOG_WARNING)<<"Failed to compute ratings for " << users_no_ratings << " Users. For those users no items are recommended (item id 0)" << std::endl;
/* Report execution metrics */
if (!quiet)
metrics_report(m);
return 0;
}