/**
* @brief Dump the momenta for staroge
* @author Alvaro Cortes Cabrera <*****@*****.**>
*
* @param mol MOL2 with the molecule
* @return null
*
*/
void dump_moments(MOL2 *mol1)
{
float *moments_a = NULL;
double **centroids_a = NULL;
int i = 0;
centroids_a = (double **) calloc(NUM_CENTROIDS,sizeof(double **));
for(i = 0; i < NUM_CENTROIDS; i++)
{
centroids_a[i] = (double *) calloc(DIMENSION, sizeof(double *));
}
getCentroids(mol1,¢roids_a);
moments_a = (float *) calloc(NUM_MOMENTS,sizeof(float*));
calculateMoments(mol1, centroids_a, &moments_a);
for(i = 0; i < NUM_MOMENTS; i++)
{
printf("%.3f;",moments_a[i]);
}
for(i = 0; i < NUM_CENTROIDS; i++)
{
free(centroids_a[i]);
}
free(centroids_a);
free(moments_a);
}
/**
* @brief Compare two molecules using ElectroShape method
* @author Alvaro Cortes Cabrera <*****@*****.**>
*
* @param mol1 MOL2 with the molecule
* @param mol1 MOL2 with the molecule
* @return Similarity
*
*/
float USR_compare_molecules(MOL2 *mol1, MOL2 *mol2)
{
float *moments_a = NULL, *moments_b = NULL;
double **centroids_a = NULL, **centroids_b = NULL;
float dist = 0.0f;
int i = 0;
centroids_a = (double **) calloc(NUM_CENTROIDS,sizeof(double **));
centroids_b = (double **) calloc(NUM_CENTROIDS,sizeof(double **));
for(i = 0; i < NUM_CENTROIDS; i++)
{
centroids_a[i] = (double *) calloc(DIMENSION, sizeof(double *));
centroids_b[i] = (double *) calloc(DIMENSION, sizeof(double *));
}
getCentroids(mol1,¢roids_a);
getCentroids(mol2,¢roids_b);
moments_a = (float *) calloc(NUM_MOMENTS,sizeof(float*));
moments_b = (float *) calloc(NUM_MOMENTS,sizeof(float*));
calculateMoments(mol1, centroids_a, &moments_a);
calculateMoments(mol2, centroids_b, &moments_b);
dist = shapeDistance(moments_a,moments_b);
for(i = 0; i < NUM_CENTROIDS; i++)
{
free(centroids_a[i]);
free(centroids_b[i]);
}
free(centroids_a);
free(centroids_b);
free(moments_a);
free(moments_b);
return dist;
}
/**
* @brief Main program
* @param argc The number of arguments of the program
* @param argv Arguments of the program
* @return Returns nothing if successful or a negative number if incorrect
*/
int main(const int argc, const char **argv) {
/********** Get the configuration data from the XML file or from the command-line ***********/
const Config conf(argv, argc);
// Generic variables
float dataBase[conf.nInstances * conf.nFeatures];
float dataBaseTransposed[conf.nInstances * conf.nFeatures];
int selInstances[conf.nCentroids];
double referencePoint[conf.nObjectives];
Individual populationOrig[conf.totalIndividuals];
/********** Get the data base and its normalization ***********/
readDataBase(dataBase, &conf);
normDataBase(dataBase, &conf);
transposeDataBase(dataBase, dataBaseTransposed, &conf); // Matrix transposed
/********** Get the initial "conf.nCentroids" centroids ***********/
getCentroids(selInstances, &conf);
/********** Set the reference point ***********/
// The reference point will be (X_1 = 1.0, X_2 = 1.0, .... X_conf.nObjectives = 1.0)
for (int i = 0; i < conf.nObjectives; ++i) {
referencePoint[i] = 1.0;
}
/********** Initialize the population and the individuals ***********/
srand((u_int) time(NULL));
// Population will have the parents and children (left half and right half respectively)
// This way is better for the performance
initPopulation(populationOrig, &conf);
/********** OpenCL init ***********/
// OpenCL mode
if (conf.nDevices > 0) {
CLDevice *devices = createDevices(dataBase, selInstances, dataBaseTransposed, &conf);
// Benchmark mode (Sequential, heterogeneous and all devices per separate)
if (conf.benchmarkMode) {
// Each device per separate
for (int i = 0; i < conf.nDevices; ++i) {
agAlgorithm(populationOrig, devices[i].deviceType, &devices[i], NULL, NULL, referencePoint, &conf);
}
// Heterogeneous mode if more than 1 device is available
if (conf.nDevices > 1) {
agAlgorithm(populationOrig, CL_DEVICE_TYPE_ALL, devices, NULL, NULL, referencePoint, &conf);
}
// Sequential mode
agAlgorithm(populationOrig, CL_DEVICE_TYPE_DEFAULT, NULL, dataBase, selInstances, referencePoint, &conf);
}
// Only 1 device (CPU or GPU)
else if (conf.nDevices == 1) {
agAlgorithm(populationOrig, devices[0].deviceType, &devices[0], NULL, NULL, referencePoint, &conf);
}
// Heterogeneous mode if more than 1 device is available
else {
agAlgorithm(populationOrig, CL_DEVICE_TYPE_ALL, devices, NULL, NULL, referencePoint, &conf);
}
/********** Resources used are released ***********/
// OpenCL resources
delete[] devices;
}
// Sequential mode
else {
agAlgorithm(populationOrig, CL_DEVICE_TYPE_DEFAULT, NULL, dataBase, selInstances, referencePoint, &conf);
}
// Generation of the Gnuplot file for display the Pareto front
generateGnuplot(referencePoint, &conf);
}