void Letterbox::writeFile()
{
outputResults();
setModified(false);
statusBar()->showMessage(tr("Saved results to file."));
}
bool Sobel::runHalideGPU(Image input, Image output, const Params& params)
{
#if ENABLE_HALIDE
// Create halide buffers
buffer_t inputBuffer = createHalideBuffer(input);
buffer_t outputBuffer = createHalideBuffer(output);
reportStatus("Running Halide GPU filter");
// Warm-up run
inputBuffer.host_dirty = true;
halide_sobel_gpu(&inputBuffer, &outputBuffer);
halide_dev_sync(NULL);
// Timed runs
startTiming();
for (int i = 0; i < params.iterations; i++)
{
halide_sobel_gpu(&inputBuffer, &outputBuffer);
}
halide_dev_sync(NULL);
stopTiming();
halide_copy_to_host(NULL, &outputBuffer);
halide_release(NULL);
return outputResults(input, output, params);
#else
reportStatus("Halide not enabled during build.");
return false;
#endif
}
bool Bilateral::runHalideCPU(Image input, Image output, const Params& params)
{
#if ENABLE_HALIDE
// Create halide buffers
buffer_t inputBuffer = createHalideBuffer(input);
buffer_t outputBuffer = createHalideBuffer(output);
reportStatus("Running Halide CPU filter");
// Warm-up run
halide_bilateral_cpu(&inputBuffer, &outputBuffer);
// Timed runs
startTiming();
for (int i = 0; i < params.iterations; i++)
{
halide_bilateral_cpu(&inputBuffer, &outputBuffer);
}
stopTiming();
halide_release(NULL);
return outputResults(input, output, params);
#else
reportStatus("Halide not enabled during build.");
return false;
#endif
}
/* Create a steady state solver, solve the constraints. */
void solveSteadyStates(const string & path_to_model, const Model & model) {
// Create the output file and label columns
ofstream output_file = initFile(path_to_model, model.name);
outputLegend(model.species, output_file);
// Create the solver together with the constraints
SpaceSolver<SteadySpace> solver(new SteadySpace(model.species.size(), model.max_value));
for (const size_t i : cscope(model.species))
solver->boundSpecie(i, model.species[i].max_val);
solver->applyModel(model);
// Output the results
outputResults(output_file, solver);
}
int main(int argc,char* argv[]){
time_t timer_start,timer_end;
setGlobalParameters(argc,argv);
registerProNdAlg();
setAddtParameters();
time(&timer_start);
run();
time(&timer_end);
cout<<"Time used: "<<difftime(timer_end,timer_start)<<" seconds"<<endl;
outputResults();
return 0;
}
int main()
{
srand(time(NULL));
//Declare Variables
FILE *fp;
char *line = NULL;
size_t len = 0;
ssize_t read;
char filename[99];
char *numLine;
char *userInput = (char*) malloc(100);
char *valueLine;
char buffer[100];
int n = 0;
clock_t start, end;
float elapsed_time;
//For random generation
int maxValue = 10000;
int maxNumOfCoins = 5;
int maxCoinValue = 50;
//regular variables
int v[maxNumOfCoins];
int c[maxNumOfCoins];
int a, m; //start value
//prep arrays
for(int x = 0; x < maxNumOfCoins; x++)
{
c[x] = 0;
v[x] = 0;
}
//ask user for file or random generator
printf("What do you want to run:\n");
printf("1) Load from File\n");
printf("2) Random Generator\n");
//Get user input
scanf ("%[^\n]%*c", userInput);
if (strcmp(userInput,"1") == 0)
{
//Run LoadFile
}
else if (strcmp(userInput,"2") == 0)
{
//Run Random Generator
randomNum(&v, &a, maxNumOfCoins, maxCoinValue, maxValue);
}
//start = clock();
runGreedyAlgorithm(v, a, &c, &m, maxNumOfCoins);
//end = clock();
//elapsed_time = (float)(end - start) / (1.0*CLOCKS_PER_SEC);
printf("%d\n", a);
//fprintf(fp,"%d %s %f %s",a, "\t", elapsed_time ,"\n");
printf("\nmaxNumOfCoins=%d\n", maxNumOfCoins);
printf("maxCoinValue=%d\n", maxCoinValue);
printf("maxValue=%d\n", maxValue);
outputResults(v, maxNumOfCoins, a, 'V');
printf("Elapsed time: %f seconds\n", elapsed_time);
printf("\nResults:\n");
outputResults(c, maxNumOfCoins, m, 'C');
// printf("Enter filename: ");
// fgets(filename, 99, stdin);
// char *p = strchr(filename, '\n'); // p will point to the newline in filename
// if(p) *p = 0; // if p is not null, terminate filename at p
// fp = fopen(filename, "r");
// if(!fp)
// perror("File not found");
// else
// {
// printf("opening file: %s...\n", filename);
// while ((read = getline(&line, &len, fp)) != -1) {
// if (n == 1)
// {
// numLine = (char *) realloc (numLine, strlen(line)+1);
// strncpy(numLine, line, strlen(line));
// *p = strchr(numLine, '\n'); // p will point to the newline in filename
// if(p) *p = 0; // if p is not null, terminate filename at p
// }
// if (n == 2)
// {
// printf("n=2\n");
// printf("strlen=%d\n",strlen(line));
// valueLine = (char *) realloc (valueLine, strlen(line)+1);
//strncpy(valueLine, line, strlen(line));
// }
// n++;
// }
// }
// printf("numLine=%s\n", numLine);
// printf("valueLine=%s\n", valueLine);
/*
//parse numbers from lines into array
for (int i = 0; i < line[0].noOfLines; i++)
{
line[i].noOfnums = 0;
//printf("Words[%d]=%s\n", i, line[i].words); //Test Only
char *pt;
pt = strtok(line[i].words,",");
while (pt != NULL) {
if (pt[0] == '[')
pt[0] = ' ';
line[i].num[line[i].noOfnums] = atoi(pt);
pt = strtok (NULL, ",");
line[i].noOfnums++;
}
}
*/
//close file
//fclose(fp);
//Exit
printf("\nHave a nice day.\n");
return 0;
}
// std::cout << currentRead.BPLeft << " " << BoxSize << " " << NumBoxes << " " << TempBoxIndex << std::endl;
int SearchVariant::Search(BDData & g_bdData, ControlState& currentState, const unsigned NumBoxes, const SearchWindow& window)
{
std::vector<unsigned> Vars[NumBoxes];
unsigned TempBoxIndex;
unsigned int farEndExists = 0;
unsigned int readsUsed = 0;
unsigned int bpSum = 0;
for (unsigned ReadIndex = 0; ReadIndex < currentState.Reads_SR.size(); ReadIndex++) {
SPLIT_READ& currentRead = currentState.Reads_SR[ReadIndex];
if (currentRead.Used) {
readsUsed++;
}
if (!currentRead.UP_Far.empty()) {
farEndExists++;
bpSum += currentRead.UP_Far[ currentRead.UP_Far.size()-1 ].AbsLoc;
}
if (bpSum>1000000000) {
bpSum -= 1000000000;
}
}
*logStream << "Reads already used: " << readsUsed << std::endl;
*logStream << "Far ends already mapped " << farEndExists << std::endl;
*logStream << "Checksum of far ends: " << bpSum << std::endl;
//UserDefinedSettings* userSettings = UserDefinedSettings::Instance();
LOG_INFO(*logStream << "Searching " << typeOfVariant << " ... " << std::endl);
const std::string ChrSeq = window.getChromosome()->getSeq();
for (unsigned ReadIndex = 0; ReadIndex < currentState.Reads_SR.size(); ReadIndex++) {
SPLIT_READ& currentRead = currentState.Reads_SR[ReadIndex];
//std::cout << ReadIndex << std::endl;
//std::cout << currentRead << std::endl;
if (currentRead.FragName != currentRead.FarFragName) {
//std::cout << "inter-chromosome split-read" << std::endl;
continue;
}
if (currentRead.Used || currentRead.UP_Far.empty()) {
continue;
}
if (currentRead.MatchedD == Plus) {
for (short MAX_SNP_ERROR_index = 0; MAX_SNP_ERROR_index <= currentRead.getMAX_SNP_ERROR(); MAX_SNP_ERROR_index++) {
if (currentRead.Used) {
break;
}
for (unsigned int CloseIndex = 0; CloseIndex
< currentRead.UP_Close.size(); CloseIndex++) {
if (currentRead.Used) {
break;
}
if (currentRead.UP_Close[CloseIndex].Mismatches > MAX_SNP_ERROR_index) {
continue;
}
for (int FarIndex = currentRead.UP_Far.size() - 1; FarIndex >= 0; FarIndex--) {
if (currentRead.Used) {
break;
}
if (currentRead.UP_Far[FarIndex]. Mismatches > MAX_SNP_ERROR_index) {
continue;
}
if (currentRead.UP_Far[FarIndex]. Mismatches + currentRead.UP_Close[CloseIndex]. Mismatches > MAX_SNP_ERROR_index) {
continue;
}
if (currentRead.UP_Far[FarIndex]. Direction == Minus) {
if (decisionBranch1(currentRead, CloseIndex, FarIndex)) {
currentRead.Left = currentRead. UP_Close[CloseIndex].AbsLoc - currentRead. UP_Close[CloseIndex].LengthStr + 1;
currentRead.Right = currentRead.UP_Far[FarIndex]. AbsLoc + currentRead.UP_Far[FarIndex]. LengthStr - 1;
currentRead.BP = currentRead. UP_Close[CloseIndex].LengthStr - 1;
currentRead.IndelSize = calculateIndelSize(currentRead);
currentRead.NT_str = getInsertedStr1(currentRead);
currentRead.BPLeft = currentRead. UP_Close[CloseIndex].AbsLoc - g_SpacerBeforeAfter;
currentRead.BPRight = currentRead.UP_Far[FarIndex]. AbsLoc - g_SpacerBeforeAfter;
unsigned RealBP_left= currentRead.BPLeft;
unsigned RealBP_right = currentRead.BPRight;//, DIFF;
if (ChrSeq.size() < RealBP_left || ChrSeq.size() < RealBP_right) {
currentRead.Used = true;
break;
}
if (currentRead.NT_str.size()) {
//std::cout << "ns i currentRead.NT_str.size()" << std::endl;
//std::cout << currentRead.NT_str << " " << RealBP_left << " " << RealBP_right << std::endl;
GetRealStart4Insertion(ChrSeq, currentRead.NT_str, RealBP_left, RealBP_right);
//std::cout << "ne i currentRead.NT_str.size()" << std::endl;
} else {
//std::cout << "no_ns d currentRead.NT_str.size()" << std::endl;
//std::cout << RealBP_left << " " << RealBP_right << std::endl;
GetRealStart4Deletion(ChrSeq, RealBP_left, RealBP_right);
//std::cout << "no_ns d currentRead.NT_str.size()" << std::endl;
}
short DIFF = currentRead.BPLeft - RealBP_left;
DIFF = !((currentRead.BP - 1)<DIFF)?DIFF:(currentRead.BP - 1); // min(DIFF, currentRead.BP - 1);
if (DIFF > 0) {
//std::cout << "DIFF " << DIFF << std::endl;
currentRead.BP -= DIFF;
currentRead.BPLeft -= DIFF;
currentRead.BPRight -= DIFF;
}
if (readTransgressesBinBoundaries( currentRead, window.getEnd())) {
saveReadForNextCycle( currentRead, currentState.FutureReads_SR);
} else {
if (readInSpecifiedRegion( currentRead, userSettings->getRegion())) {
TempBoxIndex = (int) (currentRead. BPLeft) / BoxSize;
//std::cout << currentRead.BPLeft << " " << BoxSize << " " << NumBoxes << " " << TempBoxIndex << std::endl;
if (TempBoxIndex < NumBoxes) {
Vars[TempBoxIndex].push_back(ReadIndex);
currentRead.Used = true;
Count_Var_Plus++;
Count_Var++;
}
}
}
}
}
}
}
}
} else if (currentRead.MatchedD == Minus) {
for (short MAX_SNP_ERROR_index = 0; MAX_SNP_ERROR_index <= currentRead.getMAX_SNP_ERROR(); MAX_SNP_ERROR_index++) {
if (currentRead.Used) {
break;
}
for (int CloseIndex = currentRead.UP_Close.size() - 1; CloseIndex >= 0; CloseIndex--) {
if (currentRead.Used) {
break;
}
if (currentRead.UP_Close[CloseIndex]. Mismatches > MAX_SNP_ERROR_index) {
continue;
}
for (int FarIndex = currentRead.UP_Far.size() - 1; FarIndex >= 0; FarIndex--) {
if (currentRead.Used) {
break;
}
if (currentRead.UP_Far[FarIndex]. Mismatches > MAX_SNP_ERROR_index) {
continue;
}
if (currentRead.UP_Far[FarIndex]. Mismatches + currentRead.UP_Close[CloseIndex]. Mismatches > MAX_SNP_ERROR_index) {
continue;
}
if (currentRead.UP_Far[FarIndex]. Direction == Plus) {
if (decisionBranch2(currentRead, CloseIndex, FarIndex)) {
currentRead.Left = currentRead.UP_Far[FarIndex]. AbsLoc - currentRead.UP_Far[FarIndex]. LengthStr + 1;
currentRead.Right = currentRead. UP_Close[CloseIndex].AbsLoc + currentRead. UP_Close[CloseIndex].LengthStr - 1;
currentRead.BP = currentRead.UP_Far[FarIndex]. LengthStr - 1;
currentRead.IndelSize = calculateIndelSize(currentRead);
currentRead.NT_str = getInsertedStr2(currentRead);
currentRead.BPLeft = currentRead.UP_Far[FarIndex].AbsLoc - g_SpacerBeforeAfter;
currentRead.BPRight = currentRead.UP_Close[CloseIndex].AbsLoc - g_SpacerBeforeAfter;
unsigned RealBP_left= currentRead.BPLeft;
unsigned RealBP_right = currentRead.BPRight;//, DIFF;
if (ChrSeq.size() < RealBP_left || ChrSeq.size() < RealBP_right) {
currentRead.Used = true;
break;
}
if (currentRead.NT_str.size()) {
//std::cout << "ns i currentRead.NT_str.size()" << std::endl;
//std::cout << currentRead.NT_str << " " << RealBP_left << " " << RealBP_right << std::endl;
GetRealStart4Insertion(ChrSeq, currentRead.NT_str, RealBP_left, RealBP_right);
//std::cout << "ne i currentRead.NT_str.size()" << std::endl;
} else {
//std::cout << "no_ns d currentRead.NT_str.size()" << std::endl;
//std::cout << RealBP_left << " " << RealBP_right << std::endl;
GetRealStart4Deletion(ChrSeq, RealBP_left, RealBP_right);
//std::cout << "no_ne d currentRead.NT_str.size()" << std::endl;
}
short DIFF = currentRead.BPLeft - RealBP_left;
DIFF = !((currentRead.BP - 1)<DIFF)?DIFF:(currentRead.BP - 1);
if (DIFF > 0) {
// std::cout << DIFF << std::endl;
//std::cout << "DIFF " << DIFF << std::endl;
currentRead.BP -= DIFF;
currentRead.BPLeft -= DIFF;
currentRead.BPRight -= DIFF;
}
if (readTransgressesBinBoundaries( currentRead, window.getEnd())) {
saveReadForNextCycle( currentRead, currentState.FutureReads_SR);
} else {
if (readInSpecifiedRegion( currentRead, userSettings->getRegion())) {
TempBoxIndex = (int) (currentRead. BPLeft) / BoxSize;
//std::cout << currentRead.BPLeft << " " << BoxSize << " " << NumBoxes << " " << TempBoxIndex << std::endl;
if (TempBoxIndex < NumBoxes) {
Vars[TempBoxIndex]. push_back(ReadIndex);
currentRead.Used = true;
Count_Var++;
Count_Var_Minus++;
}
}
}
}
}
}
}
}
}
}
LOG_INFO(*logStream << "Total: " << Count_Var << "\t+" << Count_Var_Plus << "\t-" << Count_Var_Minus << std::endl);
outputResults(g_bdData, currentState, Vars, NumBoxes, window);
for (unsigned int i = 0; i < NumBoxes; i++) {
Vars[i].clear();
}
return EXIT_SUCCESS;
}
int main(int argc, char** argv)
{
if(argc < 6)
{
printf("usage: sum <distr. mode = 0/1> <block cyclic factor = R [1, n/P]> <N: matrix is NxN> <input file name> <output ux = 0/1>\n");
return 0;
}
// Read arguments
DISTRIBUTE_READ = atoi(argv[1]);
R = atoi(argv[2]);
N = atoi(argv[3]);
OUTPUT_UX = atoi(argv[5]);
char* inputFile = argv[4];
// Initialize MPI
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &P);
MPI_Comm_rank(MPI_COMM_WORLD, &PID);
RPP = N / P;
if(R < 1 || R > N / P)
{
printf("ERROR: R (%d) must be between 1 and N/P (%d)\n", R, N/P);
return -1;
}
// Broadcast matrix size and block cyclic factor
MPI_Bcast(&N, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&R, 1, MPI_INT, 0, MPI_COMM_WORLD);
// This array stores the rows of the augmented matrix associated to this processor.
double* localRows = malloc(RPP * (N + 1) * sizeof(double));
double x[MAX_N];
memset(x, 0, MAX_N * sizeof(double));
// These variables will store times for data loading (and distribution)
// Forward elimination and back substitution.
float ddtime;
float fetime;
float bstime;
float pvtime;
// Load the matrix data
loadMatrix(inputFile, localRows, &ddtime);
// Solve the system
solve(localRows, x, &fetime, &bstime, &pvtime);
// Output solution and statistics
outputResults(inputFile, localRows, x, ddtime, bstime, fetime, pvtime);
// Free memory
//free(localRowIds);
//free(localRows);
// Finalize MPI
MPI_Finalize();
return 0;
}
int _tmain(int argc, _TCHAR* argv[])
{
//In order to accelerate the access to the system state, we code the system state into a double which is calculated as followed
//for each server, state_index = (cpu_residual+mem_residual+disk_residual) * server_id
//for the whole system, state_index = sum the state_index over the all servers.
//With this method, we can quickly locate the state and its corresponding value.
vector<cConfiguration> config_vec;
initialInputfile(config_vec);
vector<cConfiguration>::iterator iter_config_vec = config_vec.begin();
for (;iter_config_vec != config_vec.end();iter_config_vec++)
{
//reset the seed of random number generator for generating arrival times
interval_timeSeed = 10;
//reset the seed of random number generator for generating duration times
duration_time_seed = 100;
//reset the system state value
system_state_value_map.clear();
//store the system state visited ever
system_state_policy_map.clear();
//initial the set of policies
policy_vec.clear();
//initial the input parameters
initialInputParameter(iter_config_vec);
average_accepted_rate = 0;
average_allocation_fail_rate = 0;
system_value_map *p_system_value_map = new system_value_map[total_request + 1];
system_policy_map *p_system_policy_map = new system_policy_map[total_request + 1];
global_point_system_value_map = p_system_value_map;
global_point_system_policy_map = p_system_policy_map;
//unsigned int sample_index;
for (sample_index = 0;sample_index < sample_request_num; sample_index++)
{
accepted_requests_num = 0;
allocation_fail_num = 0;
cout<<"The "<<sample_index<<" sample path"<<endl;
//initial request sequence
//vector<cRequest> request_vec;
vector<cRequest> *p_request_vec = new vector<cRequest>;
multimap<double,cEvent> *p_event_multimap = new multimap<double,cEvent>;
//multimap<double,cEvent> event_multimap;
//initial the set of physical servers
vector<cServer> *p_server_vec = new vector<cServer>;
//vector<cServer> server_vec;
initialPhyServers(*p_server_vec);
if (iter_config_vec == config_vec.begin() && sample_index == 0)
{
initialCommuCost(*p_server_vec);
//initialBasisFuncParameters(server_vec);
}
initialSystemState(*p_server_vec);
generateSampleEvent(*p_request_vec,*p_event_multimap);
obtainOptimalStateValue(*p_event_multimap,*p_server_vec);
//reset the event indicator
event_id = 1;
average_accepted_rate += accepted_requests_num/total_request;
average_allocation_fail_rate += allocation_fail_num/total_request;
delete p_request_vec;
delete p_server_vec;
delete p_event_multimap;
}//end...for (sample_index...)
outputResults();
delete[] p_system_policy_map;
delete[] p_system_value_map;
//outputResultsBasisFunct();
}//end...for (iter_config_vec)
return 0;
}
