int main(int argc, char * argv[]){
/* MPI Initialization */
int nprocs, rank;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (argc!=4){
fprintf(stderr, "Usage: %s\n", argv[0]);
exit(EXIT_FAILURE);
}
/* number of steps in mcmc */
int max_steps;
/* flag to indicate starting parameters */
int param_flag;
/* name of file to output -- not including path */
char file_string[256];
sscanf(argv[1], "%d", &max_steps);
sscanf(argv[2], "%d", ¶m_flag);
if(rank==0) fprintf(stderr, "%d steps in mcmc chain.\n", max_steps);
sscanf(argv[3], "%s", file_string);
/* -- Initialize parameters --*/
STEP_DATA initial;
load_step_data(&initial, param_flag, rank);
/* -- Load data from various files --*/
int i, j;
int N_plist;
int N_bins;
POINTING *plist;
/* have each process separately access these files */
int current_rank = 0;
while ( current_rank < nprocs ){
if (current_rank == rank) {
load_pointingID(&N_plist, &plist);
if(rank == 0) fprintf(stderr, "%d pointings to do\n", N_plist);
N_bins = load_Nbins();
if(rank == 0) fprintf(stderr, "%d bins per pointing\n", N_bins);
}
MPI_Barrier(MPI_COMM_WORLD);
current_rank++;
}
/* Establish slice of pointings for each process to handle */
int slice_length;
int remain = N_plist % nprocs;
int lower_ind, upper_ind;
/* Make slices as even as possible */
slice_length = N_plist / nprocs;
lower_ind = rank * slice_length;
if (rank < remain){
lower_ind += rank;
slice_length++;
}
else lower_ind += remain;
upper_ind = lower_ind + slice_length;
/* Each process now loads data for its slice only */
load_ZRW(plist, lower_ind, upper_ind, rank);
load_rbins(plist, N_bins, lower_ind, upper_ind, rank);
load_pairs(plist, N_bins, lower_ind, upper_ind, rank);
// load_covariance(plist, N_bins, lower_ind, upper_ind, rank);
// load_correlation(plist, N_bins, lower_ind, upper_ind, rank);
load_inv_covariance(plist, N_bins, lower_ind, upper_ind, rank);
/* test loading of covariance */
// if(rank==0){
// for(i=0; i<N_bins; i++){
// for(j=0; j<N_bins; j++){
// fprintf(stderr, "Value: %le, Row: %d, Col: %d \n",
// plist[1].cov_row[i].cov_col[j], i, j);
// }
// }
// }
// MPI_Barrier(MPI_COMM_WORLD);
/* Calculate DD/RR */
/* Only must be done once */
calculate_DD_RR(plist, N_bins, lower_ind, upper_ind);
/* Run mcmc */
run_mcmc(plist, initial, N_bins, max_steps, lower_ind, upper_ind,
rank, nprocs, file_string);
/* Free allocated values */
for(i=lower_ind; i<upper_ind; i++){
for(j=0; j<N_bins; j++){
free(plist[i].rbin[j].pair1);
free(plist[i].rbin[j].pair2);
// free(plist[i].cov_row[j].cov_col);
// free(plist[i].cor_row[j].cor_col);
free(plist[i].invcov_row[j].invcov_col);
}
free(plist[i].rbin);
// free(plist[i].cov_row);
// free(plist[i].cor_row);
free(plist[i].invcov_row);
free(plist[i].Z);
free(plist[i].R);
free(plist[i].weight);
}
free(plist);
if(rank==0) fprintf(stderr, "Allocated space cleared. \n");
/* barrier to ensure all procs clear space before MPI_Finalize */
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
return EXIT_SUCCESS;
}
int main (int argc, char* argv[]) {
char filename1[200];
char filename2[200];
char pairs_file[200];
char fileout[200];
FILE* query_fp = 0;
FILE* reference_fp = 0;
FILE* fp_pairs = 0;
FILE* fpout = stdout;
int total_pairs = 0;
pair_struct* pairs = 0;
extern FILE *scaninfo_file;
setup_match_types();
/* Set Default Parameter Values*/
length_5p_for_weighting = 8; /* The 5' sequence length to be weighted except for the last residue */
scale = 4.0; /* The 5' miRNA scaling parameter */
strict = 0; /* Strict seed model on/off*/
debug = 0; /* Debugging mode on/off*/
key_value_pairs = 0;
gap_open = -9.0; /* Gap-open Penalty*/
gap_extend = -4.0; /* Gap-extend Penalty*/
score_threshold = 140.0; /* SW Score Threshold for reporting hits*/
score_ceiling = 0; /* Default upper limit to score. If zero, this is not used. */
energy_threshold = 1.0; /* Energy Threshold (DG) for reporting hits*/
verbosity = 1; /* Verbose mode on/off*/
brief_output = 0; /* Brief output off by default */
rusage_output = 0; /* rusage output off by default */
outfile = 0; /* Dump to file on/off*/
truncated = 0; /* Truncate sequences on/off*/
no_energy = 1; /* Turn off Energy Calcs - FASTER*/
restricted = 0; /* Perform restricted search space*/
parse_command_line(argc, argv, filename1, filename2, fileout, pairs_file);
if (gap_open > 0.0 || gap_extend > 0.0) {
fprintf(stderr, "Error: gap penalties may not be greater than 0\n");
return 1;
}
if (truncated < 0) {
fprintf(stderr, "Error: negative value give for UTR truncation\n");
return 1;
}
if ((query_fp = fopen(filename1, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename1);
return 1;
}
if ((reference_fp = fopen(filename2, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename2);
return 1;
}
fclose(reference_fp);
if ((outfile) && ((fpout = fopen(fileout, "w")) == NULL)) {
fprintf(stderr, "Error: Cannot create output file %s\n", fileout);
return 1;
}
if (restricted) {
if ((fp_pairs = fopen(pairs_file, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open restrict pairs file %s\n", pairs_file);
return 1;
}
/* Initialize the pairs list for restriced searches*/
total_pairs = load_pairs(fp_pairs, &pairs);
fclose(fp_pairs);
}
fflush(fpout);
initialize_globals();
if(!brief_output)
print_parameters(filename1, filename2, fpout);
if (restricted && verbosity) {
printf("Performing Restricted Scan on:%d pairs\n", total_pairs);
}
find_targets(query_fp, fpout, pairs, total_pairs, filename2);
#ifdef USE_RUSAGE
if(rusage_output)
{
struct rusage ru;
if(getrusage(RUSAGE_SELF,&ru) != 0)
{
fprintf(stderr,"Could not get rusage data\n");
if(errno)
fprintf(stderr,"Reason: %s",strerror(errno));
}
else
{
printf("User CPU time: %ld.%06ld\n",ru.ru_utime.tv_sec,ru.ru_utime.tv_usec);
printf("Max RSS: %ld KB\n",ru.ru_maxrss);
}
}
#endif // RUSAGE
destroy_globals();
if (outfile) fclose(fpout);
if (scaninfo_file != stdout && scaninfo_file != stderr && scaninfo_file != NULL)
fclose(scaninfo_file);
json_close();
fclose(query_fp);
return 0;
}
int main(int argc, char * argv[]){
/* MPI Initialization */
int nprocs, rank;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
/* parse command line for starting params, steps, and filename */
ARGS cl = parse_command_line( argc, argv );
if(rank==0){
fprintf(stderr, "N_parameters: %d\n", cl.N_params);
fprintf(stderr, "Starting parameters: r0_thin = %lf , z0_thin = %lf , r0_thick = %lf , z0_thick = %lf , ratio = %lf\n",
cl.r0_thin, cl.z0_thin, cl.r0_thick, cl.z0_thick, cl.ratio);
fprintf(stderr, "%d steps in MCMC chain...\n", cl.max_steps);
fprintf(stderr, "Results will be output to %s\n", cl.filename);
}
/* Assign cl arguments to initial parameters */
STEP_DATA initial;
initial.r0_thin = cl.r0_thin;
initial.z0_thin = cl.z0_thin;
initial.r0_thick = cl.r0_thick;
initial.z0_thick = cl.z0_thick;
initial.ratio_thick_thin = cl.ratio;
initial.chi2 = 0.0;
initial.chi2_reduced = 0.0;
/* -- Load data from various files --*/
int i, j;
int N_plist;
int N_bins;
POINTING *plist;
/* have each process separately access these files */
int current_rank = 0;
while ( current_rank < nprocs ){
if (current_rank == rank){
load_pointingID(&N_plist, &plist);
if(rank == 0) fprintf(stderr, "%d pointings to do\n", N_plist);
N_bins = load_Nbins();
if(rank == 0) fprintf(stderr, "%d bins per pointing\n", N_bins);
}
MPI_Barrier(MPI_COMM_WORLD);
current_rank++;
}
/* Establish slice of pointings for each process to handle */
int slice_length;
int remain = N_plist % nprocs;
int lower_ind, upper_ind;
/* Make slices as even as possible */
slice_length = N_plist / nprocs;
lower_ind = rank * slice_length;
if (rank < remain){
lower_ind += rank;
slice_length++;
}
else lower_ind += remain;
upper_ind = lower_ind + slice_length;
/* Each process now loads data for its slice only */
load_ZRW(plist, lower_ind, upper_ind, rank);
load_rbins(plist, N_bins, lower_ind, upper_ind, rank);
load_pairs(plist, N_bins, lower_ind, upper_ind, rank);
load_inv_correlation(plist, N_bins, lower_ind, upper_ind, rank);
/* Run mcmc */
run_mcmc(plist, cl.N_params, initial, N_bins, cl.max_steps, lower_ind, upper_ind,
rank, nprocs, cl.filename);
/* Free allocated values */
for(i=lower_ind; i<upper_ind; i++){
for(j=0; j<N_bins; j++){
free(plist[i].rbin[j].pair1);
free(plist[i].rbin[j].pair2);
}
free(plist[i].rbin);
free(plist[i].Z);
free(plist[i].R);
free(plist[i].weight);
}
free(plist);
if(rank==0) fprintf(stderr, "Allocated space cleared. \n");
/* barrier to ensure all procs clear space before MPI_Finalize */
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
return EXIT_SUCCESS;
}
int main(int argc, char * argv[]){
/* MPI Initialization */
int nprocs, rank;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
// if (argc!=4){
// fprintf(stderr, "Usage: %s\n", argv[0]);
// exit(EXIT_FAILURE);
// }
// /* number of steps in mcmc */
// int max_steps;
// /* flag to indicate starting parameters */
// int param_flag;
// /* name of file to output -- not including path */
// char file_string[256];
// sscanf(argv[1], "%d", &max_steps);
// sscanf(argv[2], "%d", ¶m_flag);
// if(rank==0) fprintf(stderr, "%d steps in mcmc chain.\n", max_steps);
// sscanf(argv[3], "%s", file_string);
// /* -- Initialize parameters --*/
// STEP_DATA initial;
// load_step_data(&initial, param_flag, rank);
/* parse command line for starting params, steps, and filename */
ARGS cl = parse_command_line( argc, argv );
if(rank==0){
fprintf(stderr, "N_parameters: %d\n", cl.N_params);
fprintf(stderr, "Starting parameters: r0_thin = %lf , z0_thin = %lf , r0_thick = %lf , z0_thick = %lf , ratio = %lf\n", cl.r0_thin, cl.z0_thin, cl.r0_thick, cl.z0_thick, cl.ratio);
fprintf(stderr, "%d steps in MCMC chain...\n", cl.max_steps);
fprintf(stderr, "Results will be output to %s\n", cl.filename);
}
/* Assign cl arguments to initial parameters */
STEP_DATA initial;
initial.r0_thin = cl.r0_thin;
initial.z0_thin = cl.z0_thin;
initial.r0_thick = cl.r0_thick;
initial.z0_thick = cl.z0_thick;
initial.ratio_thick_thin = cl.ratio;
initial.chi2 = 0.0;
initial.chi2_reduced = 0.0;
/* -- Load data from various files --*/
int i, j;
int N_plist;
int N_bins;
POINTING *plist;
/* have each process separately access these files */
int current_rank = 0;
while ( current_rank < nprocs ){
if (current_rank == rank) {
load_pointingID(&N_plist, &plist);
if(rank == 0) fprintf(stderr, "%d pointings to do\n", N_plist);
N_bins = load_Nbins();
if(rank == 0) fprintf(stderr, "%d bins per pointing\n", N_bins);
}
MPI_Barrier(MPI_COMM_WORLD);
current_rank++;
}
/* Establish slice of pointings for each process to handle */
int slice_length;
int remain = N_plist % nprocs;
int lower_ind, upper_ind;
/* Make slices as even as possible */
slice_length = N_plist / nprocs;
lower_ind = rank * slice_length;
if (rank < remain){
lower_ind += rank;
slice_length++;
}
else lower_ind += remain;
upper_ind = lower_ind + slice_length;
/* Each process now loads data for its slice only */
load_ZRW(plist, lower_ind, upper_ind, rank);
load_rbins(plist, N_bins, lower_ind, upper_ind, rank);
load_pairs(plist, N_bins, lower_ind, upper_ind, rank);
/* Calculate fractional error in DD/MM */
/* Only must be done once */
calculate_frac_error(plist, N_bins, lower_ind, upper_ind);
/* Run mcmc */
run_mcmc(plist, cl.N_params, initial, N_bins, cl.max_steps, lower_ind, upper_ind,
rank, nprocs, cl.filename);
/* Free allocated values */
for(i=lower_ind; i<upper_ind; i++){
for(j=0; j<N_bins; j++){
free(plist[i].rbin[j].pair1);
free(plist[i].rbin[j].pair2);
}
free(plist[i].rbin);
free(plist[i].Z);
free(plist[i].R);
free(plist[i].weight);
}
free(plist);
if(rank==0) fprintf(stderr, "Allocated space cleared. \n");
/* barrier to ensure all procs clear space before MPI_Finalize */
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
return EXIT_SUCCESS;
}
int main (int argc, char* argv[]) {
char filename1[200];
char filename2[200];
char pairs_file[200];
char fileout[200];
FILE* query_fp = 0;
FILE* reference_fp = 0;
FILE* fp_pairs = 0;
FILE* fpout = stdout;
int total_pairs = 0;
pair_struct* pairs = 0;
/* Set Default Parameter Values*/
length_5p_for_weighting = 8; /* The 5' sequence length to be weighed except for the last residue*/
scale = 4.0; /* The 5' miRNA scaling parameter*/
strict = 0; /* Strict seed model on/off*/
debug = 0; /* Debugging mode on/off*/
key_value_pairs = 0;
gap_open = -9.0; /* Gap-open Penalty*/
gap_extend = -4.0; /* Gap-extend Penalty*/
score_threshold = 140.0; /* SW Score Threshold for reporting hits*/
energy_threshold = 1.0; /* Energy Threshold (DG) for reporting hits*/
verbosity = 1; /* Verbose mode on/off*/
outfile = 0; /* Dump to file on/off*/
truncated = 0; /* Truncate sequences on/off*/
no_energy = 0; /* Turn off Vienna Energy Calcs - FASTER*/
restricted = 0; /* Perform restricted search space*/
parse_command_line(argc, argv, filename1, filename2, fileout, pairs_file);
if (gap_open > 0.0 || gap_extend > 0.0) {
fprintf(stderr, "Error: gap penalties may not be greater than 0\n");
return 1;
}
if (truncated < 0) {
fprintf(stderr, "Error: negative value give for UTR truncation\n");
return 1;
}
if ((query_fp = fopen(filename1, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename1);
return 1;
}
if ((reference_fp = fopen(filename2, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename2);
return 1;
}
fclose(reference_fp);
if ((outfile) && ((fpout = fopen(fileout, "w")) == NULL)) {
fprintf(stderr, "Error: Cannot create output file %s\n", fileout);
return 1;
}
if (restricted) {
if ((fp_pairs = fopen(pairs_file, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open restrict pairs file %s\n", pairs_file);
return 1;
}
/* Initialize the pairs list for restriced searches*/
total_pairs = load_pairs(fp_pairs, &pairs);
fclose(fp_pairs);
}
initialize_globals();
print_parameters(filename1, filename2, fpout);
if (restricted && verbosity) {
printf("Performing Restricted Scan on:%d pairs\n", total_pairs);
}
find_targets(query_fp, fpout, pairs, total_pairs, filename2);
destroy_globals();
if (outfile) fclose(fpout);
fclose(query_fp);
return 0;
}
