Model::Model(shared_ptr<RInside>& ri, const std::string& net_var) :
R(ri), net(false), trans_runner(create_transmission_runner()), cd4_calculator(create_CD4Calculator()), viral_load_calculator(
create_ViralLoadCalculator()), popsize(), max_id(0), stage_map(), stats() {
List rnet = as<List>((*R)[net_var]);
PersonCreator person_creator(trans_runner);
initialize_network(rnet, net, person_creator);
init_stage_map(stage_map);
popsize.push_back(net.vertexCount());
max_id = net.vertexCount();
// get initial stats
stats.incrementCurrentEdgeCount(net.edgeCount());
stats.incrementCurrentSize(net.vertexCount());
for (auto iter = net.verticesBegin(); iter != net.verticesEnd(); ++iter) {
if ((*iter)->isInfected()) {
stats.incrementCurrentTotalInfectedCount(1);
}
}
stats.resetForNextTimeStep();
float art_coverage_rate = Parameters::instance()->getDoubleParameter(ART_COVERAGE_RATE);
BinomialGen coverage(repast::Random::instance()->engine(),
boost::random::binomial_distribution<>(1, art_coverage_rate));
Random::instance()->putGenerator(ART_COVERAGE_BINOMIAL, new DefaultNumberGenerator<BinomialGen>(coverage));
}
int main(int argc, char** argv) {
int NUM_PASSES = 100;
if (argc < 3) {
fprintf(stderr, "Usage: ./mnist <test|inference> [NUMBER_PASSES]\n");
return 2;
}
else{
NUM_PASSES = atoi(argv[2]);
}
Network* net = construct_scene_labeling_net();
initialize_network(net, 1);
if (!strcmp(argv[1], "inference")) {
//net_measure_inference_time(net);
return 1;
}
if (!strcmp(argv[1], "test")){
// net_test(net, input, labels, NUM_PASSES);
}
free_network(net);
return 2;
}
void net_info(char* ip_address, char* mask) {
host h1;
initialize_host(&h1, ip_address, mask);
network n1;
initialize_network(&n1, &h1);
print_network_info(&n1);
}
void *_serverstart()
{
android_log(ANDROID_LOG_VERBOSE,"ntripcaster status before starting:%d",get_ntripcaster_state());
set_run_path(appPath);
thread_lib_init ();
init_thread_tree (__LINE__, __FILE__);
setup_defaults ();
setup_signal_traps ();
allocate_resources ();
init_authentication_scheme ();
parse_default_config_file ();
initialize_network ();
startup_mode ();
android_log(ANDROID_LOG_VERBOSE,"ntripcaster status after ending:%d",get_ntripcaster_state());
pthread_exit(0);
android_log(ANDROID_LOG_VERBOSE,"ntripcaster ended");
}
int main(int argc, char *argv[])
{
struct State S;
S.is_2D = false;
int N_trials = 200;
double time_formation;
double angle_location;
char filename[100];
read_network_parameters(argc, argv, &S);
initialize_rng();
initialize_network(&S);
initialize_circular_buffer(&S);
double m_s = 5.0;
double dispersion;
double duration = 0.10;
double intensity = 0.2;
double location[1] = {0};
FILE *fin;
for (int i=0; i < 12; i++) {
dispersion = 15 + 5 * i;
sprintf(filename,
"bump_formation_times_ms_%02d_duration_%4.2f_i_%3.1f_dispersion_%02d",
(int) m_s, duration, intensity, (int)dispersion);
fin = fopen(filename, "w");
for (int j=0; j < N_trials; j++) {
printf("%d\n", j);
generate_pulses(&S, 1, location, dispersion, duration, intensity, m_s);
simulate_single_trajectory_self_stop(&S, &time_formation, &angle_location);
fprintf(fin, "% 8.3f % 10.3f\n", time_formation, angle_location);
printf("% 8.3f % 10.3f\n", time_formation, angle_location);
reset_rates_and_inputs(&S);
free_extinputs(S.pulse_list);
}
fclose(fin);
}
free_network_variables(&S);
fclose(fin);
return 0;
}
int main(int argc, char** argv) {
int NUM_PASSES = 100;
if (argc < 3) {
fprintf(stderr, "Usage: ./gtsrb <test|inference> [NUMBER_PASSES]\n");
return 2;
}
else{
NUM_PASSES = atoi(argv[2]);
}
Network* net = construct_gtsrb_net();
initialize_network(net, 1);
vol_t** input = (vol_t**)malloc(sizeof(vol_t*)*NUM_PASSES);
label_t* labels = (label_t*)malloc(sizeof(label_t)*NUM_PASSES);
load_gtsrb_data(input, labels, NUM_PASSES);
int valid = 0;
if (!strcmp(argv[1], "inference")) {
net_predict_Multiple(net, input, NUM_PASSES);
valid = 1;
}
if (!strcmp(argv[1], "test")){
net_test(net, input, labels, NUM_PASSES);
valid = 1;
}
#ifdef DEBUGG
print_vol(net->buffer[4][0],0);
#endif
free_network(net);
for(int i = 0; i < NUM_PASSES; i++)
free(input[i]);
free(input);
free(labels);
if(valid) return 0;
fprintf(stderr,"unrecognised command\n");
return 2;
}
void host_tree(char* ip_address, char* mask, int hosts) {
host h1;
initialize_host(&h1, ip_address, mask);
tnode* t1;
t1 = (tnode *) malloc(sizeof(tnode));
t1->right = NULL;
t1->left = NULL;
t1->parent = NULL;
initialize_network(&t1->n, &h1);
build_tree_host_count(t1, hosts);
print_network_tree(t1, 0, verbose);
free_network_tree(t1);
}
void vlsm_tree(char* ip_address, char* mask, char* nets) {
host h1;
initialize_host(&h1, ip_address, mask);
tnode *t1;
t1 = (tnode *) malloc(sizeof(tnode));
t1->right = NULL;
t1->left = NULL;
t1->parent = NULL;
initialize_network(&t1->n, &h1);
//int j = 0;
char* tok;
char* sep = ",";
for(tok = strtok(nets, sep); tok; tok = strtok(NULL,sep)) {
//verify host counts are legit
if(!is_number(tok))
g_error("vlsm string contains non-numeric values");
// we should have left and right as an option here, set by CLI flag
// default is left
build_tree_vlsm(t1, atoi(tok), 0);
}
print_network_tree(t1, 0, verbose);
free_network_tree(t1);
}
int main(int argc, char **argv)
{
int status;
struct sigaction usr_action;
struct sigaction term_action;
sigset_t block_mask;
int socks_status;
connections.last_slot = -1;
connections.running_pid = getpid();
status = init(argc, argv, &connections);
if (status == INIT_FAILURE)
{
if (to_printhelp == 1)
print_help(argc, argv);
exit(EXIT_FAILURE);
}
if (status == INIT_SUCCESS && to_printhelp == 1)
{
print_help(argc, argv);
exit(EXIT_SUCCESS);
}
if (to_command_mode)
{
status = execute_command(&connections);
exit(status);
}
Log(LOG_NOTICE, "Program started by User %d \n", getuid());
/* Daemon-specific initialization */
if (to_demonize)
{
status = daemonize(&connections);
switch (status)
{
case DAEMONIZE_FAILURE:
/*something gone wrong exit from parent */
printf("Failed to daemonize.Check permissions\n");
exit(EXIT_FAILURE);
break;
case DAEMONIZE_SUCCESS:
/*ok we are the parent, we can exit gracefully */
Log(LOG_INFO, "Starting as a daemon.Parent exit\n");
printf("Starting as a daemon.Parent exit\n");
exit(EXIT_SUCCESS);
break;
}
}
/* Establish the signal handler. */
sigfillset(&block_mask);
usr_action.sa_handler = sleep_signal;
usr_action.sa_mask = block_mask;
usr_action.sa_flags = 0;
sigaction(SIGUSR1, &usr_action, NULL);
term_action.sa_handler = term_signal;
term_action.sa_mask = block_mask;
term_action.sa_flags = 0;
sigaction(SIGTERM, &term_action, NULL);
Log(LOG_INFO, "Init networking\n");
status = initialize_network(&connections);
Log(LOG_INFO, "Init timers\n");
status = initialize_timers(&connections);
/* The Big Loop */
while (1)
{
Log(LOG_DEBUG, "Main loop\n");
rebuild_connection_set(&connections);
socks_status = select(connections.max_socket + 1, &connections.socket_set, NULL, NULL, NULL);
if (socks_status < 0)
{
status = errno;
/* We had an error, signal it */
if (status != EINTR)
{
Log(LOG_ERR, "Error in select socket (%s) \n", strerror(status));
exit(EXIT_FAILURE);
}
}
else
if (socks_status == 0)
{
/* Nothing to do probably a staying alive msg in debug mode */
}
else
{
read_sockets(&connections);
}
}
closelog();
exit(EXIT_SUCCESS);
}
//rtems_task Init(rtems_task_argument Argument)
void *POSIX_Init(void *argument)
{
pthread_attr_t threadAttr;
pthread_t theThread;
struct sched_param sched_param;
size_t stack_size;
int result;
char data[1000];
memset(data, 1, sizeof(data));
/* Set the TOD clock, so that gettimeofday() will work */
rtems_time_of_day fakeTime = { 2006, 3, 15, 17, 30, 0, 0 };
if (RTEMS_SUCCESSFUL != rtems_clock_set(&fakeTime))
{
assert(0);
}
/* Bring up the network stack so we can run the socket tests. */
initialize_network();
/* Start a POSIX thread for pjlib_test_main(), since that's what it
* thinks it is running in.
*/
/* Initialize attribute */
TEST( pthread_attr_init(&threadAttr) );
/* Looks like the rest of the attributes must be fully initialized too,
* or otherwise pthread_create will return EINVAL.
*/
/* Specify explicit scheduling request */
TEST( pthread_attr_setinheritsched(&threadAttr, PTHREAD_EXPLICIT_SCHED));
/* Timeslicing is needed by thread test, and this is accomplished by
* SCHED_RR.
*/
TEST( pthread_attr_setschedpolicy(&threadAttr, SCHED_RR));
/* Set priority */
TEST( pthread_attr_getschedparam(&threadAttr, &sched_param));
sched_param.sched_priority = NETWORK_STACK_PRIORITY - 10;
TEST( pthread_attr_setschedparam(&threadAttr, &sched_param));
/* Must have sufficient stack size (large size is needed by
* logger, because default settings for logger is to use message buffer
* from the stack).
*/
TEST( pthread_attr_getstacksize(&threadAttr, &stack_size));
if (stack_size < 8192)
TEST( pthread_attr_setstacksize(&threadAttr, 8192));
/* Create the thread for application */
result = pthread_create(&theThread, &threadAttr, &pjlib_test_main, NULL);
if (result != 0) {
my_perror(PJ_STATUS_FROM_OS(result),
"Error creating pjlib_test_main thread");
assert(!"Error creating main thread");
}
return NULL;
}
void net_summary() {
tnode* networks[MAX_NUM_TREES];
host h1;
char ip[16];
char mask[16];
int i;
/* initialize the nodes to NULL */
for(i = 0; i < MAX_NUM_TREES; i++)
networks[i] = NULL;
/* populate the array with the networks from the input */
for(i = 0; scanf("%s %s", ip, mask) != EOF; i++) {
initialize_host(&h1, ip, mask);
networks[i] = g_malloc(sizeof(tnode));
initialize_network(&networks[i]->n, &h1);
networks[i]->left = NULL;
networks[i]->right = NULL;
networks[i]->parent = NULL;
// printf("Added network %s %s\n", ip, mask);
}
//printf("%i\n", i);
int j;
int k;
int l;
tnode *t1;
int made_changes = 1;
/* loop until there are no summarization left to do */
while(made_changes) {
made_changes = 0;
/* loop through each member */
for(j = 0; j < i; j++) {
/* compare each member for summarization*/
for(k = 0; k < i; k++) {
if((j != k) && (t1 = combine_networks(networks[j], networks[k])) != NULL) {
// printf("Combined networks\n[%i:%i]\n", j,k);
networks[j] = NULL;
networks[k] = NULL;
for(l = 0; networks[l] != NULL; l++)
;
networks[l] = t1;
made_changes = 1;
}
}
}
}
printf("Networks were summarized as follows:\n\n");
for(i = 0; i < MAX_NUM_TREES; i++) {
if(networks[i] != NULL) {
if(verbose)
{
print_network_tree(networks[i], 0, TRUE);
printf("\n");
}
else
{
char ip_address[16];
inttodd(ip_address, networks[i]->n.address.ip_address);
printf("%s/%i\n", ip_address, get_bits_in_mask(networks[i]->n.address.mask));
}
free_network_tree(networks[i]);
}
}
}
