void VariantJobServer::PushCurVariantOntoJobs(ofstream &outVCFFile,
ofstream &filterVCFFile,
vcf::VariantCallFile &vcfFile,
InputStructures &global_context,
ExtendParameters *parameters) {
variant->isHotSpot = isHotSpot; // see TODO above
//@TODO: the logic here is slightly more complex than optimal
if (variant_thread_job_spec == NULL) {
variant_thread_job_spec = new variantThreadInfo(outVCFFile, filterVCFFile, parameters, &global_context, all_thread_master);
}
if (variant_thread_job_spec->ReadyForAnotherVariant()) {
variant_thread_job_spec->PushVariantOntoJob(variant);
}
else {
//check for the number of running threads and if less than MAX create new thread and pass the job
all_thread_master.WaitForFreeThread();
if (all_thread_master.max_threads_sem.count < all_thread_master.max_threads_available) {
all_thread_master.StartJob(variant_thread_job_spec, false, global_context.DEBUG);
variant_thread_job_spec = NULL;
variant_thread_job_spec = new variantThreadInfo(outVCFFile, filterVCFFile, parameters, &global_context, all_thread_master);
variant_thread_job_spec->PushVariantOntoJob(variant);
}
else {
cerr << "FATAL: thought I had a thread available but I didn't" << endl;
exit(-1);
}
//Added for 3.6.1 Patch to clear thread resource after they terminate. Need to move this to use thread pools instead.
if (all_thread_master.thread_tracker.size() > (size_t) 3*all_thread_master.max_threads_available) {
std::vector<pthread_t*>::iterator thread_itr = all_thread_master.thread_tracker.begin();
int counter = 0;
int rc = 0;
while (counter < all_thread_master.max_threads_available && thread_itr != all_thread_master.thread_tracker.end()) {
rc = pthread_join(**thread_itr, NULL);
if (rc) {
cerr << "FATAL: pthread_join returned non-zero return code " << rc << endl;
exit(-1);
}
//remove the thread reference since it has completed successfully to release it's resources
delete *thread_itr;
thread_itr = all_thread_master.thread_tracker.erase(thread_itr);
counter++;
}
}
}
NewVariant(vcfFile);
}
void VariantJobServer::PushCurVariantOntoJobs(ofstream &outVCFFile,
ofstream &filterVCFFile,
vcf::VariantCallFile &vcfFile,
InputStructures &global_context,
ExtendParameters *parameters) {
variant->isHotSpot = isHotSpot; // see TODO above
//@TODO: the logic here is slightly more complex than optimal
// need a new job, create one
if (variant_thread_job_spec == NULL) {
variant_thread_job_spec = new variantThreadInfo(outVCFFile, filterVCFFile, parameters, &global_context, all_thread_master);
}
// if job can take another variant, go for it
if (variant_thread_job_spec->ReadyForAnotherVariant()) {
variant_thread_job_spec->PushVariantOntoJob(variant);
}
else {
// ready to fire off the job
//check for the number of running threads and if less than MAX create new thread and pass the job
all_thread_master.WaitForFreeThread();
if (all_thread_master.max_threads_sem.count < all_thread_master.max_threads_available) {
all_thread_master.StartJob(variant_thread_job_spec, false, global_context.DEBUG);
// generate a new job to handle the variant we were passed
variant_thread_job_spec = NULL;
variant_thread_job_spec = new variantThreadInfo(outVCFFile, filterVCFFile, parameters, &global_context, all_thread_master);
variant_thread_job_spec->PushVariantOntoJob(variant);
}
else {
cerr << "FATAL: thought I had a thread available but I didn't" << endl;
exit(-1);
}
//Added for 3.6.1 Patch to clear thread resource after they terminate. Need to move this to use thread pools instead.
RefreshThreadPool();
}
// get a new variant to handle the next case
NewVariant(vcfFile);
}
