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Fix race condition when placing sample #307

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merged 2 commits into from
Dec 8, 2022
Merged

Fix race condition when placing sample #307

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b711f5c
fix race
yceh Dec 8, 2022
37b1149
Merge branch 'master' of https://github.com/yatisht/usher
yceh Dec 8, 2022
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6 changes: 3 additions & 3 deletions src/usher-sampled/place_sample.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -446,15 +446,14 @@ typedef tbb::flow::function_node<Preped_Sample_To_Place *,size_t> placer_node_t;
typedef tbb::concurrent_bounded_queue<Sample_Muts*> retry_place_t;
typedef tbb::flow::multifunction_node<Sample_Muts*,tbb::flow::tuple<Sample_Muts*>> Pusher_Node_T;
typedef tbb::flow::function_node<print_format> Printer_Node_t;
static void place_sample_thread( MAT::Tree &main_tree,std::vector<MAT::Node *> &deleted_nodes,
static void place_sample_thread(int start_idx, MAT::Tree &main_tree,std::vector<MAT::Node *> &deleted_nodes,
Placed_move_sended_state& send_queue,found_place_t& found_place_queue,Pusher_Node_T& retry_queue
,int all_size,std::atomic_bool& stop,std::atomic_size_t& curr_idx,
const int parsimony_increase_threshold, size_t sample_start_idx,bool dry_run,
int max_parsimony,size_t max_uncertainty,bool multi_processing,Printer_Node_t& printer_node,bool do_print) {
int redo=0;
int total=0;
int parsimony_increase=0;
int start_idx=curr_idx;
int stop_count=all_size-start_idx;
while (total<stop_count) {
move_type* in;
Expand Down Expand Up @@ -727,6 +726,7 @@ void place_sample_leader(std::vector<Sample_Muts> &sample_to_place,
size_t sample_start_idx,std::vector<size_t>* idx_map,
bool do_print
) {
int start_idx=curr_idx;
std::vector<MAT::Node *> deleted_nodes;
size_t node_count=main_tree.depth_first_expansion().size();
deleted_nodes.reserve(sample_to_place.size());
Expand Down Expand Up @@ -787,7 +787,7 @@ void place_sample_leader(std::vector<Sample_Muts> &sample_to_place,
if (dry_run) {
send_queue.try_push(nullptr);
}
place_sample_thread(main_tree, deleted_nodes, send_queue, found_queue,
place_sample_thread(start_idx,main_tree, deleted_nodes, send_queue, found_queue,
init, sample_to_place.size(), stop, curr_idx,
parsimony_increase_threshold,
sample_start_idx, dry_run,max_parsimony,max_uncertainty,process_count>1,printer_node,do_print);
Expand Down