merge master

yatisht · Nov 2, 2021 · 14e1434 · 14e1434
2 parents 43d008f + 0cc02c3
commit 14e1434
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Showing 10 changed files with 440 additions and 215 deletions.
diff --git a/install/Dockerfile b/install/Dockerfile
@@ -1,11 +1,11 @@
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 ENV APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=DontWarn
 ENV DEBIAN_FRONTEND=noninteractive
 USER root
 RUN apt-get update && apt-get install -yq --no-install-recommends \
     git wget \
     ca-certificates \
-    sudo 
+    sudo python3
 WORKDIR /HOME/kentsource
 RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords
 RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSize

diff --git a/src/.DS_Store b/src/.DS_Store
diff --git a/src/matOptimize/main.cpp b/src/matOptimize/main.cpp
@@ -380,7 +380,7 @@ int main(int argc, char **argv) {
                 fprintf(stderr, "Defered %zu nodes\n",defered_nodes.size());
                 nodes_to_search=std::move(defered_nodes);
                 new_score=t.get_parsimony_score();
-                fprintf(stderr, "parsimony score after optimizing: %zu,with radius %d, second from start %ld \n\n",
+                fprintf(stderr, "parsimony score after optimizing: %zu,with radius %d, second from start %lld \n\n",
                         new_score,std::abs(radius),std::chrono::duration_cast<std::chrono::seconds>(std::chrono::steady_clock::now()-start_time).count());
                 if(!no_write_intermediate) {
                     intermediate_writing=intermediate_template;
@@ -389,7 +389,7 @@ int main(int argc, char **argv) {
                     t.save_detailed_mutations(intermediate_writing);
                     rename(intermediate_writing.c_str(), intermediate_pb_base_name.c_str());
                     last_save_time=std::chrono::steady_clock::now();
-                    fprintf(stderr, "Took %ldsecond to save intermediate protobuf\n",std::chrono::duration_cast<std::chrono::seconds>(last_save_time-save_start).count());
+                    fprintf(stderr, "Took %lldsecond to save intermediate protobuf\n",std::chrono::duration_cast<std::chrono::seconds>(last_save_time-save_start).count());
                 }
                 if (std::chrono::steady_clock::now()>=search_end_time) {
                     break;

diff --git a/src/matOptimize/optimize_tree.cpp b/src/matOptimize/optimize_tree.cpp
@@ -229,7 +229,7 @@ struct fetcher {
             }else {
                 update_rate=std::min(0.5,update_rate+0.01);
             }*/
-            fprintf(stderr, "requesting %zu nodes from %d after %zu seconds, got %d nodes \n",req_size,this_rank,request_period,recieve_count);
+            fprintf(stderr, "requesting %zu nodes from %d after %lld seconds, got %d nodes \n",req_size,this_rank,request_period,recieve_count);
             release_rate=1+recieve_count/num_threads;
             last_request_time=this_request_time;
             if (recieve_count==0) {
@@ -276,9 +276,9 @@ void optimize_tree_main_thread(std::vector<size_t> &nodes_to_search,
     tbb::flow::graph g;
     std::vector<std::string> defered_node_identifier;
     resolver_node_t resover_node(g, 1,
-                                          Conflict_Resolver(potential_crosses,
-                                                  deferred_moves,
-                                                  &defered_node_identifier));
+                                 Conflict_Resolver(potential_crosses,
+                                         deferred_moves,
+                                         &defered_node_identifier));
     std::thread move_reciever(MPI_recieve_move,std::ref(dfs_ordered_nodes),std::ref(resover_node));
     //progress bar
     searcher_node_t searcher(g,num_threads+1,move_searcher{dfs_ordered_nodes,radius,allow_drift,set_reachable(radius, t,search_all_dir)});
@@ -330,7 +330,7 @@ void optimize_tree_main_thread(std::vector<size_t> &nodes_to_search,
                );
     auto apply_end=std::chrono::steady_clock::now();
     auto elpased_time =std::chrono::duration_cast<std::chrono::seconds>(apply_end-apply_start);
-    fprintf(stderr, "apply moves took %ld seconds\n",elpased_time.count());
+    fprintf(stderr, "apply moves took %lld seconds\n",elpased_time.count());
     //recycle conflicting moves
     int init_deferred=deferred_moves.size();
     int recycled=0;
@@ -404,7 +404,7 @@ void optimize_tree_main_thread(std::vector<size_t> &nodes_to_search,
         }
     }
     fprintf(stderr, "recycled %f of conflicting moves \n",(double)recycled/(double)init_deferred);
-    fprintf(stderr, "recycling moves took %ld seconds\n",elpased_time.count());
+    fprintf(stderr, "recycling moves took %lld seconds\n",elpased_time.count());
     t.populate_ignored_range();
 }
 void optimize_tree_worker_thread(MAT::Tree &t,int radius,bool do_drift,bool search_all_dir) {
@@ -425,4 +425,4 @@ void optimize_tree_worker_thread(MAT::Tree &t,int radius,bool do_drift,bool sear
 tbb::concurrent_unordered_map<MAT::Mutation,
     tbb::concurrent_unordered_map<std::string, nuc_one_hot> *,
     Mutation_Pos_Only_Hash, Mutation_Pos_Only_Comparator>
-    mutated_positions;
+    mutated_positions;