yatisht · ognian- · Jun 28, 2022 · Jul 8, 2022 · Jul 8, 2022 · Jul 8, 2022
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 
-cmake_minimum_required (VERSION 3.8) 
+cmake_minimum_required (VERSION 3.14) 
 cmake_policy(SET CMP0069 NEW)
 project(usher)
 if(NOT CMAKE_BUILD_TYPE)
@@ -16,14 +16,28 @@ if ("${VERSION_PATCH}" MATCHES "[0-9]+")
 endif()
 message(STATUS "${usher_VERSION}")
 
+include(FetchContent)
+set(TBB_VERSION "v2022.2.0")
+FetchContent_Declare(oneTBB
+  GIT_REPOSITORY https://github.com/oneapi-src/oneTBB
+  GIT_TAG ${TBB_VERSION}
+  GIT_SHALLOW true
+  GIT_PROGRESS true
+  UPDATE_DISCONNECTED true
+  CMAKE_ARGS -DTBB_TEST:BOOL=OFF
+)
+set(TBB_TEST OFF CACHE INTERNAL "" FORCE)
+FetchContent_MakeAvailable(oneTBB)
+
 configure_file(src/version.hpp.in version.hpp)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -Wall -pipe -g -ggdb3 -Wno-unused-function  -Wno-deprecated-declarations") 
 #-DDEBUG_PARSIMONY_SCORE_CHANGE_CORRECT -fsanitize=address -DCHECK_PAR_MAIN  -DEASY_DEBUG -DSTOP_ON_ERROR  -DDETAILED_MERGER_CHECK -O0
 set(CMAKE_CXX_FLAGS_DEBUG "  -fno-eliminate-unused-debug-symbols -O0")
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-DNDEBUG -O3")
 set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 ")
-set(CMAKE_INCLUDE_CURRENT_DIR ON) 
+set(CMAKE_INCLUDE_CURRENT_DIR ON)
+set(CMAKE_EXE_LINKER_FLAGS "-Wl,--copy-dt-needed-entries")
 
 if(DEFINED Protobuf_PATH) 
     find_package(Protobuf REQUIRED HINTS ${Protobuf_PATH}) 
@@ -39,11 +53,7 @@ find_package(MPI REQUIRED)
 include_directories(SYSTEM ${MPI_INCLUDE_PATH})
 include_directories(${Protobuf_INCLUDE_DIRS})
 
-include(${TBB_DIR}/cmake/TBBBuild.cmake)
-tbb_build(TBB_ROOT ${TBB_DIR} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1)
-find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview)
-
-FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED)
+FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED CONFIG)
 
 #find_package(OpenMP REQUIRED)
 
@@ -475,47 +485,48 @@ endif()
 
 if(SAVE_PROFILE)
     if(DEBUG)
-        TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DSAVE_PROFILE=1 -DDEBUG=1)
+        TARGET_COMPILE_OPTIONS(usher PRIVATE  -DSAVE_PROFILE=1 -DDEBUG=1)
     else(DEBUG)
-        TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DSAVE_PROFILE=1)
+        TARGET_COMPILE_OPTIONS(usher PRIVATE  -DSAVE_PROFILE=1)
     endif(DEBUG)
 else(SAVE_PROFILE)
     if(DEBUG)
-        TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES -DDEBUG=1)
+        TARGET_COMPILE_OPTIONS(usher PRIVATE  -DDEBUG=1)
     else(DEBUG)
-        TARGET_COMPILE_OPTIONS(usher PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
+        TARGET_COMPILE_OPTIONS(usher PRIVATE )
     endif(DEBUG)
 endif(SAVE_PROFILE)
 #set_property(TARGET matOptimize PROPERTY INTERPROCEDURAL_OPTIMIZATION TRUE)
-TARGET_LINK_LIBRARIES(compareVCF PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(compareVCF PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
 
 
-TARGET_LINK_LIBRARIES(check_samples_place PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(matOptimize PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(usher-sampled PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
-#TARGET_LINK_LIBRARIES(output_final_protobuf PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(transpose_vcf PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(transposed_vcf_to_vcf PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(transposed_vcf_to_fa PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(transposed_vcf_print_name PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(check_samples_place PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(matOptimize PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
+target_include_directories(usher-sampled PUBLIC taskflow)
+TARGET_LINK_LIBRARIES(usher-sampled PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
+#TARGET_LINK_LIBRARIES(output_final_protobuf PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(transpose_vcf PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(transposed_vcf_to_vcf PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(transposed_vcf_to_fa PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(transposed_vcf_print_name PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
 
-TARGET_LINK_LIBRARIES(usher PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(usher PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
 target_include_directories(usher PUBLIC "${PROJECT_BINARY_DIR}")
 
-TARGET_COMPILE_OPTIONS(matUtils PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
-TARGET_LINK_LIBRARIES(matUtils PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_COMPILE_OPTIONS(matUtils PRIVATE)
+TARGET_LINK_LIBRARIES(matUtils PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
 
-TARGET_LINK_LIBRARIES(ripplesUtils PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(ripplesInit PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(ripplesUtils PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(ripplesInit PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
 
-TARGET_COMPILE_OPTIONS(ripples PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
-TARGET_LINK_LIBRARIES(ripples PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
-TARGET_LINK_LIBRARIES(ripples-fast PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_COMPILE_OPTIONS(ripples PRIVATE)
+TARGET_LINK_LIBRARIES(ripples PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(ripples-fast PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
 
 if(USHER_SERVER)
-    TARGET_COMPILE_OPTIONS(usher_server PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
-    TARGET_LINK_LIBRARIES(usher_server PRIVATE stdc++ ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
-    TARGET_LINK_LIBRARIES(usher-sampled-server PRIVATE stdc++ ${CMAKE_DL_LIBS} ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
+    TARGET_COMPILE_OPTIONS(usher_server PRIVATE)
+    TARGET_LINK_LIBRARIES(usher_server PRIVATE stdc++ ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB) # OpenMP::OpenMP_CXX)
+    TARGET_LINK_LIBRARIES(usher-sampled-server PRIVATE stdc++ ${CMAKE_DL_LIBS} ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES} ZLIB::ZLIB  ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS} ${ISAL_LIB} ) # OpenMP::OpenMP_CXX)
     install(TARGETS usher matUtils matOptimize ripples usher_server DESTINATION bin)
 else()
     install(TARGETS usher matUtils matOptimize ripples DESTINATION bin)

diff --git a/src/check_samples_place/check_samples.cpp b/src/check_samples_place/check_samples.cpp
@@ -5,7 +5,7 @@
 #include <cstdio>
 #include <string>
 #include <tbb/concurrent_unordered_set.h>
-#include <tbb/task.h>
+#include <tbb/task_group.h>
 #include <unordered_map>
 #include <unordered_set>
 #include <utility>
@@ -37,123 +37,109 @@ void ins_mut(Mutation_Set &parent_mutations,const Mutation_Annotated_Tree::Mutat
     }
 }
 //functor for getting state of all leaves
-struct insert_samples_worker:public tbb::task {
-    const Mutation_Annotated_Tree::Node *root; //starting node whose subtree need to be processed
-    Mutation_Set parent_mutations; //mutation of parent of "root" relative to the root of the entire tree
-    Original_State_t &samples; //output
-    insert_samples_worker(const Mutation_Annotated_Tree::Node *root,
+void insert_samples_worker(const Mutation_Annotated_Tree::Node *root,
                           const Mutation_Set &parent_mutations,
-                          Original_State_t &samples)
-        : root(root), parent_mutations(parent_mutations),
-          samples(samples) {}
-    tbb::task* execute() override {
-        //add mutation of "root"
-        for (const Mutation_Annotated_Tree::Mutation &m : root->mutations) {
-            if(m.is_valid()||root->is_leaf()) {
-                ins_mut(parent_mutations, m,root->is_leaf());
-            }
-        }
-        //output
-        if (root->is_leaf()) {
-            samples.insert(std::make_pair(root->node_id, parent_mutations));
-        }
-        //continuation
-        tbb::empty_task* empty=new(allocate_continuation()) tbb::empty_task();
-        //spawn a task for each children
-        empty->set_ref_count(root->children.size());
-        for (auto child : root->children) {
-            assert(child->parent==root);
-            empty->spawn(*new (empty->allocate_child())insert_samples_worker(child, parent_mutations, samples));
+                          Original_State_t &samples,
+                          tbb::task_group &tg) {
+    //add mutation of "root"
+    Mutation_Set local_parent_mutations = parent_mutations;
+    for (const Mutation_Annotated_Tree::Mutation &m : root->mutations) {
+        if(m.is_valid()||root->is_leaf()) {
+            ins_mut(local_parent_mutations, m,root->is_leaf());
         }
-        //bypass the scheduler to execute continuation task directly to fix ref count
-        // if no child spawned (otherwise it will hang)
-        return root->children.empty()?empty:nullptr;
     }
-};
+    //output
+    if (root->is_leaf()) {
+        samples.insert(std::make_pair(root->node_id, local_parent_mutations));
+    }
+    //spawn a task for each children
+    for (auto child : root->children) {
+        assert(child->parent==root);
+        tg.run([=, &samples, &tg]() {
+            insert_samples_worker(child, local_parent_mutations, samples, tg);
+        });
+    }
+}
 
 //functor for checking state of all leaves
-struct check_samples_worker:public tbb::task {
-    const Mutation_Annotated_Tree::Node *root;
-    Mutation_Set parent_mutations;
-    const Original_State_t &samples;
-    tbb::concurrent_unordered_set<size_t>& visited_samples;
-    const MAT::Tree* tree;
-    check_samples_worker(const Mutation_Annotated_Tree::Node *root,
+void check_samples_worker(const Mutation_Annotated_Tree::Node *root,
                          const Mutation_Set& parent_mutations,
                          const Original_State_t &samples,
-                         tbb::concurrent_unordered_set<size_t>& visited_samples
-    ,const MAT::Tree* tree):root(root),parent_mutations(parent_mutations),samples(samples),visited_samples(visited_samples),tree(tree) {}
-    tbb::task* execute() override {
-        tbb::empty_task* empty=new(allocate_continuation()) tbb::empty_task();
-        empty->set_ref_count(root->children.size());
-        for (const Mutation_Annotated_Tree::Mutation &m : root->mutations) {
-            if(m.is_valid()||root->is_leaf()) {
-                ins_mut(parent_mutations, m,root->is_leaf());
-            };
-        }
+                         tbb::concurrent_unordered_set<size_t>& visited_samples,
+                         const MAT::Tree* tree,
+                         tbb::task_group &tg) {
+    Mutation_Set local_parent_mutations = parent_mutations;
+    for (const Mutation_Annotated_Tree::Mutation &m : root->mutations) {
+        if(m.is_valid()||root->is_leaf()) {
+            ins_mut(local_parent_mutations, m,root->is_leaf());
+        };
+    }
 
-        if (root->is_leaf()) {
-            auto iter = samples.find(root->node_id);
-            if (iter == samples.end()) {
-                fprintf(stderr, "[ERROR] Extra Sample %s \n",
-                        tree->get_node_name(root->node_id).c_str());
-                //raise(SIGTRAP);
-            } else {
-                Mutation_Set to_check(iter->second);
-                for (auto m : parent_mutations) {
-                    auto m_iter = to_check.find(m);
-                    if (m_iter == to_check.end()) {
-                        fprintf(
-                            stderr,
-                            "[ERROR] Extra mutation to\t%c\%d\t of Sample\t%s at bfs_index %zu \n",
-                            Mutation_Annotated_Tree::get_nuc(m.get_all_major_allele()), m.get_position(),
-                            tree->get_node_name(root->node_id).c_str(),root->bfs_index);
-                        //raise(SIGTRAP);
+    if (root->is_leaf()) {
+        auto iter = samples.find(root->node_id);
+        if (iter == samples.end()) {
+            fprintf(stderr, "[ERROR] Extra Sample %s \n",
+                    tree->get_node_name(root->node_id).c_str());
+            //raise(SIGTRAP);
+        } else {
+            Mutation_Set to_check(iter->second);
+            for (auto m : local_parent_mutations) {
+                auto m_iter = to_check.find(m);
+                if (m_iter == to_check.end()) {
+                    fprintf(
+                        stderr,
+                        "[ERROR] Extra mutation to\t%c\%d\t of Sample\t%s at bfs_index %zu \n",
+                        Mutation_Annotated_Tree::get_nuc(m.get_all_major_allele()), m.get_position(),
+                        tree->get_node_name(root->node_id).c_str(),root->bfs_index);
+                    //raise(SIGTRAP);
 
-                    } else {
-                        if (!(m.get_all_major_allele()&m_iter->get_all_major_allele())) {
-                            fprintf(stderr, "Mut Nuc Mismatch at \t %d of sample \t %s at bfs_index \t %zu: original \t %d , altered :\t %d \n",m.get_position(),tree->get_node_name(root->node_id).c_str(),root->bfs_index,(int)m_iter->get_all_major_allele(),(int)m.get_all_major_allele());
-                            //raise(SIGTRAP);
-                        }
-                        to_check.erase(m_iter);
+                } else {
+                    if (!(m.get_all_major_allele()&m_iter->get_all_major_allele())) {
+                        fprintf(stderr, "Mut Nuc Mismatch at \t %d of sample \t %s at bfs_index \t %zu: original \t %d , altered :\t %d \n",m.get_position(),tree->get_node_name(root->node_id).c_str(),root->bfs_index,(int)m_iter->get_all_major_allele(),(int)m.get_all_major_allele());
+                        //raise(SIGTRAP);
                     }
+                    to_check.erase(m_iter);
                 }
+            }
 
-                for (auto m_left : to_check) {
-                    if (m_left.get_all_major_allele()&m_left.get_par_one_hot()) {
-                        continue;
-                    }
-                    fprintf(stderr,
-                            "[ERROR] Lost mutation to\t%c\t%d\t of Sample\t%s at bfs_index %zu \n",
-                            Mutation_Annotated_Tree::get_nuc(m_left.get_all_major_allele()),
-                            m_left.get_position(), tree->get_node_name(root->node_id).c_str(),root->bfs_index);
-                    //raise(SIGTRAP);
+            for (auto m_left : to_check) {
+                if (m_left.get_all_major_allele()&m_left.get_par_one_hot()) {
+                    continue;
                 }
-
-                visited_samples.insert(iter->first);
+                fprintf(stderr,
+                        "[ERROR] Lost mutation to\t%c\t%d\t of Sample\t%s at bfs_index %zu \n",
+                        Mutation_Annotated_Tree::get_nuc(m_left.get_all_major_allele()),
+                        m_left.get_position(), tree->get_node_name(root->node_id).c_str(),root->bfs_index);
+                //raise(SIGTRAP);
             }
-            return empty;
+
+            visited_samples.insert(iter->first);
         }
-        for (auto child : root->children) {
-            if (child->parent!=root) {
-                fprintf(stderr, "%lx\n", (long)child);
-                //std::raise(SIGTRAP);
-            }
-            empty->spawn(*new (empty->allocate_child())check_samples_worker(child, parent_mutations, samples,visited_samples,tree));
+        return;
+    }
+    for (auto child : root->children) {
+        if (child->parent!=root) {
+            fprintf(stderr, "%lx\n", (long)child);
+            //std::raise(SIGTRAP);
         }
-        return nullptr;
+        tg.run([=, &samples, &visited_samples, &tg]() {
+            check_samples_worker(child, local_parent_mutations, samples, visited_samples, tree, tg);
+        });
     }
-};
+}
 //top level
 void check_samples(const Mutation_Annotated_Tree::Node *root,
                    Original_State_t &samples,const MAT::Tree* tree,bool ignore_missed_samples) {
     Mutation_Set mutations;
     if (samples.empty()) {
-        tbb::task::spawn_root_and_wait(*new(tbb::task::allocate_root())
-                                       insert_samples_worker(root, mutations, samples));
+        tbb::task_group tg;
+        insert_samples_worker(root, mutations, samples, tg);
+        tg.wait();
     } else {
         tbb::concurrent_unordered_set<size_t> visited_sample;
-        tbb::task::spawn_root_and_wait(*new(tbb::task::allocate_root())check_samples_worker(root, mutations, samples,visited_sample,tree));
+        tbb::task_group tg;
+        check_samples_worker(root, mutations, samples, visited_sample, tree, tg);
+        tg.wait();
         if (!ignore_missed_samples) {
             bool have_missed=false;
             for (auto s : samples) {