removed paryfor dependency: with omp is faster

pangenome · Nov 25, 2020 · 4352669 · 4352669
1 parent 8bcc6de
commit 4352669
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Showing 5 changed files with 12 additions and 25 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -73,9 +73,6 @@
 [submodule "deps/dirtyzipf"]
 	path = deps/dirtyzipf
 	url = https://github.com/ekg/dirtyzipf.git
-[submodule "deps/paryfor"]
-	path = deps/paryfor
-	url = https://github.com/ekg/paryfor.git
 [submodule "deps/atomicbitvector"]
 	path = deps/atomicbitvector
 	url = https://github.com/ekg/atomicbitvector.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -298,16 +298,6 @@ ExternalProject_Add(xoshiro
 ExternalProject_Get_property(xoshiro SOURCE_DIR)
 set(xoshiro_INCLUDE "${SOURCE_DIR}")
 
-# paryfor parallel_for
-ExternalProject_Add(paryfor
-  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/paryfor"
-  UPDATE_COMMAND ""
-  INSTALL_COMMAND ""
-  BUILD_COMMAND ""
-  CONFIGURE_COMMAND "")
-ExternalProject_Get_property(paryfor SOURCE_DIR)
-set(paryfor_INCLUDE "${SOURCE_DIR}")
-
 ExternalProject_Add(atomicbitvector
         SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/atomicbitvector/include"
         UPDATE_COMMAND ""
@@ -446,8 +436,7 @@ set(odgi_DEPS
     mmmulti
     ips4o
     xoshiro
-    atomicqueue
-    paryfor)
+    atomicqueue)
 add_dependencies(odgi_objs ${odgi_DEPS})
 
 set(odgi_INCLUDES
@@ -479,7 +468,6 @@ set(odgi_INCLUDES
   "${random_distributions_INCLUDE}"
   "${dirtyzipf_INCLUDE}"
   "${xoshiro_INCLUDE}"
-  "${paryfor_INCLUDE}"
   "${atomicbitvector_INCLUDE}")
 
 set(odgi_LIBS

diff --git a/deps/paryfor b/deps/paryfor
diff --git a/src/odgi.cpp b/src/odgi.cpp
@@ -2,6 +2,7 @@
 //  graph.cpp
 //  
 
+#include <thread>
 #include "odgi.hpp"
 
 namespace odgi {
@@ -814,13 +815,14 @@ void graph_t::apply_ordering(const std::vector<handle_t>& order_in, bool compact
     std::mutex node_unavailable_mutex;
     atomicbitvector::atomic_bv_t node_unavailable(ids.size());
 
-    paryfor::parallel_for<uint64_t>(
-        0, path_metadata_v.size(), 16,
-        [&](uint64_t idx, int tid) {
+    uint64_t path_metadata_v_size = path_metadata_v.size();
+
+#pragma omp parallel for schedule(static,1) num_threads(16)
+   for (uint64_t idx = 0; idx < path_metadata_v_size; ++idx) {
             if (path_metadata_v[idx].length > 0) {
-                bool from_left_else_right = (tid % 2 == 0);
+                bool from_left_else_right = (idx & 1);
 
-                auto& p = path_metadata_v.at(idx);
+                auto& p = path_metadata_v[idx];
                 step_handle_t step = from_left_else_right ? p.first : p.last;
                 step_handle_t xxx_step = from_left_else_right ? p.last : p.first;
 
@@ -920,8 +922,9 @@ void graph_t::apply_ordering(const std::vector<handle_t>& order_in, bool compact
                     }
                 } while (true);
             }
-        });
-    *this = ordered;
+        };
+
+   *this = ordered;
 }
 
 void graph_t::apply_path_ordering(const std::vector<path_handle_t>& order) {

diff --git a/src/odgi.hpp b/src/odgi.hpp
@@ -30,7 +30,7 @@
 #include "hash_map.hpp"
 #include "node.hpp"
 
-#include "paryfor.hpp"
+#include <omp.h>
 #include "atomic_bitvector.hpp"
 #include <mutex>