Fix Cmake

veg · Mar 24, 2022 · 55565df · 55565df
1 parent 2ecb352
commit 55565df
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Showing 3 changed files with 27 additions and 75 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 project(TN93)
 
 #-------------------------------------------------------------------------------
@@ -33,7 +33,6 @@ add_executable(
     src/argparse_cluster.cpp
 )
 
-
 add_executable(
     seqcoverage
     src/charfreqs.cpp
@@ -87,65 +86,28 @@ add_executable(
     src/argparse_fasta_diff.cpp
 )
 
-#set(DEFAULT_COMPILE_FLAGS "-O3 -march=native -g -mveclibabi=svml -mstringop-strategy=vector_loop -Wa,-q")
-set(DEFAULT_COMPILE_FLAGS "-O3 -std=c++11 -march=native -funroll-loops -g")
+set(DEFAULT_COMPILE_OPTIONS -O3 -std=c++14 -funroll-loops )
+set(DEFAULT_LINK_OPTIONS ${DEFAULT_COMPILE_OPTIONS})
+
+add_definitions(${DEFAULT_COMPILE_OPTIONS})
 
-set(DEFAULT_LINK_FLAGS "${DEFAULT_COMPILE_FLAGS}")
+
+#add_compile_options (-O3 -std=c++14 -march=native -funroll-loops )
 
 find_package(OpenMP)
 
-if (${OPENMP_FOUND})
-	set_target_properties(
-		tn93
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-	)
-	set_target_properties(
-		tn93-cluster
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-	)
-	set_target_properties(
-		selectreads
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-	)
-	set_target_properties(
-		seqcoverage
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-	)
-	set_target_properties(
-		ShortestPathTN93
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-    )
-	set_target_properties(
-		readreduce
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
-    )
-
-	set_target_properties(
-		fasta_diff
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
-		LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS} "
-    )
-
-endif (${OPENMP_FOUND})
-
-	set_target_properties(
-		fasta_diff
-		PROPERTIES
-		COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -std=c++14 "
-   )
+if(${OPENMP_FOUND})
+   add_definitions(${OpenMP_CXX_FLAGS})
+   target_link_libraries(tn93 PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(tn93-cluster PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(selectreads PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(seqcoverage PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(readreduce PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(fasta_diff PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+   target_link_libraries(ShortestPathTN93 PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+endif(${OPENMP_FOUND})
+
+
 
 install(
     TARGETS tn93
@@ -199,10 +161,6 @@ add_custom_target(TN93SP
 )
 
 
-#add_custom_target(SEQCOVERAGE
-#  DEPENDS seqcoverage
-#)
-
 install(
     TARGETS nucfreqsfasta
 	RUNTIME DESTINATION bin

diff --git a/src/ShortestPathTN93.cpp b/src/ShortestPathTN93.cpp
@@ -86,14 +86,13 @@ void reportPathToSource (const unsigned long which_index, FILE* output, const bo
 void relaxDistanceEstimates (const unsigned long theSequence, const long firstSequenceLength, const char resolutionOption, const long min_overlap, const double step_penalty) {
     const unsigned long left_to_do           = workingNodes.length();
     double               my_distance_estimate = distanceEstimates.value (theSequence);
-    #ifdef _OPENMP
+
 
-    #if _OPENMP >= 201511 && __GNUC__ >= 9
+    #if _OPENMP >= 200805
       #pragma omp parallel for default(none) shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates, step_penalty, min_overlap, resolutionOption, firstSequenceLength, theSequence, left_to_do)
     #else
       #pragma omp parallel for default(none) shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates)
     #endif
-    #endif
 
 
     for (long remaining = 0; remaining < left_to_do; remaining ++) {

diff --git a/src/read_reducer.cpp b/src/read_reducer.cpp
@@ -58,12 +58,11 @@ void merge_current_clusters (StringBuffer& current_clusters, Vector& sequence_le
             long try_cluster = -1;
 
             #ifdef _OPENMP
-
-            #if _OPENMP >= 200805 
-              #pragma omp parallel shared(current_clusters, sequence_lengths, cluster_id, try_cluster, cluster_merge, cluster1, did_some_merges, merged_cluster_count)            
-            #else 
-              #pragma omp parallel shared(cluster_id, try_cluster, cluster_merge, cluster1, did_some_merges, merged_cluster_count)
-            #endif 
+                #if _OPENMP >= 200805
+                  #pragma omp parallel shared(current_clusters, sequence_lengths, cluster_id, try_cluster, cluster_merge, cluster1, did_some_merges, merged_cluster_count)
+                #else
+                  #pragma omp parallel shared(cluster_id, try_cluster, cluster_merge, cluster1, did_some_merges, merged_cluster_count)
+                #endif
             #endif
             {
                 #pragma omp for schedule (dynamic)
@@ -125,15 +124,11 @@ void handle_a_sequence (StringBuffer& current_sequence, StringBuffer& current_cl
     long try_cluster = -1;
 
         #ifdef _OPENMP
-          #if _OPENMP >= 201511 && __GNUC__ >= 9
-            #pragma omp parallel for default(none) shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters,min_overlap,firstSequenceLength)
-          #else
           #if _OPENMP >= 200805
-            #pragma omp parallel for default(none) shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters)
+            #pragma omp parallel for default(none) shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters, firstSequenceLength, min_overlap)
           #else 
             #pragma omp parallel for default(none) shared(currently_defined_clusters, try_cluster)
           #endif
-          #endif
         #endif
         for (long cluster_index = 0; cluster_index < currently_defined_clusters; cluster_index ++) {
             #pragma omp flush (try_cluster)