Changed OpenMP to be optional.

bo1929 · Feb 17, 2025 · 706611b · 706611b
1 parent 5bb7773
commit 706611b
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Showing 3 changed files with 38 additions and 11 deletions.
diff --git a/makefile b/makefile
@@ -1,17 +1,28 @@
 # compiler options
 #--------------------------------------------
 COMPILER = g++
-WLCURL=1
+WLCURL = 1
+WOPENMP = 1
+CSTATIC = 0
 
-ifeq ($(WLCURL), 0)
-	LDLIBS= -lstdc++fs -lm -lz -lstdc++
+CXXFLAGS = -std=c++17 -O3
+
+ifeq ($(CSTATIC), 0)
+	LDLIBS = -lstdc++fs -lm -lz -lstdc++
 else
-	LDLIBS= -lstdc++fs -lm -lz -lstdc++ -lcurl
+	LDLIBS = --static -lstdc++fs -lm -lz -static-libgcc -static-libstdc++
+endif
+
+ifneq ($(WLCURL), 0)
+	LDLIBS += -lcurl
 endif
 
-VARDEF= -D _WLCURL=$(WLCURL)
+ifneq ($(WOPENMP), 0)
+	LDLIBS += -lgomp
+	CXXFLAGS += -fopenmp
+endif
 
-CXXFLAGS = -std=c++17 -O3 -fopenmp
+VARDEF= -D _WLCURL=$(WLCURL) -D _WOPENMP=$(WOPENMP)
 
 INC = -Iexternal/CLI11/include/CLI \
 			-Iexternal/parallel-hashmap \
@@ -37,10 +48,10 @@ all: $(PROGRAM)
 # generic rule for compiling *.cpp -> *.o
 build/%.o: src/%.cpp
 	@mkdir -p build
-	$(COMPILER) $(WFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDLIBS) $(VARDEF) $(INC) -c src/$*.cpp -o build/$*.o
+	$(COMPILER) $(WFLAGS) $(CXXFLAGS) $(LDLIBS) $(VARDEF) $(INC) -c src/$*.cpp -o build/$*.o
 
 $(PROGRAM): $(OBJECTS)
-	$(COMPILER) $(WFLAGS) $(CXXFLAGS) $+ $(LDLIBS) $(VARDEF) $(CPPFLAGS) $(LDFLAGS) $(INC) -o $@
+	$(COMPILER) $(WFLAGS) $(CXXFLAGS) $+ $(LDLIBS) $(VARDEF) $(LDFLAGS) $(INC) -o $@
 
 clean:
 	rm -f $(PROGRAM) $(OBJECTS)

diff --git a/src/common.hpp b/src/common.hpp
@@ -31,14 +31,14 @@
 #include <vector>
 #include <zlib.h>
 #include <stdio.h>
-#if defined(_OPENMP)
+#if defined(_OPENMP) && _WOPENMP == 1
   #include "omp.h"
 #endif
-#if defined _WLCURL && _WLCURL == 1
+#if defined(_WLCURL) && _WLCURL == 1
   #include <curl/curl.h>
 #endif
 
-#define VERSION "v0.4.1"
+#define VERSION "v0.4.2"
 #define PRINT_VERSION std::cerr << "krepp version: " << VERSION << std::endl;
 
 extern uint32_t num_threads;

diff --git a/src/krepp.cpp b/src/krepp.cpp
@@ -145,8 +145,10 @@ void IndexMultiple::build_index()
 {
   record_sptr_t record = std::make_shared<Record>(tree);
   dynht_sptr_t root_dynht = std::make_shared<DynHT>(nrows, tree, record);
+#if defined(_OPENMP) && _WOPENMP == 1
   omp_set_num_threads(num_threads);
   omp_set_nested(1);
+#endif
 #pragma omp parallel
   {
 #pragma omp single
@@ -238,20 +240,28 @@ void IndexMultiple::build_for_subtree(node_sptr_t nd, dynht_sptr_t dynht)
   } else {
     assert(nd->get_nchildren() > 0);
     vec<dynht_sptr_t> children_dynht_v;
+#if defined(_OPENMP) && _WOPENMP == 1
     omp_lock_t parent_lock;
     omp_init_lock(&parent_lock);
+#endif
     for (tuint_t i = 0; i < nd->get_nchildren(); ++i) {
       children_dynht_v.emplace_back(std::make_shared<DynHT>(nrows, tree, dynht->get_record()));
 #pragma omp task untied shared(dynht)
       {
         build_for_subtree(*std::next(nd->get_children(), i), children_dynht_v[i]);
+#if defined(_OPENMP) && _WOPENMP == 1
         omp_set_lock(&parent_lock);
+#endif
         dynht->union_table(children_dynht_v[i]);
+#if defined(_OPENMP) && _WOPENMP == 1
         omp_unset_lock(&parent_lock);
+#endif
       }
     }
 #pragma omp taskwait
+#if defined(_OPENMP) && _WOPENMP == 1
     omp_destroy_lock(&parent_lock);
+#endif
 #pragma omp critical
     {
       std::cerr << "\33[2K\r" << std::flush;
@@ -278,7 +288,9 @@ void QuerySketch::seek_sequences()
 {
   strstream dreport_stream;
   header_dreport(dreport_stream);
+#if defined(_OPENMP) && _WOPENMP == 1
   omp_set_num_threads(num_threads);
+#endif
   qseq_sptr_t qs = std::make_shared<QSeq>(query);
 #pragma omp parallel shared(qs)
   {
@@ -301,7 +313,9 @@ void QueryIndex::estimate_distances()
   strstream dreport_stream;
   header_dreport(dreport_stream);
   (*output_stream) << dreport_stream.rdbuf();
+#if defined(_OPENMP) && _WOPENMP == 1
   omp_set_num_threads(num_threads);
+#endif
   qseq_sptr_t qs = std::make_shared<QSeq>(query);
 #pragma omp parallel shared(qs)
   {
@@ -348,7 +362,9 @@ void QueryIndex::place_sequences()
   strstream jplace_stream;
   begin_jplace(jplace_stream);
   (*output_stream) << jplace_stream.rdbuf();
+#if defined(_OPENMP) && _WOPENMP == 1
   omp_set_num_threads(num_threads);
+#endif
   qseq_sptr_t qs = std::make_shared<QSeq>(query);
 #pragma omp parallel shared(qs)
   {