enables concurrency in psufsort

EvolBioInf · Feb 11, 2015 · 0c98b73 · 0c98b73
1 parent 0cbd62f
commit 0c98b73
Show file tree

Hide file tree

Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/opt/psufsort/Makefile.am b/opt/psufsort/Makefile.am
@@ -1,2 +1,4 @@
 noinst_LIBRARIES = libpsufsort.a
-libpsufsort_a_SOURCES = psufsort.cxx
+libpsufsort_a_SOURCES = psufsort.cxx ../src/global.h
+libpsufsort_a_CXXFLAGS = $(OPENMP_CXXFLAGS) -W -Wall
+libpsufsort_a_CPPFLAGS = $(OPENMP_CXXFLAGS) -I$(top_srcdir)/src
diff --git a/opt/psufsort/psufsort.cxx b/opt/psufsort/psufsort.cxx
@@ -5,8 +5,8 @@
 #include <algorithm>
 #include <iostream>
 #include <cassert>
-//#include <flags.h>
 #include <cmath>
+#include <global.h>
 
 void mk_sort (std::vector<int>& SA, const std::string& T, size_t l, size_t r, size_t depth);
 void insertion_sort (std::vector<int>& SA, const std::string& T, size_t l, size_t r, size_t depth);
@@ -124,7 +124,7 @@ std::vector<int> psufsort(const std::string& T){
 	}
 
 	// sort all S* suffixes
-	//#pragma omp parallel for shared(SA,T) schedule(dynamic, 1) num_threads(THREADS)
+	#pragma omp parallel for shared(SA,T) schedule(dynamic, 1) num_threads( (FLAGS & F_LOW_MEMORY) ? THREADS : 1)
 	for(i=0; i<256*256; i++){
 		const auto buc = bucket_SS[i];
 		if( buc.size > 1){

diff --git a/test/Makefile.am b/test/Makefile.am
@@ -11,8 +11,8 @@ test_seq_CXXFLAGS = -W -Wall $(GLIB_CFLAGS)
 test_seq_LDADD = $(GLIB_LIBS)
 
 test_esa_SOURCES = test_esa.cxx ../src/esa.cpp ../src/sequence.cpp $(top_srcdir)/src/esa.h
-test_esa_CPPFLAGS = -I$(top_srcdir)/libs -I$(top_srcdir)/libs/RMQ -I$(top_srcdir)/src -DDEBUG
-test_esa_CXXFLAGS = -W -Wall $(GLIB_CFLAGS)
+test_esa_CPPFLAGS = $(OPENMP_CXXFLAGS) -I$(top_srcdir)/libs -I$(top_srcdir)/libs/RMQ -I$(top_srcdir)/src -DDEBUG
+test_esa_CXXFLAGS = $(OPENMP_CXXFLAGS) -W -Wall $(GLIB_CFLAGS)
 test_esa_LDADD = $(top_builddir)/libs/RMQ/libRMQ_improved.a $(GLIB_LIBS) $(PSUFSORT)
 
 test_fasta_SOURCES = test_fasta.cxx

diff --git a/test/test_esa.cxx b/test/test_esa.cxx
@@ -5,6 +5,7 @@
 #include <string.h>
 
 int FLAGS = F_NONE;
+int THREADS = 1;
 
 extern const int CACHE_LENGTH;