trying to bring thread affinitization, various lock types, TBB fully …

…over from Bowtie2

Makefile

@@ -46,19 +46,19 @@ ifneq (,$(findstring Darwin,$(shell uname)))
 	ifneq (,$(findstring 13,$(shell uname -r)))
 		CPP = clang++
 		CC = clang
-		EXTRA_FLAGS += -stdlib=libstdc++
+		override EXTRA_FLAGS += -stdlib=libstdc++
 	endif
 	ifneq (,$(findstring 14,$(shell uname -r)))
 		CPP = clang++
 		CC = clang
-		EXTRA_FLAGS += -stdlib=libstdc++
+		override EXTRA_FLAGS += -stdlib=libstdc++
 	endif
 endif
 
 LINUX = 0
 ifneq (,$(findstring Linux,$(shell uname)))
     LINUX = 1
-    EXTRA_FLAGS += -Wl,--hash-style=both
+    override EXTRA_FLAGS += -Wl,--hash-style=both
 endif
 
 MM_DEF = 
@@ -75,21 +75,25 @@ PTHREAD_DEF =
 
 ifeq (1,$(MINGW))
 	PTHREAD_LIB = 
-	EXTRA_FLAGS += -static-libgcc -static-libstdc++
+	override EXTRA_FLAGS += -static-libgcc -static-libstdc++
 else
     PTHREAD_LIB = -lpthread
 endif
 
+ifeq (1,$(NO_SPINLOCK))
+	override EXTRA_FLAGS += -DNO_SPINLOCK
+endif
+
 ifeq (1,$(WITH_TBB))
 	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
-	EXTRA_FLAGS += -DWITH_TBB
+	override EXTRA_FLAGS += -DWITH_TBB
 else
 	LIBS = $(PTHREAD_LIB)
 endif
 
 POPCNT_CAPABILITY ?= 1
 ifeq (1, $(POPCNT_CAPABILITY))
-    EXTRA_FLAGS += -DPOPCNT_CAPABILITY
+    override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
     INC += -I third_party
 endif
 
@@ -110,12 +114,27 @@ ifeq (1,$(WITH_THREAD_PROFILING))
 	override EXTRA_FLAGS += -DPER_THREAD_TIMING=1
 endif
 
+ifeq (1,$(WITH_AFFINITY))
+	override EXTRA_FLAGS += -DWITH_AFFINITY=1
+endif
+
+ifeq (1,$(WITH_QUEUELOCK))
+	override EXTRA_FLAGS += -DWITH_QUEUELOCK=1
+endif
+
 ifeq (1,$(WITH_FINE_TIMER))
 	override EXTRA_FLAGS += -DUSE_FINE_TIMER=1
 endif
 
 OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
              edit.cpp ebwt.cpp
+
+ifeq (1,$(WITH_COHORTLOCK))
+	LIBS += -lnuma
+	override EXTRA_FLAGS += -DWITH_COHORTLOCK=1
+	OTHER_CPPS += cohort.cpp cpu_numa_info.cpp
+endif
+
 ifneq (1,$(WITH_TBB))
 	OTHER_CPPS += tinythread.cpp
 endif

SeqAn-1.1/seqan/file/file_format_cgviz.h

@@ -63,7 +63,6 @@ void _write_impl(TFile& target, Align<TSource, TSpec>& align, TStringContainer&
 	SEQAN_CHECKPOINT
 
 	typedef Align<TSource, TSpec> const TAlign;
-	typedef typename Row<TAlign>::Type TRow;
 	typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
 	typedef typename Position<TAlign>::Type TPosition;
 	TRowsPosition row_count = length(rows(align));

SeqAn-1.1/seqan/file/file_format_fasta_align.h

@@ -134,9 +134,6 @@ SEQAN_CHECKPOINT
 	TSize numRows=length(beg_end_length) / 3;
 	resize(rows(align), numRows);	//rows
 		
-	typedef Align<TSource, TSpec> TAlign;
-	typedef typename Row<TAlign>::Type TRow;
-	
 	for(TSize i=0;i<numRows;++i) {
 		TSize begin = beg_end_length[i*3];
 //		TSize end = beg_end_length[i*3+1];
@@ -249,7 +246,6 @@ void _write_impl(TFile& file, Align<TSource, TSpec>& align, TStringContainer& id
 	typedef Align<TSource, TSpec> const TAlign;
 	typedef typename Row<TAlign>::Type TRow;
 	typedef typename Position<typename Rows<TAlign>::Type>::Type TRowsPosition;
-	typedef typename Position<TAlign>::Type TPosition;
 	TRowsPosition row_count = length(rows(align));
 
 	for(TRowsPosition i=0;i<row_count;++i) {

aligner_0mm.h

@@ -58,8 +58,7 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtFw.isInMemory());
 	}
@@ -133,7 +132,6 @@ class UnpairedExactAlignerV1Factory : public AlignerFactory {
 	bool rangeMode_;
 	bool verbose_;
 	bool quiet_;
-	uint32_t seed_;
 };
 
 /**
@@ -201,8 +199,7 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtFw.isInMemory());
 	}
@@ -376,7 +373,6 @@ class PairedExactAlignerV1Factory : public AlignerFactory {
 	const bool rangeMode_;
 	const bool verbose_;
 	const bool quiet_;
-	const uint32_t seed_;
 };
 
 #endif /* ALIGNER_0MM_H_ */

aligner_1mm.h

@@ -59,8 +59,7 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtFw.isInMemory());
 		assert(ebwtBw != NULL);
@@ -170,7 +169,6 @@ class Unpaired1mmAlignerV1Factory : public AlignerFactory {
 	bool rangeMode_;
 	bool verbose_;
 	bool quiet_;
-	uint32_t seed_;
 };
 
 /**
@@ -239,8 +237,7 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtBw != NULL);
 		assert(ebwtFw.isInMemory());
@@ -488,7 +485,6 @@ class Paired1mmAlignerV1Factory : public AlignerFactory {
 	const bool rangeMode_;
 	const bool verbose_;
 	const bool quiet_;
-	const uint32_t seed_;
 };
 
 #endif /* ALIGNER_1MM_H_ */

aligner_23mm.h

@@ -60,8 +60,7 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtFw.isInMemory());
 		assert(ebwtBw != NULL);
@@ -240,7 +239,6 @@ class Unpaired23mmAlignerV1Factory : public AlignerFactory {
 	const bool rangeMode_;
 	const bool verbose_;
 	const bool quiet_;
-	uint32_t seed_;
 };
 
 /**
@@ -312,8 +310,7 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 			strandFix_(strandFix),
 			rangeMode_(rangeMode),
 			verbose_(verbose),
-			quiet_(quiet),
-			seed_(seed)
+			quiet_(quiet)
 	{
 		assert(ebwtBw != NULL);
 		assert(ebwtFw.isInMemory());
@@ -685,7 +682,6 @@ class Paired23mmAlignerV1Factory : public AlignerFactory {
 	const bool rangeMode_;
 	const bool verbose_;
 	const bool quiet_;
-	const uint32_t seed_;
 };
 
 #endif /* ALIGNER_23MM_H_ */

bitset.h

@@ -93,7 +93,7 @@ class SyncBitset {
 	 */
 	bool test(uint32_t i) {
 		bool ret;
-        GUARD_LOCK(mutex_m);
+        ThreadSafe _ts(&mutex_m);
 		ret = testUnsync(i);
 		return ret;
 	}
@@ -103,7 +103,7 @@ class SyncBitset {
 	 * it has been set.  Uses synchronization.
 	 */
 	void set(uint32_t i) {
-		GUARD_LOCK(mutex_m);
+        ThreadSafe _ts(&mutex_m);
 		while(i >= _sz) {
 			// Slow path: bitset needs to be expanded before the
 			// specified bit can be set
@@ -123,7 +123,7 @@ class SyncBitset {
 	 * synchronization.
 	 */
 	void setOver(uint32_t i) {
-		GUARD_LOCK(mutex_m);
+        ThreadSafe _ts(&mutex_m);
 		while(i >= _sz) {
 			// Slow path: bitset needs to be expanded before the
 			// specified bit can be set

ebwt_search.cpp

@@ -1138,7 +1138,7 @@ static Ebwt<String<Dna> >*    exactSearch_ebwt;
 static vector<String<Dna5> >* exactSearch_os;
 static BitPairReference*      exactSearch_refs;
 #ifdef WITH_TBB
-void exactSearchWorker::operator()() {
+void exactSearchWorker::operator()() const {
 #else
 static void exactSearchWorker(void *vp) {
 	int tid = *((int*)vp);
@@ -1218,7 +1218,7 @@ static void exactSearchWorker(void *vp) {
  * A statefulness-aware worker driver.  Uses UnpairedExactAlignerV1.
  */
 #ifdef WITH_TBB
-void exactSearchWorkerStateful::operator()() {
+void exactSearchWorkerStateful::operator()() const {
 #else
 static void exactSearchWorkerStateful(void *vp) {
 	int tid = *((int*)vp);
@@ -1402,7 +1402,7 @@ static BitPairReference*              mismatchSearch_refs;
  * A statefulness-aware worker driver.  Uses Unpaired/Paired1mmAlignerV1.
  */
 #ifdef WITH_TBB
-void mismatchSearchWorkerFullStateful::operator()() {
+void mismatchSearchWorkerFullStateful::operator()() const {
 #else
 static void mismatchSearchWorkerFullStateful(void *vp) {
 	int tid = *((int*)vp);
@@ -1487,7 +1487,7 @@ static void mismatchSearchWorkerFullStateful(void *vp) {
 	return;
 }
 #ifdef WITH_TBB
-void mismatchSearchWorkerFull::operator()(){
+void mismatchSearchWorkerFull::operator()() const {
 #else
 static void mismatchSearchWorkerFull(void *vp){
 	int tid = *((int*)vp);
@@ -1734,7 +1734,7 @@ static BitPairReference*              twoOrThreeMismatchSearch_refs;
  * A statefulness-aware worker driver.  Uses UnpairedExactAlignerV1.
  */
 #ifdef WITH_TBB
-void twoOrThreeMismatchSearchWorkerStateful::operator()(){
+void twoOrThreeMismatchSearchWorkerStateful::operator()() const {
 #else
 static void twoOrThreeMismatchSearchWorkerStateful(void *vp) {
 	int tid = *((int*)vp);
@@ -1822,7 +1822,7 @@ static void twoOrThreeMismatchSearchWorkerStateful(void *vp) {
 	return;
 }
 #ifdef WITH_TBB
-void twoOrThreeMismatchSearchWorkerFull::operator()(){
+void twoOrThreeMismatchSearchWorkerFull::operator()() const {
 #else
 static void twoOrThreeMismatchSearchWorkerFull(void *vp) {
 	int tid = *((int*)vp);
@@ -2042,7 +2042,7 @@ static int                      seededQualSearch_qualCutoff;
 static BitPairReference*        seededQualSearch_refs;
 
 #ifdef WITH_TBB
-void seededQualSearchWorkerFull::operator()(){
+void seededQualSearchWorkerFull::operator()() const {
 #else
 static void seededQualSearchWorkerFull(void *vp) {
 	int tid = *((int*)vp);
@@ -2268,7 +2268,7 @@ static void seededQualSearchWorkerFull(void *vp) {
 	WORKER_EXIT();
 }
 #ifdef WITH_TBB
-void seededQualSearchWorkerFullStateful::operator()(){
+void seededQualSearchWorkerFullStateful::operator()() const {
 #else
 static void seededQualSearchWorkerFullStateful(void *vp) {
 	int tid = *((int*)vp);

ebwt_search.h

@@ -18,7 +18,7 @@ class exactSearchWorkerStateful {
 public:
 	exactSearchWorkerStateful(const exactSearchWorkerStateful& W): tid(W.tid) {};
 	exactSearchWorkerStateful(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 };
 
 class exactSearchWorker {
@@ -27,7 +27,7 @@ class exactSearchWorker {
 public:
 	exactSearchWorker(const exactSearchWorker& W): tid(W.tid) {};
 	exactSearchWorker(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 
@@ -37,7 +37,7 @@ class mismatchSearchWorkerFull {
 public:
 	mismatchSearchWorkerFull(const mismatchSearchWorkerFull& W): tid(W.tid) {};
 	mismatchSearchWorkerFull(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 
@@ -47,7 +47,7 @@ class mismatchSearchWorkerFullStateful {
 public:
 	mismatchSearchWorkerFullStateful(const mismatchSearchWorkerFullStateful& W): tid(W.tid) {};
 	mismatchSearchWorkerFullStateful(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 class twoOrThreeMismatchSearchWorkerStateful {
@@ -56,7 +56,7 @@ class twoOrThreeMismatchSearchWorkerStateful {
 public:
 	twoOrThreeMismatchSearchWorkerStateful(const twoOrThreeMismatchSearchWorkerStateful& W): tid(W.tid) {};
 	twoOrThreeMismatchSearchWorkerStateful(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 class twoOrThreeMismatchSearchWorkerFull {
@@ -65,7 +65,7 @@ class twoOrThreeMismatchSearchWorkerFull {
 public:
 	twoOrThreeMismatchSearchWorkerFull(const twoOrThreeMismatchSearchWorkerFull& W): tid(W.tid) {};
 	twoOrThreeMismatchSearchWorkerFull(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 
@@ -75,7 +75,7 @@ class seededQualSearchWorkerFullStateful {
 public:
 	seededQualSearchWorkerFullStateful(const seededQualSearchWorkerFullStateful& W): tid(W.tid) {};
 	seededQualSearchWorkerFullStateful(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };
 class seededQualSearchWorkerFull {
@@ -84,7 +84,7 @@ class seededQualSearchWorkerFull {
 public:
 	seededQualSearchWorkerFull(const seededQualSearchWorkerFull& W): tid(W.tid) {};
 	seededQualSearchWorkerFull(int id):tid(id) {};
-	void operator()();
+	void operator()() const;
 
 };