Removed unused AVX code

ut80.fmindex/Makefile

@@ -37,7 +37,7 @@ BWAMEM2_PATH=./bwa-mem2
 
 CXXFLAGS=-std=c++11 -fopenmp
 CPPFLAGS=-DENABLE_PREFETCH -DBWA_OTHER_ELE=0
-INCLUDES=-I$(BWAMEM2_PATH)/src -I$(BWAMEM2_PATH)/ext/safestringlib/include 
+INCLUDES=-I$(BWAMEM2_PATH)/src -I$(BWAMEM2_PATH)/ext/safestringlib/include -I/usr/include/
 LIBS=-L$(BWAMEM2_PATH) -L$(BWAMEM2_PATH)/ext/safestringlib -lsafestring -fopenmp -lz -lbwa -ldl
 
 .PHONY:all clean depend

ut80.fmindex/bwa-mem2/Makefile

@@ -35,7 +35,7 @@ EXE=bwa-mem2
 	
 MEM_FLAGS=-DSAIS=1
 CPPFLAGS+=-DENABLE_PREFETCH -DV17=1 $(MEM_FLAGS) 
-INCLUDES=-Isrc -I./ext/safestringlib/include
+INCLUDES=-Isrc -I./ext/safestringlib/include -I/usr/include/
 LIBS=-lpthread -lm -lz -L. -lbwa -L./ext/safestringlib -lsafestring 
 OBJS=src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o \
 			src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o \

ut80.fmindex/bwa-mem2/ext/safestringlib/makefile

@@ -5,7 +5,7 @@ CXX=$(EPI_TOOLCHAIN)/bin/clang++
 IDIR = include
 MKDIR_P = mkdir -p
 CFLAGS=-I$(IDIR) -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
-LDFLAGS=-z noexecstack -z relo -z now
+#LDFLAGS=-z noexecstack -z relo -z now
 
 ODIR=obj
 OTDIR=objtest

ut80.fmindex/bwa-mem2/src/FMI_search.cpp

@@ -41,6 +41,14 @@ extern "C" {
 }
 #endif
 
+/*
+ * Compatibility MACROS
+ */
+#define _mm_malloc(size,align) malloc(size)
+#define _mm_free(addr) free(addr)
+#define __rdtsc() clock()
+#define _mm_prefetch(addr,mode) __builtin_prefetch(addr)
+
 FMI_search::FMI_search(const char *fname)
 {
     fprintf(stderr, "* Entering FMI_search\n");

ut80.fmindex/bwa-mem2/src/bwamem.cpp

@@ -32,6 +32,14 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 #include "FMI_search.h"
 #include "memcpy_bwamem.h"
 
+/*
+ * Compatibility MACROS
+ */
+#define _mm_malloc(size,align) malloc(size)
+#define _mm_free(addr) free(addr)
+#define __rdtsc() clock()
+#define _mm_prefetch(addr,mode) __builtin_prefetch(addr)
+
 //----------------
 extern uint64_t tprof[LIM_R][LIM_C];
 //----------------
@@ -1946,15 +1954,7 @@ inline void sortPairsLen(SeqPair *pairArray, int32_t count, SeqPair *tempArray,
 {
 
     int32_t i;
-#if ((!__AVX512BW__) & (__AVX2__ | __SSE2__))
     for(i = 0; i <= MAX_SEQ_LEN16; i++) hist[i] = 0;
-#else   
-    __m512i zero512 = _mm512_setzero_si512();
-    for(i = 0; i <= MAX_SEQ_LEN16; i+=16)
-    {
-        _mm512_store_si512((__m512i *)(hist + i), zero512);
-    }
-#endif
     
     for(i = 0; i < count; i++)
     {

ut80.fmindex/bwa-mem2/src/bwamem_pair.cpp

@@ -41,11 +41,12 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 #include "bandedSWA.h"
 #include "kswv.h"
 
+#define __rdtsc() clock()
+
 #ifdef USE_MALLOC_WRAPPERS
 #  include "malloc_wrap.h"
 #endif
 
-
 #define MIN_RATIO     0.8
 #define MIN_DIR_CNT   10
 #define MIN_DIR_RATIO 0.05

ut80.fmindex/bwa-mem2/src/fastmap.cpp

@@ -32,9 +32,6 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#if NUMA_ENABLED
-#include <numa.h>
-#endif
 #include <sstream>
 #include "fastmap.h"
 #include "FMI_search.h"
@@ -44,21 +41,18 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 int affy[256];
 #endif
 
+/*
+ * Compatibility MACROS
+ */
+#define _mm_malloc(size,align) malloc(size)
+#define _mm_free(addr) free(addr)
+#define __rdtsc() clock()
+
 // --------------
 extern uint64_t tprof[LIM_R][LIM_C];
 // ---------------
 
-void __cpuid(unsigned int i, unsigned int cpuid[4]) {
-#ifdef _WIN32
-    __cpuid((int *) cpuid, (int)i);
-
-#else
-    asm volatile
-        ("cpuid" : "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
-            : "0" (i), "2" (0));
-#endif
-}
-
+void __cpuid(unsigned int i, unsigned int cpuid[4]) {}
 
 int HTStatus()
 {

ut80.fmindex/bwa-mem2/src/ksort.h

@@ -75,7 +75,7 @@ typedef struct {
 	int depth;
 } ks_isort_stack_t;
 
-#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
+#define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; }
 
 #define KSORT_INIT(name, type_t, __sort_lt)								\
 	void ks_mergesort_##name(size_t n, type_t array[], type_t temp[])	\

ut80.fmindex/bwa-mem2/src/ksw.cpp

@@ -128,7 +128,7 @@ kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target,
 	// q = (qry && *qry)? *qry : ksw_qinit(2, qlen, query, m, mat); //test
 	
 	if (qry && *qry == 0) *qry = q;
-	func = q->size == 2? ksw_i16 : ksw_u8;
+	//func = q->size == 2? ksw_i16 : ksw_u8;
 	size = q->size;
 	
 	r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);
@@ -163,7 +163,7 @@ kswr_t ksw_align2_orig_bak(int qlen, uint8_t *query, int tlen, uint8_t *target,
 	q = (qry && *qry)? *qry : ksw_qinit((xtra & KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
 	
 	if (qry && *qry == 0) *qry = q;
-	func = q->size == 2? ksw_i16 : ksw_u8;
+	//func = q->size == 2? ksw_i16 : ksw_u8;
 	size = q->size;
 	// uint64_t tim = __rdtsc();
 	r = func(q, tlen, target, o_del, e_del, o_ins, e_ins, xtra);

ut80.fmindex/bwa-mem2/src/ksw.h

@@ -27,6 +27,12 @@
 
 #include <stdint.h>
 
+/*
+ * Compatibility
+ */
+#define __m128i uint64_t
+#define __rdtsc() clock()
+
 #define KSW_XBYTE  0x10000
 #define KSW_XSTOP  0x20000
 #define KSW_XSUBO  0x40000

ut80.fmindex/bwa-mem2/src/utils.h

@@ -48,24 +48,6 @@
 
 #define xassert(cond, msg) if ((cond) == 0) _err_fatal_simple_core(__func__, msg)
 
-#if defined(__GNUC__) && !defined(__clang__)
-#if defined(__i386__)
-static inline unsigned long long __rdtsc(void)
-{
-    unsigned long long int x;
-    __asm__ volatile (".byte 0x0f, 0x31" : "=A" (x));
-    return x;
-}
-#elif defined(__x86_64__)
-static inline unsigned long long __rdtsc(void)
-{
-    unsigned hi, lo;
-    __asm__ __volatile__ ("rdtsc" : "=a"(lo), "=d"(hi));
-    return ( (unsigned long long)lo)|( ((unsigned long long)hi)<<32 );
-}
-#endif
-#endif
-
 typedef struct {
 	uint64_t x, y;
 } pair64_t;

ut80.fmindex/fmi.cpp

@@ -38,6 +38,13 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 #include "bwa.h"
 #include "FMI_search.h"
 
+/*
+ * Compatibility MACROS
+ */
+#define _mm_malloc(size,align) malloc(size)
+#define _mm_free(addr) free(addr)
+#define __rdtsc() clock()
+
 #ifdef ENABLE_PARSEC_HOOKS
 #include "hooks.h"
 #endif