From 567e316a090ea3def969b5edd2ac2ce822e21e5d Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Mon, 5 Jul 2021 15:26:48 -0400
Subject: [PATCH] revert to upstream master

---
 Makefile                   | 13 ++++---------
 include/simd_instruction.h |  2 +-
 src/simd_instruction.h     |  2 +-
 src/utils.c                | 10 +++-------
 4 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/Makefile b/Makefile
index 9fff7ba..132fb0c 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 #CC          = gcc
 EXTRA_FLAGS = -Wno-unused-function -Wno-misleading-indentation
-CFLAGS      += -Wall -O3 $(EXTRA_FLAGS)
+CFLAGS      = -Wall -O3 $(EXTRA_FLAGS)
 
 # for debug
 ifneq ($(debug),)
@@ -8,9 +8,9 @@ ifneq ($(debug),)
 endif
 # for gdb
 ifneq ($(gdb),)
-	CFLAGS   += -Wall -g ${DFLAGS} $(EXTRA_FLAGS)
+	CFLAGS   = -Wall -g ${DFLAGS} $(EXTRA_FLAGS)
 else
-	CFLAGS   += -Wall -O3 ${DFLAGS} $(EXTRA_FLAGS)
+	CFLAGS   = -Wall -O3 ${DFLAGS} $(EXTRA_FLAGS)
 endif
 
 # for gprof
@@ -62,11 +62,6 @@ else ifneq ($(avx512bw),)
 	py_SIMD_FLAG = AVX512BW=1
 endif
 
-# Let CACTUS_ARCH override this (it'll add -march to CFLAGS) in order to avoid -march native for more portable binaries
-ifneq ($(CACTUS_ARCH),)
-	SIMD_FLAG =
-endif
-
 .c.o:
 		$(CC) -c $(CFLAGS) $< -o $@
 
@@ -107,7 +102,7 @@ $(SRC_DIR)/simd_abpoa_align.o:$(SRC_DIR)/simd_abpoa_align.c $(SRC_DIR)/abpoa_gra
 
 install_py: python/cabpoa.pxd python/pyabpoa.pyx python/README.md
 	${py_SIMD_FLAG} python setup.py install
-
+	
 sdist: install_py
 	${py_SIMD_FLAG} python setup.py sdist #bdist_wheel
 
diff --git a/include/simd_instruction.h b/include/simd_instruction.h
index 8395621..202c521 100644
--- a/include/simd_instruction.h
+++ b/include/simd_instruction.h
@@ -574,7 +574,7 @@ extern "C" {
 
 int simd_check(void);
 
-static inline void *SIMDMalloc(size_t size, size_t align) {
+static void *SIMDMalloc(size_t size, size_t align) {
     void *ret = (void*)_mm_malloc(size, align);
     if (ret == NULL) {
         fprintf(stderr, "[%s] mm_Malloc fail!\nSize: %ld\n", __func__, size);
diff --git a/src/simd_instruction.h b/src/simd_instruction.h
index 8395621..202c521 100644
--- a/src/simd_instruction.h
+++ b/src/simd_instruction.h
@@ -574,7 +574,7 @@ extern "C" {
 
 int simd_check(void);
 
-static inline void *SIMDMalloc(size_t size, size_t align) {
+static void *SIMDMalloc(size_t size, size_t align) {
     void *ret = (void*)_mm_malloc(size, align);
     if (ret == NULL) {
         fprintf(stderr, "[%s] mm_Malloc fail!\nSize: %ld\n", __func__, size);
diff --git a/src/utils.c b/src/utils.c
index 83a8595..a5d7f42 100644
--- a/src/utils.c
+++ b/src/utils.c
@@ -354,9 +354,9 @@ double cputime()
 double realtime()
 {
 	struct timeval tp;
-	//struct timezone tzp;
-	gettimeofday(&tp, NULL);
-	return tp.tv_sec*1e6 + tp.tv_usec * 1e-6;
+	struct timezone tzp;
+	gettimeofday(&tp, &tzp);
+	return tp.tv_sec + tp.tv_usec * 1e-6;
 }
 
 long peakrss(void)
@@ -393,7 +393,6 @@ void print_format_time(FILE *out)
 
 int err_func_format_printf(const char *func, const char *format, ...)
 {
-#ifdef ENABLE_ABPOA_LOG
     print_format_time(stderr);
     fprintf(stderr, "[%s] ", func);
 	va_list arg;
@@ -405,7 +404,4 @@ int err_func_format_printf(const char *func, const char *format, ...)
 	va_end(arg);
 	if (done < 0) _err_fatal_simple("vfprintf(stderr)", strerror(saveErrno));
 	return done;
-#else
-        return 0;
-#endif
 }