Make SIMD tests work when building multiarch binaries

MacOS multiarch binaries compile source code for each architecture
and then join them together using 'lipo'.  This means architecture
specific code both in the actual source and configure tests need
to be compilable on both architectures.

Switch the configure tests and hts_probe_cc.sh so that they check
if a given flag is needed to compile the test code instead of
just testing to see if the flag works.  By adding #ifdef __x86_64__
guards around the test code, compilation will work on non-x86_64
returning the result that no special compiler flag is needed.
Similar #ifdef guards are added to the source files so that the
SIMD-specific code only gets compiled for x86_64.  The
htscodecs submodule is updated to pull in these source file
changes.

The SIMD parts of built-in htscodecs are now compiled
unconditionally.  Tests for NEON have also been removed as they
weren't really doing anything.

The configure and hts_probe_cc.sh are adjusted to exactly match
those used by htscodecs' configure, for ease of maintenance.

Makefile

@@ -126,10 +126,18 @@ srcdir = .
 srcprefix =
 HTSPREFIX =
 
+# Flags for SIMD code
 HTS_CFLAGS_AVX2 =
 HTS_CFLAGS_AVX512 =
 HTS_CFLAGS_SSE4 =
 
+# Control building of SIMD code.  Not used if configure has been run.
+HTS_BUILD_AVX2 =
+HTS_BUILD_AVX512 =
+HTS_BUILD_SSSE3 =
+HTS_BUILD_POPCNT =
+HTS_BUILD_SSE4_1 =
+
 include htslib_vars.mk
 include htscodecs.mk
 
@@ -274,18 +282,20 @@ config.h:
 	echo '#endif' >> $@
 	echo '#define HAVE_DRAND48 1' >> $@
 	echo '#define HAVE_LIBCURL 1' >> $@
-	if [ "x$(HTS_CFLAGS_SSE4)" != "x" ] ; then \
+	if [ "x$(HTS_BUILD_POPCNT)" != "x" ] && \
+	   [ "x$(HTS_BUILD_SSE4_1)" != "x" ] && \
+	   [ "x$(HTS_BUILD_SSSE3)" != "x" ]; then \
 	    echo '#define HAVE_POPCNT 1' >> $@ ; \
 	    echo '#define HAVE_SSE4_1 1' >> $@ ; \
 	    echo '#define HAVE_SSSE3 1' >> $@ ; \
 	    echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> $@ ; \
 	    echo '#define UBSAN 1' >> $@ ; \
 	    echo '#endif' >> $@ ; \
 	fi
-	if [ "x$(HTS_CFLAGS_AVX2)" != "x" ] ; then \
+	if [ "x$(HTS_BUILD_AVX2)" != "x" ] ; then \
 	    echo '#define HAVE_AVX2 1' >> $@ ; \
 	fi
-	if [ "x$(HTS_CFLAGS_AVX512)" != "x" ] ; then \
+	if [ "x$(HTS_BUILD_AVX512)" != "x" ] ; then \
 	    echo '#define HAVE_AVX512 1' >> $@ ; \
 	fi
 

configure.ac

@@ -30,7 +30,7 @@ AC_CONFIG_SRCDIR(hts.c)
 AC_CONFIG_HEADERS(config.h)
 
 m4_include([m4/hts_prog_cc_warnings.m4])
-m4_include([m4/ax_check_compile_flag.m4])
+m4_include([m4/hts_check_compile_flags_needed.m4])
 m4_include([m4/hts_hide_dynamic_syms.m4])
 m4_include([m4/pkg.m4])
 
@@ -71,16 +71,53 @@ dnl later as they can interfere with some of the tests (notably AC_SEARCH_LIBS)
 HTS_PROG_CC_WERROR(hts_late_cflags)
 
 dnl Check for various compiler flags to enable SIMD features
-dnl Options for rANS32x16 sse4.1 version
-AX_CHECK_COMPILE_FLAG([-mssse3 -mpopcnt -msse4.1], [
-  hts_cflags_sse4="-mssse3 -mpopcnt -msse4.1"
-  AC_SUBST([hts_cflags_sse4])
-  AC_DEFINE([HAVE_SSSE3],1,
-            [Defined to 1 if the compiler can issue SSSE3 instructions.])
-  AC_DEFINE([HAVE_POPCNT],1,
-            [Defined to 1 if the compiler can issue popcnt instructions.])
-  AC_DEFINE([HAVE_SSE4_1],1,
-            [Defined to 1 if the compiler can issue SSE4.1 instructions.])
+dnl Options for rANS32x16 sse4.1 version - ssse3
+hts_cflags_sse4=""
+HTS_CHECK_COMPILE_FLAGS_NEEDED([ssse3], [-mssse3], [AC_LANG_PROGRAM([[
+    #ifdef __x86_64__
+    #include "x86intrin.h"
+    #endif
+  ]],[[
+    #ifdef __x86_64__
+    __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1);
+    __m128i c = _mm_shuffle_epi8(a, b);
+    return *((char *) &c);
+    #endif
+  ]])], [
+  hts_cflags_sse4="$flags_needed $hts_cflags_sse4"
+  AC_DEFINE([HAVE_SSSE3],1,[Defined to 1 if rANS source using SSSE3 can be compiled.])
+])
+
+dnl Options for rANS32x16 sse4.1 version - popcnt
+HTS_CHECK_COMPILE_FLAGS_NEEDED([popcnt], [-mpopcnt], [AC_LANG_PROGRAM([[
+    #ifdef __x86_64__
+    #include "x86intrin.h"
+    #endif
+  ]],[[
+    #ifdef __x86_64__
+    unsigned int i = _mm_popcnt_u32(1);
+    return i != 1;
+    #endif
+  ]])], [
+  hts_cflags_sse4="$flags_needed $hts_cflags_sse4"
+  AC_DEFINE([HAVE_POPCNT],1,[Defined to 1 if rANS source using popcnt can be compiled.])
+])
+
+dnl Options for rANS32x16 sse4.1 version - sse4.1
+HTS_CHECK_COMPILE_FLAGS_NEEDED([sse4.1], [-msse4.1], [AC_LANG_PROGRAM([[
+    #ifdef __x86_64__
+    #include "x86intrin.h"
+    #endif
+  ]],[[
+    #ifdef __x86_64__
+    __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1);
+    __m128i c = _mm_max_epu32(a, b);
+    return *((char *) &c);
+    #endif
+  ]])], [
+  hts_cflags_sse4="$flags_needed $hts_cflags_sse4"
+  AC_DEFINE([HAVE_SSE4_1],1,[Defined to 1 if rANS source using SSE4.1 can be compiled.
+])
 dnl Propagate HTSlib's unaligned access preference to htscodecs
   AH_VERBATIM([UBSAN],[
 /* Prevent unaligned access in htscodecs SSE4 rANS codec */
@@ -89,60 +126,43 @@ dnl Propagate HTSlib's unaligned access preference to htscodecs
 #endif
   ])
   AC_DEFINE([UBSAN],1,[])
-  ], [], [], [AC_LANG_PROGRAM([[
-    #include "x86intrin.h"
-  ]],[[
-    unsigned int i = _mm_popcnt_u32(1);
-    __m128i a = _mm_set_epi32(1, 2, 3, i), b = _mm_set_epi32(4, 3, 2, 1);
-    __m128i c = _mm_max_epu32(a, b);
-    b = _mm_shuffle_epi8(a, c);
-    return *((char *) &b);
-  ]])])
+])
+AC_SUBST([hts_cflags_sse4])
 
 dnl Options for rANS32x16 avx2 version
-AX_CHECK_COMPILE_FLAG([-mavx2], [
-  hts_cflags_avx2="-mavx2"
-  AC_SUBST([hts_cflags_avx2])
-  AC_DEFINE([HAVE_AVX2],1,
-            [Defined to 1 if the compiler can issue AVX2 instructions.])
-  ], [], [], [AC_LANG_PROGRAM([[
-  #include "x86intrin.h"
+HTS_CHECK_COMPILE_FLAGS_NEEDED([avx2], [-mavx2], [AC_LANG_PROGRAM([[
+    #ifdef __x86_64__
+    #include "x86intrin.h"
+    #endif
   ]],[[
+    #ifdef __x86_64__
     __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8);
     __m256i b = _mm256_add_epi32(a, a);
     long long c = _mm256_extract_epi64(b, 0);
     return (int) c;
-  ]])])
+    #endif
+  ]])], [
+  hts_cflags_avx2="$flags_needed"
+  AC_SUBST([hts_cflags_avx2])
+  AC_DEFINE([HAVE_AVX2],1,[Defined to 1 if rANS source using AVX2 can be compiled.])
+])
 
 dnl Options for rANS32x16 avx512 version
-AX_CHECK_COMPILE_FLAG([-mavx512f], [
-  hts_cflags_avx512="-mavx512f"
-  AC_SUBST([hts_cflags_avx512])
-  AC_DEFINE([HAVE_AVX512],1,
-            [Defined to 1 if the compiler can issue AVX512 instructions.])
-  ], [], [], [AC_LANG_PROGRAM([[
+HTS_CHECK_COMPILE_FLAGS_NEEDED([avx512f], [-mavx512f], [AC_LANG_PROGRAM([[
+    #ifdef __x86_64__
     #include "x86intrin.h"
+    #endif
   ]],[[
+    #ifdef __x86_64__
     __m512i a = _mm512_set1_epi32(1);
     __m512i b = _mm512_add_epi32(a, a);
     return *((char *) &b);
-  ]])])
-
-dnl Detect ARM Neon availability
-AC_CACHE_CHECK([whether C compiler supports ARM Neon], [hts_cv_have_neon], [
-  AC_COMPILE_IFELSE([
-    AC_LANG_PROGRAM([[
-      #include "arm_neon.h"
-    ]], [[
-      int32x4_t a = vdupq_n_s32(1);
-      int32x4_t b = vaddq_s32(a, a);
-      return *((char *) &b);
-    ]])], [hts_cv_have_neon=yes], [hts_cv_have_neon=no])])
-if test "$hts_cv_have_neon" = yes; then
-  hts_have_neon=yes
-  AC_SUBST([hts_have_neon])
-fi
-
+    #endif
+  ]])], [
+  hts_cflags_avx512="$flags_needed"
+  AC_SUBST([hts_cflags_avx512])
+  AC_DEFINE([HAVE_AVX512],1,[Defined to 1 if rANS source using AVX512F can be compiled.])
+])
 
 dnl Avoid chicken-and-egg problem where pkg-config supplies the
 dnl PKG_PROG_PKG_CONFIG macro, but we want to use it to check

hts_probe_cc.sh

@@ -43,72 +43,101 @@ run_compiler ()
     return $retval
 }
 
+# Run a test.  $1 is the flag to try, $2 is the Makefile variable to set
+# with the flag probe result, $3 is a Makefile variable which will be
+# set to 1 if the code was built successfully.  The code to test should
+# be passed in via fd 0.
+# First try compiling conftest.c without the flag.  If that fails, try
+# again with it to see if the flag is needed.
+run_test ()
+{
+    rm -f conftest conftest.err conftest.c
+    cat - > conftest.c
+    if run_compiler ; then
+        echo "$2 ="
+        echo "$3 = 1"
+    elif run_compiler "$1" ; then
+        echo "$2 = $1"
+        echo "$3 = 1"
+    else
+        echo "$3 ="
+    fi
+}
+
 echo "# Compiler probe results, generated by $0"
 
-# Check for sse4.1 etc. support
+# Check for ssse3
+run_test "-mssse3" HTS_CFLAGS_SSSE3 HTS_BUILD_SSSE3 <<'EOF'
+#ifdef __x86_64__
+#include "x86intrin.h"
+int main(int argc, char **argv) {
+    __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1);
+    __m128i c = _mm_shuffle_epi8(a, b);
+    return *((char *) &c);
+}
+#else
+int main(int argc, char **argv) { return 0; }
+#endif
+EOF
 
-rm -f conftest conftest.err conftest.c
-cat - <<'EOF' > conftest.c
+# Check for popcnt
+run_test "-mpopcnt" HTS_CFLAGS_POPCNT HTS_BUILD_POPCNT <<'EOF'
+#ifdef __x86_64__
 #include "x86intrin.h"
 int main(int argc, char **argv) {
     unsigned int i = _mm_popcnt_u32(1);
-    __m128i a = _mm_set_epi32(1, 2, 3, i), b = _mm_set_epi32(4, 3, 2, 1);
+    return i != 1;
+}
+#else
+int main(int argc, char **argv) { return 0; }
+#endif
+EOF
+
+# Check for sse4.1 etc. support
+run_test "-msse4.1" HTS_CFLAGS_SSE4_1 HTS_BUILD_SSE4_1 <<'EOF'
+#ifdef __x86_64__
+#include "x86intrin.h"
+int main(int argc, char **argv) {
+    __m128i a = _mm_set_epi32(1, 2, 3, 4), b = _mm_set_epi32(4, 3, 2, 1);
     __m128i c = _mm_max_epu32(a, b);
-    b = _mm_shuffle_epi8(a, c);
-    return *((char *) &b);
+    return *((char *) &c);
 }
+#else
+int main(int argc, char **argv) { return 0; }
+#endif
 EOF
-FLAGS="-mpopcnt -msse4.1 -mssse3"
-if run_compiler "$FLAGS" ; then
-    echo "HTS_CFLAGS_SSE4 = $FLAGS"
-fi
+
+echo 'HTS_CFLAGS_SSE4 = $(HTS_CFLAGS_SSSE3) $(HTS_CFLAGS_POPCNT) $(HTS_CFLAGS_SSE4_1)'
 
 # Check for avx2
 
-rm -f conftest.c
-cat - <<'EOF' > conftest.c
+run_test -mavx2 HTS_CFLAGS_AVX2 HTS_BUILD_AVX2 <<'EOF'
+#ifdef __x86_64__
 #include "x86intrin.h"
 int main(int argc, char **argv) {
     __m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8);
     __m256i b = _mm256_add_epi32(a, a);
     long long c = _mm256_extract_epi64(b, 0);
     return (int) c;
 }
+#else
+int main(int argc, char **argv) { return 0; }
+#endif
 EOF
-FLAGS="-mavx2"
-if run_compiler "$FLAGS" ; then
-    echo "HTS_CFLAGS_AVX2 = $FLAGS"
-fi
 
 # Check for avx512
 
-rm -f conftest.c
-cat - <<'EOF' > conftest.c
+run_test -mavx512f HTS_CFLAGS_AVX512 HTS_BUILD_AVX512 <<'EOF'
+#ifdef __x86_64__
 #include "x86intrin.h"
 int main(int argc, char **argv) {
     __m512i a = _mm512_set1_epi32(1);
     __m512i b = _mm512_add_epi32(a, a);
     return *((char *) &b);
 }
+#else
+int main(int argc, char **argv) { return 0; }
+#endif
 EOF
-FLAGS="-mavx512f"
-if run_compiler "$FLAGS" ; then
-    echo "HTS_CFLAGS_AVX512 = $FLAGS"
-fi
-
-# Check for neon
-
-rm -f conftest.c
-cat - <<'EOF' > conftest.c
-#include "arm_neon.h"
-int main(int argc, char **argv) {
-    int32x4_t a = vdupq_n_s32(1);
-    int32x4_t b = vaddq_s32(a, a);
-    return *((char *) &b);
-}
-EOF
-if run_compiler "" ; then
-    echo "HTS_HAVE_NEON = yes"
-fi
 
 rm -f conftest.c

htscodecs_bundled.mk

@@ -28,10 +28,10 @@ HTSCODECS_SOURCES = $(HTSPREFIX)htscodecs/htscodecs/arith_dynamic.c \
         $(HTSPREFIX)htscodecs/htscodecs/htscodecs.c \
         $(HTSPREFIX)htscodecs/htscodecs/pack.c \
         $(HTSPREFIX)htscodecs/htscodecs/rANS_static4x16pr.c \
-	$(if $(HTS_CFLAGS_AVX2),$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx2.c) \
-	$(if $(HTS_CFLAGS_AVX512),$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx512.c) \
-	$(if $(HTS_CFLAGS_SSE4),$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_sse4.c) \
-	$(if $(HTS_HAVE_NEON),$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_neon.c) \
+	$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx2.c \
+	$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_avx512.c \
+	$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_sse4.c \
+	$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr_neon.c \
 	$(HTSPREFIX)htscodecs/htscodecs/rANS_static32x16pr.c \
         $(HTSPREFIX)htscodecs/htscodecs/rANS_static.c \
         $(HTSPREFIX)htscodecs/htscodecs/rle.c \