@@ -92,8 +92,13 @@ DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \

 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4

 am__aclocal_m4_deps = $(top_srcdir)/config/acx_mmap_fixed.m4 \

 	$(top_srcdir)/config/acx_mmap_variable.m4 \

-	$(top_srcdir)/config/expand.m4 $(top_srcdir)/config/fopen.m4 \

-	$(top_srcdir)/config/libtool.m4 \

+	$(top_srcdir)/config/asm-bsr.m4 \

+	$(top_srcdir)/config/ax_check_compile_flag.m4 \

+	$(top_srcdir)/config/ax_ext.m4 \

+	$(top_srcdir)/config/ax_gcc_x86_avx_xgetbv.m4 \

+	$(top_srcdir)/config/ax_gcc_x86_cpuid.m4 \

+	$(top_srcdir)/config/builtin.m4 $(top_srcdir)/config/expand.m4 \

+	$(top_srcdir)/config/fopen.m4 $(top_srcdir)/config/libtool.m4 \

 	$(top_srcdir)/config/ltoptions.m4 \

 	$(top_srcdir)/config/ltsugar.m4 \

 	$(top_srcdir)/config/ltversion.m4 \

@@ -101,6 +106,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/acx_mmap_fixed.m4 \

 	$(top_srcdir)/config/madvise-flags.m4 \

 	$(top_srcdir)/config/mmap-flags.m4 \

 	$(top_srcdir)/config/pagesize.m4 $(top_srcdir)/config/perl.m4 \

+	$(top_srcdir)/config/sse2_shift_defect.m4 \

 	$(top_srcdir)/config/struct-stat64.m4 \

 	$(top_srcdir)/configure.ac

 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \

@@ -287,6 +293,7 @@ SAMTOOLS_LIBS = @SAMTOOLS_LIBS@

 SED = @SED@

 SET_MAKE = @SET_MAKE@

 SHELL = @SHELL@

+SIMD_FLAGS = @SIMD_FLAGS@

 STATIC_LDFLAG = @STATIC_LDFLAG@

 STRIP = @STRIP@

 UNIQSCAN = @UNIQSCAN@

@@ -1185,6 +1185,12 @@ AC_SUBST([am__untar])

 m4_include([config/acx_mmap_fixed.m4])

 m4_include([config/acx_mmap_variable.m4])

+m4_include([config/asm-bsr.m4])

+m4_include([config/ax_check_compile_flag.m4])

+m4_include([config/ax_ext.m4])

+m4_include([config/ax_gcc_x86_avx_xgetbv.m4])

+m4_include([config/ax_gcc_x86_cpuid.m4])

+m4_include([config/builtin.m4])

 m4_include([config/expand.m4])

 m4_include([config/fopen.m4])

 m4_include([config/libtool.m4])

@@ -1196,4 +1202,5 @@ m4_include([config/madvise-flags.m4])

 m4_include([config/mmap-flags.m4])

 m4_include([config/pagesize.m4])

 m4_include([config/perl.m4])

+m4_include([config/sse2_shift_defect.m4])

 m4_include([config/struct-stat64.m4])

new file mode 100644

@@ -0,0 +1,16 @@

+

+AC_DEFUN([ACX_ASM_BSR], [

+AC_LANG_SAVE

+AC_LANG(C)

+

+AC_MSG_CHECKING(for bsr instruction in assembly)

+AC_COMPILE_IFELSE(

+  [AC_LANG_PROGRAM([[ ]],

+                   [[int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));]])],

+  [AC_MSG_RESULT(yes)

+   AC_DEFINE([HAVE_ASM_BSR],[1],[Define to 1 if bsr command is available in assembly])],

+  [AC_MSG_RESULT(no)])

+

+AC_LANG_RESTORE

+])

+

new file mode 100644

@@ -0,0 +1,72 @@

+# ===========================================================================

+#   http://www.gnu.org/software/autoconf-archive/ax_check_compile_flag.html

+# ===========================================================================

+#

+# SYNOPSIS

+#

+#   AX_CHECK_COMPILE_FLAG(FLAG, [ACTION-SUCCESS], [ACTION-FAILURE], [EXTRA-FLAGS])

+#

+# DESCRIPTION

+#

+#   Check whether the given FLAG works with the current language's compiler

+#   or gives an error.  (Warnings, however, are ignored)

+#

+#   ACTION-SUCCESS/ACTION-FAILURE are shell commands to execute on

+#   success/failure.

+#

+#   If EXTRA-FLAGS is defined, it is added to the current language's default

+#   flags (e.g. CFLAGS) when the check is done.  The check is thus made with

+#   the flags: "CFLAGS EXTRA-FLAGS FLAG".  This can for example be used to

+#   force the compiler to issue an error when a bad flag is given.

+#

+#   NOTE: Implementation based on AX_CFLAGS_GCC_OPTION. Please keep this

+#   macro in sync with AX_CHECK_{PREPROC,LINK}_FLAG.

+#

+# LICENSE

+#

+#   Copyright (c) 2008 Guido U. Draheim <guidod@gmx.de>

+#   Copyright (c) 2011 Maarten Bosmans <mkbosmans@gmail.com>

+#

+#   This program is free software: you can redistribute it and/or modify it

+#   under the terms of the GNU General Public License as published by the

+#   Free Software Foundation, either version 3 of the License, or (at your

+#   option) any later version.

+#

+#   This program is distributed in the hope that it will be useful, but

+#   WITHOUT ANY WARRANTY; without even the implied warranty of

+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General

+#   Public License for more details.

+#

+#   You should have received a copy of the GNU General Public License along

+#   with this program. If not, see <http://www.gnu.org/licenses/>.

+#

+#   As a special exception, the respective Autoconf Macro's copyright owner

+#   gives unlimited permission to copy, distribute and modify the configure

+#   scripts that are the output of Autoconf when processing the Macro. You

+#   need not follow the terms of the GNU General Public License when using

+#   or distributing such scripts, even though portions of the text of the

+#   Macro appear in them. The GNU General Public License (GPL) does govern

+#   all other use of the material that constitutes the Autoconf Macro.

+#

+#   This special exception to the GPL applies to versions of the Autoconf

+#   Macro released by the Autoconf Archive. When you make and distribute a

+#   modified version of the Autoconf Macro, you may extend this special

+#   exception to the GPL to apply to your modified version as well.

+

+#serial 2

+

+AC_DEFUN([AX_CHECK_COMPILE_FLAG],

+[AC_PREREQ(2.59)dnl for _AC_LANG_PREFIX

+AS_VAR_PUSHDEF([CACHEVAR],[ax_cv_check_[]_AC_LANG_ABBREV[]flags_$4_$1])dnl

+AC_CACHE_CHECK([whether _AC_LANG compiler accepts $1], CACHEVAR, [

+  ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS

+  _AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $4 $1"

+  AC_COMPILE_IFELSE([AC_LANG_PROGRAM()],

+    [AS_VAR_SET(CACHEVAR,[yes])],

+    [AS_VAR_SET(CACHEVAR,[no])])

+  _AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags])

+AS_IF([test x"AS_VAR_GET(CACHEVAR)" = xyes],

+  [m4_default([$2], :)],

+  [m4_default([$3], :)])

+AS_VAR_POPDEF([CACHEVAR])dnl

+])dnl AX_CHECK_COMPILE_FLAGS

new file mode 100644

@@ -0,0 +1,346 @@

+# ===========================================================================

+#          http://www.gnu.org/software/autoconf-archive/ax_ext.html

+# ===========================================================================

+#

+# SYNOPSIS

+#

+#   AX_EXT

+#

+# DESCRIPTION

+#

+#   Find supported SIMD extensions by requesting cpuid. When an SIMD

+#   extension is found, the -m"simdextensionname" is added to SIMD_FLAGS if

+#   compiler supports it. For example, if "sse2" is available, then "-msse2"

+#   is added to SIMD_FLAGS.

+#

+#   This macro calls:

+#

+#     AC_SUBST(SIMD_FLAGS)

+#

+#   And defines:

+#

+#     HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4.1 / HAVE_SSE4.2 / HAVE_AVX

+#

+# LICENSE

+#

+#   Copyright (c) 2007 Christophe Tournayre <turn3r@users.sourceforge.net>

+#   Copyright (c) 2013 Michael Petch <mpetch@capp-sysware.com>

+#

+#   Copying and distribution of this file, with or without modification, are

+#   permitted in any medium without royalty provided the copyright notice

+#   and this notice are preserved. This file is offered as-is, without any

+#   warranty.

+

+#serial 13

+

+AC_DEFUN([AX_EXT],

+[

+  AC_REQUIRE([AC_CANONICAL_HOST])

+

+  case $host_cpu in

+    powerpc*)

+      AC_CACHE_CHECK([whether altivec is enabled and supported], [ax_cv_have_altivec_ext],

+          [

+            if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then

+                if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then

+                  ax_cv_have_altivec_ext=yes

+                fi

+            fi

+          ])

+

+          if test "$ax_cv_have_altivec_ext" = yes; then

+            AC_DEFINE(HAVE_ALTIVEC,1,[Define to 1 if you support Altivec instructions])

+            AX_CHECK_COMPILE_FLAG(-faltivec, SIMD_FLAGS="$SIMD_FLAGS -faltivec", [])

+          fi

+    ;;

+

+

+    i[[3456]]86*|x86_64*|amd64*)

+

+      AC_REQUIRE([AX_GCC_X86_CPUID])

+      AC_REQUIRE([AX_GCC_X86_AVX_XGETBV])

+

+      AX_GCC_X86_CPUID(0x00000001)

+      ecx=0

+      edx=0

+      if test "$ax_cv_gcc_x86_cpuid_0x00000001" != "unknown";

+      then

+        ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 3`

+        edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`

+      fi

+

+      AC_CACHE_CHECK([whether mmx is enabled and supported], [ax_cv_have_mmx_ext],

+      [

+        ax_cv_have_mmx_ext=no

+        if test "$((0x$edx>>23&0x01))" = 1; then

+          ax_cv_have_mmx_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether sse is enabled and supported], [ax_cv_have_sse_ext],

+      [

+        ax_cv_have_sse_ext=no

+        if test "$((0x$edx>>25&0x01))" = 1; then

+          ax_cv_have_sse_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether sse2 is enabled and supported], [ax_cv_have_sse2_ext],

+      [

+        ax_cv_have_sse2_ext=no

+        if test "$ax_cv_want_sse2_ext" = yes; then

+          if test "$((0x$edx>>26&0x01))" = 1; then

+            ax_cv_have_sse2_ext=yes

+          fi

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether sse3 is enabled and supported], [ax_cv_have_sse3_ext],

+      [

+        ax_cv_have_sse3_ext=no

+        if test "$((0x$ecx&0x01))" = 1; then

+          ax_cv_have_sse3_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether ssse3 is enabled and supported], [ax_cv_have_ssse3_ext],

+      [

+        ax_cv_have_ssse3_ext=no

+        if test "$((0x$ecx>>9&0x01))" = 1; then

+          ax_cv_have_ssse3_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether sse4.1 is enabled and supported], [ax_cv_have_sse41_ext],

+      [

+        ax_cv_have_sse41_ext=no

+        if test "$ax_cv_want_sse41_ext" = yes; then

+          if test "$((0x$ecx>>19&0x01))" = 1; then

+            ax_cv_have_sse41_ext=yes

+          fi

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether sse4.2 is enabled and supported], [ax_cv_have_sse42_ext],

+      [

+        ax_cv_have_sse42_ext=no

+        if test "$((0x$ecx>>20&0x01))" = 1; then

+          ax_cv_have_sse42_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether avx is enabled and supported by processor], [ax_cv_have_avx_cpu_ext],

+      [

+        ax_cv_have_avx_cpu_ext=no

+        if test "$((0x$ecx>>28&0x01))" = 1; then

+          ax_cv_have_avx_cpu_ext=yes

+        fi

+      ])

+

+      if test x"$ax_cv_have_avx_cpu_ext" = x"yes"; then

+        AX_GCC_X86_AVX_XGETBV(0x00000000)

+

+        xgetbv_eax="0"

+        if test x"$ax_cv_gcc_x86_avx_xgetbv_0x00000000" != x"unknown"; then

+          xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`

+        fi

+

+        AC_CACHE_CHECK([whether avx is supported by operating system], [ax_cv_have_avx_ext],

+        [

+          ax_cv_have_avx_ext=no

+

+          if test "$((0x$ecx>>27&0x01))" = 1; then

+            if test "$((0x$xgetbv_eax&0x6))" = 6; then

+              ax_cv_have_avx_ext=yes

+            fi

+          fi

+        ])

+        if test x"$ax_cv_have_avx_ext" = x"no"; then

+          AC_MSG_WARN([Your processor supports AVX, but your operating system doesn't])

+        fi

+      fi

+

+

+      AC_CACHE_CHECK([whether popcnt is enabled and supported], [ax_cv_have_popcnt_ext],

+      [

+        ax_cv_have_popcnt_ext=no

+        if test "$((0x$ecx>>23&0x01))" = 1; then

+          ax_cv_have_popcnt_ext=yes

+        fi

+      ])

+

+

+      AX_GCC_X86_CPUID(0x80000001)

+      ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`

+      edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`

+

+      AC_CACHE_CHECK([whether lzcnt is enabled and supported], [ax_cv_have_lzcnt_ext],

+      [

+        ax_cv_have_lzcnt_ext=no

+        if test "$((0x$ecx>>5&0x01))" = 1; then

+          ax_cv_have_lzcnt_ext=yes

+        fi

+      ])

+

+

+      AX_GCC_X86_CPUID(0x00000007)

+      ebx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 2`

+      ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`

+      edx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 4`

+

+      AC_CACHE_CHECK([whether avx2 is enabled and supported], [ax_cv_have_avx2_ext],

+      [

+        ax_cv_have_avx2_ext=no

+        if test "$((0x$ebx>>5&0x01))" = 1; then

+          ax_cv_have_avx2_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether bmi1 is enabled and supported], [ax_cv_have_bmi1_ext],

+      [

+        ax_cv_have_bmi1_ext=no

+        if test "$((0x$ebx>>3&0x01))" = 1; then

+          ax_cv_have_bmi1_ext=yes

+        fi

+      ])

+

+      AC_CACHE_CHECK([whether bmi2 is enabled and supported], [ax_cv_have_bmi2_ext],

+      [

+        ax_cv_have_bmi2_ext=no

+        if test "$((0x$ebx>>8&0x01))" = 1; then

+          ax_cv_have_bmi2_ext=yes

+        fi

+      ])

+

+

+

+      if test "$ax_cv_have_mmx_ext" = yes; then

+        AX_CHECK_COMPILE_FLAG(-mmmx, ax_cv_support_mmx_ext=yes, [])

+        if test x"$ax_cv_support_mmx_ext" = x"yes"; then

+          SIMD_FLAGS="$SIMD_FLAGS -mmmx"

+          AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support mmx instructions])

+        else

+          AC_MSG_WARN([Your processor supports mmx instructions but not your compiler.  Can you try another compiler or update yours?])

+        fi

+      fi

+

+      if test "$ax_cv_have_sse_ext" = yes; then

+        AX_CHECK_COMPILE_FLAG(-msse, ax_cv_support_sse_ext=yes, [])

+        if test x"$ax_cv_support_sse_ext" = x"yes"; then

+          SIMD_FLAGS="$SIMD_FLAGS -msse"

+          AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions])

+        else

+          AC_MSG_WARN([Your processor supports sse instructions but not your compiler.  Can you try another compiler or update yours?])

+        fi

+      fi

+

+      if test "$ax_cv_have_sse2_ext" = yes; then

+	AX_CHECK_COMPILE_FLAG(-msse2, ax_cv_support_sse2_ext=yes, [])

+	if test x"$ax_cv_support_sse2_ext" = x"yes"; then

+	  SIMD_FLAGS="$SIMD_FLAGS -msse2"

+	  AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions])

+	else

+	  AC_MSG_WARN([Your processor supports sse2 instructions but not your compiler.  Can you try another compiler or update yours?])

+	fi

+      fi

+

+      if test "$ax_cv_have_sse3_ext" = yes; then

+        AX_CHECK_COMPILE_FLAG(-msse3, ax_cv_support_sse3_ext=yes, [])

+        if test x"$ax_cv_support_sse3_ext" = x"yes"; then

+          SIMD_FLAGS="$SIMD_FLAGS -msse3"

+          AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions])

+        else

+          AC_MSG_WARN([Your processor supports sse3 instructions but not your compiler.  Can you try another compiler or update yours?])

+        fi

+      fi

+

+      if test "$ax_cv_have_ssse3_ext" = yes; then

+        AX_CHECK_COMPILE_FLAG(-mssse3, ax_cv_support_ssse3_ext=yes, [])

+        if test x"$ax_cv_support_ssse3_ext" = x"yes"; then

+          SIMD_FLAGS="$SIMD_FLAGS -mssse3"

+          AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions])

+        else

+          AC_MSG_WARN([Your processor supports ssse3 instructions but not your compiler.  Can you try another compiler or update yours?])

+        fi

+      fi

+

+      if test "$ax_cv_have_sse41_ext" = yes; then

+	AX_CHECK_COMPILE_FLAG(-msse4.1, ax_cv_support_sse41_ext=yes, [])

+	if test x"$ax_cv_support_sse41_ext" = x"yes"; then

+	  SIMD_FLAGS="$SIMD_FLAGS -msse4.1"

+	  AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions])

+	else

+	  AC_MSG_WARN([Your processor supports sse4.1 instructions but not your compiler.  Can you try another compiler or update yours?])

+	fi

+      fi

+

+      if test "$ax_cv_have_sse42_ext" = yes; then

+        AX_CHECK_COMPILE_FLAG(-msse4.2, ax_cv_support_sse42_ext=yes, [])

+        if test x"$ax_cv_support_sse42_ext" = x"yes"; then

+          SIMD_FLAGS="$SIMD_FLAGS -msse4.2"

+          AC_DEFINE(HAVE_SSE4_2,1,[Define to 1 if you support SSE4.2 (Streaming SIMD Extensions 4.2) instructions])

+        else

+          AC_MSG_WARN([Your processor supports sse4.2 instructions but not your compiler.  Can you try another compiler or update yours?])

+        fi

+      fi

+

+#      if test "$ax_cv_have_avx_ext" = yes; then

+#        AX_CHECK_COMPILE_FLAG(-mavx, ax_cv_support_avx_ext=yes, [])

+#        if test x"$ax_cv_support_avx_ext" = x"yes"; then

+#          SIMD_FLAGS="$SIMD_FLAGS -mavx"

+#          AC_DEFINE(HAVE_AVX,1,[Define to 1 if you support AVX (Advanced Vector Extensions) instructions])

+#        else

+#          AC_MSG_WARN([Your processor supports avx instructions but not your compiler.  Can you try another compiler or update yours?])

+#        fi

+#      fi

+

+      AC_MSG_CHECKING(for immintrin.h header file)

+      AC_TRY_LINK([#include <immintrin.h>],

+                  [ ],

+                  [ax_cv_have_immintrin_h=yes])

+

+      if test x"$a_cv_have_immintrin_h" = x"yes"; then

+        AC_MSG_RESULT([yes])

+        if test "$ax_cv_have_popcnt_ext" = yes; then

+          AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])

+        fi

+

+        if test "$ax_cv_have_lzcnt_ext" = yes; then

+          AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])

+        fi

+

+        if test "$ax_cv_have_bmi1_ext" = yes; then

+          AC_DEFINE(HAVE_BMI1,1,[Define to 1 if you support BMI1 (Bit Manipulation Instruction set 1)])

+        fi

+      else

+        AC_MSG_RESULT([no])

+        if test "$ax_cv_have_popcnt_ext" = yes; then

+          AC_MSG_WARN([Your processor supports _popcnt instructions but your compiler cannot find immintrin.h.  Will try another method.])

+        fi

+        if test "$ax_cv_have_lzcnt_ext" = yes; then

+          AC_MSG_WARN([Your processor supports _lzcnt instructions but your compiler cannot find immintrin.h.  Will try another method.])

+        fi

+        if test "$ax_cv_have_bmi1_ext" = yes; then

+          AC_MSG_WARN([Your processor supports bmi instructions but your compiler cannot find immintrin.h.  Will try another method.])

+        fi

+      fi

+

+      if test "$ax_cv_have_bmi2_ext" = yes; then

+        AC_DEFINE(HAVE_BMI2,1,[Define to 1 if you support BMI2 (Bit Manipulation Instruction set 2)])

+      fi

+

+#      if test "$ax_cv_have_avx2_ext" = yes; then

+#        AX_CHECK_COMPILE_FLAG(-mavx2, ax_cv_support_avx2_ext=yes, [])

+#        if test x"$ax_cv_support_avx2_ext" = x"yes"; then

+#          SIMD_FLAGS="$SIMD_FLAGS -mavx2"

+#          AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])

+#        else

+#          AC_MSG_WARN([Your processor supports avx2 instructions but not your compiler.  Can you try another compiler or update yours?])

+#        fi

+#      fi

+

+  ;;

+  esac

+

+  AC_SUBST(SIMD_FLAGS)

+])

new file mode 100644

@@ -0,0 +1,79 @@

+# ===========================================================================

+#   http://www.gnu.org/software/autoconf-archive/ax_gcc_x86_avx_xgetbv.html

+# ===========================================================================

+#

+# SYNOPSIS

+#

+#   AX_GCC_X86_AVX_XGETBV

+#

+# DESCRIPTION

+#

+#   On later x86 processors with AVX SIMD support, with gcc or a compiler

+#   that has a compatible syntax for inline assembly instructions, run a

+#   small program that executes the xgetbv instruction with input OP. This

+#   can be used to detect if the OS supports AVX instruction usage.

+#

+#   On output, the values of the eax and edx registers are stored as

+#   hexadecimal strings as "eax:edx" in the cache variable

+#   ax_cv_gcc_x86_avx_xgetbv.

+#

+#   If the xgetbv instruction fails (because you are running a

+#   cross-compiler, or because you are not using gcc, or because you are on

+#   a processor that doesn't have this instruction),

+#   ax_cv_gcc_x86_avx_xgetbv_OP is set to the string "unknown".

+#

+#   This macro mainly exists to be used in AX_EXT.

+#

+# LICENSE

+#

+#   Copyright (c) 2013 Michael Petch <mpetch@capp-sysware.com>

+#

+#   This program is free software: you can redistribute it and/or modify it

+#   under the terms of the GNU General Public License as published by the

+#   Free Software Foundation, either version 3 of the License, or (at your

+#   option) any later version.

+#

+#   This program is distributed in the hope that it will be useful, but

+#   WITHOUT ANY WARRANTY; without even the implied warranty of

+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General

+#   Public License for more details.

+#

+#   You should have received a copy of the GNU General Public License along

+#   with this program. If not, see <http://www.gnu.org/licenses/>.

+#

+#   As a special exception, the respective Autoconf Macro's copyright owner

+#   gives unlimited permission to copy, distribute and modify the configure

+#   scripts that are the output of Autoconf when processing the Macro. You

+#   need not follow the terms of the GNU General Public License when using

+#   or distributing such scripts, even though portions of the text of the

+#   Macro appear in them. The GNU General Public License (GPL) does govern

+#   all other use of the material that constitutes the Autoconf Macro.

+#

+#   This special exception to the GPL applies to versions of the Autoconf

+#   Macro released by the Autoconf Archive. When you make and distribute a

+#   modified version of the Autoconf Macro, you may extend this special

+#   exception to the GPL to apply to your modified version as well.

+

+#serial 1

+

+AC_DEFUN([AX_GCC_X86_AVX_XGETBV],

+[AC_REQUIRE([AC_PROG_CC])

+AC_LANG_PUSH([C])

+AC_CACHE_CHECK(for x86-AVX xgetbv $1 output, ax_cv_gcc_x86_avx_xgetbv_$1,

+ [AC_RUN_IFELSE([AC_LANG_PROGRAM([#include <stdio.h>], [

+     int op = $1, eax, edx;

+     FILE *f;

+      /* Opcodes for xgetbv */

+      __asm__(".byte 0x0f, 0x01, 0xd0"

+        : "=a" (eax), "=d" (edx)

+        : "c" (op));

+     f = fopen("conftest_xgetbv", "w"); if (!f) return 1;

+     fprintf(f, "%x:%x\n", eax, edx);

+     fclose(f);

+     return 0;

+])],

+     [ax_cv_gcc_x86_avx_xgetbv_$1=`cat conftest_xgetbv`; rm -f conftest_xgetbv],

+     [ax_cv_gcc_x86_avx_xgetbv_$1=unknown; rm -f conftest_xgetbv],

+     [ax_cv_gcc_x86_avx_xgetbv_$1=unknown])])

+AC_LANG_POP([C])

+])

new file mode 100644

@@ -0,0 +1,79 @@

+# ===========================================================================

+#     http://www.gnu.org/software/autoconf-archive/ax_gcc_x86_cpuid.html

+# ===========================================================================

+#

+# SYNOPSIS

+#

+#   AX_GCC_X86_CPUID(OP)

+#

+# DESCRIPTION

+#

+#   On Pentium and later x86 processors, with gcc or a compiler that has a

+#   compatible syntax for inline assembly instructions, run a small program

+#   that executes the cpuid instruction with input OP. This can be used to

+#   detect the CPU type.

+#

+#   On output, the values of the eax, ebx, ecx, and edx registers are stored

+#   as hexadecimal strings as "eax:ebx:ecx:edx" in the cache variable

+#   ax_cv_gcc_x86_cpuid_OP.

+#

+#   If the cpuid instruction fails (because you are running a

+#   cross-compiler, or because you are not using gcc, or because you are on

+#   a processor that doesn't have this instruction), ax_cv_gcc_x86_cpuid_OP

+#   is set to the string "unknown".

+#

+#   This macro mainly exists to be used in AX_GCC_ARCHFLAG.

+#

+# LICENSE

+#

+#   Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu>

+#   Copyright (c) 2008 Matteo Frigo

+#

+#   This program is free software: you can redistribute it and/or modify it

+#   under the terms of the GNU General Public License as published by the

+#   Free Software Foundation, either version 3 of the License, or (at your

+#   option) any later version.

+#

+#   This program is distributed in the hope that it will be useful, but

+#   WITHOUT ANY WARRANTY; without even the implied warranty of

+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General

+#   Public License for more details.

+#

+#   You should have received a copy of the GNU General Public License along

+#   with this program. If not, see <http://www.gnu.org/licenses/>.

+#

+#   As a special exception, the respective Autoconf Macro's copyright owner

+#   gives unlimited permission to copy, distribute and modify the configure

+#   scripts that are the output of Autoconf when processing the Macro. You

+#   need not follow the terms of the GNU General Public License when using

+#   or distributing such scripts, even though portions of the text of the

+#   Macro appear in them. The GNU General Public License (GPL) does govern

+#   all other use of the material that constitutes the Autoconf Macro.

+#

+#   This special exception to the GPL applies to versions of the Autoconf

+#   Macro released by the Autoconf Archive. When you make and distribute a

+#   modified version of the Autoconf Macro, you may extend this special

+#   exception to the GPL to apply to your modified version as well.

+

+#serial 7

+

+AC_DEFUN([AX_GCC_X86_CPUID],

+[AC_REQUIRE([AC_PROG_CC])

+AC_LANG_PUSH([C])

+AC_CACHE_CHECK(for x86 cpuid $1 output, ax_cv_gcc_x86_cpuid_$1,

+ [AC_RUN_IFELSE([AC_LANG_PROGRAM([#include <stdio.h>], [

+     int op = $1, eax, ebx, ecx, edx;

+     FILE *f;

+      __asm__("cpuid"

+        : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)

+        : "a" (op));

+     f = fopen("conftest_cpuid", "w"); if (!f) return 1;

+     fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);

+     fclose(f);

+     return 0;

+])],

+     [ax_cv_gcc_x86_cpuid_$1=`cat conftest_cpuid`; rm -f conftest_cpuid],

+     [ax_cv_gcc_x86_cpuid_$1=unknown; rm -f conftest_cpuid],

+     [ax_cv_gcc_x86_cpuid_$1=unknown])])

+AC_LANG_POP([C])

+])

new file mode 100644

@@ -0,0 +1,33 @@

+

+AC_DEFUN([ACX_BUILTIN], [

+AC_LANG_SAVE

+AC_LANG(C)

+

+AC_MSG_CHECKING(for __builtin_popcount)

+AC_RUN_IFELSE(

+  [AC_LANG_PROGRAM([[]],

+                   [[return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;]])],

+  [AC_MSG_RESULT(yes)

+   AC_DEFINE([HAVE_BUILTIN_POPCOUNT],[1],[Define to 1 if __builtin_popcount works.])],

+  [AC_MSG_RESULT(no)])

+

+AC_MSG_CHECKING(for __builtin_clz)

+AC_RUN_IFELSE(

+  [AC_LANG_PROGRAM([[]],

+                   [[return (__builtin_clz(0x1u) == 31) ? 0 : 9;]])],

+  [AC_MSG_RESULT(yes)

+   AC_DEFINE([HAVE_BUILTIN_CLZ],[1],[Define to 1 if __builtin_clz works.])],

+  [AC_MSG_RESULT(no)])

+

+AC_MSG_CHECKING(for __builtin_ctz)

+AC_RUN_IFELSE(

+  [AC_LANG_PROGRAM([[]],

+                   [[return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;]])],

+  [AC_MSG_RESULT(yes)

+   AC_DEFINE([HAVE_BUILTIN_CTZ],[1],[Define to 1 if __builtin_ctz works.])],

+  [AC_MSG_RESULT(no)])

+

+AC_LANG_RESTORE

+])

+

+

@@ -30,6 +30,15 @@ AC_COMPILE_IFELSE(

    AC_DEFINE([HAVE_MADVISE_MADV_RANDOM],[1],[Define to 1 if MADV_RANDOM available for madvise])],

   [AC_MSG_RESULT(no)])

+AC_MSG_CHECKING(for MADV_SEQUENTIAL in madvise)

+AC_COMPILE_IFELSE(

+  [AC_LANG_PROGRAM([[#include <sys/types.h>

+#include <sys/mman.h>]],

+                   [[int flags = MADV_SEQUENTIAL;]])],

+  [AC_MSG_RESULT(yes)

+   AC_DEFINE([HAVE_MADVISE_MADV_SEQUENTIAL],[1],[Define to 1 if MADV_SEQUENTIAL available for madvise])],

+  [AC_MSG_RESULT(no)])

+

 AC_LANG_RESTORE

 ])

new file mode 100644

@@ -0,0 +1,26 @@

+

+AC_DEFUN([ACX_SSE2_SHIFT_DEFECT], [

+  AC_REQUIRE([AC_CANONICAL_HOST])

+  AC_LANG_SAVE

+  AC_LANG_C

+

+  AC_MSG_CHECKING(compiler is defective and requires an immediate in sse2 shift commands)

+  AC_COMPILE_IFELSE(

+  [AC_LANG_PROGRAM([[#include <stdio.h>

+#include <stdlib.h>

+#include <emmintrin.h>]],

+                   [[int nshift = rand() % 32;

+__m128i shifted;

+shifted = _mm_slli_epi32(_mm_set1_epi32(1),nshift);

+]])],

+  [ax_cv_sse2_shift_defect=no],

+  [ax_cv_sse2_shift_defect=yes])

+

+  AC_MSG_RESULT($ax_cv_sse2_shift_defect)

+  if test "$ax_cv_sse2_shift_defect" = yes; then

+    AC_DEFINE(DEFECTIVE_SSE2_COMPILER,1,[Define to 1 if your compiler is defective and requires an immediate in sse2 shift commands.])

+  fi

+

+AC_LANG_RESTORE

+])dnl

+

@@ -646,6 +646,7 @@ ZLIB_LIBS

 MAKE_BINARIES_FALSE

 MAKE_BINARIES_TRUE

 GMAPDB

+SIMD_FLAGS

 UNIQSCAN

 GSNAP

 GMAP

@@ -801,6 +802,10 @@ with_gnu_ld

 with_sysroot

 enable_libtool_lock

 with_gmap

+enable_popcnt

+enable_sse2

+enable_sse4_1

+enable_simd

 with_gmapdb

 enable_binaries

 enable_zlib

@@ -1452,6 +1457,15 @@ Optional Features:

   --enable-fast-install[=PKGS]

                           optimize for fast installation [default=yes]

   --disable-libtool-lock  avoid locking (might break parallel builds)

+  --enable-popcnt         Enable -mpopcnt if it compiles and runs

+                          (default=yes). May want to disable if compiling on

+                          one machine and running on another.

+  --enable-sse2           Enable sse2 simd commands if they compile and run

+                          (default=yes).

+  --enable-sse4.1         Enable sse4.1 simd commands if they compile and run

+                          (default=yes). Requires that sse2 be enabled.

+  --enable-simd           Enable simd commands in general if they compile and

+                          run (default=yes).

   --enable-binaries       Enable building of binaries (default=yes)

   --enable-zlib           Enable zlib support (option needed for uncompressing

                           gzip files) (default=yes)

@@ -14657,6 +14671,32 @@ $as_echo "no" >&6; }

 fi

 rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for MADV_SEQUENTIAL in madvise" >&5

+$as_echo_n "checking for MADV_SEQUENTIAL in madvise... " >&6; }

+cat confdefs.h - <<_ACEOF >conftest.$ac_ext

+/* end confdefs.h.  */

+#include <sys/types.h>

+#include <sys/mman.h>

+int

+main ()

+{

+int flags = MADV_SEQUENTIAL;

+  ;

+  return 0;

+}

+_ACEOF

+if ac_fn_c_try_compile "$LINENO"; then :

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5

+$as_echo "yes" >&6; }

+

+$as_echo "#define HAVE_MADVISE_MADV_SEQUENTIAL 1" >>confdefs.h

+

+else

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5

+$as_echo "no" >&6; }

+fi

+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

+

 ac_ext=c

 ac_cpp='$CPP $CPPFLAGS'

 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'

@@ -14866,6 +14906,2477 @@ $as_echo "#define USE_FOPEN_TEXT 1" >>confdefs.h

 fi

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for popcnt feature" >&5

+$as_echo_n "checking for popcnt feature... " >&6; }

+# Check whether --enable-popcnt was given.

+if test "${enable_popcnt+set}" = set; then :

+  enableval=$enable_popcnt; answer="$enableval"

+else

+  answer=""

+fi

+

+case x"$answer" in

+	xyes)

+        { $as_echo "$as_me:${as_lineno-$LINENO}: result: enabled" >&5

+$as_echo "enabled" >&6; }

+

+

+ac_ext=c

+ac_cpp='$CPP $CPPFLAGS'

+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'

+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'

+ac_compiler_gnu=$ac_cv_c_compiler_gnu

+

+

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for __builtin_popcount" >&5

+$as_echo_n "checking for __builtin_popcount... " >&6; }

+if test "$cross_compiling" = yes; then :

+  { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5

+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}

+as_fn_error $? "cannot run test program while cross compiling

+See \`config.log' for more details" "$LINENO" 5; }

+else

+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

+/* end confdefs.h.  */

+

+int

+main ()

+{

+return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;

+  ;

+  return 0;

+}

+_ACEOF

+if ac_fn_c_try_run "$LINENO"; then :

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5

+$as_echo "yes" >&6; }

+

+$as_echo "#define HAVE_BUILTIN_POPCOUNT 1" >>confdefs.h

+

+else

+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5

+$as_echo "no" >&6; }

+fi

+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \

+  conftest.$ac_objext conftest.beam conftest.$ac_ext

+fi

+

+

+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for __builtin_clz" >&5

+$as_echo_n "checking for __builtin_clz... " >&6; }

+if test "$cross_compiling" = yes; then :

+  { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5

+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}