C++0x and Mersenne Twister update

gtfold-mfe/configure.in

@@ -1,185 +1,191 @@
-dnl Process this file with autoconf to produce a configure script.
-
-dnl AC_PREREQ([2.67])
-dnl AC 2.62 needed for OpenMP
-AC_PREREQ([2.63])
-
-dnl AC_INIT (package, version, [bug-report-email], [tarname])
-AC_INIT([gtfold],[2.0])
-
-dnl check for this file's existence to make sure that the directory
-dnl specified by --srcdir is the right one
-AC_CONFIG_SRCDIR([README])
-
-dnl Specify a header configuration file
-AC_CONFIG_HEADERS([gtfold_config.h])
-
-dnl Compute the canonical host-system type variable, host, and its
-dnl three individual parts host_cpu, host_vendor, and host_os.
-AC_CANONICAL_TARGET
-
-dnl Initialize Automake
-AM_INIT_AUTOMAKE
-
-dnl Argument -enable-64bit specifies that the library should be
-dnl compiled for 64-bit environments, if possible. 
-AC_ARG_ENABLE(64bit,
-  [  --enable-64bit          compile for 64-bit environments],
-  [case "${enableval}" in
-    "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;;
-    n | no) gtfold_cv_enable_64bit=no ;;
-    *) AC_MSG_ERROR(bad value ${enableval} for --enable-64bit) ;;
-  esac],
-  [gtfold_cv_enable_64bit=no])
-
-if test "$gtfold_cv_enable_64bit" == "yes" ; 
-then 
-   if test "$gtfold_cv_check_sunpro_cc" == "yes" ; then
-      CFLAGS=$(echo $CFLAGS | sed -e 's/-fast\|-xarch=.*//g') 
-      CFLAGS="$CFLAGS -fast -xarch=v9 -lgmp" 
-   else
-      if test "$GCC" == "yes"; then
-         CFLAGS=$(echo $CFLAGS | sed -e 's/-m32\|-m64//g') 
-         CFLAGS="$CFLAGS -m64 -lgmp" 
-      fi
-   fi
-fi
-
-
-dnl Search for a C compiler starting with the specified list
-AC_PROG_CC([xlc gcc icc cc])
-dnl Search for a C++ compiler starting with the specified list
-AC_PROG_CXX([xlC g++ iCC CC])
-dnl Check for programs
-#AC_PROG_LIBTOOL
-AC_PROG_INSTALL
-
-AC_OPENMP
-
-#AC_DEFINE([_RAND],[],[RNG library to use])
-
-dnl Check for libraries
-AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present]))
-
-dnl Check for header files
-AC_HEADER_STDC
-#AC_CHECK_HEADERS(sys/resource.h)
-#AC_CHECK_HEADERS(getopt.h)
-AC_CHECK_HEADERS([stdlib.h string.h sys/time.h])
-
-dnl Check for typedefs, structures, C compiler characteristics
-AC_C_CONST
-AC_C_INLINE
-AC_TYPE_SIZE_T
-AC_HEADER_TIME
-AC_STRUCT_TM
-
-dnl If using xlC add OPENMP_CFLAGS to the link flags
-if test "x$CXX" = "xxlC"; then
-  LDFLAGS="-qsmp=omp"
-fi
-
-dnl This is an example how to specify different CFLAGS depending on
-dnl the C compiler detected: 
-
-dnl If gcc is present, use -Wall
-if test "x$GCC" = "xyes"; then
-  if test -z "`echo "$CFLAGS" | grep "\-Wall" 2> /dev/null`" ; then
-    CFLAGS="$CFLAGS -Wall"
-  fi
-fi
-
-dnl If g++ is present, use -Wall
-if test "x$GXX" = "xyes"; then
-  if test -z "`echo "$CXXFLAGS" | grep "\-Wall" 2> /dev/null`" ; then
-    CXXFLAGS="$CXXFLAGS -Wall -lgmp"
-  fi
-fi
-
-dnl This is an example how to check for compiler characteristics that
-dnl are not a part of the standard Autoconf tests:
-
-#If Sun cc is present, define appropriate compiler flags  
-AC_MSG_CHECKING(for Sun C compiler)
-AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C
-                    #include "error: this is not a Sun C compiler."
-                    #endif 
-                   ]])],[AC_MSG_RESULT(yes)
-                    gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no)
-                    gtfold_cv_check_sunpro_cc=no])
-
-if test "$gtfold_cv_check_sunpro_cc" == "yes";
-then
-	AC_MSG_CHECKING(for Sun C compiler architecture target)
-	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc
-                    #include "error: this is not a Sun Sparc processor."
-                    #endif 
-                   ]])],[AC_MSG_RESULT(yes)
-                    gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no)
-                    gtfold_cv_check_sun_sparc=no])
-fi
-
-if test "$gtfold_cv_check_sunpro_cc" == "yes";
-then
-	if test "$gtfold_cv_check_sun_sparc" == "yes";
-	then	
-		AC_MSG_CHECKING(for Sun sparc v9 architecture)
-		AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9
-				    #include "error: this is not a Sun Sparc V9 processor."
-				    #endif 
-				    ]])],[AC_MSG_RESULT(yes)
-				    gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no)
-				    gtfold_cv_check_sun_sparcv9=no])
-        fi				    
-fi
-
-if test "$gtfold_cv_check_sunpro_cc" == "yes";
-then
-	CFLAGS="$CFLAGS -mt -fast"
-        LIBS="$LIBS -lmtsk"
-	if test "$gtfold_cv_check_sun_sparc" == "yes";
-	then
-		if test "$gtfold_cv_check_sun_sparcv9" == "yes";
-		then
-			CFLAGS="$CFLAGS -xarch=v9"
-                else
-			CFLAGS="$CFLAGS -xarch=v8plusa"
-                fi
-        fi
-fi
-
-
-if test "$enable_openmp" != 'no'; then  
-   if test "x${GCC}" = "xyes"; then  
-      AC_CHECK_LIB( omp,GOMP_parallel_start,LIB_OMP="-lgomp",,)  
-      AC_CHECK_LIB(gomp,GOMP_parallel_start,GOMP_LIBS="-lgomp",,)  
-   else  
-      AC_CHECK_LIB(mtsk,sunw_mp_register_warn,LIB_OMP="-lmtsk",,)  
-      AC_CHECK_LIB(mtsk,sunw_mp_register_warn,GOMP_LIBS="-lmtsk",,)  
-   fi  
-   LIBS="$GOMP_LIBS $LIBS"  
-fi
-
-
-dnl Check for library functions
-AC_CHECK_FUNCS(floor gettimeofday pow)
-
-dnl debug flag 
-AC_ARG_ENABLE(debug,
-  [  --enable-debug          turn on debugging],
-  [case "${enableval}" in
-    "" | y | ye | yes) debug=true; 
-		       CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;;
-    n | no) debug=false ;;
-    *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;;
-  esac],
-  [debug=false])
-AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue)
-
-dnl Create makefiles and other configuration files
-AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile])
-AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile])
-
-dnl Generate `config.status' and launch it
-AC_OUTPUT
-
+dnl Process this file with autoconf to produce a configure script.
+
+dnl AC_PREREQ([2.67])
+dnl AC 2.62 needed for OpenMP
+AC_PREREQ([2.63])
+
+dnl AC_INIT (package, version, [bug-report-email], [tarname])
+AC_INIT([gtfold],[2.0])
+
+dnl check for this file's existence to make sure that the directory
+dnl specified by --srcdir is the right one
+AC_CONFIG_SRCDIR([README])
+
+dnl Specify a header configuration file
+AC_CONFIG_HEADERS([gtfold_config.h])
+
+dnl Compute the canonical host-system type variable, host, and its
+dnl three individual parts host_cpu, host_vendor, and host_os.
+AC_CANONICAL_TARGET
+
+dnl Initialize Automake
+AM_INIT_AUTOMAKE
+
+dnl Argument -enable-64bit specifies that the library should be
+dnl compiled for 64-bit environments, if possible. 
+AC_ARG_ENABLE(64bit,
+  [  --enable-64bit          compile for 64-bit environments],
+  [case "${enableval}" in
+    "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;;
+    n | no) gtfold_cv_enable_64bit=no ;;
+    *) AC_MSG_ERROR(bad value ${enableval} for --enable-64bit) ;;
+  esac],
+  [gtfold_cv_enable_64bit=no])
+
+if test "$gtfold_cv_enable_64bit" == "yes" ; 
+then 
+   if test "$gtfold_cv_check_sunpro_cc" == "yes" ; then
+      CFLAGS=$(echo $CFLAGS | sed -e 's/-fast\|-xarch=.*//g') 
+      CFLAGS="$CFLAGS -fast -xarch=v9 -lgmp" 
+   else
+      if test "$GCC" == "yes"; then
+         CFLAGS=$(echo $CFLAGS | sed -e 's/-m32\|-m64//g') 
+         CFLAGS="$CFLAGS -m64 -lgmp" 
+      fi
+   fi
+fi
+
+
+dnl Search for a C compiler starting with the specified list
+AC_PROG_CC([xlc gcc icc cc])
+dnl Search for a C++ compiler starting with the specified list
+AC_PROG_CXX([xlC g++ iCC CC])
+dnl Check for programs
+#AC_PROG_LIBTOOL
+AC_PROG_INSTALL
+
+AC_OPENMP
+
+#AC_DEFINE([_RAND],[],[RNG library to use])
+
+dnl Check for libraries
+AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present]))
+
+dnl Check for header files
+AC_HEADER_STDC
+#AC_CHECK_HEADERS(sys/resource.h)
+#AC_CHECK_HEADERS(getopt.h)
+AC_CHECK_HEADERS([stdlib.h string.h sys/time.h])
+
+dnl Check for typedefs, structures, C compiler characteristics
+AC_C_CONST
+AC_C_INLINE
+AC_TYPE_SIZE_T
+AC_HEADER_TIME
+AC_STRUCT_TM
+
+dnl If using xlC add OPENMP_CFLAGS to the link flags
+if test "x$CXX" = "xxlC"; then
+  LDFLAGS="-qsmp=omp"
+fi
+
+dnl This is an example how to specify different CFLAGS depending on
+dnl the C compiler detected: 
+
+dnl If gcc is present, use -Wall
+if test "x$GCC" = "xyes"; then
+  if test -z "`echo "$CFLAGS" | grep "\-Wall" 2> /dev/null`" ; then
+    CFLAGS="$CFLAGS -Wall"
+  fi
+fi
+
+dnl If g++ is present, use -Wall
+if test "x$GXX" = "xyes"; then
+  if test -z "`echo "$CXXFLAGS" | grep "\-Wall" 2> /dev/null`" ; then
+    CXXFLAGS="$CXXFLAGS -Wall -lgmp"
+  fi
+fi
+
+dnl hopefully this works every time?
+if test true; then
+   CFLAGS="$CFLAGS -std=c++0x"
+   CXXFLAGS="$CXXFLAGS -std=c++0x"
+fi
+
+dnl This is an example how to check for compiler characteristics that
+dnl are not a part of the standard Autoconf tests:
+
+#If Sun cc is present, define appropriate compiler flags  
+AC_MSG_CHECKING(for Sun C compiler)
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C
+                    #include "error: this is not a Sun C compiler."
+                    #endif 
+                   ]])],[AC_MSG_RESULT(yes)
+                    gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no)
+                    gtfold_cv_check_sunpro_cc=no])
+
+if test "$gtfold_cv_check_sunpro_cc" == "yes";
+then
+	AC_MSG_CHECKING(for Sun C compiler architecture target)
+	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc
+                    #include "error: this is not a Sun Sparc processor."
+                    #endif 
+                   ]])],[AC_MSG_RESULT(yes)
+                    gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no)
+                    gtfold_cv_check_sun_sparc=no])
+fi
+
+if test "$gtfold_cv_check_sunpro_cc" == "yes";
+then
+	if test "$gtfold_cv_check_sun_sparc" == "yes";
+	then	
+		AC_MSG_CHECKING(for Sun sparc v9 architecture)
+		AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9
+				    #include "error: this is not a Sun Sparc V9 processor."
+				    #endif 
+				    ]])],[AC_MSG_RESULT(yes)
+				    gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no)
+				    gtfold_cv_check_sun_sparcv9=no])
+        fi				    
+fi
+
+if test "$gtfold_cv_check_sunpro_cc" == "yes";
+then
+	CFLAGS="$CFLAGS -mt -fast"
+        LIBS="$LIBS -lmtsk"
+	if test "$gtfold_cv_check_sun_sparc" == "yes";
+	then
+		if test "$gtfold_cv_check_sun_sparcv9" == "yes";
+		then
+			CFLAGS="$CFLAGS -xarch=v9"
+                else
+			CFLAGS="$CFLAGS -xarch=v8plusa"
+                fi
+        fi
+fi
+
+
+if test "$enable_openmp" != 'no'; then  
+   if test "x${GCC}" = "xyes"; then  
+      AC_CHECK_LIB( omp,GOMP_parallel_start,LIB_OMP="-lgomp",,)  
+      AC_CHECK_LIB(gomp,GOMP_parallel_start,GOMP_LIBS="-lgomp",,)  
+   else  
+      AC_CHECK_LIB(mtsk,sunw_mp_register_warn,LIB_OMP="-lmtsk",,)  
+      AC_CHECK_LIB(mtsk,sunw_mp_register_warn,GOMP_LIBS="-lmtsk",,)  
+   fi  
+   LIBS="$GOMP_LIBS $LIBS"  
+fi
+
+
+dnl Check for library functions
+AC_CHECK_FUNCS(floor gettimeofday pow)
+
+dnl debug flag 
+AC_ARG_ENABLE(debug,
+  [  --enable-debug          turn on debugging],
+  [case "${enableval}" in
+    "" | y | ye | yes) debug=true; 
+		       CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;;
+    n | no) debug=false ;;
+    *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;;
+  esac],
+  [debug=false])
+AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue)
+
+dnl Create makefiles and other configuration files
+AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile])
+AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile])
+
+dnl Generate `config.status' and launch it
+AC_OUTPUT
+