First addition of files to do the cuda queue. Makefiles and configure now compile with cuda

Makefile.in

-# Makefile.in generated by automake 1.11.6 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -31,23 +31,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 VPATH = @srcdir@
-am__make_dryrun = \
-  { \
-    am__dry=no; \
-    case $$MAKEFLAGS in \
-      *\\[\ \	]*) \
-        echo 'am--echo: ; @echo "AM"  OK' | $(MAKE) -f - 2>/dev/null \
-          | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
-      *) \
-        for am__flg in $$MAKEFLAGS; do \
-          case $$am__flg in \
-            *=*|--*) ;; \
-            *n*) am__dry=yes; break;; \
-          esac; \
-        done;; \
-    esac; \
-    test $$am__dry = yes; \
-  }
 pkgdatadir = $(datadir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
 pkglibdir = $(libdir)/@PACKAGE@
@@ -102,11 +85,6 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
 	install-pdf-recursive install-ps-recursive install-recursive \
 	installcheck-recursive installdirs-recursive pdf-recursive \
 	ps-recursive uninstall-recursive
-am__can_run_installinfo = \
-  case $$AM_UPDATE_INFO_DIR in \
-    n|no|NO) false;; \
-    *) (install-info --version) >/dev/null 2>&1;; \
-  esac
 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
   distclean-recursive maintainer-clean-recursive
 AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
@@ -119,11 +97,9 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
 am__remove_distdir = \
-  if test -d "$(distdir)"; then \
-    find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
-      && rm -rf "$(distdir)" \
-      || { sleep 5 && rm -rf "$(distdir)"; }; \
-  else :; fi
+  { test ! -d "$(distdir)" \
+    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+         && rm -fr "$(distdir)"; }; }
 am__relativize = \
   dir0=`pwd`; \
   sed_first='s,^\([^/]*\)/.*$$,\1,'; \
@@ -152,8 +128,6 @@ am__relativize = \
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 distuninstallcheck_listfiles = find . -type f -print
-am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
-  | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
 distcleancheck_listfiles = find . -type f -print
 ACLOCAL = @ACLOCAL@
 AMTAR = @AMTAR@
@@ -167,10 +141,11 @@ CCDEPMODE = @CCDEPMODE@
 CFLAGS = @CFLAGS@
 CPP = @CPP@
 CPPFLAGS = @CPPFLAGS@
+CUDA_CFLAGS = @CUDA_CFLAGS@
+CUDA_LIBS = @CUDA_LIBS@
 CYGPATH_W = @CYGPATH_W@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
-DLLTOOL = @DLLTOOL@
 DOXYGEN_PAPER_SIZE = @DOXYGEN_PAPER_SIZE@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
@@ -218,10 +193,10 @@ LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 MAKEINFO = @MAKEINFO@
-MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
 NM = @NM@
 NMEDIT = @NMEDIT@
+NVCC = @NVCC@
 OBJDUMP = @OBJDUMP@
 OBJEXT = @OBJEXT@
 OPENMP_CFLAGS = @OPENMP_CFLAGS@
@@ -232,7 +207,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
-PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 PRTDIAG = @PRTDIAG@
@@ -250,7 +224,6 @@ abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
-ac_ct_AR = @ac_ct_AR@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 acx_pthread_config = @acx_pthread_config@
@@ -284,6 +257,7 @@ libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -310,7 +284,7 @@ all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 
 .SUFFIXES:
-am--refresh: Makefile
+am--refresh:
 	@:
 $(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	@for dep in $?; do \
@@ -346,8 +320,10 @@ $(ACLOCAL_M4):  $(am__aclocal_m4_deps)
 $(am__aclocal_m4_deps):
 
 config.h: stamp-h1
-	@if test ! -f $@; then rm -f stamp-h1; else :; fi
-	@if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+	@if test ! -f $@; then \
+	  rm -f stamp-h1; \
+	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
+	else :; fi
 
 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
 	@rm -f stamp-h1
@@ -540,10 +516,13 @@ distdir: $(DISTFILES)
 	done
 	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
 	  if test "$$subdir" = .; then :; else \
-	    $(am__make_dryrun) \
-	      || test -d "$(distdir)/$$subdir" \
-	      || $(MKDIR_P) "$(distdir)/$$subdir" \
-	      || exit 1; \
+	    test -d "$(distdir)/$$subdir" \
+	    || $(MKDIR_P) "$(distdir)/$$subdir" \
+	    || exit 1; \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
 	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
 	    $(am__relativize); \
 	    new_distdir=$$reldir; \
@@ -575,11 +554,7 @@ dist-gzip: distdir
 	$(am__remove_distdir)
 
 dist-bzip2: distdir
-	tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
-	$(am__remove_distdir)
-
-dist-lzip: distdir
-	tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
+	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
 	$(am__remove_distdir)
 
 dist-lzma: distdir
@@ -587,7 +562,7 @@ dist-lzma: distdir
 	$(am__remove_distdir)
 
 dist-xz: distdir
-	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
+	tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
 	$(am__remove_distdir)
 
 dist-tarZ: distdir
@@ -618,8 +593,6 @@ distcheck: dist
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lzma*) \
 	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
-	*.tar.lz*) \
-	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
 	*.tar.xz*) \
 	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
 	*.tar.Z*) \
@@ -639,7 +612,6 @@ distcheck: dist
 	  && am__cwd=`pwd` \
 	  && $(am__cd) $(distdir)/_build \
 	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
-	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
@@ -668,16 +640,8 @@ distcheck: dist
 	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
 	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
 distuninstallcheck:
-	@test -n '$(distuninstallcheck_dir)' || { \
-	  echo 'ERROR: trying to run $@ with an empty' \
-	       '$$(distuninstallcheck_dir)' >&2; \
-	  exit 1; \
-	}; \
-	$(am__cd) '$(distuninstallcheck_dir)' || { \
-	  echo 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
-	  exit 1; \
-	}; \
-	test `$(am__distuninstallcheck_listfiles) | wc -l` -eq 0 \
+	@$(am__cd) '$(distuninstallcheck_dir)' \
+	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
 	   || { echo "ERROR: files left after uninstall:" ; \
 	        if test -n "$(DESTDIR)"; then \
 	          echo "  (check DESTDIR support)"; \
@@ -708,15 +672,10 @@ install-am: all-am
 
 installcheck: installcheck-recursive
 install-strip:
-	if test -z '$(STRIP)'; then \
-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	      install; \
-	else \
-	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
-	fi
+	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	  `test -z '$(STRIP)' || \
+	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
 mostlyclean-generic:
 
 clean-generic:
@@ -804,8 +763,8 @@ uninstall-am:
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
 	all all-am am--refresh check check-am clean clean-generic \
 	clean-libtool ctags ctags-recursive dist dist-all dist-bzip2 \
-	dist-gzip dist-lzip dist-lzma dist-shar dist-tarZ dist-xz \
-	dist-zip distcheck distclean distclean-generic distclean-hdr \
+	dist-gzip dist-lzma dist-shar dist-tarZ dist-xz dist-zip \
+	distcheck distclean distclean-generic distclean-hdr \
 	distclean-libtool distclean-tags distcleancheck distdir \
 	distuninstallcheck dvi dvi-am html html-am info info-am \
 	install install-am install-data install-data-am install-dvi \

aclocal.m4

-# generated automatically by aclocal 1.11.6 -*- Autoconf -*-
+# generated automatically by aclocal 1.11.1 -*- Autoconf -*-
 
 # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation,
-# Inc.
+# 2005, 2006, 2007, 2008, 2009  Free Software Foundation, Inc.
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -14,21 +13,18 @@
 
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
-[m4_warning([this file was generated for autoconf 2.69.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.63],,
+[m4_warning([this file was generated for autoconf 2.63.
 You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
 To do so, use the procedure documented by the package, typically `autoreconf'.])])
 
-# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_AUTOMAKE_VERSION(VERSION)
 # ----------------------------
 # Automake X.Y traces this macro to ensure aclocal.m4 has been
@@ -38,7 +34,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
 [am__api_version='1.11'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.11.6], [],
+m4_if([$1], [1.11.1], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -54,21 +50,19 @@ m4_define([_AM_AUTOCONF_VERSION], [])
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.11.6])dnl
+[AM_AUTOMAKE_VERSION([1.11.1])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
 # $ac_aux_dir to `$srcdir/foo'.  In other projects, it is set to
 # `$srcdir', `$srcdir/..', or `$srcdir/../..'.
@@ -150,14 +144,14 @@ AC_CONFIG_COMMANDS_PRE(
 Usually this means the macro was only invoked conditionally.]])
 fi])])
 
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009,
-# 2010, 2011 Free Software Foundation, Inc.
+# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009
+# Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 12
+# serial 10
 
 # There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
 # written in clear, in which case automake, when reading aclocal.m4,
@@ -197,7 +191,6 @@ AC_CACHE_CHECK([dependency style of $depcc],
   # instance it was reported that on HP-UX the gcc test will end up
   # making a dummy file named `D' -- because `-MD' means `put the output
   # in D'.
-  rm -rf conftest.dir
   mkdir conftest.dir
   # Copy depcomp to subdir because otherwise we won't find it if we're
   # using a relative directory.
@@ -262,7 +255,7 @@ AC_CACHE_CHECK([dependency style of $depcc],
 	break
       fi
       ;;
-    msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+    msvisualcpp | msvcmsys)
       # This compiler won't grok `-c -o', but also, the minuso test has
       # not run yet.  These depmodes are late enough in the game, and
       # so weak that their functioning should not be impacted.
@@ -327,13 +320,10 @@ AC_DEFUN([AM_DEP_TRACK],
 if test "x$enable_dependency_tracking" != xno; then
   am_depcomp="$ac_aux_dir/depcomp"
   AMDEPBACKSLASH='\'
-  am__nodep='_no'
 fi
 AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
 AC_SUBST([AMDEPBACKSLASH])dnl
 _AM_SUBST_NOTMAKE([AMDEPBACKSLASH])dnl
-AC_SUBST([am__nodep])dnl
-_AM_SUBST_NOTMAKE([am__nodep])dnl
 ])
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
@@ -567,15 +557,12 @@ for _am_header in $config_headers :; do
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001, 2003, 2005, 2008, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 2001, 2003, 2005, 2008  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_PROG_INSTALL_SH
 # ------------------
 # Define $install_sh.
@@ -742,15 +729,12 @@ else
 fi
 ])
 
-# Copyright (C) 2003, 2004, 2005, 2006, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_PROG_MKDIR_P
 # ---------------
 # Check for `mkdir -p'.
@@ -773,14 +757,13 @@ esac
 
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001, 2002, 2003, 2005, 2008, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 2001, 2002, 2003, 2005, 2008  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 5
+# serial 4
 
 # _AM_MANGLE_OPTION(NAME)
 # -----------------------
@@ -788,13 +771,13 @@ AC_DEFUN([_AM_MANGLE_OPTION],
 [[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
 
 # _AM_SET_OPTION(NAME)
-# --------------------
+# ------------------------------
 # Set option NAME.  Presently that only means defining a flag for this option.
 AC_DEFUN([_AM_SET_OPTION],
 [m4_define(_AM_MANGLE_OPTION([$1]), 1)])
 
 # _AM_SET_OPTIONS(OPTIONS)
-# ------------------------
+# ----------------------------------
 # OPTIONS is a space-separated list of Automake options.
 AC_DEFUN([_AM_SET_OPTIONS],
 [m4_foreach_w([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
@@ -870,14 +853,12 @@ Check your system clock])
 fi
 AC_MSG_RESULT(yes)])
 
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001, 2003, 2005  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_PROG_INSTALL_STRIP
 # ---------------------
 # One issue with vendor `install' (even GNU) is that you can't
@@ -900,13 +881,13 @@ fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006, 2008, 2010 Free Software Foundation, Inc.
+# Copyright (C) 2006, 2008  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 3
+# serial 2
 
 # _AM_SUBST_NOTMAKE(VARIABLE)
 # ---------------------------
@@ -915,13 +896,13 @@ AC_SUBST([INSTALL_STRIP_PROGRAM])])
 AC_DEFUN([_AM_SUBST_NOTMAKE])
 
 # AM_SUBST_NOTMAKE(VARIABLE)
-# --------------------------
+# ---------------------------
 # Public sister of _AM_SUBST_NOTMAKE.
 AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
+# Copyright (C) 2004, 2005  Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -943,11 +924,10 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
 # a tarball read from stdin.
 #     $(am__untar) < result.tar
 AC_DEFUN([_AM_PROG_TAR],
-[# Always define AMTAR for backward compatibility.  Yes, it's still used
-# in the wild :-(  We should find a proper way to deprecate it ...
-AC_SUBST([AMTAR], ['$${TAR-tar}'])
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
 m4_if([$1], [v7],
-     [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
+     [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
      [m4_case([$1], [ustar],, [pax],,
               [m4_fatal([Unknown tar format])])
 AC_MSG_CHECKING([how to create a $1 tar archive])

autom4te.cache/requests

-# This file was generated by Autom4te Sat May 26 18:17:46 UTC 2012.
+# This file was generated.
 # It contains the lists of macros which have been traced.
 # It can be safely removed.
 
@@ -58,9 +58,9 @@
                         '_LT_AC_LANG_CXX_CONFIG' => 1,
                         'AM_PROG_MKDIR_P' => 1,
                         'DX_IF_FEATURE' => 1,
-                        'DX_CHM_FEATURE' => 1,
                         'DX_FEATURE_doc' => 1,
                         'AM_AUTOMAKE_VERSION' => 1,
+                        'DX_CHM_FEATURE' => 1,
                         'DX_PDF_FEATURE' => 1,
                         'AM_SUBST_NOTMAKE' => 1,
                         'AM_MISSING_PROG' => 1,

config.h.in

@@ -6,6 +6,9 @@
 /* Define to 1 if you have the `clock_gettime' function. */
 #undef HAVE_CLOCK_GETTIME
 
+/* The cuda compiler is installed. */
+#undef HAVE_CUDA
+
 /* Define to 1 if you have the <c_asm.h> header file. */
 #undef HAVE_C_ASM_H
 
@@ -118,9 +121,6 @@
 /* Define to the one symbol short name of this package. */
 #undef PACKAGE_TARNAME
 
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
 /* Define to the version of this package. */
 #undef PACKAGE_VERSION
 

configure.in

@@ -78,6 +78,34 @@ AC_TRY_LINK([#ifdef HAVE_INTRINSICS_H
 #endif], [_rtc()], [AC_DEFINE(HAVE__RTC,1,[Define if you have the UNICOS _rtc() intrinsic.])], [rtc_ok=no])
 AC_MSG_RESULT($rtc_ok)
 
+# Check for CUDA
+AC_ARG_WITH([cuda],
+    [AS_HELP_STRING([--with-cuda=PATH],[prefix where cuda is installed @<:@default=no@:>@])],
+    [if test "x$with_cuda" != "xno"
+     then
+        if test "x$with_cuda" != "xyes"
+        then
+            CUDA_CFLAGS="-I$with_cuda/include"
+            CUDA_LIBS="-L$with_cuda/lib -L$with_cuda/lib64 -lcudart"
+            NVCC="$with_cuda/bin/nvcc"
+        else
+            AC_CHECK_PROG([NVCC],nvcc)
+            if test -n "$NVCC"
+            then
+                CUDA_CFLAGS="-I/usr/local/cuda/include"
+                CUDA_LIBS="-L/usr/local/cuda/lib -L/usr/local/cuda/lib64 -lcudart"
+            fi
+        fi
+        if test -n "$NVCC"; then
+            AC_DEFINE([HAVE_CUDA],[1],[The cuda compiler is installed.])
+        fi
+    fi])
+AC_SUBST(CUDA_CFLAGS)
+AC_SUBST(CUDA_LIBS)
+AC_SUBST(NVCC)
+AM_CONDITIONAL([HAVE_CUDA],[test -n "$NVCC"])
+
+
 
 # make the documentation
 DX_INIT_DOXYGEN(libchebfun,doc/Doxyfile,doc/)

m4/ltoptions.m4

 # Helper functions for option handling.                    -*- Autoconf -*-
 #
-#   Copyright (C) 2004, 2005, 2007, 2008, 2009 Free Software Foundation,
-#   Inc.
+#   Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
 #   Written by Gary V. Vaughan, 2004
 #
 # This file is free software; the Free Software Foundation gives
 # unlimited permission to copy and/or distribute it, with or without
 # modifications, as long as this notice is preserved.
 
-# serial 7 ltoptions.m4
+# serial 6 ltoptions.m4
 
 # This is to help aclocal find these macros, as it can't see m4_define.
 AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
@@ -126,7 +125,7 @@ LT_OPTION_DEFINE([LT_INIT], [win32-dll],
 [enable_win32_dll=yes
 
 case $host in
-*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-cegcc*)
+*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
   AC_CHECK_TOOL(AS, as, false)
   AC_CHECK_TOOL(DLLTOOL, dlltool, false)
   AC_CHECK_TOOL(OBJDUMP, objdump, false)
@@ -134,13 +133,13 @@ case $host in
 esac
 
 test -z "$AS" && AS=as
-_LT_DECL([], [AS],      [1], [Assembler program])dnl
+_LT_DECL([], [AS],      [0], [Assembler program])dnl
 
 test -z "$DLLTOOL" && DLLTOOL=dlltool
-_LT_DECL([], [DLLTOOL], [1], [DLL creation program])dnl
+_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
 
 test -z "$OBJDUMP" && OBJDUMP=objdump
-_LT_DECL([], [OBJDUMP], [1], [Object dumper program])dnl
+_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
 ])# win32-dll
 
 AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
@@ -326,24 +325,9 @@ dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
 # MODE is either `yes' or `no'.  If omitted, it defaults to `both'.
 m4_define([_LT_WITH_PIC],
 [AC_ARG_WITH([pic],
-    [AS_HELP_STRING([--with-pic@<:@=PKGS@:>@],
+    [AS_HELP_STRING([--with-pic],
 	[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
-    [lt_p=${PACKAGE-default}
-    case $withval in
-    yes|no) pic_mode=$withval ;;
-    *)
-      pic_mode=default
-      # Look at the argument we got.  We use all the common list separators.
-      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
-      for lt_pkg in $withval; do
-	IFS="$lt_save_ifs"
-	if test "X$lt_pkg" = "X$lt_p"; then
-	  pic_mode=yes
-	fi
-      done
-      IFS="$lt_save_ifs"
-      ;;
-    esac],
+    [pic_mode="$withval"],
     [pic_mode=default])
 
 test -z "$pic_mode" && pic_mode=m4_default([$1], [default])

m4/ltversion.m4

@@ -7,17 +7,17 @@
 # unlimited permission to copy and/or distribute it, with or without
 # modifications, as long as this notice is preserved.
 
-# @configure_input@
+# Generated from ltversion.in.
 
-# serial 3337 ltversion.m4
+# serial 3017 ltversion.m4
 # This file is part of GNU Libtool
 
-m4_define([LT_PACKAGE_VERSION], [2.4.2])
-m4_define([LT_PACKAGE_REVISION], [1.3337])
+m4_define([LT_PACKAGE_VERSION], [2.2.6b])
+m4_define([LT_PACKAGE_REVISION], [1.3017])
 
 AC_DEFUN([LTVERSION_VERSION],
-[macro_version='2.4.2'
-macro_revision='1.3337'
+[macro_version='2.2.6b'
+macro_revision='1.3017'
 _LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
 _LT_DECL(, macro_revision, 0)
 ])

m4/lt~obsolete.m4

 # lt~obsolete.m4 -- aclocal satisfying obsolete definitions.    -*-Autoconf-*-
 #
-#   Copyright (C) 2004, 2005, 2007, 2009 Free Software Foundation, Inc.
+#   Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
 #   Written by Scott James Remnant, 2004.
 #
 # This file is free software; the Free Software Foundation gives
 # unlimited permission to copy and/or distribute it, with or without
 # modifications, as long as this notice is preserved.
 
-# serial 5 lt~obsolete.m4
+# serial 4 lt~obsolete.m4
 
 # These exist entirely to fool aclocal when bootstrapping libtool.
 #
@@ -77,6 +77,7 @@ m4_ifndef([AC_DISABLE_FAST_INSTALL],	[AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
 m4_ifndef([_LT_AC_LANG_CXX],		[AC_DEFUN([_LT_AC_LANG_CXX])])
 m4_ifndef([_LT_AC_LANG_F77],		[AC_DEFUN([_LT_AC_LANG_F77])])
 m4_ifndef([_LT_AC_LANG_GCJ],		[AC_DEFUN([_LT_AC_LANG_GCJ])])
+m4_ifndef([AC_LIBTOOL_RC],		[AC_DEFUN([AC_LIBTOOL_RC])])
 m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG],	[AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
 m4_ifndef([_LT_AC_LANG_C_CONFIG],	[AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
 m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG],	[AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
@@ -89,10 +90,3 @@ m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG],	[AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
 m4_ifndef([_LT_AC_LANG_RC_CONFIG],	[AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
 m4_ifndef([AC_LIBTOOL_CONFIG],		[AC_DEFUN([AC_LIBTOOL_CONFIG])])
 m4_ifndef([_LT_AC_FILE_LTDLL_C],	[AC_DEFUN([_LT_AC_FILE_LTDLL_C])])
-m4_ifndef([_LT_REQUIRED_DARWIN_CHECKS],	[AC_DEFUN([_LT_REQUIRED_DARWIN_CHECKS])])
-m4_ifndef([_LT_AC_PROG_CXXCPP],		[AC_DEFUN([_LT_AC_PROG_CXXCPP])])
-m4_ifndef([_LT_PREPARE_SED_QUOTE_VARS],	[AC_DEFUN([_LT_PREPARE_SED_QUOTE_VARS])])
-m4_ifndef([_LT_PROG_ECHO_BACKSLASH],	[AC_DEFUN([_LT_PROG_ECHO_BACKSLASH])])
-m4_ifndef([_LT_PROG_F77],		[AC_DEFUN([_LT_PROG_F77])])
-m4_ifndef([_LT_PROG_FC],		[AC_DEFUN([_LT_PROG_FC])])
-m4_ifndef([_LT_PROG_CXX],		[AC_DEFUN([_LT_PROG_CXX])])

src/Makefile.am

@@ -33,3 +33,22 @@ libquicksched_la_SOURCES = qsched.c queue.c
 # List required headers
 include_HEADERS = atomic.h lock.h queue.h qsched.h task.h res.h error.h
 
+# CUDA sources 
+if HAVE_CUDA
+    SOURCES_CUDA = qsched.c queue.c cuda_queue.cu
+    CUDA_MYFLAGS = -O3 -g -DCPU_TPS=3.1e9 -lineinfo -src-in-ptx --maxrregcount=32 -Xptxas="-v" -Xptxas -dlcm=cg -gencode arch=compute_30,code=sm_30 -ftz=true -fmad=true -DFPTYPE_SINGLE -DWITH_CUDA
+.cu: qsched.c queue.c
+.cu.o:
+	$(NVCC) -c $(NVCCFLAGS) $(CUDA_CFLAGS) $(CUDA_MYFLAGS) $< -o $@
+.cu.lo:
+	$(top_srcdir)/cudalt.py $@ $(NVCC) -c $(NVCCFLAGS) $(CUDA_CFLAGS) $(CUDA_MYFLAGS) $<
+else
+    SOURCES_CUDA =
+endif
+
+# Build a CUDA-enabled version too?
+if HAVE_CUDA
+lib_LTLIBRARIES += libquicksched_cuda.la
+libquicksched_cuda_la_SOURCES = $(SOURCES_CUDA)
+libquicksched_cuda_la_CFLAGS = -DFPTYPE_SINGLE $(AM_CFLAGS) $(CUDA_CFLAGS)
+endif

src/cuda_queue.cu

+/*******************************************************************************
+ * This file is part of QuickSched.
+ * Coypright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk), Aidan Chalk (aidan.chalk@durham.ac.uk)
+ * 
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ ******************************************************************************/
+
+#include "cuda_queue.h"
+
+/*Define if conflicts are enabled or not.*/
+
+//#define GPU_locks
+
+/*Declare variables required for the queue*/
+__device__ struct queue_cuda cuda_queues[ cuda_numqueues ];
+__constant__ int cuda_nrqueues;
+__constant__ int cuda_queue_size;
+
+/**
+ * @brief Get a task ID from the given queue.
+ *
+ */
+ 
+__device__ int cuda_queue_gettask ( struct queue_cuda *q ) {
+
+    int ind, tid = -1;
+    
+    /* Don't even try... */
+    if ( q->rec_count == q->count )
+        return -1;
+
+    /* Get the index of the next task. */
+    ind = atomicAdd( &q->first , 1 );
+
+    /* Wrap the index. */
+    ind %= cuda_queue_size; 
+    /* Loop until there is a valid task at that index. */
+    while ( q->rec_count < q->count && ( tid = q->data[ind] ) < 0 );
+    
+    /* Scratch the task from the queue */
+    if ( tid >= 0 )
+        q->data[ind] = -1;
+
+    /* Return the acquired task ID. */
+    return tid;
+    
+    }
+
+
+/**
+ * @brief Put a task onto the given queue.
+ *
+ * @param tid The task ID to add to the end of the queue.
+ */
+ 
+__device__ void cuda_queue_puttask ( struct queue_cuda *q , int tid ) {
+
+    int ind;
+
+    /* Get the index of the next task. */
+    ind = atomicAdd( &q->last , 1 ) % cuda_queue_size;
+    
+    /* Wait for the slot in the queue to be empty. */
+    while ( q->data[ind] != -1 );
+
+    /* Write the task back to the queue. */
+    q->data[ind] = tid;
+    
+    }
+
+
+
+
+#ifdef GPU_locks
+
+
+//TODO
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#else
+
+/**
+ * @brief Get a task from the given task queue.
+ *
+ * Picks tasks from the queue sequentially and checks if they
+ * can be computed. If not, they are returned to the queue.
+ *
+ * This version of the routine does not check for conflicts.
+ *
+ * This routine blocks until a valid task is picked up, or the
+ * specified queue is empty.
+ */
+__device__ int runner_cuda_gettask ( struct queue_cuda *q ) {
+
+    int tid = -1;
+    
+    
+    /* Main loop. */
+    while ( ( tid = cuda_queue_gettask( q ) ) >= 0 ) {
+        break;    
+        }
+        
+    /* Put this task into the recycling queue, if needed. */
+    if ( tid >= 0 ) {
+            q->rec_data[ atomicAdd( (int *)&q->rec_count , 1 ) ] = tid;
+        }
+        
+        
+    /* Return whatever we got. */
+    return tid;
+
+    }
+
+
+#endif
+

src/cuda_queue.h

+/*******************************************************************************
+ * This file is part of QuickSched.
+ * Coypright (c) 2013 Pedro Gonnet (pedro.gonnet@durham.ac.uk), Aidan Chalk (aidan.chalk@durham.ac.uk)
+ * 
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ ******************************************************************************/
+#define cuda_max_unlock 128
+#define cuda_numqueues 2
+
+
+/** Struct for a task queue. */
+struct queue_cuda {
+
+    /* Indices to the first and last elements. */
+    int first, last;
+    
+    /* Number of elements in this queue. */
+    volatile int count;
+    
+    /* Number of elements in the recycled list. */
+    volatile int rec_count;
+    
+    /* The queue data. */
+    volatile int *data;
+    
+    /* The recycling list. */
+    volatile int *rec_data;
+
+    };
+
+
+/** Struct for each task. */
+struct task_cuda {
+
+    /** Task type and subtype. */
+    short int type, subtype;
+
+    /** Wait counters. */
+    volatile int wait;
+    
+    /** Task flags. */
+    int flags;
+
+    /** Indices of the cells involved. */
+    int i, j;
+    
+    /** Nr of task that this task unlocks. */
+    int nr_unlock;
+    
+    /** List of task that this task unlocks (dependencies). */
+    int unlock[ cuda_max_unlock ];
+    
+    };