* Small bugfix of VtkWriter. writeFiles(const std::string) should now work.

AMDiS/libtool

@@ -30,10 +30,10 @@
 # the same distribution terms that you use for the rest of that program.
 
 # A sed program that does not truncate output.
-SED="/bin/sed"
+SED="/usr/bin/sed"
 
 # Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/bin/sed -e 1s/^X//"
+Xsed="/usr/bin/sed -e 1s/^X//"
 
 # The HP-UX ksh and POSIX shell print the target directory to stdout
 # if CDPATH is set.
@@ -44,7 +44,7 @@ available_tags=" CXX F77"
 
 # ### BEGIN LIBTOOL CONFIG
 
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1s060:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=i686-redhat-linux-gnu
+host=x86_64-unknown-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i686-redhat-linux-gnu
+build=x86_64-unknown-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -82,25 +82,25 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="gcc"
+LTCC="icc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="gcc"
+CC="icc"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
 
-gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
 gcc_ver=`gcc -dumpversion`
 
 # An ERE matcher.
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/bin/ld -m elf_x86_64"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -177,7 +177,7 @@ dlopen_self_static=unknown
 link_static_flag="-static"
 
 # Compiler flag to turn off builtin functions.
-no_builtin_flag=" -fno-builtin"
+no_builtin_flag=" -fno-builtin -fno-rtti -fno-exceptions"
 
 # Compiler flag to allow reflexive dlopens.
 export_dynamic_flag_spec="\${wl}--export-dynamic"
@@ -328,10 +328,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
 link_all_deplibs=unknown
 
 # Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7266,7 +7266,7 @@ disable_libs=static
 # End:
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1s060:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7288,12 +7288,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=i686-redhat-linux-gnu
+host=x86_64-unknown-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i686-redhat-linux-gnu
+build=x86_64-unknown-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -7304,25 +7304,25 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="gcc"
+LTCC="icc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="g++"
+CC="icpc"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
 
-gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
 gcc_ver=`gcc -dumpversion`
 
 # An ERE matcher.
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/bin/ld -m elf_x86_64"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -7436,8 +7436,8 @@ old_archive_from_new_cmds=""
 old_archive_from_expsyms_cmds=""
 
 # Commands used to build and install a shared archive.
-archive_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
-archive_expsym_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-retain-symbols-file \$wl\$export_symbols -o \$lib"
+archive_cmds="\$CC -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
+archive_expsym_cmds="\$CC -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-retain-symbols-file \$wl\$export_symbols -o \$lib"
 postinstall_cmds=""
 postuninstall_cmds=""
 
@@ -7451,11 +7451,11 @@ striplib="strip --strip-unneeded"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+predep_objects=`echo "-mIPOPT_obj_output_file_name=/tmp/ipo_icpcNKAC6p.o -mGLOB_obj_output_file=/tmp/ipo_icpcNKAC6p.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdep_objects=`echo "/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+postdep_objects=`echo "/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtbeginS.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/crtn.o" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -7463,11 +7463,11 @@ predeps=""
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-L/work/licsoft/compilers/intel/cce/10.1.015/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/ -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -limf -lsvml -lm -lipgo -lstdc++ -lintlc -lgcc_s -lintlc -lc -lgcc_s -lirc_s -ldl -lc"
 
 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path=`echo "-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+compiler_lib_search_path=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Method to check whether dependent libraries are shared objects.
 deplibs_check_method="pass_all"
@@ -7513,7 +7513,7 @@ hardcode_into_libs=yes
 
 # Flag to hardcode $libdir into a binary during linking.
 # This must work even if $libdir does not exist.
-hardcode_libdir_flag_spec="\${wl}--rpath \${wl}\$libdir"
+hardcode_libdir_flag_spec="\${wl}-rpath,\$libdir"
 
 # If ld is used when linking, flag to hardcode $libdir into
 # a binary during linking. This must work even if $libdir does
@@ -7547,10 +7547,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
 link_all_deplibs=unknown
 
 # Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../i386-redhat-linux/4.1.2/ /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ /lib/i386-redhat-linux/4.1.2/ /lib/ /usr/lib/i386-redhat-linux/4.1.2/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7574,7 +7574,7 @@ include_expsyms=""
 
 # ### BEGIN LIBTOOL TAG CONFIG: F77
 
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p1s060:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7596,12 +7596,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=i686-redhat-linux-gnu
+host=x86_64-unknown-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i686-redhat-linux-gnu
+build=x86_64-unknown-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -7612,7 +7612,7 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="gcc"
+LTCC="icc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
@@ -7621,16 +7621,16 @@ LTCFLAGS="-g -O2"
 CC="g77"
 
 # Is the compiler the GNU C compiler?
-with_gcc=yes
+with_gcc=
 
-gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_dir=`gcc -print-file-name=. | /usr/bin/sed 's,/\.$,,'`
 gcc_ver=`gcc -dumpversion`
 
 # An ERE matcher.
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/bin/ld -m elf_x86_64"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -7858,10 +7858,10 @@ variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COM
 link_all_deplibs=unknown
 
 # Compile-time system search path for libraries
-sys_lib_search_path_spec=`echo " /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../i386-redhat-linux/lib/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../i386-redhat-linux/3.4.6/ /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../ /lib/i386-redhat-linux/3.4.6/ /lib/ /usr/lib/i386-redhat-linux/3.4.6/ /usr/lib/" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+sys_lib_search_path_spec=`echo "/lib64 /usr/lib64 /usr/local/lib64" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib "
+sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/x86_64-suse-linux/lib /usr/local/lib64 /usr/local/lib /opt/kde3/lib64 /opt/kde3/lib /opt/gnome/lib64 /opt/gnome/lib /lib64 /lib /usr/lib64 /usr/lib /opt/cluster/intel/cce/9.1.042/lib /opt/cluster/intel/fce/9.1.036/lib /opt/cluster/Pathscale3.0/lib/2.9.99 /opt/cluster/Pathscale3.0/lib/2.9.99/32 /work/licsoft/compilers/pgi/linux86-64/6.2/lib /work/licsoft/compilers/pgi/linux86-64/6.2/libso "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""

AMDiS/src/VtkWriter.cc

@@ -11,7 +11,7 @@
 
 namespace AMDiS { 
 
-  int VtkWriter::writeFile(const std::string &name)
+  int VtkWriter::writeFile(const std::string name)
   {
 #ifdef HAVE_BOOST
     
@@ -29,14 +29,14 @@ namespace AMDiS {
       file.push(boost::iostreams::file_descriptor_sink(name));
       break;
     } 
-    writeFile(file);
+    writeFileToStream(file);
 
 #else
 
     std::ofstream file;
     file.open(name.c_str());
     TEST_EXIT(file.is_open())("Cannot open file %s for writing\n", name.c_str());
-    writeFile(file);    
+    writeFileToStream(file);    
     file.close();
 
 #endif

AMDiS/src/VtkWriter.h

@@ -49,7 +49,7 @@ namespace AMDiS {
 
 
     /// Writes a ParaView-VTK file.
-    int writeFile(const std::string &name);
+    int writeFile(const std::string name);
 
     /// May be used to simply write ParaView files.
     static void writeFile(DOFVector<double> *values,
@@ -65,62 +65,38 @@ namespace AMDiS {
 			    std::vector< std::string > *paraViewAnimationFrames,
 			    const std::string &animationFilename);
   protected:
-    /** \brief
-     * Writes the VTU file to an arbitrary stream.
-     */
+    /// Writes the VTK file to an arbitrary stream.
     template<typename T>
-    void writeFile(T &file);
+    void writeFileToStream(T &file);
 
-    /** \brief
-     * Writes all coordinates of vertices and interpolation points to an
-     * output file.
-     */
+    /// Writes all coordinates of vertices and interpolation points to an output file.
     template<typename T>
     void writeVertexCoords(T &file);
 
-
-    /** \brief
-     * Writes all values of vertices and interpolation point to an output 
-     * file.
-     */
+    /// Writes all values of vertices and interpolation point to an output file.
     template<typename T>
     void writeVertexValues(T &file, int componentNo);
 
-
-    /** \brief
-     * Writes the connectivity of all simplices to an output file.
-     */
+    /// Writes the connectivity of all simplices to an output file.
     template<typename T>
     void writeConnectivity(T &file);
 
-    /** \brief
-     * Writes the connectivity for the case dim = 2 and degree = 2 to
-     * an output file.
-     */
+    /// Writes the connectivity for the case dim = 2 and degree = 2 to an output file.
     template<typename T>
     void writeConnectivity_dim2_degree2(T &file);
 
-
-    /** \brief
-     * Writes the connectivity for the case dim = 2 and degree = 3 to
-     * an output file.
-     */
+    /// Writes the connectivity for the case dim = 2 and degree = 3 to an output file.
     template<typename T>
     void writeConnectivity_dim2_degree3(T &file);
 
-
-    /** \brief
-     * Writes the connectivity for the case dim = 2 and degree = 4 to
-     * an output file.
-     */
+    /// Writes the connectivity for the case dim = 2 and degree = 4 to an output file.
     template<typename T>
     void writeConnectivity_dim2_degree4(T &file);
 
 #ifdef HAVE_BOOST
-    /** \brief
-     * Writes a world coordinate to a given file.
-     */
-    inline void writeCoord(boost::iostreams::filtering_ostream &file, WorldVector<double> coord) {
+    /// Writes a world coordinate to a given file.
+    inline void writeCoord(boost::iostreams::filtering_ostream &file, 
+			   WorldVector<double> coord) {
       for (int i = 0; i < Global::getGeo(WORLD); i++) {
 	file << " " << std::scientific << coord[i];
       }
@@ -131,9 +107,7 @@ namespace AMDiS {
     }
 #endif
 
-    /** \brief
-     * Writes a world coordinate to a given file.
-     */
+    /// Writes a world coordinate to a given file.
     inline void writeCoord(std::ofstream &file, WorldVector<double> coord) {
       for (int i = 0; i < Global::getGeo(WORLD); i++) {
 	file << " " << std::scientific << coord[i];
@@ -145,27 +119,19 @@ namespace AMDiS {
     }
 
   private:
-    /** \brief
-     * List of DataCollectors, for each component of the problem one.
-     */
+    /// List of DataCollectors, for each component of the problem one.
     std::vector<DataCollector*> *dataCollector;
 
-
     /** \brief
      * Defines if the file has to be compressed for ouput, and with which
      * kind of compress method.
      */
     FileCompression compress;
 
-    /** \brief
-     * Degree of the basis function of the problem.
-     */
+    /// Degree of the basis function of the problem.
     int degree;
     
-
-    /** \brief
-     * Dimension of the geometry.
-     */
+    /// Dimension of the geometry.
     int dim;
   };
 }

AMDiS/src/VtkWriter.hh

@@ -5,7 +5,7 @@
 namespace AMDiS {
 
   template<typename T>
-  void VtkWriter::writeFile(T &file)
+  void VtkWriter::writeFileToStream(T &file)
   {
     int nVertices = (*dataCollector)[0]->getNumberVertices();
     int nElements = (*dataCollector)[0]->getNumberElements();