Added matlab output functions for matrices and vectors.

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="/usr/bin/sed"
+SED="/bin/sed"
 
 # Sed that helps us avoid accidentally triggering echo(1) options like -n.
-Xsed="/usr/bin/sed -e 1s/^X//"
+Xsed="/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 deimos103:
+# Libtool was configured on host NWRW15:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -82,13 +82,13 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+CC="gcc"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
@@ -97,7 +97,7 @@ with_gcc=yes
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -171,7 +171,7 @@ dlopen_self=unknown
 dlopen_self_static=unknown
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
 
 # Compiler flag to turn off builtin functions.
 no_builtin_flag=" -fno-builtin"
@@ -325,10 +325,10 @@ 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=" /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
+sys_lib_search_path_spec=" /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/"
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
 # End:
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
-# Libtool was configured on host deimos103:
+# Libtool was configured on host NWRW15:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -6782,12 +6782,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -6798,13 +6798,13 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
 
 # A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
+CC="g++"
 
 # Is the compiler the GNU C compiler?
 with_gcc=yes
@@ -6813,7 +6813,7 @@ with_gcc=yes
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -6887,7 +6887,7 @@ dlopen_self=unknown
 dlopen_self_static=unknown
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
 
 # Compiler flag to turn off builtin functions.
 no_builtin_flag=" -fno-builtin"
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects="/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"
+predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdep_objects="/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"
+postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -6954,11 +6954,11 @@ predeps=""
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
 
 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path="-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
+compiler_lib_search_path="-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/../../.."
 
 # Method to check whether dependent libraries are shared objects.
 deplibs_check_method="pass_all"
@@ -7038,10 +7038,10 @@ 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=" /usr/lib64/gcc/x86_64-suse-linux/4.1.2/ /usr/lib/gcc/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../x86_64-suse-linux/4.1.2/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64/ /lib/x86_64-suse-linux/4.1.2/ /lib/../lib64/ /usr/lib/x86_64-suse-linux/4.1.2/ /usr/lib/../lib64/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../ /lib/ /usr/lib/"
+sys_lib_search_path_spec=" /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/"
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7065,7 +7065,7 @@ include_expsyms=""
 
 # ### BEGIN LIBTOOL TAG CONFIG: F77
 
-# Libtool was configured on host deimos103:
+# Libtool was configured on host NWRW15:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7087,12 +7087,12 @@ fast_install=yes
 
 # The host system.
 host_alias=
-host=x86_64-unknown-linux-gnu
+host=i686-pc-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=x86_64-unknown-linux-gnu
+build=i686-pc-linux-gnu
 build_os=linux-gnu
 
 # An echo program that does not interpret backslashes.
@@ -7103,7 +7103,7 @@ AR="ar"
 AR_FLAGS="cru"
 
 # A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
@@ -7112,13 +7112,13 @@ LTCFLAGS="-g -O2"
 CC="g77"
 
 # Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
 
 # An ERE matcher.
 EGREP="grep -E"
 
 # The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
+LD="/usr/bin/ld"
 
 # Whether we need hard or soft links.
 LN_S="ln -s"
@@ -7346,10 +7346,10 @@ 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=" /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/ /usr/lib/gcc/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../x86_64-suse-linux/3.3.5/ /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../ /lib/x86_64-suse-linux/3.3.5/ /lib/ /usr/lib/x86_64-suse-linux/3.3.5/ /usr/lib/"
+sys_lib_search_path_spec=" /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/"
 
 # Run-time system search path for libraries
-sys_lib_dlsearch_path_spec="/lib /usr/lib /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 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""

AMDiS/src/Debug.cc

+#include <iostream>
+#include <fstream>
 #include <boost/lexical_cast.hpp>
 #include "Debug.h"
 #include "DOFVector.h"
@@ -191,6 +193,45 @@ namespace AMDiS {
       ElementFileWriter::writeFile(vec, feSpace, filename);
     }
 
+    void writeMatlabMatrix(DOFMatrix &mat, std::string filename)
+    {
+      using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+      namespace traits = mtl::traits;
+      typedef DOFMatrix::base_matrix_type Matrix;
+
+      traits::row<Matrix>::type row(mat.getBaseMatrix());
+      traits::col<Matrix>::type col(mat.getBaseMatrix());
+      traits::const_value<Matrix>::type value(mat.getBaseMatrix());
+
+      typedef traits::range_generator<major, Matrix>::type cursor_type;
+      typedef traits::range_generator<nz, cursor_type>::type icursor_type;
+
+      std::ofstream out;
+      out.open(filename.c_str());
+    
+      for (cursor_type cursor = begin<major>(mat.getBaseMatrix()), 
+	     cend = end<major>(mat.getBaseMatrix()); cursor != cend; ++cursor)
+	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); icursor != icend; ++icursor)
+	  out << row(*icursor) + 1 << " " 
+	      << col(*icursor) + 1 << " " 
+	      << value(*icursor) << "\n";
+
+      out.close();
+    }
+
+    void writeMatlabVector(DOFVector<double> &vec, std::string filename)
+    {
+      std::ofstream out;    
+      out.open(filename.c_str());
+
+      DOFIterator<double> it(&vec, USED_DOFS);
+      int counter = 1;
+      for (it.reset(); !it.end(); ++it)
+	out << counter++ << " " << *it << "\n";
+
+      out.close();      
+    }
+
   } // namespace debug
   
 } // namespace AMDiS

AMDiS/src/Debug.h

@@ -51,6 +51,10 @@ namespace AMDiS {
     void printMatValuesStatistics(Matrix<DOFMatrix*> *mat);
 
     void writeElementIndexMesh(FiniteElemSpace *feSpace, std::string filename);
+
+    void writeMatlabMatrix(DOFMatrix &mat, std::string filename);
+
+    void writeMatlabVector(DOFVector<double> &vec, std::string filename);
   }
 }
 

AMDiS/src/ProblemScal.cc

@@ -23,6 +23,7 @@
 #include "ValueReader.h"
 #include "ElementFileWriter.h"
 #include "ProblemVec.h"
+#include "Debug.h"
 
 namespace AMDiS {
 
@@ -232,7 +233,10 @@ namespace AMDiS {
 #ifdef _OPENMP
     double wtime = omp_get_wtime();
 #endif
-    clock_t first = clock();
+    clock_t first = clock();    
+
+    debug::writeMatlabMatrix(*systemMatrix, "ac.dat");
+    exit(0);
 
     SolverMatrix<DOFMatrix> solverMatrix;
     solverMatrix.setMatrix(*systemMatrix);