Work on Makefiles.

1efe388f · Thomas Witkowski · 2c1294eb · 1efe388f · 1efe388f · 1efe388f
Commit 1efe388f authored Mar 17, 2011 by Thomas Witkowski
--- a/AMDiS/Makefile.am
+++ b/AMDiS/Makefile.am
-SUBDIRS = lib bin
-
-EXTRA_DIST = demo
+SUBDIRS = src lib
--- a/AMDiS/Makefile.in
+++ b/AMDiS/Makefile.in
@@ -142,6 +142,7 @@ PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 PETSC_DIR = @PETSC_DIR@
 RANLIB = @RANLIB@
+SED = @SED@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -193,8 +194,7 @@ sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
-SUBDIRS = lib bin
-EXTRA_DIST = demo
+SUBDIRS = src lib
 all: all-recursive

 .SUFFIXES:
@@ -418,7 +418,7 @@ distdir: $(DISTFILES)
 	      || exit 1; \
 	  fi; \
 	done
-	-find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+	-find $(distdir) -type d ! -perm -755 -exec chmod a+rwx,go+rx {} \; -o \
 	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -444 -exec $(SHELL) $(install_sh) -c -m a+r {} {} \; \

--- a/AMDiS/aclocal.m4
+++ b/AMDiS/aclocal.m4
@@ -1578,10 +1578,27 @@ linux*)
  # before this can be enabled.
  hardcode_into_libs=yes

+  # find out which ABI we are using
+  libsuff=
+  case "$host_cpu" in
+  x86_64*|s390x*|powerpc64*)
+    echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+    if AC_TRY_EVAL(ac_compile); then
+      case `/usr/bin/file conftest.$ac_objext` in
+      *64-bit*)
+        libsuff=64
+        sys_lib_search_path_spec="/lib${libsuff} /usr/lib${libsuff} /usr/local/lib${libsuff}"
+        ;;
+      esac
+    fi
+    rm -rf conftest*
+    ;;
+  esac
+
  # Append ld.so.conf contents to the search path
  if test -f /etc/ld.so.conf; then
-    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
-    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+    lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+    sys_lib_dlsearch_path_spec="/lib${libsuff} /usr/lib${libsuff} $lt_ld_extra"
  fi

  # We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -4288,6 +4305,9 @@ CC=$lt_[]_LT_AC_TAGVAR(compiler, $1)
 # Is the compiler the GNU C compiler?
 with_gcc=$_LT_AC_TAGVAR(GCC, $1)

+gcc_dir=\`gcc -print-file-name=. | $SED 's,/\.$,,'\`
+gcc_ver=\`gcc -dumpversion\`
+
 # An ERE matcher.
 EGREP=$lt_EGREP

@@ -4421,11 +4441,11 @@ striplib=$lt_striplib

 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects=$lt_[]_LT_AC_TAGVAR(predep_objects, $1)
+predep_objects=\`echo $lt_[]_LT_AC_TAGVAR(predep_objects, $1) | \$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=$lt_[]_LT_AC_TAGVAR(postdep_objects, $1)
+postdep_objects=\`echo $lt_[]_LT_AC_TAGVAR(postdep_objects, $1) | \$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.
@@ -4437,7 +4457,7 @@ postdeps=$lt_[]_LT_AC_TAGVAR(postdeps, $1)

 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path=$lt_[]_LT_AC_TAGVAR(compiler_lib_search_path, $1)
+compiler_lib_search_path=\`echo $lt_[]_LT_AC_TAGVAR(compiler_lib_search_path, $1) | \$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=$lt_deplibs_check_method
@@ -4517,7 +4537,7 @@ variables_saved_for_relink="$variables_saved_for_relink"
 link_all_deplibs=$_LT_AC_TAGVAR(link_all_deplibs, $1)

 # Compile-time system search path for libraries
-sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+sys_lib_search_path_spec=\`echo $lt_sys_lib_search_path_spec | \$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=$lt_sys_lib_dlsearch_path_spec
@@ -6353,6 +6373,7 @@ do
    done
  done
 done
+IFS=$as_save_IFS
 lt_ac_max=0
 lt_ac_count=0
 # Add /usr/xpg4/bin/sed as it is typically found on Solaris
@@ -6385,6 +6406,7 @@ for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
 done
 ])
 SED=$lt_cv_path_SED
+AC_SUBST([SED])
 AC_MSG_RESULT([$SED])
 ])


--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
-lib_LTLIBRARIES = libamdis.la libcompositeFEM.la
-
-SOURCE_DIR = ../src
-LIB_DIR = ../lib
-PARALLEL_DIR = $(SOURCE_DIR)
-
-PARMETIS_DIR = ../lib/ParMetis-3.1
-
-AMDIS_INCLUDES = -I$(SOURCE_DIR) 
-
-libamdis_la_CXXFLAGS = 
-
-PARALLEL_AMDIS_SOURCES = 
-PARALLEL_INCLUDES =
-
-if USE_PARALLEL_DOMAIN_AMDIS
-  PARALLEL_AMDIS_SOURCES += \
-  $(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
-  $(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
-  $(SOURCE_DIR)/parallel/ZoltanPartitioner.h $(SOURCE_DIR)/parallel/ZoltanPartitioner.cc \
-  $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
-  $(SOURCE_DIR)/parallel/MeshPartitioner.h $(SOURCE_DIR)/parallel/MeshPartitioner.cc \
-  $(SOURCE_DIR)/parallel/MeshManipulation.h $(SOURCE_DIR)/parallel/MeshManipulation.cc \
-  $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
-  $(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
-  $(SOURCE_DIR)/parallel/ParallelProblemStatBase.cc \
-  $(SOURCE_DIR)/parallel/PetscSolver.h $(SOURCE_DIR)/parallel/PetscSolver.cc \
-  $(SOURCE_DIR)/parallel/MpiHelper.h $(SOURCE_DIR)/parallel/MpiHelper.cc \
-  $(SOURCE_DIR)/parallel/ElementObjectData.h $(SOURCE_DIR)/parallel/ElementObjectData.cc
-  libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
-  AMDIS_INCLUDES += -I$(PARMETIS_DIR)
-  AMDIS_INCLUDES += -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
-  AMDIS_INCLUDES += -I$(LIB_DIR)/zoltan_build/include
-endif
-
-if ENABLE_UMFPACK
-  libamdis_la_CXXFLAGS += -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
-  AMDIS_INCLUDES += -I$(LIB_DIR)/UFconfig \
-	            -I$(LIB_DIR)/AMD/Include \
-                    -I$(LIB_DIR)/UMFPACK/Include  
-endif
-
-if ENABLE_MKL
-  libamdis_la_CXXFLAGS += -DHAVE_MKL=1 -I${MKL_INC}
-endif
-
-if ENABLE_DUNE
-  libamdis_la_CXXFLAGS += -DHAVE_DUNE=1
-  AMDIS_INCLUDES += -I$(DUNE_DIR)
-endif
-
-if ENABLE_BOOST
-  libamdis_la_CXXFLAGS += -DHAVE_BOOST=1
-endif
-
-TEMPLATE_INCLUDES = -I../lib/mtl4 
-
-INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES) $(TEMPLATE_INCLUDES)
-
-if AMDIS_DEBUG
-  libamdis_la_CXXFLAGS += -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
-else
-  libamdis_la_CXXFLAGS += -O3 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
-endif
-
-
-libamdis_la_SOURCES =  \
-$(PARALLEL_AMDIS_SOURCES) \
-$(SOURCE_DIR)/DOFIndexed.h $(SOURCE_DIR)/DOFIndexed.cc \
-$(SOURCE_DIR)/io/GNUPlotWriter.h $(SOURCE_DIR)/io/GNUPlotWriter.cc \
-$(SOURCE_DIR)/VertexVector.h $(SOURCE_DIR)/VertexVector.cc \
-$(SOURCE_DIR)/PeriodicBC.h $(SOURCE_DIR)/PeriodicBC.cc \
-$(SOURCE_DIR)/Recovery.h $(SOURCE_DIR)/Recovery.cc \
-$(SOURCE_DIR)/RecoveryEstimator.h $(SOURCE_DIR)/RecoveryEstimator.cc \
-$(SOURCE_DIR)/ResidualEstimator.h $(SOURCE_DIR)/ResidualEstimator.cc \
-$(SOURCE_DIR)/Cholesky.h $(SOURCE_DIR)/Cholesky.cc \
-$(SOURCE_DIR)/AdaptBase.h $(SOURCE_DIR)/AdaptBase.cc \
-$(SOURCE_DIR)/ProblemIterationInterface.h \
-$(SOURCE_DIR)/StandardProblemIteration.h $(SOURCE_DIR)/StandardProblemIteration.cc \
-$(SOURCE_DIR)/ProblemScal.h $(SOURCE_DIR)/ProblemScal.cc \
-$(SOURCE_DIR)/ProblemVec.h $(SOURCE_DIR)/ProblemVec.cc \
-$(SOURCE_DIR)/ProblemVecDbg.h $(SOURCE_DIR)/ProblemVecDbg.cc \
-$(SOURCE_DIR)/DualTraverse.h $(SOURCE_DIR)/DualTraverse.cc \
-$(SOURCE_DIR)/ElementPartition_ED.h $(SOURCE_DIR)/SurfacePartition_ED.h \
-$(SOURCE_DIR)/ElementData.h $(SOURCE_DIR)/ElementData.cc \
-$(SOURCE_DIR)/ComponentTraverseInfo.h $(SOURCE_DIR)/ComponentTraverseInfo.cc \
-$(SOURCE_DIR)/CreatorMap.h $(SOURCE_DIR)/CreatorMap.hh $(SOURCE_DIR)/CreatorMap.cc \
-$(SOURCE_DIR)/CreatorInterface.h \
-$(SOURCE_DIR)/ElementFunction.h \
-$(SOURCE_DIR)/ProblemInterpolScal.h $(SOURCE_DIR)/ProblemInterpolScal.cc \
-$(SOURCE_DIR)/ProblemInterpolVec.h $(SOURCE_DIR)/ProblemInterpolVec.cc \
-$(SOURCE_DIR)/Serializable.h \
-$(SOURCE_DIR)/Serializer.cc \
-$(SOURCE_DIR)/BallProject.h \
-$(SOURCE_DIR)/CylinderProject.h \
-$(SOURCE_DIR)/io/MacroInfo.h $(SOURCE_DIR)/io/MacroInfo.cc \
-$(SOURCE_DIR)/io/MacroReader.h $(SOURCE_DIR)/io/MacroReader.cc \
-$(SOURCE_DIR)/io/ValueReader.h $(SOURCE_DIR)/io/ValueReader.cc \
-$(SOURCE_DIR)/Projection.h $(SOURCE_DIR)/Projection.cc \
-$(SOURCE_DIR)/SubAssembler.h $(SOURCE_DIR)/SubAssembler.cc \
-$(SOURCE_DIR)/ZeroOrderAssembler.h $(SOURCE_DIR)/ZeroOrderAssembler.cc \
-$(SOURCE_DIR)/FirstOrderAssembler.h $(SOURCE_DIR)/FirstOrderAssembler.cc \
-$(SOURCE_DIR)/SecondOrderAssembler.h $(SOURCE_DIR)/SecondOrderAssembler.cc \
-$(SOURCE_DIR)/Assembler.h $(SOURCE_DIR)/Assembler.cc \
-$(SOURCE_DIR)/AdaptInfo.h $(SOURCE_DIR)/AdaptInfo.cc \
-$(SOURCE_DIR)/Marker.h $(SOURCE_DIR)/Marker.cc \
-$(SOURCE_DIR)/SystemVector.h \
-$(SOURCE_DIR)/SurfaceQuadrature.h $(SOURCE_DIR)/SurfaceQuadrature.cc \
-$(SOURCE_DIR)/LeafData.h $(SOURCE_DIR)/LeafData.cc \
-$(SOURCE_DIR)/BoundaryManager.h $(SOURCE_DIR)/BoundaryManager.cc \
-$(SOURCE_DIR)/BoundaryCondition.h \
-$(SOURCE_DIR)/DirichletBC.h $(SOURCE_DIR)/DirichletBC.cc \
-$(SOURCE_DIR)/RobinBC.h $(SOURCE_DIR)/RobinBC.cc \
-$(SOURCE_DIR)/AbstractFunction.h \
-$(SOURCE_DIR)/ProblemStatBase.h \
-$(SOURCE_DIR)/DOFContainer.h \
-$(SOURCE_DIR)/io/FileWriter.h $(SOURCE_DIR)/io/FileWriter.hh $(SOURCE_DIR)/io/FileWriter.cc \
-$(SOURCE_DIR)/io/ElementFileWriter.h $(SOURCE_DIR)/io/ElementFileWriter.cc \
-$(SOURCE_DIR)/ElInfo.cc \
-$(SOURCE_DIR)/ElInfoStack.h $(SOURCE_DIR)/ElInfoStack.cc \
-$(SOURCE_DIR)/OperatorTerm.h $(SOURCE_DIR)/OperatorTerm.cc \
-$(SOURCE_DIR)/ZeroOrderTerm.h $(SOURCE_DIR)/ZeroOrderTerm.cc \
-$(SOURCE_DIR)/FirstOrderTerm.h $(SOURCE_DIR)/FirstOrderTerm.cc \
-$(SOURCE_DIR)/SecondOrderTerm.h $(SOURCE_DIR)/SecondOrderTerm.cc \
-$(SOURCE_DIR)/Operator.h $(SOURCE_DIR)/Operator.cc \
-$(SOURCE_DIR)/Mesh.cc \
-$(SOURCE_DIR)/MeshStructure.h $(SOURCE_DIR)/MeshStructure.cc \
-$(SOURCE_DIR)/MeshStructure_ED.h \
-$(SOURCE_DIR)/AMDiS.h \
-$(SOURCE_DIR)/AdaptStationary.h $(SOURCE_DIR)/AdaptStationary.cc \
-$(SOURCE_DIR)/AdaptInstationary.h $(SOURCE_DIR)/AdaptInstationary.cc \
-$(SOURCE_DIR)/QPsiPhi.h \
-$(SOURCE_DIR)/BasisFunction.h \
-$(SOURCE_DIR)/Boundary.h \
-$(SOURCE_DIR)/ITL_Solver.h \
-$(SOURCE_DIR)/CoarseningManager.h \
-$(SOURCE_DIR)/CoarseningManager1d.h $(SOURCE_DIR)/CoarseningManager2d.h $(SOURCE_DIR)/CoarseningManager3d.h \
-$(SOURCE_DIR)/DOFAdmin.h \
-$(SOURCE_DIR)/DOFIterator.h \
-$(SOURCE_DIR)/DOFMatrix.h \
-$(SOURCE_DIR)/DOFVector.h $(SOURCE_DIR)/DOFVector.hh $(SOURCE_DIR)/DOFVector.cc \
-$(SOURCE_DIR)/Element.h $(SOURCE_DIR)/ElementConnection.h \
-$(SOURCE_DIR)/ElInfo.h $(SOURCE_DIR)/ElInfo1d.h $(SOURCE_DIR)/ElInfo2d.h $(SOURCE_DIR)/ElInfo3d.h \
-$(SOURCE_DIR)/Error.h $(SOURCE_DIR)/Error.hh \
-$(SOURCE_DIR)/Estimator.h $(SOURCE_DIR)/Estimator.cc \
-$(SOURCE_DIR)/FiniteElemSpace.h \
-$(SOURCE_DIR)/FixVec.h $(SOURCE_DIR)/FixVec.hh \
-$(SOURCE_DIR)/FixVecConvert.h \
-$(SOURCE_DIR)/Flag.h \
-$(SOURCE_DIR)/Global.h \
-$(SOURCE_DIR)/UmfPackSolver.h \ $(SOURCE_DIR)/UmfPackSolver.hh \
-$(SOURCE_DIR)/Lagrange.h $(SOURCE_DIR)/Line.h \
-$(SOURCE_DIR)/MacroElement.h $(SOURCE_DIR)/MacroWriter.h \
-$(SOURCE_DIR)/Markings.h $(SOURCE_DIR)/Markings.hh \
-$(SOURCE_DIR)/Mesh.h \
-$(SOURCE_DIR)/Parameters.h \
-$(SOURCE_DIR)/Parametric.h \
-$(SOURCE_DIR)/Quadrature.h \
-$(SOURCE_DIR)/RCNeighbourList.h \
-$(SOURCE_DIRe)/RefinementManager.h \
-$(SOURCE_DIR)/RefinementManager1d.h \
-$(SOURCE_DIR)/RefinementManager2d.h \
-$(SOURCE_DIR)/RefinementManager3d.h \
-$(SOURCE_DIR)/Tetrahedron.h \
-$(SOURCE_DIR)/Traverse.h \
-$(SOURCE_DIR)/Triangle.h \
-$(SOURCE_DIR)/NonLinSolver.h $(SOURCE_DIR)/NonLinSolver.hh \
-$(SOURCE_DIR)/ProblemInstat.h $(SOURCE_DIR)/ProblemInstat.cc \
-$(SOURCE_DIR)/ProblemTimeInterface.h \
-$(SOURCE_DIR)/ProblemNonLin.h $(SOURCE_DIR)/ProblemNonLin.cc \
-$(SOURCE_DIR)/NonLinUpdater.h $(SOURCE_DIR)/NonLinUpdater.cc \
-$(SOURCE_DIR)/Newton.h $(SOURCE_DIR)/Newton.hh  \
-$(SOURCE_DIR)/NewtonFS.h $(SOURCE_DIR)/NewtonFS.hh \
-$(SOURCE_DIR)/io/GridWriter.h $(SOURCE_DIR)/io/GridWriter.hh \
-$(SOURCE_DIR)/io/ValueWriter.h \
-$(SOURCE_DIR)/QPsiPhi.cc \
-$(SOURCE_DIR)/BasisFunction.cc \
-$(SOURCE_DIR)/Boundary.cc \
-$(SOURCE_DIR)/CoarseningManager.cc \
-$(SOURCE_DIR)/CoarseningManager1d.cc \
-$(SOURCE_DIR)/CoarseningManager2d.cc \
-$(SOURCE_DIR)/CoarseningManager3d.cc \
-$(SOURCE_DIR)/DOFAdmin.cc \
-$(SOURCE_DIR)/DOFMatrix.cc \
-$(SOURCE_DIR)/Element.cc \
-$(SOURCE_DIR)/ElInfo1d.cc \
-$(SOURCE_DIR)/ElInfo2d.cc \
-$(SOURCE_DIR)/ElInfo3d.cc \
-$(SOURCE_DIR)/FiniteElemSpace.cc \
-$(SOURCE_DIR)/FixVec.cc \
-$(SOURCE_DIR)/Global.cc \
-$(SOURCE_DIR)/Lagrange.cc \
-$(SOURCE_DIR)/Line.cc \
-$(SOURCE_DIR)/MacroElement.cc \
-$(SOURCE_DIR)/io/MacroWriter.cc \
-$(SOURCE_DIR)/Parameters.cc \
-$(SOURCE_DIR)/Parametric.cc \
-$(SOURCE_DIR)/Quadrature.cc \
-$(SOURCE_DIR)/RCNeighbourList.cc \
-$(SOURCE_DIR)/RefinementManager.cc \
-$(SOURCE_DIR)/RefinementManager1d.cc \
-$(SOURCE_DIR)/RefinementManager2d.cc \
-$(SOURCE_DIR)/RefinementManager3d.cc \
-$(SOURCE_DIR)/Tetrahedron.cc \
-$(SOURCE_DIR)/Traverse.cc \
-$(SOURCE_DIR)/TraverseParallel.h $(SOURCE_DIR)/TraverseParallel.cc \
-$(SOURCE_DIR)/Triangle.cc \
-$(SOURCE_DIR)/io/ValueWriter.cc \
-$(SOURCE_DIR)/io/VtkWriter.h $(SOURCE_DIR)/io/VtkWriter.cc \
-$(SOURCE_DIR)/io/DofWriter.h $(SOURCE_DIR)/io/DofWriter.cc \
-$(SOURCE_DIR)/io/PngWriter.h $(SOURCE_DIR)/io/PngWriter.cc \
-$(SOURCE_DIR)/io/PovrayWriter.h $(SOURCE_DIR)/io/PovrayWriter.cc \
-$(SOURCE_DIR)/io/DataCollector.h $(SOURCE_DIR)/io/DataCollector.cc \
-$(SOURCE_DIR)/ElementInfo.h \
-$(SOURCE_DIR)/VertexInfo.h \
-$(SOURCE_DIR)/PeriodicInfo.h \
-$(SOURCE_DIR)/OpenMP.h \
-$(SOURCE_DIR)/ScalableQuadrature.h $(SOURCE_DIR)/ScalableQuadrature.cc \
-$(SOURCE_DIR)/SubElInfo.h $(SOURCE_DIR)/SubElInfo.cc \
-$(SOURCE_DIR)/SolutionDataStorage.h $(SOURCE_DIR)/SolutionDataStorage.hh \
-$(SOURCE_DIR)/ElementDofIteartor.h $(SOURCE_DIR)/ElementDofIterator.cc \
-$(SOURCE_DIR)/parallel/InteriorBoundary.h $(SOURCE_DIR)/parallel/InteriorBoundary.cc \
-$(SOURCE_DIR)/Debug.h $(SOURCE_DIR)/Debug.cc \
-$(SOURCE_DIR)/io/ArhReader.h $(SOURCE_DIR)/io/ArhReader.cc \
-$(SOURCE_DIR)/io/ArhWriter.h $(SOURCE_DIR)/io/ArhWriter.cc \
-$(SOURCE_DIR)/time/RosenbrockAdaptInstationary.h $(SOURCE_DIR)/time/RosenbrockAdaptInstationary.cc \
-$(SOURCE_DIR)/time/RosenbrockStationary.h $(SOURCE_DIR)/time/RosenbrockStationary.cc \
-$(SOURCE_DIR)/time/RosenbrockMethod.h $(SOURCE_DIR)/time/RosenbrockMethod.cc 
-
-COMPOSITE_SOURCE_DIR = ../compositeFEM/src
-
-libcompositeFEM_la_CXXFLAGS = $(libamdis_la_CXXFLAGS)
-
-
-libcompositeFEM_la_SOURCES = $(COMPOSITE_SOURCE_DIR)/CFE_Integration.h \
-$(COMPOSITE_SOURCE_DIR)/CFE_Integration.cc \
-$(COMPOSITE_SOURCE_DIR)/CFE_NormAndErrorFcts.h \
-$(COMPOSITE_SOURCE_DIR)/CFE_NormAndErrorFcts.cc \
-$(COMPOSITE_SOURCE_DIR)/CompositeFEMMethods.h \
-$(COMPOSITE_SOURCE_DIR)/CompositeFEMMethods.cc \
-$(COMPOSITE_SOURCE_DIR)/LevelSetAdaptMesh.h \
-$(COMPOSITE_SOURCE_DIR)/LevelSetAdaptMesh.cc \
-$(COMPOSITE_SOURCE_DIR)/PenaltyOperator.h \
-$(COMPOSITE_SOURCE_DIR)/PenaltyOperator.cc \
-$(COMPOSITE_SOURCE_DIR)/ElementLevelSet.h \
-$(COMPOSITE_SOURCE_DIR)/ElementLevelSet.cc \
-$(COMPOSITE_SOURCE_DIR)/CompositeFEMOperator.h \
-$(COMPOSITE_SOURCE_DIR)/CompositeFEMOperator.cc \
-$(COMPOSITE_SOURCE_DIR)/SubPolytope.h $(COMPOSITE_SOURCE_DIR)/SubPolytope.cc \
-$(COMPOSITE_SOURCE_DIR)/SubElementAssembler.h \
-$(COMPOSITE_SOURCE_DIR)/SubElementAssembler.cc \
-$(COMPOSITE_SOURCE_DIR)/TranslateLsFct.h
-
--- a/AMDiS/configure
+++ b/AMDiS/configure
--- a/AMDiS/configure.ac
+++ b/AMDiS/configure.ac
@@ -125,7 +125,7 @@ AC_PROG_CXX
 AC_PROG_LIBTOOL
 AC_CONFIG_FILES([
 	Makefile
+	src/Makefile
 	lib/Makefile
-	bin/Makefile
 	])
 AC_OUTPUT
--- a/AMDiS/libtool
+++ b/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 deimos102:
+# 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.
@@ -82,22 +82,25 @@ 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

+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`
+
 # 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"
@@ -171,7 +174,7 @@ 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"
@@ -229,11 +232,11 @@ striplib="strip --strip-unneeded"

 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects=""
+predep_objects=`echo "" | $SED -e "s@${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=""
+postdep_objects=`echo "" | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`

 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -245,7 +248,7 @@ postdeps=""

 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path=""
+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"
@@ -325,10 +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=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /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/ /fastfs/wir/local/lib/ /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=`echo " /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/i386-redhat-linux/4.1.2/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/ /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"`

 # 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/mysql /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "

 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -6760,7 +6763,7 @@ 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 deimos102:
+# Libtool was configured on host NWRW15:

 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -6782,12 +6785,12 @@ 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.
@@ -6798,22 +6801,25 @@ 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/mpicxx"
+CC="g++"

 # Is the compiler the GNU C compiler?
 with_gcc=yes

+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`
+
 # 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"
@@ -6887,7 +6893,7 @@ 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 +6948,11 @@ 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=`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"`

 # 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=`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"`

 # Dependencies to place before the objects being linked to create a
 # shared library.
@@ -6954,11 +6960,11 @@ 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/fastfs/wir/local/lib -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=`echo "-L/u/witkowski/local/lib -L/u/witkowski/local/intel/mkl/10.0.1.014/lib/32 -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"`

 # Method to check whether dependent libraries are shared objects.
 deplibs_check_method="pass_all"
@@ -7038,10 +7044,10 @@ 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=" /fastfs/wir/local/lib/x86_64-suse-linux/4.1.2/ /fastfs/wir/local/lib/../lib64/ /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/ /fastfs/wir/local/lib/ /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=`echo " /u/witkowski/local/lib/i386-redhat-linux/4.1.2/ /u/witkowski/local/lib/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/i386-redhat-linux/4.1.2/ /u/witkowski/local/intel/mkl/10.0.1.014/lib/32/ /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"`

 # 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/mysql /usr/lib/octave-2.9.9 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "

 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""
@@ -7065,7 +7071,7 @@ include_expsyms=""

 # ### BEGIN LIBTOOL TAG CONFIG: F77

-# Libtool was configured on host deimos102:
+# Libtool was configured on host NWRW15:

 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7087,12 +7093,12 @@ 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 +7109,7 @@ 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 +7118,16 @@ LTCFLAGS="-g -O2"
 CC="g77"

 # Is the compiler the GNU C compiler?
-with_gcc=
+with_gcc=yes
+
+gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+gcc_ver=`gcc -dumpversion`

 # An ERE matcher.
 EGREP="grep -E"

 # The linker used to build libraries.
-LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"