made something wrong in last commit with parallel domain amdis

AMDiS/bin/Makefile.am

@@ -31,6 +31,7 @@ if USE_PARALLEL_DOMAIN_AMDIS
   PARALLEL_AMDIS_SOURCES += \
   $(PARALLEL_DIR)/ParallelDomainProblem.h $(PARALLEL_DIR)/ParallelDomainProblem.cc
   libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
+  AMDIS_INCLUDES += -I/work/home7/witkowsk/local/include
 endif
 
 if ENABLE_UMFPACK

AMDiS/bin/Makefile.in

@@ -41,17 +41,18 @@ host_triplet = @host@
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@  $(PARALLEL_DIR)/ParallelDomainProblem.h $(PARALLEL_DIR)/ParallelDomainProblem.cc
 
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
-@ENABLE_UMFPACK_TRUE@am__append_4 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
-@ENABLE_UMFPACK_TRUE@am__append_5 = -I$(LIB_DIR)/UFconfig \
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I/work/home7/witkowsk/local/include
+@ENABLE_UMFPACK_TRUE@am__append_5 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
+@ENABLE_UMFPACK_TRUE@am__append_6 = -I$(LIB_DIR)/UFconfig \
 @ENABLE_UMFPACK_TRUE@	            -I$(LIB_DIR)/AMD/Include \
 @ENABLE_UMFPACK_TRUE@                    -I$(LIB_DIR)/UMFPACK/Include  
 
-@ENABLE_MKL_TRUE@am__append_6 = -DHAVE_MKL=1 -I${MKL_INC}
-@ENABLE_DUNE_TRUE@am__append_7 = -DHAVE_DUNE=1
-@ENABLE_DUNE_TRUE@am__append_8 = -I$(DUNE_DIR)
-@ENABLE_BOOST_TRUE@am__append_9 = -DHAVE_BOOST=1
-@AMDIS_DEBUG_TRUE@am__append_10 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
-@AMDIS_DEBUG_FALSE@am__append_11 = -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
+@ENABLE_MKL_TRUE@am__append_7 = -DHAVE_MKL=1 -I${MKL_INC}
+@ENABLE_DUNE_TRUE@am__append_8 = -DHAVE_DUNE=1
+@ENABLE_DUNE_TRUE@am__append_9 = -I$(DUNE_DIR)
+@ENABLE_BOOST_TRUE@am__append_10 = -DHAVE_BOOST=1
+@AMDIS_DEBUG_TRUE@am__append_11 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) $(INCLUDES) #-pedantic
+@AMDIS_DEBUG_FALSE@am__append_12 = -O2 -Wall -DDEBUG=0 -DNDEBUG $(OPENMP_FLAG) -ftemplate-depth-100 $(INCLUDES) #-pedantic
 subdir = bin
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -440,10 +441,11 @@ SOURCE_DIR = ../src
 LIB_DIR = ../lib
 PARALLEL_DIR = $(SOURCE_DIR)
 PARMETIS_DIR = ../lib/ParMetis-3.1
-AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_5) $(am__append_8)
-libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_3) $(am__append_4) \
-	$(am__append_6) $(am__append_7) $(am__append_9) \
-	$(am__append_10) $(am__append_11)
+AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_4) $(am__append_6) \
+	$(am__append_9)
+libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_3) $(am__append_5) \
+	$(am__append_7) $(am__append_8) $(am__append_10) \
+	$(am__append_11) $(am__append_12)
 @USE_PARALLEL_AMDIS_FALSE@PARALLEL_AMDIS_SOURCES = $(am__append_2)
 @USE_PARALLEL_AMDIS_TRUE@PARALLEL_AMDIS_SOURCES = $(PARALLEL_DIR)/ConditionalEstimator.h \
 @USE_PARALLEL_AMDIS_TRUE@	$(PARALLEL_DIR)/ConditionalEstimator.cc \

AMDiS/configure

@@ -2102,9 +2102,9 @@ else
 fi
-# Check whether --enable-paralleldomain or --disable-paralleldomain was given.
-if test "${enable_paralleldomain+set}" = set; then
-  enableval="$enable_paralleldomain"
+# Check whether --enable-parallel-domain or --disable-parallel-domain was given.
+if test "${enable_parallel_domain+set}" = set; then
+  enableval="$enable_parallel_domain"
   case "${enableval}" in
     yes) paralleldomain=true ;;
     no)  paralleldomain=false ;;

AMDiS/configure.ac

@@ -63,7 +63,7 @@ AC_ARG_ENABLE(parmetis,
   esac],[parmetis=false])
 AM_CONDITIONAL(USE_PARALLEL_AMDIS, test $parmetis = true)
 
-AC_ARG_ENABLE(paralleldomain,
+AC_ARG_ENABLE(parallel-domain,
   [  --enable-parallel-domain  Parallelization with classical domain decomposition],
   [case "${enableval}" in
     yes) paralleldomain=true ;;

AMDiS/src/ParallelDomainProblem.cc

@@ -285,7 +285,7 @@ namespace AMDiS {
   void ParallelDomainProblemBase::fillPetscMatrix(DOFMatrix *mat, 
 						  DOFVector<double> *vec)
   {
-    DOFMatrix::Iterator rowIt(mat, USED_DOFS);
+    /*   DOFMatrix::Iterator rowIt(mat, USED_DOFS);
     for (rowIt.reset(); !rowIt.end(); ++rowIt) {
       for (int i = 0; i < static_cast<int>((*rowIt).size()); i++) {
 	if ((*rowIt)[i].col >= 0) {
@@ -303,7 +303,7 @@ namespace AMDiS {
       double value = *dofIt;
 
       VecSetValues(petscRhsVec, 1, &index, &value, ADD_VALUES);
-    }
+      }*/
   }
 
   double ParallelDomainProblemBase::setElemWeights(AdaptInfo *adaptInfo)