From d5c8e677c8c15f282c0dbefa833082531444725c Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Tue, 21 Apr 2009 11:25:23 +0000
Subject: [PATCH] Changes for parallelization
---
AMDiS/libtool | 70 ++++++------
AMDiS/src/CoarseningManager.h | 10 --
AMDiS/src/DOFAdmin.h | 173 ++++++++---------------------
AMDiS/src/ElementFileWriter.cc | 6 +-
AMDiS/src/MacroReader.cc | 169 ++++++++++++++--------------
AMDiS/src/MacroReader.h | 59 +++-------
AMDiS/src/Mesh.cc | 45 ++------
AMDiS/src/Mesh.h | 10 --
AMDiS/src/ParallelDomainProblem.cc | 14 ++-
AMDiS/src/ProblemNonLin.cc | 27 +++--
AMDiS/src/ProblemScal.cc | 65 +++++------
AMDiS/src/ProblemScal.h | 22 ++--
12 files changed, 257 insertions(+), 413 deletions(-)
diff --git a/AMDiS/libtool b/AMDiS/libtool
index 3b667337..54b3e258 100755
--- 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="/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 p2s118:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -66,12 +66,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-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="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="gcc"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# 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/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -174,7 +174,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -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=""
@@ -6763,7 +6763,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p2s118:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -6785,12 +6785,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -6801,25 +6801,25 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="g++"
+CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpiCC"
# Is the compiler the GNU C compiler?
with_gcc=yes
-gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+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/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -6893,7 +6893,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6948,11 +6948,11 @@ 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 "/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" | $SED -e "s@${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/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.
@@ -6960,11 +6960,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
# 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 "-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/../../.." | $SED -e "s@${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"
@@ -7044,10 +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=`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 $srcfile for the compiler.
fix_srcfile_path=""
@@ -7071,7 +7071,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
-# Libtool was configured on host NWRW15:
+# Libtool was configured on host p2s118:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
@@ -7093,12 +7093,12 @@ fast_install=yes
# The host system.
host_alias=
-host=i686-pc-linux-gnu
+host=x86_64-unknown-linux-gnu
host_os=linux-gnu
# The build system.
build_alias=
-build=i686-pc-linux-gnu
+build=x86_64-unknown-linux-gnu
build_os=linux-gnu
# An echo program that does not interpret backslashes.
@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="gcc"
+LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
@@ -7118,16 +7118,16 @@ LTCFLAGS="-g -O2"
CC="g77"
# Is the compiler the GNU C compiler?
-with_gcc=yes
+with_gcc=
-gcc_dir=`gcc -print-file-name=. | /bin/sed 's,/\.$,,'`
+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/x86_64-suse-linux/bin/ld -m elf_x86_64"
# Whether we need hard or soft links.
LN_S="ln -s"
@@ -7355,10 +7355,10 @@ 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=""
diff --git a/AMDiS/src/CoarseningManager.h b/AMDiS/src/CoarseningManager.h
index 6c91164e..4e88dcf9 100644
--- a/AMDiS/src/CoarseningManager.h
+++ b/AMDiS/src/CoarseningManager.h
@@ -74,16 +74,6 @@ namespace AMDiS {
*/
inline Mesh* getMesh() { return mesh; };
- // /** \brief
- // * Coarsens a single Element by decrement its mark and then coarsen
- // * the mesh.
- // */
- // void coarsenElement(Element *element) {
- // FUNCNAME("CoarseninManager::coarseElement");
- // element->decrementMark();
- // coarsenMesh();
- // };
-
/** \brief
* Tries to coarsen every element of mesh at least mark times. First
* all elements are marked for coarsening and then coarsenMesh will
diff --git a/AMDiS/src/DOFAdmin.h b/AMDiS/src/DOFAdmin.h
index fb91a520..440fc321 100644
--- a/AMDiS/src/DOFAdmin.h
+++ b/AMDiS/src/DOFAdmin.h
@@ -62,24 +62,16 @@ namespace AMDiS {
DOFAdmin();
- /** \brief
- * constructor
- */
+ /// Constructor
DOFAdmin(Mesh* m);
- /** \brief
- * constructor
- */
+ /// Constructor
DOFAdmin(Mesh* m, std::string aName);
- /** \brief
- * copy constructor
- */
+ /// Copy constructor
DOFAdmin(const DOFAdmin&);
- /** \brief
- * destructor
- */
+ /// Destructor
~DOFAdmin();
/** \brief
@@ -88,19 +80,13 @@ namespace AMDiS {
*/
void enlargeDOFLists(int minsize);
- /** \brief
- * assignment operator
- */
+ /// assignment operator
DOFAdmin& operator=(const DOFAdmin&);
- /** \brief
- * Compares two DOFAdmins by their names.
- */
+ /// Compares two DOFAdmins by their names.
bool operator==(const DOFAdmin&) const;
- /** \brief
- * Compares two DOFAdmins by their names.
- */
+ /// Compares two DOFAdmins by their names.
inline bool operator!=(const DOFAdmin& ad) const {
return !(ad==*this);
}
@@ -111,19 +97,13 @@ namespace AMDiS {
*/
void addDOFIndexed(DOFIndexedBase* dofIndexed);
- /** \brief
- * Adds a DOFContainer object to the DOFAdmin.
- */
+ /// Adds a DOFContainer object to the DOFAdmin.
void addDOFContainer(DOFContainer* dofContainer);
- /** \brief
- * Removes the given DOFIndexedBase object from DOFAdmin.
- */
+ /// Removes the given DOFIndexedBase object from DOFAdmin.
void removeDOFIndexed(DOFIndexedBase* dofIndexed);
- /** \brief
- * Removes the given DOFContainer object from DOFAdmin.
- */
+ /// Removes the given DOFContainer object from DOFAdmin.
void removeDOFContainer(DOFContainer* dofContainer);
/** \brief
@@ -135,16 +115,12 @@ namespace AMDiS {
*/
void compress(std::vector<DegreeOfFreedom> &new_dof);
- /** \brief
- * Returns an iterator to the begin of \ref dofIndexedList
- */
+ /// Returns an iterator to the begin of \ref dofIndexedList
std::list<DOFIndexedBase*>::iterator beginDOFIndexed() {
return dofIndexedList.begin();
}
- /** \brief
- * Returns an iterator to the end of \ref dofIndexedList
- */
+ /// Returns an iterator to the end of \ref dofIndexedList
std::list<DOFIndexedBase*>::iterator endDOFIndexed() {
return dofIndexedList.end();
}
@@ -153,87 +129,62 @@ namespace AMDiS {
* \{
*/
- /** \brief
- * Returns \ref sizeUsed.
- */
+ /// Returns \ref sizeUsed.
inline const int getUsedSize() const {
return sizeUsed;
}
- /** \brief
- * Returns \ref size
- */
+ /// Returns \ref size
inline const int getSize() const {
return size;
}
- /** \brief
- * Returns \ref usedCount
- */
+ /// Returns \ref usedCount
inline const int getUsedDOFs() const {
return usedCount;
}
- /** \brief
- * Returns \ref holeCount
- */
+ /// Returns \ref holeCount
inline const int getHoleCount() const {
return holeCount;
}
- /** \brief
- * Returns \ref name
- */
+ /// Returns \ref name
inline const std::string& getName() const {
return name;
}
- /** \brief
- * Returns \ref nrDOF[i], i.e., the number of dofs for the
- * position i.
- */
+ /// Returns \ref nrDOF[i], i.e., the number of dofs for the position i.
inline const int getNumberOfDOFs(int i) const {
return nrDOF[i];
}
- /** \brief
- * Returns \ref nrDOF
- */
+ /// Returns \ref nrDOF
inline const DimVec<int>& getNumberOfDOFs() const {
return nrDOF;
}
- /** \brief
- * Returns \ref nr0DOF[i]
- */
+ /// Returns \ref nr0DOF[i]
inline const int getNumberOfPreDOFs(int i) const {
return nr0DOF[i];
}
- /** \brief
- * Returns \ref nr0DOF
- */
+ /// Returns \ref nr0DOF
inline const DimVec<int>& getNumberOfPreDOFs() const {
return nr0DOF;
}
- /** \brief
- * Returns \ref mesh
- */
+ /// Returns \ref mesh
inline const Mesh* getMesh() const {
return mesh;
}
- /** \brief
- * Returns \ref dofFree, the array denoting DOFs to be either free or used.
- */
+ /// Returns \ref dofFree, the array denoting DOFs to be either free or used.
inline const std::vector<bool>& getDOFFree() const {
return dofFree;
}
- /** \brief
- * Returns if the given DOF is free.
- */
+ /// Returns if the given DOF is free.
inline const bool isDOFFree(int i) const {
return dofFree[i];
}
@@ -244,26 +195,18 @@ namespace AMDiS {
* \{
*/
- /** \brief
- * Sets \ref nrDOF[i] = v
- */
+ /// Sets \ref nrDOF[i] = v
void setNumberOfDOFs(int i, int v);
- /** \brief
- * Sets \ref nr0DOF[i] = v
- */
+ /// Sets \ref nr0DOF[i] = v
void setNumberOfPreDOFs(int i, int v);
- /** \brief
- * Sets \ref name = n
- */
+ /// Sets \ref name = n
inline void setName(const std::string& n) {
name = n;
}
- /** \brief
- * Sets \ref mesh = m
- */
+ /// Sets \ref mesh = m
inline void setMesh(Mesh* m) {
mesh = m;
}
@@ -273,9 +216,7 @@ namespace AMDiS {
/** \} */
protected:
- /** \brief
- * initializes this DOFAdmin
- */
+ /// Initializes this DOFAdmin
void init();
/** \brief
@@ -284,9 +225,7 @@ namespace AMDiS {
*/
int getDOFIndex();
- /** \brief
- * Frees index dof. Used by Mesh::getDOF()
- */
+ /// Frees index dof. Used by Mesh::getDOF()
void freeDOFIndex(int dof);
///
@@ -296,70 +235,46 @@ namespace AMDiS {
void deserialize(std::istream &in);
protected:
- /** \brief
- * name of this DOFAdmin
- */
+ /// name of this DOFAdmin
std::string name;
- /** \brief
- * the mesh this DOFAdmin belongs to
- */
+ /// the mesh this DOFAdmin belongs to
Mesh *mesh;
- /** \brief
- * the dofFree vector stores for each index whether it is used or not
- */
+ /// The dofFree vector stores for each index whether it is used or not
std::vector<bool> dofFree;
- /** \brief
- * index of the first free value in \ref dofFree
- */
+ /// index of the first free value in \ref dofFree
int firstHole;
- /** \brief
- * allocated size of managed vectors and matrices
- */
+ /// allocated size of managed vectors and matrices
int size;
- /** \brief
- * number of used dof indices
- */
+ /// number of used dof indices
int usedCount;
- /** \brief
- * number of FREED dof indices (NOT size-sizeUsed)
- */
+ /// number of FREED dof indices (NOT size-sizeUsed)
int holeCount;
- /** \brief
- * > max. index of a used entry
- */
+ /// > max. index of a used entry
int sizeUsed;
/** \brief
- * Number of dofs for each position, i.e., vertex,
- * edge, ..., center, for this DOFAdmin.
+ * Number of dofs for each position, i.e., vertex, edge, ..., center,
+ * for this DOFAdmin.
*/
DimVec<int> nrDOF;
- /** \brief
- * dofs from previous DOFAdmins
- */
+ /// Dofs from previous DOFAdmins
DimVec<int> nr0DOF;
- /** \brief
- * list of all managed DOFIndexed objects.
- */
+ /// List of all managed DOFIndexed objects.
std::list<DOFIndexedBase*> dofIndexedList;
- /** \brief
- * list of all managed DOFContainer objects
- */
+ /// List of all managed DOFContainer objects
std::list<DOFContainer*> dofContainerList;
- /** \brief
- * size increment used by \ref enlargeDOFLists.
- */
+ /// Size increment used by \ref enlargeDOFLists.
static const int sizeIncrement;
friend class DOFIteratorBase;
diff --git a/AMDiS/src/ElementFileWriter.cc b/AMDiS/src/ElementFileWriter.cc
index a0b1a169..35884163 100644
--- a/AMDiS/src/ElementFileWriter.cc
+++ b/AMDiS/src/ElementFileWriter.cc
@@ -107,7 +107,7 @@ namespace AMDiS {
FUNCNAME("ElementFileWriter::writeTecPlotValues()");
std::ofstream fout(filename.c_str());
- TEST_EXIT(fout)("Could not open file %s !\n", filename);
+ TEST_EXIT(fout)("Could not open file %s !\n", filename.c_str());
fout.setf(std::ios::scientific,std::ios::floatfield);
int dim = mesh->getDim();
@@ -187,7 +187,7 @@ namespace AMDiS {
FUNCNAME("ElementFileWriter::writeMeshDatValues()");
std::ofstream fout(filename.c_str());
- TEST_EXIT(fout)("Could not open file %s !\n", filename);
+ TEST_EXIT(fout)("Could not open file %s !\n", filename.c_str());
int dim = mesh->getDim();
double val;
@@ -286,7 +286,7 @@ namespace AMDiS {
FUNCNAME("ElementFileWriter::writeVtkValues()");
std::ofstream fout(filename.c_str());
- TEST_EXIT(fout)("Could not open file %s !\n", filename);
+ TEST_EXIT(fout)("Could not open file %s !\n", filename.c_str());
int dim = mesh->getDim();
int vertices = mesh->getGeo(VERTEX);
diff --git a/AMDiS/src/MacroReader.cc b/AMDiS/src/MacroReader.cc
index 2409b0ec..b002a7b4 100644
--- a/AMDiS/src/MacroReader.cc
+++ b/AMDiS/src/MacroReader.cc
@@ -1870,10 +1870,8 @@ namespace AMDiS {
fill_flag |= Mesh::FILL_NEIGH;
- for (mesh->iadmin = 0;
- mesh->iadmin < static_cast<int>(mesh->admin.size());
- mesh->iadmin++) {
- localAdmin = mesh->admin[mesh->iadmin];
+ for (int iadmin = 0; iadmin < static_cast<int>(mesh->admin.size()); iadmin++) {
+ localAdmin = mesh->admin[iadmin];
if (localAdmin->getSize() > 0) {
if (static_cast<int>(mesh->dof_used.size()) < localAdmin->getSize()) {
@@ -1883,38 +1881,40 @@ namespace AMDiS {
mesh->dof_used[i] = 0;
nused = nfree = 0;
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, fill_flag | Mesh::FILL_ADD_ALL);
+ while (elInfo) {
+ basicDOFCheckFct(elInfo, mesh, iadmin);
+ elInfo = stack.traverseNext(elInfo);
+ }
- Mesh::traversePtr = mesh;
- error_detected += mesh->traverse(-1,
- fill_flag | Mesh::FILL_ADD_ALL,
- basicDOFCheckFct);
-
- DOFIteratorBase it(localAdmin, USED_DOFS);
- for(it.reset(); !it.end(); ++it) {
- nused++;
- if (!mesh->dof_used[it.getDOFIndex()]) {
- error_detected++;
- MSG("dof[%d] not used??\n",it.getDOFIndex());
- }
+ DOFIteratorBase it(localAdmin, USED_DOFS);
+ for (it.reset(); !it.end(); ++it) {
+ nused++;
+ if (!mesh->dof_used[it.getDOFIndex()]) {
+ error_detected++;
+ MSG("dof[%d] not used??\n",it.getDOFIndex());
}
-
- DOFIteratorBase freeIt(localAdmin, FREE_DOFS);
- for(freeIt.reset(); !freeIt.end(); ++freeIt) {
- nfree++;
- if(mesh->dof_used[freeIt.getDOFIndex()]) {
- error_detected++;
- MSG("dof[%d] used??\n",freeIt.getDOFIndex());
- }
+ }
+
+ DOFIteratorBase freeIt(localAdmin, FREE_DOFS);
+ for (freeIt.reset(); !freeIt.end(); ++freeIt) {
+ nfree++;
+ if(mesh->dof_used[freeIt.getDOFIndex()]) {
+ error_detected++;
+ MSG("dof[%d] used??\n",freeIt.getDOFIndex());
}
-
- TEST(nused + nfree == localAdmin->getSize())
- ("nused = %d, nfree = %d, admin.size = %d ????\n",
- nused, nfree, localAdmin->getSize());
- TEST(nused == localAdmin->getUsedDOFs())
- ("nused = %d, admin.used_count = %d ?????\n",
- nused, localAdmin->getUsedDOFs());
}
+
+ TEST(nused + nfree == localAdmin->getSize())
+ ("nused = %d, nfree = %d, admin.size = %d ????\n",
+ nused, nfree, localAdmin->getSize());
+ TEST(nused == localAdmin->getUsedDOFs())
+ ("nused = %d, admin.used_count = %d ?????\n",
+ nused, localAdmin->getUsedDOFs());
}
+ }
if (!error_detected) {
MSG("checking done; no error detected\n");
@@ -1930,10 +1930,11 @@ namespace AMDiS {
int MacroReader::basicCheckFct(ElInfo* elinfo)
{
- FUNCNAME("MacroReader::basicCheckFct");
- int i, j, k, opp_v;
- Element *el = elinfo->getElement();
- const Element *neig;
+ FUNCNAME("MacroReader::basicCheckFct()");
+
+ int j, k, opp_v;
+ Element *el = elinfo->getElement();
+ const Element *neig;
int error_detected=0;
Mesh* mesh = Mesh::traversePtr;
@@ -1942,79 +1943,75 @@ namespace AMDiS {
elinfo->testFlag(Mesh::FILL_NEIGH);
- for (i = 0; i < mesh->getGeo(NEIGH); i++)
- {
- if ((neig = elinfo->getNeighbour(i)))
- {
- if(elinfo->getBoundary(i) > 0) { // < 0 => periodic boundary
+ for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
+ if ((neig = elinfo->getNeighbour(i))) {
+ if(elinfo->getBoundary(i) > 0) { // < 0 => periodic boundary
+ if (!error_detected)
+ MSG("error detected!!!\n");
+ error_detected++;
+ MSG("interior (*boundary)[%d] non NULL on element = %d\n",
+ i, el->getIndex());
+ }
+
+ opp_v = elinfo->getOppVertex(i);
+ if(opp_v < 0 || opp_v >= mesh->getGeo(NEIGH)) {
+ if (!error_detected)
+ MSG("error detected!!!\n");
+ error_detected++;
+ MSG("opp_v = %d\n", opp_v);
+ }
+
+ if(elinfo->getBoundary(i) > 0) { // < 0 => periodic boundary
+ if(dim == 1) {
+ if(el->getDOF(i) != neig->getDOF(opp_v)) {
if (!error_detected)
MSG("error detected!!!\n");
error_detected++;
- MSG("interior (*boundary)[%d] non NULL on element = %d\n",
- i, el->getIndex());
+ MSG("neighbour error\n");
}
-
- opp_v = elinfo->getOppVertex(i);
- if(opp_v < 0 || opp_v >= mesh->getGeo(NEIGH))
- {
+ } else {
+ for (j = 1; j < mesh->getGeo(VERTEX); j++) {
+ for (k = 1; k < mesh->getGeo(VERTEX); k++)
+ if (el->getDOF((i+j) % mesh->getGeo(VERTEX)) ==
+ neig->getDOF((opp_v+k) % mesh->getGeo(VERTEX)))
+ break;
+
+ if (k >= mesh->getGeo(VERTEX)) {
if (!error_detected)
MSG("error detected!!!\n");
error_detected++;
- MSG("opp_v = %d\n", opp_v);
- }
-
- if(elinfo->getBoundary(i) > 0) { // < 0 => periodic boundary
- if(dim == 1) {
- if(el->getDOF(i) != neig->getDOF(opp_v)) {
- if (!error_detected)
- MSG("error detected!!!\n");
- error_detected++;
- MSG("neighbour error\n");
- }
- } else {
- for (j = 1; j < mesh->getGeo(VERTEX); j++) {
- for (k = 1; k < mesh->getGeo(VERTEX); k++)
- if (el->getDOF((i+j) % mesh->getGeo(VERTEX)) ==
- neig->getDOF((opp_v+k) % mesh->getGeo(VERTEX)))
- break;
-
- if (k >= mesh->getGeo(VERTEX)) {
- if (!error_detected)
- MSG("error detected!!!\n");
- error_detected++;
- MSG("dof %d of el %d at face %d isn't dof of neigh %d at face %d\n",
- el->getDOF((i+j) % 3,0), el->getIndex(), i, neig->getIndex(),
- opp_v);
- }
- }
- }
+ MSG("dof %d of el %d at face %d isn't dof of neigh %d at face %d\n",
+ el->getDOF((i+j) % 3,0), el->getIndex(), i, neig->getIndex(),
+ opp_v);
+ }
}
- } else {
- if (elinfo->getBoundary(i) == INTERIOR) {
- if (!error_detected)
- MSG("error detected!!!\n");
- error_detected++;
- MSG("(*boundary)[%d] on domains boundary is NULL on element = %d\n",
- i, el->getIndex());
}
}
+ } else {
+ if (elinfo->getBoundary(i) == INTERIOR) {
+ if (!error_detected)
+ MSG("error detected!!!\n");
+ error_detected++;
+ MSG("(*boundary)[%d] on domains boundary is NULL on element = %d\n",
+ i, el->getIndex());
+ }
}
+ }
return error_detected;
}
- int MacroReader::basicDOFCheckFct(ElInfo* elinfo)
+ void MacroReader::basicDOFCheckFct(ElInfo* elinfo, Mesh *mesh, int iadmin)
{
FUNCNAME("MacroReader::basicDOFCheckFct()");
- Mesh* mesh = Mesh::traversePtr;
Element* el = elinfo->getElement();
- const DOFAdmin& admin = mesh->getDOFAdmin(mesh->iadmin);
+ const DOFAdmin& admin = mesh->getDOFAdmin(iadmin);
const Element *neig;
const DegreeOfFreedom *dof;
if (0 == mesh->dof_used.size())
- return 0;
+ return;
int ndof = admin.getNumberOfDOFs(VERTEX);
if (ndof) {
@@ -2140,8 +2137,6 @@ namespace AMDiS {
mesh->dof_used[jdof]++;
}
}
-
- return 0;
}
int MacroReader::basicNodeFct(ElInfo* elinfo)
diff --git a/AMDiS/src/MacroReader.h b/AMDiS/src/MacroReader.h
index f52ea898..e2b58f35 100644
--- a/AMDiS/src/MacroReader.h
+++ b/AMDiS/src/MacroReader.h
@@ -36,10 +36,6 @@ namespace AMDiS {
/** \defgroup Input Input module */
- // ===========================================================================
- // ===== class MacroReader ===================================================
- // ===========================================================================
-
/** \ingroup Input
*
* \brief
@@ -49,9 +45,7 @@ namespace AMDiS {
class MacroReader
{
public:
- /** \brief
- * Creates a Mesh by reading the macro file with the given filename
- */
+ /// Creates a Mesh by reading the macro file with the given filename.
static MacroInfo* readMacro(const char *filename,
Mesh* mesh,
const char *periodicFile,
@@ -59,6 +53,7 @@ namespace AMDiS {
protected:
static void computeNeighbours(Mesh *mesh);
+
static void boundaryDOFs(Mesh *mesh);
static void umb(int *ele, Mesh *mesh,
@@ -93,19 +88,15 @@ namespace AMDiS {
static void checkMesh(Mesh *mesh);
- static int basicCheckFct(ElInfo* e);
+ static int basicCheckFct(ElInfo* elInfo);
- static int basicDOFCheckFct(ElInfo* e);
+ static void basicDOFCheckFct(ElInfo* elInfo, Mesh *mesh, int iadmin);
- static int basicNodeFct(ElInfo* e);
+ static int basicNodeFct(ElInfo* elInfo);
friend class MacroInfo;
};
- // ==========================================================================
- // ===== class MacroInfo ====================================================
- // ==========================================================================
-
/** \ingroup Input
* \brief
* Used for reading a macro triangulation
@@ -115,45 +106,29 @@ namespace AMDiS {
public:
MEMORY_MANAGED(MacroInfo);
- /** \brief
- * Pointer to the Mesh
- */
+ /// Pointer to the Mesh
Mesh *mesh;
- /** \brief
- * list of macro elements
- */
+ /// list of macro elements
std::deque<MacroElement*> mel;
- /** \brief
- * vector of all vertex dofs
- */
+ /// vector of all vertex dofs
DegreeOfFreedom **dof;
- /** \brief
- * coords[j][k]: kth coordinate of global vertex j
- */
+ /// coords[j][k]: kth coordinate of global vertex j
WorldVector<double> *coords;
- /** \brief
- * mel_vertex[i][k]: global index of kth vertex of element i
- */
+ /// mel_vertex[i][k]: global index of kth vertex of element i
int **mel_vertex;
- /** \brief
- * true, if neighbour information is in macro file
- */
+ /// true, if neighbour information is in macro file
bool neigh_set;
- /** \brief
- * true, if boundary information is in macro file
- */
+ /// true, if boundary information is in macro file
bool bound_set;
public:
- /** \brief
- * Fills MacroInfo structure and some pointers in mesh
- */
+ /// Fills MacroInfo structure and some pointers in mesh
void fill(Mesh *mesh, int ne, int nv);
/** \brief
@@ -163,9 +138,7 @@ namespace AMDiS {
*/
void readAMDiSMacro(const char *filename, Mesh* mesh);
- /** \brief
- * Frees memory of MacroInfo
- */
+ /// Frees memory of MacroInfo
void clear(int ne, int nv);
/** \brief
@@ -177,9 +150,7 @@ namespace AMDiS {
void fillBoundaryInfo(Mesh *mesh);
protected:
- /** \brief
- * Reads indices from macro file
- */
+ /// Reads indices from macro file
int read_indices(FILE *file, DimVec<int> &id);
};
}
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index a0ad13f8..47d38e13 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -63,7 +63,6 @@ namespace AMDiS {
DOFAdmin* Mesh::compressAdmin = NULL;
Mesh* Mesh::traversePtr = NULL;
- int Mesh::iadmin = 0;
std::vector<DegreeOfFreedom> Mesh::dof_used;
const int Mesh::MAX_DOF = 100;
std::map<DegreeOfFreedom, DegreeOfFreedom*> Mesh::serializedDOFs;
@@ -285,8 +284,7 @@ namespace AMDiS {
for (int i = 0; i < 3; i++)
dofsOwner[el->getDOF(i)].insert(*macroIt);
}
-
-
+
// Remove all the given macro elements.
for (std::vector<MacroElement*>::iterator macroIt = macros.begin();
macroIt != macros.end();
@@ -330,8 +328,9 @@ namespace AMDiS {
dofsIt != dofsOwner.end();
++dofsIt) {
std::set<MacroElement*>::iterator mIt = dofsIt->second.find(*macroIt);
- if (mIt != dofsIt->second.end())
+ if (mIt != dofsIt->second.end()) {
dofsIt->second.erase(mIt);
+ }
}
// And remove the macro element from memory
@@ -345,7 +344,7 @@ namespace AMDiS {
dofsIt != dofsOwner.end();
++dofsIt) {
if (dofsIt->second.size() == 0) {
- dofsOwner.erase(dofsIt++);
+ freeDOF(const_cast<DegreeOfFreedom*>(dofsIt->first), VERTEX);
} else {
nRemainDofs++;
}
@@ -354,27 +353,6 @@ namespace AMDiS {
nVertices = nRemainDofs;
}
- void Mesh::createContinuousDofOrdering(FiniteElemSpace *feSpace, unsigned int addC)
- {
- FUNCNAME("Mesh::createContinuousDofOrdering()");
-
- const BasisFunction* basisFcts = feSpace->getBasisFcts();
-
- TEST_EXIT(dim == 2)("Not yet implemented!\n");
- TEST_EXIT(basisFcts->getNumber() == 3)("Not yet implemented!\n");
-
- std::set<DegreeOfFreedom*> dofs;
-
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(this, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- for (int i = 0; i < 3; i++) {
- dofs.insert(const_cast<DegreeOfFreedom*>(elInfo->getElement()->getDOF(i)));
- }
- elInfo = stack.traverseNext(elInfo);
- }
- }
-
int Mesh::traverse(int level, Flag flag, int (*el_fct)(ElInfo*))
{
FUNCNAME("Mesh::traverse()");
@@ -467,23 +445,18 @@ namespace AMDiS {
}
}
-
- /****************************************************************************/
- /* dofCompress: remove holes in dof vectors */
- /****************************************************************************/
-
void Mesh::dofCompress()
{
FUNCNAME("Mesh::dofCompress()");
- int size;
Flag fill_flag;
- for (iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
+ for (int iadmin = 0; iadmin < static_cast<int>(admin.size()); iadmin++) {
compressAdmin = admin[iadmin];
TEST_EXIT_DBG(compressAdmin)("no admin[%d] in mesh\n", iadmin);
- if ((size = compressAdmin->getSize()) < 1)
+ int size = compressAdmin->getSize();
+ if (size < 1)
continue;
if (compressAdmin->getUsedDOFs() < 1)
@@ -502,8 +475,8 @@ namespace AMDiS {
fill_flag = Mesh::CALL_LEAF_EL | Mesh::FILL_NOTHING;
}
- traverse( -1, fill_flag, newDOFFct1);
- traverse( -1, fill_flag, newDOFFct2);
+ traverse(-1, fill_flag, newDOFFct1);
+ traverse(-1, fill_flag, newDOFFct2);
newDOF.resize(0);
}
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 4854b733..abfcd50f 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -406,13 +406,6 @@ namespace AMDiS {
*/
void removeMacroElements(std::vector<MacroElement*>& macros);
- /* \brief
- * Creates new numbers for all dofs such that the set of dof numbers is a
- * continuous interval of natural numbers starting with 0. The constatnt addC
- * may be added to the numbers.
- */
- void createContinuousDofOrdering(FiniteElemSpace *feSpace, unsigned int addC = 0);
-
/// Frees the array of DOF pointers (see \ref createDOFPtrs)
void freeDOFPtrs(DegreeOfFreedom **ptrs);
@@ -705,9 +698,6 @@ namespace AMDiS {
*/
static Mesh* traversePtr;
- /// Used by compress- and check functions. Number of the current DOFAdmin
- static int iadmin;
-
/// Used by check functions
static std::vector<DegreeOfFreedom> dof_used;
diff --git a/AMDiS/src/ParallelDomainProblem.cc b/AMDiS/src/ParallelDomainProblem.cc
index 0aa12250..473bc60f 100644
--- a/AMDiS/src/ParallelDomainProblem.cc
+++ b/AMDiS/src/ParallelDomainProblem.cc
@@ -45,7 +45,6 @@ namespace AMDiS {
// and now partition the mesh
partitionMesh(adaptInfo);
- std::vector<int> rankDofs;
std::map<int, std::set<int> > partitionDofs;
TraverseStack stack;
@@ -69,7 +68,7 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
-
+ std::vector<int> rankDofs;
for (std::map<int, std::set<int> >::iterator it = partitionDofs.begin();
it != partitionDofs.end();
++it) {
@@ -97,6 +96,13 @@ namespace AMDiS {
}
}
+ if (mpiRank == 1) {
+ std::cout << "RANKS dofs = ";
+ for (int i = 0; i < rankDofs.size(); i++)
+ std::cout << rankDofs[i] << " ";
+ std::cout << std::endl;
+ }
+
// === Remove all macro elements that are not part of the rank partition. ===
std::vector<MacroElement*> macrosToRemove;
@@ -131,10 +137,8 @@ namespace AMDiS {
lOrder[i] = rstart + i;
}
- mesh->createContinuousDofOrdering(feSpace, rstart);
-
AOCreateBasic(PETSC_COMM_WORLD, nRankDOFs, gOrder, lOrder, &applicationOrdering);
-
+
free(gOrder);
free(lOrder);
}
diff --git a/AMDiS/src/ProblemNonLin.cc b/AMDiS/src/ProblemNonLin.cc
index e24fca17..2c0e672a 100644
--- a/AMDiS/src/ProblemNonLin.cc
+++ b/AMDiS/src/ProblemNonLin.cc
@@ -9,7 +9,8 @@ namespace AMDiS {
void ProblemNonLinScal::initialize(Flag initFlag,
ProblemScal *adoptProblem /*= NULL*/,
- Flag adoptFlag /*= INIT_NOTHING*/) {
+ Flag adoptFlag /*= INIT_NOTHING*/)
+ {
ProblemScal::initialize(initFlag, adoptProblem, adoptFlag);
@@ -52,7 +53,8 @@ namespace AMDiS {
WARNING("no nonlinear solver created\n");
}
- void ProblemNonLinScal::createNonLinSolver() {
+ void ProblemNonLinScal::createNonLinSolver()
+ {
// create non-linear solver
std::string nonLinSolverType("no");
@@ -65,19 +67,21 @@ namespace AMDiS {
nonLinSolverCreator->setName(name + "->nonlin solver");
nonLinSolverCreator->setNonLinUpdater(updater_);
nonLinSolver_ = nonLinSolverCreator->create();
- nonLinSolver_->setVectorCreator(NEW DOFVector<double>::Creator(feSpace_));
+ nonLinSolver_->setVectorCreator(NEW DOFVector<double>::Creator(feSpace));
}
- void ProblemNonLinScal::solve(AdaptInfo *adaptInfo) {
+ void ProblemNonLinScal::solve(AdaptInfo *adaptInfo)
+ {
TEST_EXIT(nonLinSolver_)("no non-linear solver!\n");
int iter = nonLinSolver_->solve(matVec, solution, rhs, leftPrecon, rightPrecon);
adaptInfo->setSolverIterations(iter);
}
- void ProblemNonLinScal::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag) {
- feSpace_->getMesh()->dofCompress();
- MSG("%d DOFs for %s\n", feSpace_->getAdmin()->getUsedSize(), feSpace_->getName().c_str());
+ void ProblemNonLinScal::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag)
+ {
+ feSpace->getMesh()->dofCompress();
+ MSG("%d DOFs for %s\n", feSpace->getAdmin()->getUsedSize(), feSpace->getName().c_str());
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1,
@@ -97,7 +101,8 @@ namespace AMDiS {
void ProblemNonLinVec::initialize(Flag initFlag,
ProblemVec *adoptProblem /*= NULL*/,
- Flag adoptFlag /*= INIT_NOTHING*/) {
+ Flag adoptFlag /*= INIT_NOTHING*/)
+ {
ProblemVec::initialize(initFlag, adoptProblem, adoptFlag);
// === create Updater ===
@@ -138,7 +143,8 @@ namespace AMDiS {
WARNING("no nonlinear solver created\n");
}
- void ProblemNonLinVec::createNonLinSolver() {
+ void ProblemNonLinVec::createNonLinSolver()
+ {
// create non-linear solver
std::string nonLinSolverType("no");
@@ -157,7 +163,8 @@ namespace AMDiS {
}
- void ProblemNonLinVec::solve(AdaptInfo *adaptInfo) {
+ void ProblemNonLinVec::solve(AdaptInfo *adaptInfo)
+ {
TEST_EXIT(nonLinSolver_)("no non-linear solver!\n");
nonLinSolver_->solve(matVec, solution, rhs, leftPrecon, rightPrecon);
}
diff --git a/AMDiS/src/ProblemScal.cc b/AMDiS/src/ProblemScal.cc
index ba622f8d..760ccf38 100644
--- a/AMDiS/src/ProblemScal.cc
+++ b/AMDiS/src/ProblemScal.cc
@@ -86,7 +86,7 @@ namespace AMDiS {
void ProblemScal::addDirichletBC(BoundaryType type,
AbstractFunction<double, WorldVector<double> >* b)
{
- DirichletBC *dirichlet = new DirichletBC(type, b, feSpace_);
+ DirichletBC *dirichlet = new DirichletBC(type, b, feSpace);
if (systemMatrix)
systemMatrix->getBoundaryManager()->addBoundaryCondition(dirichlet);
if (rhs)
@@ -111,7 +111,7 @@ namespace AMDiS {
AbstractFunction<double, WorldVector<double> > *n,
AbstractFunction<double, WorldVector<double> > *r)
{
- RobinBC *robin = new RobinBC(type, n, r, feSpace_);
+ RobinBC *robin = new RobinBC(type, n, r, feSpace);
if (rhs)
rhs->getBoundaryManager()->addBoundaryCondition(robin);
if (systemMatrix)
@@ -121,7 +121,7 @@ namespace AMDiS {
void ProblemScal::addNeumannBC(BoundaryType type,
AbstractFunction<double, WorldVector<double> > *n)
{
- NeumannBC *neumann = new NeumannBC(type, n, feSpace_);
+ NeumannBC *neumann = new NeumannBC(type, n, feSpace);
if (rhs)
rhs->getBoundaryManager()->addBoundaryCondition(neumann);
}
@@ -130,7 +130,7 @@ namespace AMDiS {
DOFVector<double> *n,
DOFVector<double> *r)
{
- RobinBC *robin = new RobinBC(type, n, r, feSpace_);
+ RobinBC *robin = new RobinBC(type, n, r, feSpace);
if (rhs)
rhs->getBoundaryManager()->addBoundaryCondition(robin);
if (systemMatrix)
@@ -139,7 +139,7 @@ namespace AMDiS {
void ProblemScal::addPeriodicBC(BoundaryType type)
{
- PeriodicBC *periodic = new PeriodicBC(type, feSpace_);
+ PeriodicBC *periodic = new PeriodicBC(type, feSpace);
if (systemMatrix)
systemMatrix->getBoundaryManager()->addBoundaryCondition(periodic);
@@ -148,10 +148,9 @@ namespace AMDiS {
}
#ifdef HAVE_PARALLEL_AMDIS
- void ProblemScal::useApplicationOrdering(AO *ao, int nDofs)
+ void ProblemScal::useApplicationOrdering(AO *ao)
{
applicationOrdering = ao;
- nRankDOFs = nDofs;
systemMatrix->useApplicationOrdering(ao);
rhs->useApplicationOrdering(ao);
}
@@ -165,7 +164,7 @@ namespace AMDiS {
// === create problems mesh ===
std::string meshName("");
- GET_PARAMETER(0, name + "->info", "%d", &info_);
+ GET_PARAMETER(0, name + "->info", "%d", &info);
GET_PARAMETER(0, name + "->mesh", &meshName);
TEST_EXIT(meshName != "")("no mesh name specified\n");
@@ -248,11 +247,11 @@ namespace AMDiS {
int iter = solver->solve(matVec, solution, rhs, leftPrecon, rightPrecon);
#ifdef _OPENMP
- INFO(info_, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
+ INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
TIME_USED(first, clock()),
omp_get_wtime() - wtime);
#else
- INFO(info_, 8)("solution of discrete system needed %.5f seconds\n",
+ INFO(info, 8)("solution of discrete system needed %.5f seconds\n",
TIME_USED(first, clock()));
#endif
@@ -293,7 +292,7 @@ namespace AMDiS {
WARNING("no mesh created\n");
// === create fespace ===
- if (feSpace_) {
+ if (feSpace) {
WARNING("feSpace already created\n");
} else {
if (initFlag.isSet(INIT_FE_SPACE) ||
@@ -302,12 +301,12 @@ namespace AMDiS {
}
if (adoptProblem &&
(adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
- TEST_EXIT(!feSpace_)("feSpace already created");
- feSpace_ = dynamic_cast<ProblemScal*>(adoptProblem)->getFESpace();
+ TEST_EXIT(!feSpace)("feSpace already created");
+ feSpace = dynamic_cast<ProblemScal*>(adoptProblem)->getFESpace();
}
}
- if (!feSpace_)
+ if (!feSpace)
WARNING("no feSpace created\n");
// === create system ===
@@ -436,7 +435,7 @@ namespace AMDiS {
// create finite element space
int degree = 1;
GET_PARAMETER(0, name + "->polynomial degree" ,"%d", °ree);
- feSpace_ = FiniteElemSpace::provideFESpace(NULL,
+ feSpace = FiniteElemSpace::provideFESpace(NULL,
Lagrange::getLagrange(mesh->getDim(), degree),
mesh,
name + "->feSpace");
@@ -452,9 +451,9 @@ namespace AMDiS {
void ProblemScal::createMatricesAndVectors()
{
// === create vectors and system matrix ===
- systemMatrix = NEW DOFMatrix(feSpace_, feSpace_, "system matrix");
- rhs = NEW DOFVector<double>(feSpace_, "rhs");
- solution = NEW DOFVector<double>(feSpace_, "solution");
+ systemMatrix = NEW DOFMatrix(feSpace, feSpace, "system matrix");
+ rhs = NEW DOFVector<double>(feSpace, "rhs");
+ solution = NEW DOFVector<double>(feSpace, "solution");
solution->setCoarsenOperation(COARSE_INTERPOL);
solution->set(0.0); /* initialize u_h ! */
@@ -510,7 +509,7 @@ namespace AMDiS {
}
// === create vector creator ===
- solver->setVectorCreator(new DOFVector<double>::Creator(feSpace_));
+ solver->setVectorCreator(new DOFVector<double>::Creator(feSpace));
}
@@ -560,7 +559,7 @@ namespace AMDiS {
if (estimator) {
clock_t first = clock();
estimator->estimate(adaptInfo->getTimestep());
- INFO(info_,8)("estimation of the error needed %.5f seconds\n",
+ INFO(info,8)("estimation of the error needed %.5f seconds\n",
TIME_USED(first,clock()));
adaptInfo->setEstSum(estimator->getErrorSum(), 0);
@@ -586,15 +585,12 @@ namespace AMDiS {
clock_t first = clock();
+#ifndef HAVE_PARALLEL_AMDIS
mesh->dofCompress();
+#endif
MSG("%d DOFs for %s\n",
-#ifdef HAVE_PARALLEL_AMDIS
- nRankDOFs,
-#else
- feSpace_->getAdmin()->getUsedSize(),
-#endif
- feSpace_->getName().c_str());
+ feSpace->getAdmin()->getUsedDOFs(), feSpace->getName().c_str());
Flag assembleFlag =
flag |
@@ -621,8 +617,8 @@ namespace AMDiS {
while (elInfo) {
if (useGetBound) {
- bound = GET_MEMORY(BoundaryType, feSpace_->getBasisFcts()->getNumber());
- feSpace_->getBasisFcts()->getBound(elInfo, bound);
+ bound = GET_MEMORY(BoundaryType, feSpace->getBasisFcts()->getNumber());
+ feSpace->getBasisFcts()->getBound(elInfo, bound);
} else {
bound = NULL;
}
@@ -631,7 +627,7 @@ namespace AMDiS {
rhs->assemble(1.0, elInfo, bound);
if (useGetBound) {
- FREE_MEMORY(bound, BoundaryType, feSpace_->getBasisFcts()->getNumber());
+ FREE_MEMORY(bound, BoundaryType, feSpace->getBasisFcts()->getNumber());
}
if (systemMatrix->getBoundaryManager())
@@ -652,8 +648,15 @@ namespace AMDiS {
if (solution->getBoundaryManager())
solution->getBoundaryManager()->exitVector(solution);
- INFO(info_, 8)("buildAfterCoarsen needed %.5f seconds\n",
- TIME_USED(first,clock()));
+ INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", TIME_USED(first,clock()));
+
+#ifdef HAVE_PARALLEL_AMDIS
+// PetscErrorCode ierr;
+// Mat A;
+
+// ierr = MatCreate(PETSC_COMM_WORLD, &A); CHKERRQ(ierr);
+#endif
+
}
void ProblemScal::writeResidualMesh(AdaptInfo *adaptInfo, const std::string name)
diff --git a/AMDiS/src/ProblemScal.h b/AMDiS/src/ProblemScal.h
index f574fdbf..3b6cd776 100644
--- a/AMDiS/src/ProblemScal.h
+++ b/AMDiS/src/ProblemScal.h
@@ -64,7 +64,7 @@ namespace AMDiS {
ProblemIterationInterface *problemIteration = NULL)
: StandardProblemIteration(this),
name(nameStr),
- feSpace_(NULL),
+ feSpace(NULL),
mesh(NULL),
marker(NULL),
estimator(NULL),
@@ -80,9 +80,8 @@ namespace AMDiS {
coarseningManager(NULL),
#ifdef HAVE_PARALLEL_AMDIS
applicationOrdering(NULL),
- nRankDOFs(0),
#endif
- info_(10)
+ info(10)
{}
/// Destructor
@@ -224,7 +223,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_AMDIS
/// Sets the petsc application ordering object to map dof indices.
- void useApplicationOrdering(AO *ao, int nDofs);
+ void useApplicationOrdering(AO *ao);
#endif
// ===== getting-methods ======================================================
@@ -253,9 +252,9 @@ namespace AMDiS {
return mesh;
}
- /// Returns \ref feSpace_.
+ /// Returns \ref feSpace.
inline FiniteElemSpace* getFESpace() {
- return feSpace_;
+ return feSpace;
}
/// Returns \ref estimator_.
@@ -314,9 +313,9 @@ namespace AMDiS {
/// Sets \ref mesh
void setMeshFromProblemVec(ProblemVec* pv, int i = 0);
- /// Sets \ref feSpace_.
+ /// Sets \ref feSpace.
inline void setFESpace(FiniteElemSpace* fe) {
- feSpace_ = fe;
+ feSpace = fe;
}
/// Sets \ref estimator_.
@@ -363,7 +362,7 @@ namespace AMDiS {
std::string name;
/// FiniteElemSpace of this problem.
- FiniteElemSpace *feSpace_;
+ FiniteElemSpace *feSpace;
/// Mesh of this problem.
Mesh *mesh;
@@ -418,13 +417,10 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_AMDIS
/// Petsc application ordering to map dof indices.
AO *applicationOrdering;
-
- /// Number of DOFs in the rank partition.
- int nRankDOFs;
#endif
/// Info level.
- int info_;
+ int info;
};
--
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