Removed small bug in serialization of parallel domain problems.

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 deimos104:
 
 # 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.
@@ -82,13 +82,13 @@ 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
@@ -97,7 +97,7 @@ with_gcc=yes
 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"
@@ -171,7 +171,7 @@ 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"
@@ -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/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/"
+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/"
 
 # 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 /usr/lib/qt4/lib "
+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 "
 
 # 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 NWRW15:
+# Libtool was configured on host deimos104:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -6782,12 +6782,12 @@ 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.
@@ -6798,13 +6798,13 @@ 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
@@ -6813,7 +6813,7 @@ with_gcc=yes
 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"
@@ -6887,7 +6887,7 @@ 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"
@@ -6942,11 +6942,11 @@ striplib="strip --strip-unneeded"
 
 # Dependencies to place before the objects being linked to create a
 # shared library.
-predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
+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"
 
 # Dependencies to place after the objects being linked to create a
 # shared library.
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
+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"
 
 # 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="-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="-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/../../.."
+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/../../.."
 
 # 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/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/"
+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/"
 
 # 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 /usr/lib/qt4/lib "
+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 "
 
 # 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 NWRW15:
+# Libtool was configured on host deimos104:
 
 # Shell to use when invoking shell scripts.
 SHELL="/bin/sh"
@@ -7087,12 +7087,12 @@ 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.
@@ -7103,7 +7103,7 @@ 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"
@@ -7112,13 +7112,13 @@ LTCFLAGS="-g -O2"
 CC="g77"
 
 # Is the compiler the GNU C compiler?
-with_gcc=yes
+with_gcc=
 
 # 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"
@@ -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/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/"
+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/"
 
 # 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 /usr/lib/qt4/lib "
+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 "
 
 # Fix the shell variable $srcfile for the compiler.
 fix_srcfile_path=""

AMDiS/src/ParallelDomainBase.cc

@@ -1933,6 +1933,7 @@ namespace AMDiS {
     SerUtil::serialize(out, isRankDof);
 
     serialize(out, vertexDof);
+    serialize(out, periodicDof);
 
     SerUtil::serialize(out, rstart);
     SerUtil::serialize(out, nRankRows);
@@ -1985,7 +1986,37 @@ namespace AMDiS {
     deserialized = true;
   }
 
+  void ParallelDomainBase::serialize(std::ostream &out, PeriodicDofMap &data)
+  {
+    int mapSize = data.size();
+    SerUtil::serialize(out, mapSize);
 
+    for (PeriodicDofMap::iterator it = data.begin(); it != data.end(); ++it) {
+      DegreeOfFreedom dof = it->first;
+      std::set<DegreeOfFreedom> dofSet = it->second;
+      SerUtil::serialize(out, dof);
+      SerUtil::serialize(out, dofSet);
+    }
+  }
+
+  void ParallelDomainBase::deserialize(std::istream &in, PeriodicDofMap &data)
+  {
+    data.clear();
+
+    int mapSize = 0;
+    SerUtil::deserialize(in, mapSize);
+    for (int i = 0; i < mapSize; i++) {
+      DegreeOfFreedom dof = 0;
+      std::set<DegreeOfFreedom> dofSet;
+
+      SerUtil::deserialize(in, dof);
+      SerUtil::deserialize(in, dofSet);
+
+      data[dof] = dofSet;
+    }
+    
+  }
+  
   void ParallelDomainBase::DbgCreateElementMap(ElementIdxToDofs &elMap)
   {
     FUNCNAME("ParallelDomainBase::DbgCreateElementMap()");

AMDiS/src/ParallelDomainBase.h

@@ -342,6 +342,12 @@ namespace AMDiS {
     void deserialize(std::istream &in, RankToDofContainer &data,
 		     std::map<int, const DegreeOfFreedom*> &dofMap);
 
+    /// Writes a periodic dof mapping to an output stream.
+    void serialize(std::ostream &out, PeriodicDofMap &data);
+
+    /// Reads a periodic dof mapping from an input stream.
+    void deserialize(std::istream &in, PeriodicDofMap &data);
+
     /// Writes a mapping from dof pointers to some values to an output stream.
     template<typename T>
     void serialize(std::ostream &out, std::map<const DegreeOfFreedom*, T> &data)

AMDiS/src/Serializer.h

@@ -134,6 +134,30 @@ namespace AMDiS {
       }
     }
 
+    template<typename T>
+    void serialize(std::ostream& out, std::set<T>& data)
+    {
+      int setSize = data.size();
+      serialize(out, setSize);
+      for (typename std::set<T>::iterator it = data.begin(); 
+	   it != data.end(); ++it) {
+	T v = *it;
+	serialize(out, v);
+      }
+    }
+
+    template<typename T>
+    void deserialize(std::istream& in, std::set<T>& data)
+    {
+      int setSize = 0;
+      deserialize(in, setSize);
+
+      for (int i = 0; i < setSize; i++) {
+	T v;
+	deserialize(in, v);
+	data.insert(v);
+      }
+    }
 
     template<typename T1, typename T2>
     void serialize(std::ostream& out, std::map<T1, T2>& data)