From: Kai L. <kai...@un...> - 2004-10-13 12:08:44
|
Hi all, just compiled libmesh-0.4.3 (g++ 3.3, SuSE Linux 9.1) without PETSc. 'make run_examples' yields ... *************************************************************** * Running Example ./ex10 *************************************************************** Mesh Information: mesh_dimension()=3D2 spatial_dimension()=3D3 n_nodes()=3D6273 n_elem()=3D13650 n_local_elem()=3D13650 n_active_elem()=3D10240 n_subdomains()=3D1 n_processors()=3D1 processor_id()=3D0 EquationSystems n_systems()=3D1 System "Convection-Diffusion" Type "TransientImplicit" Variables=3D"u" Finite Element Types=3D"0" Approximation Orders=3D"1" n_dofs()=3D6273 n_local_dofs()=3D6273 n_constrained_dofs()=3D0 n_vectors()=3D1 n_parameters()=3D2 Parameters: "linear solver maximum iterations"=3D5000 "linear solver tolerance"=3D1e-12 Solving time step 0, time=3D0.0250... Refining the mesh... ERROR: LASPACK Error: in ILUFactor: Matrix has a structure which is not allowed for ILU factorization. [0] src/numerics/laspack_interface.C, line 274, compiled Oct 13 2004 at 13:52:42 Best Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Tel.: 07071/29-73049 Mail: kai...@un... |
From: John P. <pet...@cf...> - 2004-10-13 15:42:08
|
Hmm...haven't seen that one before, will check it out. -John Kai Ludwig writes: > Hi all, >=20 > just compiled libmesh-0.4.3 (g++ 3.3, SuSE Linux 9.1) > without PETSc. 'make run_examples' > yields >=20 > ... >=20 > *************************************************************** > * Running Example ./ex10 > *************************************************************** >=20 > Mesh Information: > mesh_dimension()=3D2 > spatial_dimension()=3D3 > n_nodes()=3D6273 > n_elem()=3D13650 > n_local_elem()=3D13650 > n_active_elem()=3D10240 > n_subdomains()=3D1 > n_processors()=3D1 > processor_id()=3D0 >=20 > EquationSystems > n_systems()=3D1 > System "Convection-Diffusion" > Type "TransientImplicit" > Variables=3D"u" > Finite Element Types=3D"0" > Approximation Orders=3D"1" > n_dofs()=3D6273 > n_local_dofs()=3D6273 > n_constrained_dofs()=3D0 > n_vectors()=3D1 > n_parameters()=3D2 > Parameters: > "linear solver maximum iterations"=3D5000 > "linear solver tolerance"=3D1e-12 >=20 > Solving time step 0, time=3D0.0250... > Refining the mesh... > ERROR: LASPACK Error: > in ILUFactor: > Matrix has a structure which is not allowed for ILU factorization. > [0] src/numerics/laspack_interface.C, line 274, compiled Oct 13 2004= at > 13:52:42 >=20 > Best Regards, > Kai >=20 >=20 > --=20 > http://echempp.sourceforge.net >=20 > Kai Ludwig > Institut f=FCr Organische Chemie > Auf der Morgenstelle 18 > 72076 T=FCbingen > Tel.: 07071/29-73049 > Mail: kai...@un... >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJou= rnal > Use IT products in your business? Tell us what you think of them. Gi= ve us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find o= ut more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users |
From: Benjamin S. K. <be...@cf...> - 2004-10-15 04:29:31
|
Hmm... I cannot seem to repeat this. Could you please post the output from ./configure and your Make.common file? -Ben Kai Ludwig wrote: > Hi all, > > just compiled libmesh-0.4.3 (g++ 3.3, SuSE Linux 9.1) > without PETSc. 'make run_examples' > yields > > ... > > *************************************************************** > * Running Example ./ex10 > *************************************************************** > > Mesh Information: > mesh_dimension()=2 > spatial_dimension()=3 > n_nodes()=6273 > n_elem()=13650 > n_local_elem()=13650 > n_active_elem()=10240 > n_subdomains()=1 > n_processors()=1 > processor_id()=0 > > EquationSystems > n_systems()=1 > System "Convection-Diffusion" > Type "TransientImplicit" > Variables="u" > Finite Element Types="0" > Approximation Orders="1" > n_dofs()=6273 > n_local_dofs()=6273 > n_constrained_dofs()=0 > n_vectors()=1 > n_parameters()=2 > Parameters: > "linear solver maximum iterations"=5000 > "linear solver tolerance"=1e-12 > > Solving time step 0, time=0.0250... > Refining the mesh... > ERROR: LASPACK Error: > in ILUFactor: > Matrix has a structure which is not allowed for ILU factorization. > [0] src/numerics/laspack_interface.C, line 274, compiled Oct 13 2004 at > 13:52:42 > > Best Regards, > Kai > > |
From: Kai L. <kai...@un...> - 2004-10-15 07:57:02
|
Hi Ben, > Hmm... I cannot seem to repeat this. Could you please post the output > from ./configure and your Make.common file? > configure: --------------------------------------------- ----------- Configuring libMesh ------------- --------------------------------------------- checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed <<< C++ compiler is gcc-3.3 >>> checking how to run the C++ preprocessor... g++ -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for short int... yes checking size of short int... 2 checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for float... yes checking size of float... 4 checking for double... yes checking size of double... 8 checking for void *... yes checking size of void *... 4 checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking whether the compiler implements namespaces... yes checking whether the compiler has locale... yes checking whether the compiler has stringstream... yes checking hash_map usability... no checking hash_map presence... no checking for hash_map... no checking ext/hash_map usability... yes checking ext/hash_map presence... yes checking for ext/hash_map... yes checking hash_set usability... no checking hash_set presence... no checking for hash_set... no checking ext/hash_set usability... yes checking ext/hash_set presence... yes checking for ext/hash_set... yes <<< Configuring library with AMR support >>> <<< Configuring library with expensive data structures enabled >>> <<< Configuring library with higher order p-FEM shapes >>> checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for xdrstdio_create... yes <<< Configuring library with XDR support >>> <<< Configuring library with real number support >>> <<< Configuring library with reference counting support >>> checking for ./contrib/netcdf/lib/i686-pc-linux-gnu/libnetcdf.a... no checking for ./contrib/netcdf/include/netcdf.h... no --------------------------------------------- ----- Configuring for optional packages ----- --------------------------------------------- checking for /include/petsc.h... no <<< PETSc disabled. Please set your "$PETSC_ARCH" environment variable correctly. >>>checking for ./contrib/laspack/lastypes.h... yes <<< Configuring library with LASPACK version 1.12.3 support >>> checking for ./contrib/sfcurves/sfcurves.h... yes <<< Configuring library with SFC support >>> checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for ./contrib/gzstream/gzstream.h... yes <<< Configuring library with gzstreams support >>> checking for ./contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a... yes checking for ./contrib/tecplot/include/TECIO.h... yes <<< Configuring library with Tecplot API support >>> checking for ./contrib/metis/Lib/metis.h... yes <<< Configuring library with Metis support >>> checking for doxygen... /usr/bin/doxygen checking for dot... /usr/bin/dot ---------------------------------------------- --- Done configuring for optional packages --- ---------------------------------------------- checking for perl... /usr/bin/perl configure: creating ./config.status config.status: creating Make.common config.status: creating doc/Doxyfile config.status: creating contrib/bin/libmesh-config config.status: creating include/base/libmesh_config.h config.status: include/base/libmesh_config.h is unchanged --------------------------------------------- --------- Done Configuring libMesh ---------- --------------------------------------------- Make.common: # $Id: Make.common.in,v 1.37 2004/05/05 15:23:47 spetersen Exp $ #########################################################################= ######## Please note: ## The ./configure script generates Make.common from ## Make.common.in, so if you want to change something, ## then do it in the latter file (here!)and re-run ./configure in the ## top level directory #########################################################################= ###### #########################################################################= ####### # The Make.common file defines the build environment for libMesh # and all its helper applications. If you want to build an application # that makes use of libMesh it is highly recommended that you include # this file in your project's Makefile. # #########################################################################= ###### #########################################################################= ####### the following lines will be replaced by the output # of ./configure hosttype =3D i686-pc-linux-gnu CXX =3D g++ CC =3D gcc LDFLAGS =3D DLFLAGS =3D LIBS =3D FLIBS =3D GXX-VERSION =3D gcc3.3 CXXSHAREDFLAG =3D -shared CSHAREDFLAG =3D -shared RPATHFLAG =3D -Wl,-rpath, # Complex variable support enable-complex =3D no ifeq ($(enable-complex),yes) CXXFLAGS +=3D -DUSE_COMPLEX_NUMBERS CFLAGS +=3D -DUSE_REAL_NUMBERS endif # Petsc iterative solvers for parallel and uniprocessor # applications enable-petsc =3D no petsc-version =3D petsc-major-minor =3D PETSC_ARCH =3D PETSC_DIR =3D # TetGen tetrahedrization library enable-tetgen =3D no # MPI configuration # (only explicitly defined when PETSc is absent, otherwise snooped from PETSc)MPI_IMPL =3D MPI_INCLUDE =3D MPI_LIB =3D # Doxygen for generating documentation doxygen =3D /usr/bin/doxygen # Perl for making .depend perl =3D /usr/bin/perl # Flag for optional packages enable-optional =3D yes enable-laspack =3D yes enable-metis =3D yes enable-parmetis =3D no enable-sfcurves =3D yes enable-gzstream =3D yes # # Set the current directory. libmesh_dir :=3D /usr/local/src/libmesh/libmesh-0.4.3-rc1 #########################################################################= ###### #########################################################################= ####### # Figure out the compilation mode based on the # environment variable METHOD. opt-mode :=3D off debug-mode :=3D off prof-mode :=3D off syn-mode :=3D off obj-suffix :=3D i686-pc-linux-gnu.o # # If the user has no environment variable # called METHOD, he gets optimized mode. ifeq (x$(METHOD),x) METHOD :=3D opt opt-mode :=3D on obj-suffix :=3D i686-pc-linux-gnu.o endif # # If METHOD=3Dopt, compile in optimized mode. ifeq ($(METHOD),opt) opt-mode :=3D on obj-suffix :=3D i686-pc-linux-gnu.o endif # # If METHOD=3Ddbg, compile in debug mode. ifeq ($(METHOD),dbg) debug-mode :=3D on obj-suffix :=3D i686-pc-linux-gnu.g.o endif # # If METHOD=3Dpro, compile in profiler mode ifeq ($(METHOD),pro) prof-mode :=3D on obj-suffix :=3D i686-pc-linux-gnu.pg.o endif # # If METHOD=3Dsyn, compile in syntax-checking mode ifeq ($(METHOD),syn) syn-mode :=3D on obj-suffix :=3D i686-pc-linux-gnu.sy.o endif # # Set the option to determine what type of # library (.so or .a) will be built. enable-shared :=3D yes # # If we are profiling, we CANNOT use shared # libs. At least I don't think we can ;) ifeq ($(prof-mode),on) enable-shared :=3D no endif #########################################################################= ###### #########################################################################= ####### Compiler flags, different for optimized, debug, and profiler mode= s. ifeq ($(debug-mode),on) CXXFLAGS +=3D -O2 -felide-constructors -g -ansi -pedantic -W -Wall -Wunused -Wpointer-arith -Wimplicit -Wformat -Wparentheses -Wuninitialized -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC -DDEBUG -fPI= C CFLAGS +=3D -g -DDEBUG -fPIC endif ifeq ($(opt-mode),on) CXXFLAGS +=3D -O2 -felide-constructors -DNDEBUG -fPIC -funroll-loops -fstrict-aliasing CFLAGS +=3D -O2 -DNDEBUG -fPIC -funroll-loops -fst= rict-aliasing endif ifeq ($(prof-mode),on) CXXFLAGS +=3D -O2 -felide-constructors -DNDEBUG -g -pg -fPIC -funroll-loops -fstrict-aliasing CFLAGS +=3D -O2 -DNDEBUG -g -pg -fP= IC -funroll-loops -fstrict-aliasing endif ifeq ($(syn-mode),on) CXXFLAGS +=3D -fsyntax-only CFLAGS +=3D -fsyntax-only endif ifeq ($(prof-mode),on) LIBS +=3D -pg endif #########################################################################= ###### #########################################################################= ####### The mesh library # mesh_library_dir :=3D $(libmesh_dir)/lib/$(hosttype)_$(METHOD) mesh_library :=3D $(mesh_library_dir)/libmesh.a ifeq ($(enable-shared),yes) mesh_library :=3D $(mesh_library_dir)/libmesh.so DLFLAGS +=3D $(RPATHFLAG)$(mesh_library_dir) endif LIBS +=3D $(mesh_library) #########################################################################= ###### #########################################################################= ####### now configuration for package includes, libraries, etc... # # The include directories for libMesh LIBMESH_INCLUDES =3D -I$(libmesh_dir)/include/base \ -I$(libmesh_dir)/include/enums \ -I$(libmesh_dir)/include/fe \ -I$(libmesh_dir)/include/geom \ -I$(libmesh_dir)/include/mesh \ -I$(libmesh_dir)/include/numerics \ -I$(libmesh_dir)/include/partitioning \ -I$(libmesh_dir)/include/quadrature \ -I$(libmesh_dir)/include/solvers \ -I$(libmesh_dir)/include/utils INCLUDE +=3D $(LIBMESH_INCLUDES) # # Package-specific stuff # # Contributed source & libraries EXTERNAL_LIBDIR :=3D $(libmesh_dir)/contrib/lib/$(hosttype)_$(METHOD) EXTERNAL_LIBEXT :=3D .a ifeq ($(enable-shared),yes) EXTERNAL_LIBEXT :=3D .so DLFLAGS +=3D $(RPATHFLAG)$(EXTERNAL_LIBDIR) endif # # Optional packages ifeq ($(enable-optional),yes) # if Laspack is used we need the header path # and the lib LIBS +=3D $(EXTERNAL_LIBDIR)/liblaspack$(EXTERNAL_LIBEXT) INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/laspack # if Paretis is used we need the header path # and the lib # (Parmetis must precede Metis for static linking) LIBS +=3D INCLUDE +=3D # if Metis is used we need the header path # and the lib LIBS +=3D $(EXTERNAL_LIBDIR)/libmetis$(EXTERNAL_LIBEXT) INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/metis/L= ib # if Space filling curves are used we need the # header path and the lib LIBS +=3D $(EXTERNAL_LIBDIR)/libsfcurves$(EXTERNAL_LIBEXT) INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/sfcurve= s # if gzstreams are used, we need the # header path and the lib LIBS +=3D $(EXTERNAL_LIBDIR)/libgzstream$(EXTERNAL_LIBEXT) -lz INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/gzstrea= m #if Tecplot is used, link against tecio.a LIBS +=3D /usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/tecplot/lib/i686-pc-li= nux-gnu/tecio.a INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/tecplot/include #if TetGen is used: ifeq ($(enable-tetgen),yes) CXXFLAGS +=3D -DHAVE_TETGEN CXXFLAGS +=3D LIBS +=3D INCLUDE +=3D endif #######################################################################= ###### # Petsc ifeq ($(enable-petsc),yes) # define BOPT first since it may be used in the packages file ifeq ($(enable-complex),yes) CXXFLAGS +=3D -DPETSC_USE_COMPLEX CFLAGS +=3D -DPETSC_USE_COMPLEX PETSC_BOPT.g =3D g_complex PETSC_BOPT.o =3D O_complex else PETSC_BOPT.g =3D g PETSC_BOPT.o =3D O endif ifeq ($(debug-mode),on) BOPT =3D $(PETSC_BOPT.g) else BOPT =3D $(PETSC_BOPT.o) endif # Depending on petsc version, we include different files ifeq ($(petsc-version),2.1.0) include $(PETSC_DIR)/bmake/$(PETSC_ARCH)/base.site # 2.1.0 style else C_CLINKER_SLFLAG =3D $(RPATHFLAG)# necessary for PETSc 2.1.6 include $(PETSC_DIR)/bmake/$(PETSC_ARCH)/packages # 2.1.1 or later style endif INCLUDE +=3D -I$(PETSC_DIR)/include -I$(PETSC_DIR)/bmake/$(PETSC_ARCH= ) \ $(MPI_INCLUDE) $(BLOCKSOLVE_INCLUDE) $(HYPRE_INCLUDE) PETSC_LIB =3D $(PETSC_DIR)/lib/lib$(BOPT)/$(PETSC_ARCH) ifeq ($(enable-shared),yes) CXXFLAGS +=3D -DPETSC_USE_DYNAMIC_LIBRARIES CFLAGS +=3D -DPETSC_USE_DYNAMIC_LIBRARIES DLFLAGS +=3D $(RPATHFLAG)$(PETSC_LIB) endif # Depending on petsc version, we link with different libs :-( ifeq ($(petsc-major-minor),2.2.x) # 2.2.x & newer style libs-PETSC =3D -L$(PETSC_LIB) \ -lpetscksp \ -lpetscdm \ -lpetscmat \ -lpetscvec \ -lpetsc else # 2.1.6 & older style libs-PETSC =3D -L$(PETSC_LIB) \ -lpetscsles \ -lpetscdm \ -lpetscmat \ -lpetscvec \ -lpetsc endif LIBS +=3D $(libs-PETSC) $(BLOCKSOLVE_LIB) $(SPOOLES_LIB) \ $(HYPRE_LIB) $(BLASLAPACK_LIB) $(MPI_LIB) \ $(X11_LIB) $(MATLAB_LIB) $(FLIBS) endif #end ifeq ($(enable-petsc),yes) # MPI configuration when Petsc is absent LIBS +=3D $(MPI_LIB) INCLUDE +=3D $(MPI_INCLUDE) endif # End of disable-optional test #if Exodus is used, link against libexoIIv2c.a LIBS +=3D INCLUDE +=3D #if netCDF is used, link against libnetcdf.a # (note that netCDF is required by exodus if available, # so we need to link to this _after_ exodus. LIBS +=3D INCLUDE +=3D # # Finally, Append the linker flags to the libraries LIBS +=3D $(DLFLAGS) $(LDFLAGS) #########################################################################= ###### #########################################################################= ####### Build rules ################################## # C++ rules # ################################## # # How to compile optimized C++ # %.i686-pc-linux-gnu.o : %.C @echo "Compiling C++ (in optimized mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C++ with debugging flags # %.i686-pc-linux-gnu.g.o : %.C @echo "Compiling C++ (in debug mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C++ with profiling flags # %.i686-pc-linux-gnu.pg.o : %.C @echo "Compiling C++ (in profiler mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C++ with syntax-checking flags # %.i686-pc-linux-gnu.sy.o : %.C @echo "Compiling C++ (in syntax-checker mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< $(shell touch $@) ################################## # C rules # ################################## # do not show this to the LASPACK Makefile ifeq (x$(included-from-laspack),x) # # How to compile optimized C # %.i686-pc-linux-gnu.o : %.c @echo "Compiling C (in optimized mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C with debugging flags # %.i686-pc-linux-gnu.g.o : %.c @echo "Compiling C (in debug mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C with profiling flags # %.i686-pc-linux-gnu.pg.o : %.c @echo "Compiling C (in profiler mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ # # How to compile C with profiling flags # %.i686-pc-linux-gnu.sy.o : %.c @echo "Compiling C (in syntax-checker mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ $(shell touch $@) else # only visible for LASPACK Makefile ifeq ($(enable-complex),yes) # complex: C++ rules for .c Laspack code %.i686-pc-linux-gnu.o : %.c @echo "Compiling C++ (in optimized mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.g.o : %.c @echo "Compiling C++ (in debug mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.pg.o : %.c @echo "Compiling C++ (in profiler mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.sy.o : %.c @echo "Compiling C++ (in syntax-checker mode) "$<"..." @$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< $(shell touch $@) else # real: C rules for .c Laspack code %.i686-pc-linux-gnu.o : %.c @echo "Compiling C (in optimized mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.g.o : %.c @echo "Compiling C (in debug mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.pg.o : %.c @echo "Compiling C (in profiler mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ %.i686-pc-linux-gnu.sy.o : %.c @echo "Compiling C (in syntax-checker mode) "$<"..." @$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@ $(shell touch $@) endif endif #########################################################################= ###### # Local Variables: # mode: makefile # End: Regards, Kai --=20 http://echempp.sourceforge.net Kai Ludwig Institut f=FCr Organische Chemie Auf der Morgenstelle 18 72076 T=FCbingen Tel.: 07071/29-73049 Mail: kai...@un... |