dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Thu, Dec 18, 2008 at 04:16:47PM +0100, Thomas Gazzola wrote:
> Hello everyone!
> 
> Since I post for the first time on the M-list, I thank you all for the
> fenics suite.
> 
> I am developing some code in C++, and I use dolfin in order to solve
> some BVP problem. I did include dolfin.h and two forms compiled with
> ffc in each file. I had a trouble when linking my stuff.
> I am no C++ expert, so I don't know wether it is because of me or not.
> 
> I did use the recent revision number 5349 (result of `hg id -n`).
> 
> When compiling my stuff, I did have some _linking_ problems like:
> 
> (...snip...)
> Output.o: in function «
> boost::numeric::ublas::compressed_matrix<double,
> boost::numeric::ublas::basic_row_major<unsigned long, long>, 0ul,
> boost::numeric::ublas::unbounded_array<unsigned long,
> std::allocator<unsigned long> >,
> boost::numeric::ublas::unbounded_array<double, std::allocator<double>
> > >::size1() const»:
> $PREFIX/local/include/dolfin/fem/assemble.h:89: multiple definitions
> of « dolfin::assemble_system(dolfin::GenericMatrix&,
> dolfin::GenericVector&, dolfin::Form const&, dolfin::Form const&,
> std::vector<dolfin::DirichletBC const*,
> std::allocator<dolfin::DirichletBC const*> >&,
> dolfin::MeshFunction<unsigned int> const*,
> dolfin::MeshFunction<unsigned int> const*,
> dolfin::MeshFunction<unsigned int> const*, dolfin::GenericVector
> const*, bool)»
> main.o:/homes/tgax/local/include/dolfin/fem/assemble.h:89: first definition here
> (...snip...)
> 
> In other words, I have troubles with function assemble_system in file
> dolfin/fem/assemble.h .
> 
> I had a look at the assemble.h file. It is a file with code calling
> methods from the Assembler class (defined in files
> dolfin/fem/Assembler.*).
> 
> A `nm` on my *.o did show undefined symbols for function
> assemble_system, in several object files. Assembler::assemble_system
> were OK.
> 
> The code from assemble.h seems to be compiled in several of my object
> files, so the linker just cannot link.
> 
> In order to solve this, I did split dolfin/fem/assemble.h into a .cpp
> and a real header file. The SConstruct process automatically compiles
> assemble.cpp, and the link could be done to my program.
> 
> I don't know if it is a real problem of dolfin, or if I did something
> wrong, but I wanted to let you known. What do you think?
> 
> With the best regards,
> 
> Thomas G.

> 13,15d12
> < #ifndef __ASSEMBLE_H
> < #define __ASSEMBLE_H
> < 
> 27c24,27
> <                 bool reset_tensor);
> ---
> >                 bool reset_tensor=true)
> >   {
> >     Assembler::assemble(A, a, reset_tensor);
> >   }
> 33c33,36
> <                 bool reset_tensor);
> ---
> >                 bool reset_tensor=true)
> >   {
> >     Assembler::assemble(A, a, sub_domain, reset_tensor);
> >   }
> 41c44,47
> <                 bool reset_tensor);
> ---
> >                 bool reset_tensor=true)
> >   {
> >     Assembler::assemble(A, a, cell_domains, exterior_facet_domains, interior_facet_domains);
> >   }
> 49c55,58
> <                        bool reset_tensors);
> ---
> >                        bool reset_tensors=true)
> >   {
> >     Assembler::assemble_system(A, b, a, L, bc, reset_tensors);
> >   }
> 57c66,69
> <                        bool reset_tensors);
> ---
> >                        bool reset_tensors=true)
> >   {
> >     Assembler::assemble_system(A, b, a, L, bcs, reset_tensors);
> >   }
> 69c81,86
> <                        bool reset_tensors);
> ---
> >                        bool reset_tensors=true)
> >   {
> >     Assembler::assemble_system(A, b, a, L, bcs, 
> >                                cell_domains, exterior_facet_domains, interior_facet_domains,
> >                                x0, reset_tensors);
> >   }
> 75c92,98
> <                   bool reset_tensor);
> ---
> >                   bool reset_tensor=true)
> >   {
> >     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
> >     Scalar s;
> >     Assembler::assemble(s, a, reset_tensor);
> >     return s;
> >   }
> 80c103,109
> <                   bool reset_tensor);
> ---
> >                   bool reset_tensor=true)
> >   {
> >     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
> >     Scalar s;
> >     Assembler::assemble(s, a, sub_domain, reset_tensor);
> >     return s;
> >   }
> 87,88c116,122
> <                   bool reset_tensor);
> < }
> ---
> >                   bool reset_tensor=true)
> >   {
> >     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
> >     Scalar s;
> >     Assembler::assemble(s, a, cell_domains, exterior_facet_domains, interior_facet_domains, reset_tensor);
> >     return s;
> >   }
> 90c124
> < #endif
> ---
> > }

> // Copyright (C) 2007-2008 Anders Logg.
> // Licensed under the GNU LGPL Version 2.1.
> //
> // Modified by Garth N. Wells, 2008.
> //
> // First added:  2007-01-17
> // Last changed: 2008-11-16
> //
> // This file duplicates the Assembler::assemble* functions in
> // namespace dolfin, and adds special versions returning the value
> // directly for scalars. For documentation, refer to Assemble.h.
> 
> #include <dolfin/log/log.h>
> #include <dolfin/la/Scalar.h>
> #include "Form.h"
> #include "Assembler.h"
> #include "assemble.h"
> 
> namespace dolfin
> {
>   
>   using namespace dolfin;
>   //--- Copies of assembly functions in Assembler.h ---
>   
>   /// Assemble tensor
>   void assemble(GenericTensor& A,
>                 const Form& a,
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, reset_tensor);
>   }
> 
>   /// Assemble tensor on sub domain
>   void assemble(GenericTensor& A,
>                 const Form& a,
>                 const SubDomain& sub_domain,
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, sub_domain, reset_tensor);
>   }
> 
>   /// Assemble tensor on sub domains
>   void assemble(GenericTensor& A,
>                 const Form& a,
>                 const MeshFunction<uint>* cell_domains,
>                 const MeshFunction<uint>* exterior_facet_domains,
>                 const MeshFunction<uint>* interior_facet_domains,
>                 bool reset_tensor=true)
>   {
>     Assembler::assemble(A, a, cell_domains, exterior_facet_domains, interior_facet_domains);
>   }
> 
>   /// Assemble system (A, b) and apply Dirichlet boundary condition
>   void assemble_system(GenericMatrix& A,
>                        GenericVector& b,
>                        const Form& a,
>                        const Form& L,
>                        const DirichletBC& bc,
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bc, reset_tensors);
>   }
>  
>   /// Assemble system (A, b) and apply Dirichlet boundary conditions
>   void assemble_system(GenericMatrix& A,
>                        GenericVector& b,
>                        const Form& a,
>                        const Form& L, 
>                        std::vector<const DirichletBC*>& bcs,
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bcs, reset_tensors);
>   }
> 
>   /// Assemble system (A, b) on sub domains and apply Dirichlet boundary conditions
>   void assemble_system(GenericMatrix& A,
>                        GenericVector& b,
>                        const Form& a,
>                        const Form& L,
>                        std::vector<const DirichletBC*>& bcs,
>                        const MeshFunction<uint>* cell_domains,
>                        const MeshFunction<uint>* exterior_facet_domains,
>                        const MeshFunction<uint>* interior_facet_domains,
>                        const GenericVector* x0,
>                        bool reset_tensors=true)
>   {
>     Assembler::assemble_system(A, b, a, L, bcs, 
>                                cell_domains, exterior_facet_domains, interior_facet_domains,
>                                x0, reset_tensors);
>   }
> 
>   //--- Specialized versions for scalars ---
> 
>   /// Assemble scalar
>   double assemble(const Form& a,
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, reset_tensor);
>     return s;
>   }
> 
>   /// Assemble scalar on sub domain
>   double assemble(const Form& a,
>                   const SubDomain& sub_domain,
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, sub_domain, reset_tensor);
>     return s;
>   }
> 
>   /// Assemble scalar on sub domains
>   double assemble(const Form& a,
>                   const MeshFunction<uint>* cell_domains,
>                   const MeshFunction<uint>* exterior_facet_domains,
>                   const MeshFunction<uint>* interior_facet_domains,
>                   bool reset_tensor=true)
>   {
>     if (a.rank() != 0) error("Unable to assemble, form is not scalar.");
>     Scalar s;
>     Assembler::assemble(s, a, cell_domains, exterior_facet_domains, interior_facet_domains, reset_tensor);
>     return s;
>   }
> 
> }

Sounds like a missing #ifndef in assemble.h.

I have fixed this now, see if it works.

-- 
Anders

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