dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Aug 08, 2006 at 09:30:52AM +0200, Johan Hoffman wrote:

> I would be happy to help out, for example with renaming or updating the
> manual.

I think Garth is done with the renaming. We just need to agree on
DenseVector I think. After that, I'll take a look at it again and
update the class diagram.

It would be great if we could all look over the design and agree on it
so we can finalize it and finish the manual.

In particular, we should look closely on GenericMatrix and
GenericVector. Are we completely happy with the current interface?
Should we remove something? Or add something? There are some functions
like zero(), ident() and nzmax() that we need for assembly but that
seem to be very special.

Another thing is the design of preconditioners which is not the same
for uBlas and PETSc. Can we fix this?

We should also try to make better use of the bugzilla system for
assigning tasks. Let's throw everything in there. There are currently
4 open bugs that we need to take care of but there are plenty more
we need to fix before the next release.

> Although, I seem to have some problems compiling the current dolfin hg
> version. Anyone who recognize this? Is there a bug, or do I have some
> problem with my linking?

You seem to have an old version of ublas. Try upgrading to the latest
version.

/Anders


> /Johan
> 
> 
>  g++ -DPACKAGE_NAME=\"dolfin\" -DPACKAGE_TARNAME=\"dolfin\"
> -DPACKAGE_VERSION=\"0.6.1\" "-DPACKAGE_STRING=\"dolfin 0.6.1\""
> -DPACKAGE_BUGREPORT=\"dolfin@xxxxxxxxxx\" -DSTDC_HEADERS=1
> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
> -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1
> -I. -I. -I../../../src/kernel/common -I../../../src/kernel/fem
> -I../../../src/kernel/form -I../../../src/kernel/function
> -I../../../src/kernel/io -I../../../src/kernel/la
> -I../../../src/kernel/main -I../../../src/kernel/math
> -I../../../src/kernel/mesh -I../../../src/kernel/nls
> -I../../../src/kernel/ode -I../../../src/kernel/pde
> -I../../../src/kernel/quadrature -I../../../src/kernel/parameter
> -I../../../src/kernel/log -DHAVE_PETSC_H=1 -I/usr/local/petsc-2.3.0/
> -I/usr/local/petsc-2.3.0//bmake/linux-gnu
> -I/usr/local/petsc-2.3.0//include -I/usr/local/petsc-2.3.0/include/mpiuni
> -I/usr/include/libxml2 -g -O2 -DNDEBUG -pedantic -Wno-long-long
> -std=c++98 -MT FEM.lo -MD -MP -MF .deps/FEM.Tpo -c FEM.cpp  -fPIC -DPIC
> -o .libs/FEM.o
> In file included from ../../../src/kernel/la/dolfin/ublas.h:12,
>                  from ../../../src/kernel/la/dolfin/uBlasMatrix.h:18,
>                  from ../../../src/kernel/la/dolfin/uBlasDenseMatrix.h:10,
>                  from ../../../src/kernel/la/dolfin/DenseMatrix.h:12,
>                  from ./dolfin/FEM.h:18,
>                  from FEM.cpp:10:
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:17:2: #error class
> generalized_vector_of_vector is experiment and currently does not work
> In file included from ../../../src/kernel/la/dolfin/ublas.h:12,
>                  from ../../../src/kernel/la/dolfin/uBlasMatrix.h:18,
>                  from ../../../src/kernel/la/dolfin/uBlasDenseMatrix.h:10,
>                  from ../../../src/kernel/la/dolfin/DenseMatrix.h:12,
>                  from ./dolfin/FEM.h:18,
>                  from FEM.cpp:10:
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error:
> declaration of `class T'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows
> template parm `class T'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error:
> declaration of `class F'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows
> template parm `class F'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1203: error:
> declaration of `class A'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:32: error:  shadows
> template parm `class A'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error: type
> `boost::numeric::ublas::generalized_vector_of_vector<T, F, A>' is not
> derived from type `boost::numeric::ublas::generalized_vector_of_vector<T,
> F, A>'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error: ISO C++
> forbids initialization of member `zero_'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error: making
> `zero_' static
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: error:
> template declaration of `const typename
> boost::numeric::ublas::generalized_vector_of_vector<T, F, A>::value_type
> boost::numeric::ublas::generalized_vector_of_vector<T, F, A>::zero_'
> /usr/include/boost/numeric/ublas/vector_of_vector.hpp:1208: confused by
> earlier errors, bailing out
> make[4]: *** [FEM.lo] Error 1
> make[4]: Leaving directory
> `/afs/nada.kth.se/home/m/u1qo8adm/work/computing2/dolfin/src/kernel/fem'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/afs/nada.kth.se/home/m/u1qo8adm/work/computing2/dolfin/src/kernel/fem'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/afs/nada.kth.se/home/m/u1qo8adm/work/computing2/dolfin/src/kernel'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/afs/nada.kth.se/home/m/u1qo8adm/work/computing2/dolfin/src'
> make: *** [all-recursive] Error 1
> 
> 
> 
> 
> 
> > On Mon, Aug 07, 2006 at 03:09:57PM +0200, Garth N. Wells wrote:
> >>
> >>
> >> Anders Logg wrote:
> >> > On Mon, Aug 07, 2006 at 03:00:58PM +0200, Garth N. Wells wrote:
> >> >>
> >> >> Anders Logg wrote:
> >> >>> I have made a class diagram for the linear algebra classes, which
> >> can
> >> >>> be found either in doc/manual/{dia,eps}/class-diagram-la.{dia,eps}
> >> or
> >> >>> at
> >> >>>
> >> >>>     http://home.simula.no/~logg/tmp/class-diagram.eps
> >> >>>
> >> >> Something wrong with this link.
> >> >
> >> > Should be
> >> >
> >> >    http://home.simula.no/~logg/tmp/class-diagram-la.eps
> >> >
> >> >>> >From this diagram, it is clear there are some inconsistencies. Here
> >> >>> are some suggestions:
> >> >>>
> >> >>> 1. Rename PETScSparseMatrix --> PETScMatrix since there is only one
> >> >>> PETSc matrix.
> >> >>>
> >> >>> 2. Rename DenseVector --> uBlasVector. DenseVector can be a typedef.
> >> >>>
> >> >>> 3. Break up LinearSolver in two classes: PETScLinearSolver and
> >> >>> uBlasLinearSolver and make both pure virtual interfaces.
> >> >>>
> >> >>> 4. Rename PETScLU --> PETScLUSolver to make it consistent.
> >> >>>
> >> >>> 5. Rename VirtualMatrix --> PETScKrylovMatrix to make it consistent
> >> >>> with uBlasKrylovMatrix.
> >> >>>
> >> >>> 6. Rename Preconditioner --> PETScPreconditioner to make it
> >> consistent
> >> >>> with uBlasPreconditioner.
> >> >>>
> >> >>> 7. Typedefs for common default types should include the following:
> >> >>>
> >> >>>    Matrix
> >> >>>    Vector
> >> >>>
> >> >>>    DenseMatrix
> >> >>>    DenseVector    (something that works with DenseMatrix)
> >> >>>
> >> >>>    SparseMatrix
> >> >>>    SparseVector   (something that works with SparseVector)
> >> >>>
> >> >>>    LinearSolver
> >> >>>    KrylovSolver
> >> >>>    GMRES
> >> >>>    LU
> >> >>>
> >> >>>    VirtualMatrix  (something that works with KrylovSolver)
> >> >>>    Preconditioner (something that works with KrylovSolver)
> >> >>>
> >> >> All looks good. Can add
> >> >>
> >> >>    Rename EigenvalueSolver --> PETScEigenvalueSolver.
> >> >
> >> > Agreed.
> >> >
> >> >>> Here's a little list of things I think we should fix before
> >> releasing 0.6.2:
> >> >>>
> >> >>>  - Fix the above cleanups
> >> >>>
> >> >>>  - Make sure the linear algebra works nicely in PyDOLFIN
> >> >>>
> >> >>>  - Update the class diagram
> >> >>>
> >> >>>  - Complete the linear algebra chapter in the manual
> >> >>>
> >> >>>  - Add a linear algebra benchmark in src/bench
> >> >>>
> >> >>>  - Add a linear algebra test in src/test
> >> >>>
> >> >>>  - Add a linear algebra demo in src/demo
> >> >>>
> >> >> We should also get everything compiling working with the
> >> --disable-petsc
> >> >> flag (some demos don't compile at the moment) and remove
> >> PETSc-specific
> >> >> operations if they're not necessary.
> >> >
> >> > Agreed.
> >> >
> >> > Is it possible to divide the labor among us (Hoffman, Jansson, Logg,
> >> > Wells) and fix this quickly?
> >> >
> >>
> >> Since I messed up the naming by adding uBlas-based classes, I'm happy to
> >> take care of the class renaming. After that I can add some uBlas demos
> >> and benchmarks.
> >
> > Sounds good. (But probably I'm to blame for throwing in all the PETSc
> > ifdefs to begin with...:-)
> >
> > I'll start working on a testing framework for DOLFIN so it's simple to
> > add unit test for all modules (including linear algebra).
> >
> > /Anders
> >
> >> Garth
> >>
> >>
> >> > /Anders
> >> >
> >> >> Garth
> >> >>
> >> >>> It would be great if we could all help out so everyone agrees on and
> >> >>> knows the design of the linear algebra library. We would then have a
> >> >>> well functioning and stable linear algebra library that would
> >> require
> >> >>> little maintenance so we can focus on other things (like porting to
> >> >>> the new mesh library).
> >> >>>
> >> >>> /Anders
> >> >>> _______________________________________________
> >> >>> DOLFIN-dev mailing list
> >> >>> DOLFIN-dev@xxxxxxxxxx
> >> >>> http://www.fenics.org/mailman/listinfo/dolfin-dev
> >> >>
> >> >> _______________________________________________
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> >> >> DOLFIN-dev@xxxxxxxxxx
> >> >> http://www.fenics.org/mailman/listinfo/dolfin-dev
> >> > _______________________________________________
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> >> > http://www.fenics.org/mailman/listinfo/dolfin-dev
> >>
> >> _______________________________________________
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> >
> 
> 
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