dolfin team mailing list archive

["Garth N. Wells" <g.n.wells@xxxxxxxxxx>]

Quoting Anders Logg <logg@xxxxxxxxx>:

> On Thu, May 25, 2006 at 12:32:19PM +0200, Garth N. Wells wrote:
> > 
> > Quoting Anders Logg <logg@xxxxxxxxx>:
> > 
> > > On Thu, May 25, 2006 at 10:02:26AM +0200, Garth N. Wells wrote:
> > > > What's the motivation behind allowing PETSc to be disabled? Is it to
> allow
> > > the
> > > > mesh library to be compiled without having PETSc installed? The
> problem
> > > with
> > > > disabling PETSc is that it removes 95% of DOLFIN functionality, and
> bearing
> > > this
> > > > in mind becomes intrusive in large parts of the code (a finite element
> > > assembly
> > > > library which has no sparse linear algerbra :) ). Almost every demo
> will be
> > > full
> > > > of ifdefs. A better approach would be to set an option to get the 5%
> that
> > > is
> > > > needed. Depending exactly what's needed I would suggest
> > > > 
> > > > 1) Adding something link "make mesh" to compile individual components
> that
> > > are
> > > > desried
> > > > 
> > > > 2) Adding some basic linear algerbra functionality for sparse matrices
> and
> > > a
> > > > linear solver. uBlas could be used for this. This way, everything will
> > > work,
> > > > just not optimally or in parallel and with a reduced set of features.
> > > > 
> > > > Garth
> > > 
> > > The motivation is that the DOLFIN mesh library (but not the linear
> > > algebra and not the assembly) is used in PyCC, the Python Computing
> > > Components framework developed at Simula. Not needing to download,
> > > configure, compile and install PETSc saves a lot of work.
> > > 
> > 
> > OK. I think that this holds also for people who just want to take a first
> look
> > at DOLFIN and don't want to go through the rigmarole of installing PETSc.
> It
> > doesn't affect me, but wouldn't "make mesh" be convenient and potentially
> much
> > faster for people who just want to use the mesh library?
> 
> Yes, that's also an option but it would require us to rework the build
> process. Maybe we should allow individual compilation of all the
> different libraries:
> 
>     make la
>     make ode
>     make fem
>     make mesh
>     etc
> 
> This could be useful but it would require some work. Rumour has it
> that we will soon be able to build DOLFIN with Scons (www.scons.org)
> so maybe we can wait until then.
> 
> > > I like option 2 best. We could even use the current dense matrices and
> > > vectors for this. The current assembly works entirely through
> > > GenericMatrix so it should work fine to assemble and solve PDEs
> > > without PETSc. What about trying to implement all interfaces in terms
> > > of GenericMatrix? The demos can use Matrix/Vector. If DOLFIN is
> > > compiled with PETSc support, then Matrix is a typedef of SparseMatrix
> > > and otherwise it is a typedef of DenseMatrix. All the ifdefs should
> > > only need to be in the linear algebra classes, the rest of the code
> > > should not need to care.
> > > 
> > 
> > OK, let's use GenericMatrix as much as possible. Problem with using dense
> > matrices is that the demos might not work due to exesssive memory demands,
> and
> > the solve will take forwever.  At the risk of extra complication, we could
> have
> > the classes PETScSparseMatrix and uBlasSparseMatrix, and have a typedef
> that
> > PETScSparseMatrix is a SparseMatrix if PETSc is enabled, otherwise a
> typedef
> > that uBlasSparseMatrix is a SparseMatrix. Creating uBlasSparseMatrix will
> be
> > simple as uBlas has a number of sparse matrix classes. We can than restict
> all
> > the PETSc ifdef's to src/kernel/la.
> > 
> > Garth
> 
> Sounds good to me. So we would then have something like
> 
>     class PETScSparseMatrix : public GenericMatrix { private: Mat A; }
>     class uBlasSparseMatrix : public GenericMatrix, public
> ublas::sparse_matrix_something<double> {}
>     class uBlasDenseMatrix  : public GenericMatrix, public
> ublas::matrix<double> {}
> 
>     #ifdef HAVE_PETSC_H
>     typedef PETScSparseMatrix SparseMatrix;
>     #else
>     typedef uBlasSparseMatrix SparseMatrix;
>     #endif
>     
>     typedef uBlasDenseMatrix DenseMatrix;
> 
>     typedef SparseMatrix Matrix;
> 

Exactly. I'll take a look at adding a class uBlasSparseMatrix.

Garth


> ?
> 
> /Anders
> 
> 
> > 
> > > /Anders
> > > 
> > > 
> > > > 
> > > > Quoting DOLFIN <dolfin@xxxxxxxxxx>:
> > > > 
> > > > > One or more new changesets pushed to the primary DOLFIN repository.
> > > > > A short summary of the last three changesets is included below.
> > > > > 
> > > > > changeset:   1945:a4821a8dc6ccd257033f8ff6987c88c6c76d45e7
> > > > > tag:         tip
> > > > > user:        "Anders Logg <logg@xxxxxxxxx>"
> > > > > date:        Thu May 25 00:33:42 2006 +0200
> > > > > files:       src/demo/fem/simple/main.cpp src/kernel/fem/FEM.cpp
> > > > > src/kernel/fem/dolfin/FEM.h src/kernel/io/File.cpp
> > > > > src/kernel/io/GenericFile.cpp src/kernel/io/dolfin/File.h
> > > > > src/kernel/io/dolfin/GenericFile.h src/kernel/la/dolfin/Matrix.h
> > > > > src/kernel/la/dolfin/Vector.h src/kernel/nls/NonlinearProblem.cpp
> > > > > src/kernel/nls/dolfin/NonlinearProblem.h
> src/kernel/ode/ReducedModel.cpp
> > > > > src/kernel/ode/dolfin/ReducedModel.h
> > > > > description:
> > > > > Fix compilation with --disable-petsc. (Should work now Ã…smund.)
> > > > > 
> > > > > A number of the demos don't compile without PETSc, but all libraries
> > > compile
> > > > > fine. We should remove the dependence on PETSc and work through
> > > > > GenericMatrix
> > > > > as much as possible. We should also consider doing a typedef of
> > > DenseMatrix
> > > > > to
> > > > > Matrix when running with --disable-petsc (instead of SparseMatrix).
> > > > > 
> > > > > We should set up a compilation bot on fenics.org to create nightly
> > > builds
> > > > > for various combinations of configurations. Otherwise we'll run into
> > > trouble
> > > > > with flags that we rarely use (like --disable-petsc).
> > > > > 
> > > > > 
> > > > > changeset:   1944:21e1173b19853a06ab8f44a3a84433668134c683
> > > > > user:        "Anders Logg <logg@xxxxxxxxx>"
> > > > > date:        Thu May 25 00:08:21 2006 +0200
> > > > > files:       Makefile.in aclocal.m4 configure src/Makefile.in
> > > > > src/bench/Makefile.in src/bench/fem/Makefile.in
> > > src/bench/ode/Makefile.in
> > > > > src/config/Makefile.in src/demo/Makefile.in src/demo/fem/Makefile.in
> > > > > src/demo/nls/Makefile.in src/demo/ode/Makefile.am
> > > src/demo/ode/Makefile.in
> > > > > src/demo/ode/aliev-panfilov/Makefile
> > > src/demo/ode/aliev-panfilov/main.cpp
> > > > > src/demo/ode/courtemanche/Makefile
> src/demo/ode/courtemanche/main.cpp
> > > > > src/demo/ode/homotopy/Makefile.in src/demo/pde/Makefile.in
> > > > > src/demo/pde/nonlinear/Makefile.in src/demo/pde/stokes/Makefile.in
> > > > > src/demo/scripting/Makefile.in src/demo/solvers/Makefile.in
> > > > > src/demo/solvers/navierstokes/Makefile.in src/greeting/Makefile.in
> > > > > src/kernel/Makefile.in src/kernel/common/Makefile.in
> > > > > src/kernel/common/dolfin/Makefile.in src/kernel/fem/Makefile.in
> > > > > src/kernel/fem/dolfin/Makefile.in src/kernel/form/Makefile.in
> > > > > src/kernel/form/dolfin/Makefile.in src/kernel/function/Makefile.in
> > > > > src/kernel/function/dolfin/Makefile.in src/kernel/io/Makefile.in sr
> > > > >  c/kernel/io/dolfin/Makefile.in src/kernel/la/Makefile.in
> > > > > src/kernel/la/dolfin/Makefile.in src/kernel/log/Makefile.in
> > > > > src/kernel/log/dolfin/Makefile.in src/kernel/main/Makefile.in
> > > > > src/kernel/main/dolfin/Makefile.in src/kernel/math/Makefile.in
> > > > > src/kernel/math/dolfin/Makefile.in src/kernel/mesh/Makefile.in
> > > > > src/kernel/mesh/dolfin/Makefile.in src/kernel/nls/Makefile.in
> > > > > src/kernel/nls/dolfin/Makefile.in src/kernel/ode/Makefile.in
> > > > > src/kernel/ode/dolfin/Makefile.in src/kernel/parameter/Makefile.in
> > > > > src/kernel/parameter/dolfin/Makefile.in src/kernel/pde/Makefile.in
> > > > > src/kernel/pde/dolfin/Makefile.in src/kernel/quadrature/Makefile.in
> > > > > src/kernel/quadrature/dolfin/Makefile.in src/lib/Makefile.in
> > > > > src/modules/Makefile.in src/modules/convdiff/Makefile.in
> > > > > src/modules/convdiff/dolfin/Makefile.in
> src/modules/dolfin/Makefile.in
> > > > > src/modules/elasticity-updated/Makefile.in
> > > > > src/modules/elasticity-updated/dolfin/Makefile.in
> > > > > src/modules/elasticity/Makefile.in
> > > src/modules/elasticity/dolfin/Makefile.in
> > > > > 
> > > > >  src/modules/heat/Makefile.in src/modules/heat/dolfin/Makefile.in
> > > > > src/modules/navierstokes/Makefile.in
> > > > > src/modules/navierstokes/dolfin/Makefile.in
> > > src/modules/poisson/Makefile.in
> > > > > src/modules/poisson/dolfin/Makefile.in
> src/modules/stokes/Makefile.in
> > > > > src/modules/stokes/dolfin/Makefile.in src/post/Makefile.in
> > > > > src/pre/Makefile.in src/pydolfin/Makefile.in src/utils/Makefile.in
> > > > > src/utils/convert/Makefile.in src/utils/inp2dx/Makefile.in
> > > > > description:
> > > > > Add cell models for cardiac excitation (Aliev-Panfilov and
> Courtemanche)
> > > > > as new ODE demos. Thanks to Ola and Glenn for supplying the
> examples.
> > > > > This is just a first test but the results look reasonable. Will look
> > > > > more into speeding up the computation next.
> > > > > 
> > > > > 
> > > > > changeset:   1943:16d5a8e397c062a86a04d50418573a609f6ef321
> > > > > user:        "Garth N. Wells <g.n.wells@xxxxxxxxxx>"
> > > > > date:        Wed May 24 14:08:37 2006 +0200
> > > > > files:       src/utils/convert/dolfin-convert
> > > > > description:
> > > > > Read number of "tags" before connectivity when converting meshes
> from
> > > gmsh.
> > > > > 
> > > > > 
> > > > > -------------------------------------------------------
> > > > > For more details, visit http://www.fenics.org/hg/dolfin
> > > > > 
> > > > > _______________________________________________
> > > > > DOLFIN-dev mailing list
> > > > > DOLFIN-dev@xxxxxxxxxx
> > > > > http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> > > > > 
> > > 
>