dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Jul 01, 2005 at 12:07:16AM -0400, Faheem Mitha wrote:
> 
> Dear DOLFIN developers,
> 
> I work in a small computational immunology research group in the Dept
> of Biostatistics and Bioinformatics at Duke University in North
> Carolina. We are trying to set up simulation projects, which involve
> solving pde's. We are interested in both Petsc and DOLFIN.
> 
> I've been trying to install 0.5.7 on Debian. Unfortunately, I've been 
> having some difficulties, and I hope you can help.

It shouldn't be a problem getting PETSc + DOLFIN running on
Debian. I'm using Debian myself.

> At least part of the problems I've had involve the installation of Petsci, 
> which dolfin has difficulty compiling against.
> 
> The structure of the installation of Petsci is quite complicated, but seems 
> to consist of 4 directories, namely bin, bmake, include and lib.
> 
> For some reason, there are some header files in /bmake/linux-gnu in 
> addition to those in include. The compilation had problems locating these 
> include files.

It can be a little tricky to get PETSc installed, since they don't
follow the standard configure + make. (On the other hand, they are
using Matt Knepley's new BuildSystem which is pretty powerful.)

You need to download PETSc version 2.2.1 from the PETSc web site:

    http://www-unix.mcs.anl.gov/petsc/petsc-2/

The latest version is really 2.3.0, but we have have not yet moved to
that version (we should). It won't work with the PETSc package (2.2.0)
in Debian, so I suggest you uninstall that package if you have it
installed.

Download the PETSc tarball and unpack it somewhere (I suggest you do
it in /usr/local/lib/). Then do the following:

    export PETSC_DIR=`pwd`
    ./config/configure.py
    make BOPT=g_c++
    make BOPT=O_c++

You might run into some difficulties along the way (like getting MPI
set up correctly) but the PETSc configure script should help you with
this.

> So, my first question is, what kind of Petsci library structure does dolfin 
> expect to be compiling against?
> 
> There seem to be (at least) two possibilities.
> 
> a) Dolfin expects to compile against Petsci sources. I hope not.
> 
> b) Dolfin can compile against only the Petsci shared/static libraries and 
> header files.
> 
> If the latter, where does dolfin expect the directories listed above to be 
> located?
> 
> Let me know if you want to see a configure log or anything else. This was 
> tested on a pretty bare-bones sarge (chrooted) Debian system.

When you have PETSc installed, just do

    ./configure
    make

in the DOLFIN directory to compile DOLFIN. (And then an optional make
install to install it on your system.) DOLFIN assumes that PETSc is in
/usr/local/lib/petsc/ so either make a symlink to where you compiled
PETSc or give the full path name with --with-petsc-dir=<path>. DOLFIN
also assumes that you want PETSc BOPT=g_c++, so if you want to compile
with PETSc BOPT=O_c++, use the flag --with-petsc-bopt=O_c++.

> Just a few more questions.
> 
> In your estimation, is DOLFIN ready for general usage? The code and design 
> looks very good but the documentation is sparse.

It's getting ready. There will be a new version later today (or early
next week, as soon as a new version of FIAT comes out) with many
improvements and fixes. If you want to try out this version, download
the latest CVS snapshot of DOLFIN from

    http://www.fenics.org/pub/software/dolfin/cvs/

Take a look in the subdirectory src/demo/poisson/ of DOLFIN, which
contains a simple demo program with some instructions.

Things are starting to stabilize enough now for us to write a manual,
but I can't promise that we'll have it ready until after the summer.

What does Johan + Johan say? Are you willing to contribute to the
manual?

> Are the developers willing 
> to answer questions about the details of the library?

Yes, of course.

> I see DOLFIN is currently using Petsc 2.2.1. However, 2.3 is the most 
> recent release, and the most recent version packaged for Debian is 2.2.0. 
> Are there any plans to switch to using 2.3 in the near future? Do you have 
> any Debian packages of more recent versions of Petsci or of DOLFIN 
> available?

Yes, we will switch to 2.3 as soon as possible. I'll gladly accept any
patches for this.

There are no Debian packages yet, but I would like to see DOLFIN (and
the rest of the FEniCS projects) added to Debian at some point.

/Anders