dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On Mon, Oct 15, 2012 at 7:59 PM, Anders Logg <logg@xxxxxxxxx> wrote:
> On Mon, Oct 15, 2012 at 05:28:50PM +0100, Garth N. Wells wrote:
>
>> > Do we have that documented somewhere? It would be good to get this
>> > into Dorsal (if possible) to make it easy to share the knowledge of
>> > how to build 'hpc' versions of FEniCS on some standard systems.
>> >
>>
>> Not documented, but the issue is simple: with dynamically linked
>> libraries in standard paths it's mayhem trying figure out what's being
>> linked when different libraries link to different library versions  of
>> the same package..
>
> Could you share some pointers on how you have set up your build, which
> versions of packages (MPICH or OpenMPI), which BLAS, version numbers
> etc and I can try to replicate and think about whether this can be
> documented as part of Dorsal or somewhere else.
>

- Most important is ATLAS for BLAS (if MKL is not available)

    http://math-atlas.sourceforge.net/

I use v3.10. It can take a long time to build, and can be tricky (e.g.
it won't build if the CPU clock frequency is being dynamically
controlled).

- Build LAPACK to use ATLAS BLAS

- Build latest OpenMPI with support for threads turned on. MPICH2
works fine too.

- Build Boost so that Boost.MPI uses the manually installed MPI

- Install CGAL to use the manually installed Boost

- Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
pull in MPI)

- Build VTK (so that the Ubuntu version doesn't pull in MPI)

- Build HDF5 with parallel suppport  (so that the Ubuntu version
doesn't pull in MPI)

- Build SCOTCH and PaStiX with support for 64 bit integers

- Build PETSc, SLEPc and Trilinos, linking to the above libraries.

There are probably some tricks to getting around some changes by using
the Ubuntu 'alternatives' system.

Garth

>> I hope you're not referring to 'standard HPC' systems. They don't exist.
>
> I'm referring to having a good build of the FEniCS software stack on a
> standard desktop or laptop running the latest Ubuntu which is what
> most of us have. I've been relying on Dorsal which tries to use as
> many Debian packages as possible, but apparently that is not enough.
>
> --
> Anders