[petsc-dev] clique

[Jack Poulson]

Jed,

I completely agree that it is a nightmare. All that I want is (parallel)
nodal bisection. Right now, the best solution is to create two trivial
source files:
https://github.com/poulson/Clique/blob/master/src/parmetis/ParallelBisect.c
https://github.com/poulson/Clique/blob/master/src/metis/Bisect.c
which I removed them from the ParMeTiS source tree upon request.

It seems that, given the nightmare of forcing the user to provide me with
the directory containing their ParMeTiS thread-local support configuration
file, that I should just modify the symbol names of the ParMeTiS routines
which I include with Clique. This should fix all of the problems.

Jack

On Fri, Aug 31, 2012 at 2:28 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Jack, this bundling strategy is a distribution nightmare. Suppose that
> some other package "X" independent of clique also bundles Elemental. How
> does an application (or another library) use both X and clique?
> On Aug 31, 2012 1:49 PM, "Satish Balay" <balay at mcs.anl.gov> wrote:
>
>> Should have cc:d to petsc-dev
>>
>> context:
>>
>> clique packages metis,parmetis,elemental sources in a single bundle.
>> So we were attempting to build them separately [from petsc configure].
>>
>> Jack has extensions to metis and parmetis functionality - thats used
>> in clique. We tried to split this out into separate -lparmetis-addons
>> library [using parmetis public includes] so that our current
>> -lparmetis could be used.  But this doesn't work as it needs parmetis
>> private includes.
>>
>> So looks like we'll have to add these extensions to the metis/parmetis
>> tarballs we distribute [and have common metis/parmetis sources
>> available for both petsc an clique]
>>
>> Satish
>>
>> On Fri, 31 Aug 2012, Satish Balay wrote:
>>
>> > On Fri, 31 Aug 2012, Satish Balay wrote:
>> >
>> > > On Fri, 31 Aug 2012, Jack Poulson wrote:
>> > >
>> > > > > Also does clique also build elemental? Can we split it up aswell
>> with
>> > > > > MANUAL_ELEMENTAL, ELEMENTAL_INCLUDE_DIR, ELEMENTAL_LIBS options?
>> > > > >
>> > > > >
>> > > > I will take care of all of these issues as soon as I get a chance.
>> Clique
>> > > > does currently build Elemental (it sits in external/elemental). If
>> both
>> > > > Clique and Elemental are both to be used in the same package, I
>> would think
>> > > > it would make sense to just install Clique and use its version of
>> > > > Elemental. Is there a problem with this approach? It ensures
>> compatibility.
>> > >
>> > > I'll have to check this - but 2 ways of building the same thing is not
>> > > easy in petsc build tools. Esp when we provide --with-elemental-dir
>> > > option to configure.
>> > >
>> > > Sure we'll have to make sure the compatible elemental,clique are
>> > > installed - when both are installed by petsc [or by user]
>> >
>> > Jack,
>> >
>> > [I'm having to add the flag BUILD_PARMETIS=0.] But now I get:
>> >
>> > cd /home/balay/spetsc/externalpackages/clique/arch-clique/src/parmetis
>> && /usr/lib64/ccache/gcc   -Wall -Wwrite-strings -Wno-strict-aliasing
>> -Wno-unknown-pragmas -g3 -fno-inline -O0
>> -I/home/balay/spetsc/externalpackages/clique/arch-clique/external/elemental/include
>> -I/home/balay/soft/linux64/mpich2-1.1/include
>> -I/home/balay/spetsc/arch-clique/include
>> -I/home/balay/spetsc/externalpackages/clique/external/parmetis/include
>> -I/home/balay/spetsc/externalpackages/clique/external/parmetis/libparmetis
>> -I/home/balay/spetsc/externalpackages/clique/external/parmetis/metis/GKlib
>> -I/home/balay/spetsc/externalpackages/clique/external/parmetis/metis/include
>>    -o CMakeFiles/parmetis-addons.dir/ParallelBisect.c.o   -c
>> /home/balay/spetsc/externalpackages/clique/src/parmetis/ParallelBisect.c
>> >
>> /home/balay/spetsc/externalpackages/clique/src/parmetis/ParallelBisect.c:5:25:
>> fatal error: parmetislib.h: No such file or directory
>> >
>> > Looks like this code needs parmetis private includes. So the current
>> > stratergy [of splitting into -lparmetis-addons] isn't working.
>> >
>> > Perhaps we'll have to use a single patched metis/parmetis tarball for
>> > both petsc and clique afterall..
>> >
>> > Satish
>> >
>>
>>
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