[petsc-dev] clique

[Jed Brown]

On Fri, Aug 31, 2012 at 4:17 PM, Jack Poulson <jack.poulson at gmail.com>wrote:

> In these cases, it sounds like the current best option is then to avoid
> using the CMake build system and manually link Elemental and Clique. If you
> have any suggestions, I am happy to work towards them as soon as possible.
>
> Satish's suggestion (which I agree with) is for me to add support in
> Clique's CMake build system for a user-specified Elemental library.
>

I think this the Right Way.


>
> Yet another option is to avoid having any libelemental.a/libclique.a at
> all. There is very little in it anyway, as well over 99% of both libraries
> are in header files.
>

I'm not a fan of the rampant duplication implied by header-only, but do as
you like.

Note that elemental/config.h is somewhat concerning because if any part of
the configuration is different (even for matching versions), you can have
duplicate symbols with different implementations. The linker is free to
take any implementation from anywhere. This can cause tricky run-time bugs
such as the version used to allocate being different from the version used
to deallocate.


>
> Would you find this more convenient? If so, I am willing to make the
> transition.
>
> Jack
>
>
> On Fri, Aug 31, 2012 at 4:12 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>
>> On Fri, Aug 31, 2012 at 3:17 PM, Jack Poulson <jack.poulson at gmail.com>wrote:
>>
>>> I seemed to have ignored your question.
>>>
>>> If compatible versions of the library are used in package "X", then
>>> everything should work fine. Is there a problem which you are expecting?
>>>
>>
>> Well, we may have duplicate symbols if we link an "equivalent" library
>> twice. If we do as CMake does, the full path for the different
>> libelemental.a will be passed to the linker.
>>
>>
>>> I recognize that there is a potential issue of a newer version of
>>> Elemental or Clique conflicting with an older version, but  surely you guys
>>> are willing to deal with external libraries also changing their syntax from
>>> time to time...
>>
>>
>> I'm not concerned about version mismatch because that is an issue
>> regardless of distribution if both libs are linked into the same
>> executable. It's the duplicate symbols that bother me.
>>
>>
>>>
>>> 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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