[petsc-dev] Chaco from --download-chaco vs --download-trilinos (Re: broken stuff in next for many days)

Matthew Knepley knepley at gmail.com
Mon Apr 23 14:51:08 CDT 2018 

On Mon, Apr 23, 2018 at 3:13 PM, Satish Balay <balay at mcs.anl.gov> wrote:

> I was thinking more in terms of: our download options should match
> source distribution model of externalpackages [but not necessarily
> build all components]
>
> I see chaco is primarily part of seacas and not distributed separately.
> [and then seacas is redistributed in trilinos]
>

Here is the problem with that. Chaco is not great. Its aggressively
mediocre.
The only reason to use it was its staggering lack of dependencies and simple
build. Take that away and there is no reason whatsoever to have it.

   Matt


> So how about:
>
> --download-seacas [build chaco and exodusii]
>
> And remove the separate package support for exodusii and chaco [i.e
> remove --download-exodusii --download-chaco]
>
> [and then somehow make the seacas build via trilinos match the standalone
> build]
>
> I see zoltan is distributed separately, in seacas and also in trilinos
> [so current --download-zoltan is still ok?]
>
> ML is the odd one out - I guess we'll have to extract/repackage the
> latest version from trilinos - and use it with --download-ml.
>
> Satish
>
> On Mon, 23 Apr 2018, Smith, Barry F. wrote:
>
> >
> >   Making people install all of Trilinos for just Chaco or just ML is
> just plain mean and we are not mean.
> >
> >    Suitesparse is at least not huge and is well contained so just
> because we install all of it doesn't mean we should require the same route
> for Trilinos.
> >
> >    Barry
> >
> >
> >
> > > On Apr 23, 2018, at 10:11 AM, Balay, Satish <balay at mcs.anl.gov> wrote:
> > >
> > > Ah - yes. I did check the difference in petsc code wrt
> > > PETSC_HAVE_CHACO_INT_ASSIGNMENT - but didn't check the details inside
> > > trilinos/chaco. So the available standalone chaco tarball is version
> > > 2.2 but the version included inside seacas is 3.0.0 [with a switch
> > > from short to int]
> > >
> > > We have these hierarchy of packages - and need to figure out a better
> > > [install] interface so the same version is used irrespective of the
> > > mode of install?
> > >
> > > Right now - --download-exodusii gets and installs seacas [with only
> > > exodusii enabled]
> > >
> > > So we have:
> > >
> > > --download-ml --download-chaco --download-zoltan [separate packages]
> > >
> > > --download-exodusii [installs seacas - and enables only exodusii]
> > >
> > > --download-trilinos [installs trilinos which includes
> seacas(exodusii,chaco), ml - zoltan]
> > >
> > > since seacas is distributed separately and includes exodusii and chaco
> - have:
> > >
> > > --download-seacas=1 [with options exodusii=1,chaco=1 by default [or
> disabled?]
> > >
> > > --download-seacas=1
> > > --download-seacas=1 --download-seacas-exodusii=0 [only install chaco]
> > > --download-seacas-chaco=0 [only install exodusii]
> > >
> > > [but zoltan, ml are not distributed separately?]
> > >
> > > Or should we always use trilinos? - if one wants any of the above
> > > packages [a huge download]? and enable or disable selected
> > > sub-components as desired?
> > >
> > > Another similar package is SuiteSparse. At some point we had install
> > > for only sub-components(cholmod,umfpack) - and then merged them all
> > > into --download-suitesparse.
> > >
> > > Satish
> > >
> > > On Mon, 23 Apr 2018, Vaclav Hapla wrote:
> > >
> > >> I can confirm --download-chaco vs --download-trilinos give different
> chaco partitioning - I can reproduce on my machine. So I made some
> investigation.
> > >>
> > >> PETSC_HAVE_CHACO_INT_ASSIGNMENT is set only for --download-trilinos.
> > >> This macro makes difference only at 4 places:
> > >>
> > >> At src/mat/partition/impls/chaco/chaco.c:8 and src/dm/impls/plex/
> plexpartition.c:1192:
> > >> #if defined(PETSC_HAVE_CHACO_INT_ASSIGNMENT)
> > >> #include <chaco.h>
> > >> #else
> > >> /* Older versions of Chaco do not have an include file */
> > >> PETSC_EXTERN int interface(int nvtxs, int *start, int *adjacency, int
> *vwgts,
> > >>                     float *ewgts, float *x, float *y, float *z, char
> *outassignname,
> > >>                     char *outfilename, short *assignment, int
> architecture, int ndims_tot,
> > >>                     int mesh_dims[3], double *goal, int
> global_method, int local_method,
> > >>                     int rqi_flag, int vmax, int ndims, double eigtol,
> long seed);
> > >> #endif
> > >>
> > >> At src/mat/partition/impls/chaco/chaco.c:68 and src/dm/impls/plex/
> plexpartition.c:1227:
> > >> #if defined(PETSC_HAVE_CHACO_INT_ASSIGNMENT)
> > >>  int                   *assignment;
> > >> #else
> > >>  short                 *assignment;
> > >> #endif
> > >>
> > >> So it seems PETSc is not responsible for the different outputs.
> > >>
> > >> In Trilinos, Chaco is shipped within the Seacas package. The notice
> at http://gsjaardema.github.io/seacas/#chaco <http://gsjaardema.github.io/
> seacas/#chaco> says
> > >> "The short *assignment argument to the interface function has been
> changed to int *assignment to permit decompositions with more than 32,768
> processors."
> > >> They also say
> > >> "There are also now a CHACO_VERSION_MAJOR, CHACO_VERSION_MINOR,
> CHACO_VERSION_PATCH defines in chaco.h."
> > >> Looking there, the version is 3.0.0.
> > >>
> > >> PETSc's configure --download-chaco gets this one:
> http://ftp.mcs.anl.gov/pub/petsc/externalpackages/Chaco-2.2-p2.tar.gz <
> http://ftp.mcs.anl.gov/pub/petsc/externalpackages/Chaco-2.2-p2.tar.gz>
> > >> It actually includes a git repo. There we can see it's the original
> author's version + some updates by Barry and Satish, mainly to avoid some
> name clashes.
> > >> The original version is probably this one:
> https://www3.cs.stonybrook.edu/~algorith/implement/chaco/
> distrib/Chaco-2.2.tar.gz <https://www3.cs.stonybrook.
> edu/~algorith/implement/chaco/distrib/Chaco-2.2.tar.gz>
> > >> Looking at the contents of the tarball, these sources data back to
> 2000.
> > >> I tried comparing these two version but there are two many changes in
> formatting to identify crucial changes easily. But definitely these two
> versions differ and can give different results.
> > >>
> > >> The main intent of my tests in src/dm/impls/plex/examples/tutorials/ex5.c
> is testing HDF5 I/O with different formats and I just needed to somehow
> distribute the sequential mesh read from exodus file. So I will replace
> chaco by simple here. But still it's a question whether we want to do
> something about the confusing situation with Chaco.
> > >>
> > >> Vaclav
> > >>
> > >>> 22. 4. 2018 v 17:56, Satish Balay <balay at mcs.anl.gov>:
> > >>>
> > >>> On Sun, 22 Apr 2018, Smith, Barry F. wrote:
> > >>>
> > >>>>> It would be good to figure out exactly where the difference comes
> form
> > >>>>> [wrt chaco from trilinos vs separate install of chaco - or some
> other
> > >>>>> interaction from trilinos]
> > >>>>
> > >>>>  Different random numbers being generated?
> > >>>
> > >>> Its trilinos vs non-trilinos build of packages - so I don't think
> its 'different random number generation' issue.
> > >>>
> > >>> Trilinos install does:
> > >>>
> > >>>   if self.libraries.check(self.dlib, "interface"):
> > >>>     self.addDefine('HAVE_CHACO',1)
> > >>>     self.addDefine('HAVE_CHACO_INT_ASSIGNMENT',1)
> > >>>   if self.libraries.check(self.dlib, "ML_Set_PrintLevel"):
> > >>>     self.addDefine('HAVE_ML',1)
> > >>>   if self.libraries.check(self.dlib, "Zoltan_LB_Partition"):
> > >>>     self.addDefine('HAVE_ZOLTAN',1)
> > >>>   if self.libraries.check(self.dlib, "ex_close"):
> > >>>     self.addDefine('HAVE_EXODUSII',1)
> > >>>
> > >>>
> > >>> For one there is different chaco code in petsc based on this flag
> > >>> HAVE_CHACO_INT_ASSIGNMENT. Its not clear to me if this is causing the
> > >>> difference.
> > >>>
> > >>> --download-chaco is using 'Chaco-2.2-p2.tar.gz'. This matches the
> > >>> latest chaco tarball from their website [Chaco-2.2.tar.gz]. So I do
> > >>> not know if chaco packaged by trilinos has changes that cause this
> > >>> difference [clearly it added some change that resulted in us using
> the
> > >>> flag HAVE_CHACO_INT_ASSIGNMENT]
> > >>>
> > >>> And then there is also exodus.. --download-exodus uses the latest
> > >>> snapshot from https://github.com/gsjaardema/seacas/
> > >>>
> > >>> Satish
> > >>
> > >>
> > >
> >
> >
>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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