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

[Satish Balay]

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]

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
> >> 
> >> 
> > 
> 
>