[petsc-users] Understanding DMPlexDistribute overlap

[Francesco Caimmi]

Hi Michael, 

thank you for verifying that the test works. 

I actually was on `maint`, as per 
https://www.mcs.anl.gov/petsc/download/index.html. 

Now that I switched to `master ` everything works as expected, both my test 
example and the DMPlex test ex12, which I can now build without issue.
I thought unlikely a problem with my setup because I saw the same beahviour on 
two different machines, but actually it turned out they had the same setup.

Thank you (and Matt) for helping me  track down the source of the problem.

Best,
Francesco

On giovedì 6 aprile 2017 11:40:27 CEST Michael Lange wrote:
> Hi Francesco,
> 
> Ok, I can confirm that your test runs fine for me with the latest master
> branch. I'm attaching the log for two processes up to overlap 7, where
> the entire mesh is effectively replicated on each partition. The command
> I ran was:
> 
> for OL in 1 2 3 4 5 6 7; do mpiexec -np 2 python overlay-test.py -o $OL;
> done
> 
> Looks like this might be a problem with your local build. Can you please
> try and update to the latest master?
> 
> Hope this helps,
> 
> Michael
> 
> On 06/04/17 10:25, Francesco Caimmi wrote:
> > Dear Matt,
> > 
> > thanks for your reply.
> > 
> > On mercoledì 5 aprile 2017 21:09:43 CEST Matthew Knepley wrote:
> >> On Wed, Apr 5, 2017 at 6:03 AM, Francesco Caimmi
> >> <francesco.caimmi at polimi.it>> 
> >>> [...]
> >>> the program fails with the error message captured in the attached file
> >>> error.log. Changing the number of processors does not alter the
> >>> behavior.
> >>> Note
> >>> also that the same holds if I use a mesh generated by
> >>> DMPlexCreateBoxMesh.
> >> 
> >> Francesco, I will reproduce your problem, but it may take me a few days.
> > 
> > Thank you very much for your time.
> > 
> >> It is strange since we have tests for overlap > 1 that do use
> >> CreateBoxMesh. For example,
> >> 
> >>    cd src/dm/impls/plex/examples/tests
> >>    make ex12
> >>    mpiexec -n 8 -test_partition -overlap 2 -dm_view ::ascii_info_detail
> > 
> > Anyway, there might be something related to my install: for the records,
> > if I do
> > 
> > $cd src/dm/impls/plex/examples/tests
> > $make ex12
> > 
> > I get
> > 
> >   /home/fcaimmi/Packages/petsc/my-linux-petsc/bin/mpicc     ex12.c   -o
> >   ex12
> > 
> > ex12.c:3:25: fatal error: petscdmplex.h: No such file or directory
> > 
> >   #include <petscdmplex.h>
> >   
> >                           ^
> > 
> > compilation terminated.
> > <builtin>: recipe for target 'ex12' failed
> > make: *** [ex12] Error 1
> > 
> > I get this error I cannot explain ( I am not that much into PETSc build
> > system, I mostly use the python bindings), since for example I can
> > successfully build ex1.c or ex3.c which of course contain the same include
> > statement...
> > 
> > I don't know if this is useful to track the issue, but hope it helps.
> > 
> > Thank you again,
> > FC


-- 
Francesco Caimmi
 
Laboratorio di Ingegneria dei Polimeri
http://www.chem.polimi.it/polyenglab/

Politecnico di Milano - Dipartimento di Chimica,
Materiali e Ingegneria Chimica “Giulio Natta”

P.zza Leonardo da Vinci, 32
I-20133 Milano
Tel. +39.02.2399.4711
Fax +39.02.7063.8173

francesco.caimmi at polimi.it
Skype: fmglcaimmi (please arrange meetings by e-mail)