[petsc-users] DMMeshCreateMeshFromAdjacency

Matthew Knepley knepley at gmail.com
Sun Mar 3 17:29:44 CST 2013 

On Sun, Mar 3, 2013 at 5:04 PM, Dharmendar Reddy <dharmareddy84 at gmail.com>wrote:

> Hello,
>         We use cratisian mesh for certain problems only. The user gives
> the mesh file as one of the inputs. I do not know a-priori what mesh is
> created.
>
> On a related note, I am solving a system of equations where i need to use
> a fine cartisian mesh for one equation (Schrodinger)  but i would prefer a
> coarse traiangular or tetrahedral element mesh for another
> eqaution(Poisson). Is there an interface to interpolate data from one mesh
> to another?
>

There is an interface, which is just a Mat, but there is no infrastructure
for calculating it.


> If i create a DM with a coarse mesh, Can i give the mesh a set of vertices
> such that after re meshing the DM has the given vertices as mesh nodes ? I
> tried using the gmsh to create a mesh with give set of vertices inside a
> region but had no success.
>

I do not understand the question.

  Thanks,

     Matt


> Thanks
> Reddy
>
> On Sun, Mar 3, 2013 at 3:44 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Sun, Mar 3, 2013 at 3:48 PM, Dharmendar Reddy <dharmareddy84 at gmail.com
>> > wrote:
>>
>>> So i should use petsc-dev ? I will try that.
>>>
>>> I there any way i can have access to submesh? Consider a this scenario.
>>> I have a two dimensional mesh in a rectangle with a uniform deltaX and
>>> deltaY gridding. Is there any way i can get submesh at say x = (i-1)*deltaX
>>> where  say i = 1 to N. The dofs on the submesh will should be mapped to
>>> dofs on the original mesh. The submesh in this case will be  a 1D mesh
>>> along y-axis.
>>>
>>
>> 1) If you have a Cartesian mesh, use DMDA. This is no point in an
>> unstructured mesh.
>>
>> 2) Yes, you can extract a submesh based upon labeled vertices using
>> DMPlexCreateSubmesh(). It will have
>>     a map between points in the submesh and original mesh.
>>
>>
>>> I can create each DM with input celllist and create maps after that but
>>> i am wondering if this can be done via DMgetsubDM kind of call ?
>>>
>>
>>     Matt
>>
>>
>>> Thanks
>>> Reddy
>>>
>>> On Sun, Mar 3, 2013 at 2:11 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>
>>>> On Sun, Mar 3, 2013 at 2:37 PM, Dharmendar Reddy <
>>>> dharmareddy84 at gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>>          Thanks. I will have the code compiled with-cxx and with-sieve.
>>>>> The error is understandable when i look at the following line from
>>>>> meshcreate.c
>>>>>
>>>>> 312:   if (interpolate) {SETERRQ <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/SETERRQ.html#SETERRQ>(comm, PETSC_ERR_SUP, "Interpolation (creation of faces and edges) is not yet supported.");}
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Any idea if this feature will be implimented? I am trying to import mesh from gmsh.
>>>>> I have a Fortran code which will genrate list for faces and edges for a given mesh.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Is there a DMMEsh interface through which i can input list of edges and faces ?
>>>>>
>>>>>
>>>> DMMesh was an initial implementation of these ideas, but did not
>>>> interface well with
>>>> solvers, so it has been rewritten in C as DMPlex. The interface is
>>>> almost exactly the
>>>> same, and if you want increased functionality I would encourage you to
>>>> switch. For
>>>> example, DMMeshCreateMeshFromAdjacency() becomes
>>>>
>>>>   DMPlexCreateFromCellList()
>>>>
>>>> and you can follow this with
>>>>
>>>>   DMInterpolate()
>>>>
>>>> to automatically create the edges and faces.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> Thanks
>>>>> Reddy
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Mar 3, 2013 at 12:23 AM, Satish Balay <balay at mcs.anl.gov>wrote:
>>>>>
>>>>>> BTW: I don't get compile errors with this code using petsc-3.3 built
>>>>>> with:
>>>>>>
>>>>>>  --with-clanguage=cxx --with-sieve=1 --with-boost=1
>>>>>>
>>>>>> [the code fails to run though..]
>>>>>>
>>>>>> Satish
>>>>>>
>>>>>> ---------
>>>>>>
>>>>>> asterix:/home/balay/download-pine>make
>>>>>> PETSC_DIR=/home/balay/petsc-dist-test PETSC_ARCH=asterix64-sieve
>>>>>> petscDMTest_v2
>>>>>> /home/balay/soft/linux64/mpich2-1.1/bin/mpif90 -c  -fPIC -Wall
>>>>>> -Wno-unused-variable -Wno-unused-dummy-argument -g
>>>>>> -I/home/balay/petsc-dist-test/include
>>>>>> -I/home/balay/petsc-dist-test/asterix64-sieve/include
>>>>>> -I/home/balay/petsc-dist-test/include/sieve
>>>>>> -I/home/balay/soft/linux64/mpich2-1.1/include
>>>>>> -I/home/balay/soft/mpich2-1.5/include    -o petscDMTest_v2.o
>>>>>> petscDMTest_v2.F90
>>>>>> /home/balay/soft/linux64/mpich2-1.1/bin/mpif90 -fPIC -Wall
>>>>>> -Wno-unused-variable -Wno-unused-dummy-argument -g   -o petscDMTest_v2
>>>>>> petscDMTest_v2.o
>>>>>>  -Wl,-rpath,/home/balay/petsc-dist-test/asterix64-sieve/lib
>>>>>> -L/home/balay/petsc-dist-test/asterix64-sieve/lib  -lpetsc -lX11 -lpthread
>>>>>> -llapack -lblas -lm -Wl,-rpath,/home/balay/soft/mpich2-1.5/lib
>>>>>> -L/home/balay/soft/mpich2-1.5/lib
>>>>>> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.7.2
>>>>>> -L/usr/lib/gcc/x86_64-redhat-linux/4.7.2 -lmpichf90 -lgfortran -lm
>>>>>> -lgfortran -lm -lquadmath -lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl
>>>>>> -lrt -lgcc_s -ldl
>>>>>> /usr/bin/rm -f petscDMTest_v2.o
>>>>>> asterix:/home/balay/download-pine>./petscDMTest_v2
>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>> ------------------------------------
>>>>>> [0]PETSC ERROR: No support for this operation for this object type!
>>>>>> [0]PETSC ERROR: Interpolation (creation of faces and edges) is not
>>>>>> yet supported.!
>>>>>> [0]PETSC ERROR:
>>>>>> ------------------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 6, unknown
>>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>> [0]PETSC ERROR:
>>>>>> ------------------------------------------------------------------------
>>>>>> [0]PETSC ERROR: ./petscDMTest_v2 on a asterix64 named asterix by
>>>>>> balay Sun Mar  3 00:21:29 2013
>>>>>> [0]PETSC ERROR: Libraries linked from
>>>>>> /home/balay/petsc-dist-test/asterix64-sieve/lib
>>>>>> [0]PETSC ERROR: Configure run at Sun Mar  3 00:15:25 2013
>>>>>> [0]PETSC ERROR: Configure options
>>>>>> --with-mpi-dir=/home/balay/soft/linux64/mpich2-1.1
>>>>>> --with-shared-libraries=1 --with-clanguage=cxx --with-sieve=1
>>>>>> PETSC_ARCH=asterix64-sieve --with-boost=1
>>>>>> [0]PETSC ERROR:
>>>>>> ------------------------------------------------------------------------
>>>>>> [0]PETSC ERROR: DMMeshCreateMeshFromAdjacency() line 312 in
>>>>>> /home/balay/petsc-dist-test/src/dm/impls/mesh/meshcreate.c
>>>>>>  Surcessfully Loaded mesh into DM
>>>>>> asterix:/home/balay/download-pine>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sat, 2 Mar 2013, Satish Balay wrote:
>>>>>>
>>>>>> > Fortran compiler doesn't care about presence or absence of interface
>>>>>> > defintions. If they exist - then it does extra prototype checks. If
>>>>>> > they don't exist - it assumes f77 and chugs along].
>>>>>> >
>>>>>> > Did you build petsc with sieve [and cxx]?  send make.log for this
>>>>>> > petsc build. Also what do you get for:
>>>>>> >
>>>>>> > nm -Ao libpetsc.a |grep -i DMMeshCreateMeshFromAdjacency
>>>>>> >
>>>>>> > You can followup this issue [with logs] on petsc-maint.
>>>>>> >
>>>>>> > Satish
>>>>>> >
>>>>>> >
>>>>>> > On Sat, 2 Mar 2013, Dharmendar Reddy wrote:
>>>>>> >
>>>>>> > > As you said, I do not need, PETSC_USE_FORTRAN_INTERFACES. The
>>>>>> interface to
>>>>>> > > dmmeshcreatefromadjacency is not defined in
>>>>>> > >
>>>>>> > > finclude/ftn-custom/petscdmmesh.h90
>>>>>> > >
>>>>>> > > it is only defined in
>>>>>> > >
>>>>>> > > finclude/ftn-auto/petscdmmesh.h90
>>>>>> > >
>>>>>> > >
>>>>>> > > On Sat, Mar 2, 2013 at 7:51 PM, Dharmendar Reddy <
>>>>>> dharmareddy84 at gmail.com>wrote:
>>>>>> > >
>>>>>> > > > Hello,
>>>>>> > > >         Sorry, I was going to create a test case. Anyways here
>>>>>> is the
>>>>>> > > > error message
>>>>>> > > >
>>>>>> > > > petscDMTest_v2.o: In function `MAIN__':
>>>>>> > > > petscDMTest_v2.F90:(.text+0x354): undefined reference to
>>>>>> > > > `dmmeshcreatemeshfromad
>>>>>> > > > jacency_'
>>>>>> > > > make: [testDMMesh] Error 1 (ignored)
>>>>>> > > >
>>>>>> > > > I have attached a test case and makefile.  make all should gen
>>>>>> rate the
>>>>>> > > > executable.
>>>>>> > > >
>>>>>> > > > Thanks
>>>>>> > > > Reddy
>>>>>> > > >
>>>>>> > > >
>>>>>> > > > On Sat, Mar 2, 2013 at 7:10 PM, Satish Balay <balay at mcs.anl.gov>
>>>>>> wrote:
>>>>>> > > >
>>>>>> > > >> On Sat, 2 Mar 2013, Dharmendar Reddy wrote:
>>>>>> > > >>
>>>>>> > > >> > Hello,
>>>>>> > > >> >         I am trying to use DMMeshCreateMeshFromAdjacency in
>>>>>> a Fortran
>>>>>> > > >> code.
>>>>>> > > >> > I get undefined reference error.
>>>>>> > > >>
>>>>>> > > >> What error? please copy/paste
>>>>>> > > >>
>>>>>> > > >> > I include the following file in my program
>>>>>> > > >> > #include "finclude/petsc.h90"
>>>>>> > > >> >
>>>>>> > > >> > I see that fortran interface to
>>>>>> DMMeshCreateMeshFromAdjacency is defined
>>>>>> > > >> > only in
>>>>>> > > >> >
>>>>>> > > >> > finclude/ftn-auto/petscdmmesh.h90
>>>>>> > > >> >
>>>>>> > > >> > I am not able to figure out if PETSC_USE_FORTRAN_INTERFACES
>>>>>> is defined.
>>>>>> > > >> I
>>>>>> > > >> > did not compile the code. I am runing the code on TACC
>>>>>> stampede. I tried
>>>>>> > > >> > adding
>>>>>> > > >> >
>>>>>> > > >> > #define PETSC_USE_FORTRAN_INTERFACES 1
>>>>>> > > >> > in my program before the petsc inlcude line but i still get
>>>>>> error.
>>>>>> > > >>
>>>>>> > > >> 1. again 'get error' doesn't tell us anything.
>>>>>> > > >>
>>>>>> > > >> And you shouldn't need PETSC_USE_FORTRAN_INTERFACES to use
>>>>>> > > >> DMMeshCreateMeshFromAdjacency
>>>>>> > > >>
>>>>>> > > >> Satish
>>>>>> > > >>
>>>>>> > > >> >
>>>>>> > > >> >
>>>>>> > > >> > Thanks
>>>>>> > > >> > Reddy
>>>>>> > > >> >
>>>>>> > > >> >
>>>>>> > > >>
>>>>>> > > >>
>>>>>> > > >
>>>>>> > > >
>>>>>> > > > --
>>>>>> > > > -----------------------------------------------------
>>>>>> > > > Dharmendar Reddy Palle
>>>>>> > > > Graduate Student
>>>>>> > > > Microelectronics Research center,
>>>>>> > > > University of Texas at Austin,
>>>>>> > > > 10100 Burnet Road, Bldg. 160
>>>>>> > > > MER 2.608F, TX 78758-4445
>>>>>> > > > e-mail: dharmareddy84 at gmail.com
>>>>>> > > > Phone: +1-512-350-9082
>>>>>> > > > United States of America.
>>>>>> > > > Homepage: https://webspace.utexas.edu/~dpr342
>>>>>> > > >
>>>>>> > >
>>>>>> > >
>>>>>> > >
>>>>>> > >
>>>>>> >
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -----------------------------------------------------
>>>>> Dharmendar Reddy Palle
>>>>> Graduate Student
>>>>> Microelectronics Research center,
>>>>> University of Texas at Austin,
>>>>> 10100 Burnet Road, Bldg. 160
>>>>> MER 2.608F, TX 78758-4445
>>>>> e-mail: dharmareddy84 at gmail.com
>>>>> Phone: +1-512-350-9082
>>>>> United States of America.
>>>>> Homepage: https://webspace.utexas.edu/~dpr342
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> -----------------------------------------------------
>>> Dharmendar Reddy Palle
>>> Graduate Student
>>> Microelectronics Research center,
>>> University of Texas at Austin,
>>> 10100 Burnet Road, Bldg. 160
>>> MER 2.608F, TX 78758-4445
>>> e-mail: dharmareddy84 at gmail.com
>>> Phone: +1-512-350-9082
>>> United States of America.
>>> Homepage: https://webspace.utexas.edu/~dpr342
>>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> -----------------------------------------------------
> Dharmendar Reddy Palle
> Graduate Student
> Microelectronics Research center,
> University of Texas at Austin,
> 10100 Burnet Road, Bldg. 160
> MER 2.608F, TX 78758-4445
> e-mail: dharmareddy84 at gmail.com
> Phone: +1-512-350-9082
> United States of America.
> Homepage: https://webspace.utexas.edu/~dpr342
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20130303/2dcd94a7/attachment-0001.html>

More information about the petsc-users mailing list