[petsc-users] DMMeshCreateMeshFromAdjacency

Sun Mar 3 17:41:09 CST 2013

Let say I create triangular mesh in a square: (0,0) (0,1) (1,1) (0,1)
I want (0,0.25) and (0.25,0) to be among the mesh nodes. It can have other
nodes.

On Sun, Mar 3, 2013 at 5:29 PM, Matthew Knepley <knepley at gmail.com> wrote:

> 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
>

-- 
-----------------------------------------------------
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
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