[petsc-users] DMMeshCreateMeshFromAdjacency

Matthew Knepley knepley at gmail.com
Sun Mar 3 17:45:31 CST 2013 

On Sun, Mar 3, 2013 at 6:41 PM, Dharmendar Reddy <dharmareddy84 at gmail.com>wrote:

> 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.
>

These explanations are too short. From the above, all I understand is that
you would get
a line between (0, 1/4) and (1/4, 0).

   Matt


> 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
>



-- 
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
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