[petsc-users] DMMeshCreateMeshFromAdjacency

Sun Mar 3 15:44:45 CST 2013

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
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