[petsc-users] DMMeshCreateMeshFromAdjacency
Matthew Knepley
knepley at gmail.com
Sun Mar 3 14:11:59 CST 2013
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
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