I think i caught the issues, please see the reply inline below. It is not clear to me for which DMPlex i should include petsc.h90 or petsc.h
Still need to fix the DMPlexComputeCellGeometry though On Tue, Mar 5, 2013 at 9:52 PM, Dharmendar Reddy <dharmareddy84 at gmail.com>wrote: > Hello, > I am having trouble with a couple of DMPlex routines. > I was doing tests on various function calls that i may need to write a > test Poisson problem. > > First issue is with DMPlexComputeCellGeometry. For a rectangle cell > geometry, I get , v0, J, invJ, and detJ as zero. > > DMPlexGetConeSize gives run time error > > I had to include petsc.h90 to fix this. > DMPlexVecGetClosure gives runtime error, Should not this call be > DMPlexVecGetClosureF90 ? is there such interface ? I remember doing a > procedure like VecGetArrayF90 and VecRestoreArrayF90 when i had to pass > pointer which need to be restored. > > Looks like there is an inconsistency in interface defined on petsc-dev manual page. and the interface defined in finclude/ftn-custom/petscdmplex.h90 Fortran interface does not have the csize parameter defined below PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, const PetscScalar *values[]) I have attached test case with the make file and error.log. Please have a > look at it. > you need to run: > make all debug=0 > ./testDMView > > Also, I have trouble compiling the code with debug=1 which uses petsc > configured in debug mode everything else being same (you can see the > configure options in the error.log). > I get this error message: > login1$ make all debug=1 > make: *** /home1/00924/Reddy135/LocalApps/petsc-dev/mpi_rScalar: Is a > directory. Stop > . > > > > On Tue, Mar 5, 2013 at 9:22 AM, Matthew Knepley <knepley at gmail.com> wrote: > >> On Tue, Mar 5, 2013 at 10:20 AM, Dharmendar Reddy < >> dharmareddy84 at gmail.com> wrote: >> >>> Thanks, so numDof is basically number of dof per topological entity of a >>> cell. Did i get this right ? >>> >> >> Yes, dof per field per topological entity (sieve point depth). >> >> Matt >> >> >>> +! Let u be defined on vertices >>> >>> + numDof(0*(dim+1)+1) = 1 (should not be number of nodes) >>> >>> +! Let v be defined on cells >>> >>> + numDof(1*(dim+1)+dim+1) = dim >>> >>> +! Let v be defined on faces >>> >>> + numDof(2*(dim+1)+dim) = dim-1 (similarly, should not be number of >>> faces time (dim-1)) >>> >>> >>> >>> >>> On Tue, Mar 5, 2013 at 9:06 AM, Matthew Knepley <knepley at gmail.com>wrote: >>> >>>> On Tue, Mar 5, 2013 at 2:18 AM, Dharmendar Reddy < >>>> dharmareddy84 at gmail.com> wrote: >>>> >>>>> Hello, >>>>> >>>>> Trying to understand the DMPlexCreateSection first. I have >>>>> created a test case, can you please have a look at it? Actually the code >>>>> has a link error on my system with petsc-dev. I used DMPlexeCreateBoxMesh >>>>> to create the mesh. Looks like there is no Fortran interface to that >>>>> function. If i comment out the dmplexcreateboxmesh. It does create and >>>>> executable. >>>>> >>>> >>>> I have now pushed your example, slightly changed, to the repository: >>>> >>>> src/dm/impls/plex/examples/tutorials/ex1.c/ex1f90.F >>>> >>>> and you can run with -dim 2 or -dim 3. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>>> petscDMTest_v2.o: In function `MAIN__': >>>>> petscDMTest_v2.F90:(.text+0x9b): undefined reference to >>>>> `dmplexcreateboxmesh_' >>>>> make: [testDMMeshv2] Error 1 (ignored) >>>>> >>>>> Also, If include finclude/petsc.h90 instead of finclude/petsch.h i get >>>>> compile error : >>>>> >>>>> petscDMTest_v2.F90(73): error #6691: A pointer dummy argument may only >>>>> be argument a >>>>> ssociated with a pointer. [NUMCOMP] >>>>> call DMPlexCreateSection(dmMesh, topologyDim, numField, numComp, >>>>> numDof, & >>>>> ----------------------------------------------------------^ >>>>> petscDMTest_v2.F90(73): error #6691: A pointer dummy argument may only >>>>> be argument a >>>>> ssociated with a pointer. [NUMDOF] >>>>> call DMPlexCreateSection(dmMesh, topologyDim, numField, numComp, >>>>> numDof, & >>>>> -------------------------------------------------------------------^ >>>>> petscDMTest_v2.F90(74): error #6691: A pointer dummy argument may only >>>>> be argument a >>>>> ssociated with a pointer. [BCFIELD] >>>>> numBC, bcField, bcPointIS,section,ierr) >>>>> ----------------------------------^ >>>>> petscDMTest_v2.F90(74): error #6691: A pointer dummy argument may only >>>>> be argument a >>>>> ssociated with a pointer. [BCPOINTIS] >>>>> numBC, bcField, bcPointIS,section,ierr) >>>>> -------------------------------------------^ >>>>> >>>>> Please have a look at the attached test case and Makefile >>>>> >>>>> >>>>> On Mon, Mar 4, 2013 at 7:39 PM, Matthew Knepley <knepley at >>>>> gmail.com>wrote: >>>>> >>>>>> On Mon, Mar 4, 2013 at 7:50 PM, Dharmendar Reddy < >>>>>> dharmareddy84 at gmail.com> wrote: >>>>>> >>>>>>> Hello, >>>>>>> Is there a DMPlex based fortran example for solving a pde >>>>>>> such as laplace ? Even a c example will do. I am not able to understand >>>>>>> the >>>>>>> terminology of chart, cone etc. Is there a paper or user guide to learn >>>>>>> more about the definitions of terms such as chart cone stratum ? I >>>>>>> remember >>>>>>> reading a presentation file by mathew about sieve. Is there a newer >>>>>>> tutorial with terminology mapped to the new DMPlex/DMMesh functions. >>>>>>> >>>>>> >>>>>> There is a fully worked out Stokes example (SNES ex62) and a Finite >>>>>> Volume example (TS ex11), >>>>>> and there are a few tests. You should not need much of that stuff for >>>>>> defining a problem. I am >>>>>> writing up a paper about ex11 right now. There is a short manual >>>>>> section on unstructured grids as well. >>>>>> >>>>>> I think the key thing to understand is how to define a data layout >>>>>> over the mesh using a PetscSection. >>>>>> Once that is done, all the DM functions work as normal, and the last >>>>>> hard part is coding your residual >>>>>> loop. I have support for FEM schemes, but its undocumented and >>>>>> slightly complex in order to allow >>>>>> GPU assembly, so you may be more comfortable with your own element >>>>>> loop to start. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Matt >>>>>> >>>>>> >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 > -- ----------------------------------------------------- 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. 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