<div dir="ltr">On Wed, Mar 6, 2013 at 2:43 AM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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 <br>
<br>Still need to fix the DMPlexComputeCellGeometry though<br><br><br><div class="gmail_quote"><div class="im">
On Tue, Mar 5, 2013 at 9:52 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<div class="im"><br> I am having trouble with a couple of DMPlex routines. <br> I was doing tests on various function calls that i may need to write a test Poisson problem.<br><br>First issue is with DMPlexComputeCellGeometry. For a rectangle cell geometry, I get , v0, J, invJ, and detJ as zero.<br>
</div></blockquote></div></blockquote><div><br></div><div style>Geometric primitives of course depend on the way you specify a cell. Simplicies are nice in</div><div style>that you can only change the orientation, but hexes are harder. I specify quads so that the</div>
<div style>vertices go counter-clockwise around the boundary. Do you do this? If so, can you send</div><div style>a small example test that I can add to PETSc.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">DMPlexGetConeSize gives run time error<br><br></div></blockquote><div><font color="#3333ff"> I had to include petsc.h90 to fix this. </font></div>
</div></blockquote><div><br></div><div style>I have fixed the manpage documentation to reflect this.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote">
<div><br></div><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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. <br>
<br></blockquote></div><div> <font color="#3366ff"> Looks like there is an inconsistency in interface defined on petsc-dev manual page. and the interface defined in finclude/ftn-custom/petscdmplex.h90</font> <br><span style="color:rgb(51,102,255)">Fortran interface does not have the csize parameter defined below</span><br>
<pre>PetscErrorCode DMPlexVecGetClosure(DM dm, PetscSection section, Vec v, PetscInt point, PetscInt *csize, const PetscScalar *values[])</pre></div></div></blockquote><div style>I have noted this on the manpage.</div><div style>
<br></div><div style>Did you look at src/dm/impls/plex/examples/tests/ex2f90.F? It tests many of these operations.</div><div style><br></div><div style> Thanks,</div><div style><br></div><div style> Matt</div><div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><div> <br><br></div><div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have attached test case with the make file and error.log. Please have a look at it.<br>you need to run:<br>
make all debug=0<br>./testDMView<br><br>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). <br>
I get this error message:<br>login1$ make all debug=1<br>make: *** /home1/00924/Reddy135/LocalApps/petsc-dev/mpi_rScalar: Is a directory. Stop<br>.<div><div><br><br><br><div class="gmail_quote">
On Tue, Mar 5, 2013 at 9:22 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>On Tue, Mar 5, 2013 at 10:20 AM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br>
</div><div class="gmail_extra"><div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Thanks, so numDof is basically number of dof per topological entity of a cell. Did i get this right ?<br>
</blockquote><div><br></div></div><div>Yes, dof per field per topological entity (sieve point depth).</div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<pre>+! Let u be defined on vertices</pre>
<div>
<pre>+ numDof(0*(dim+1)+1) = 1 (should not be number of nodes)</pre>
</div>
<div>
<pre>+! Let v be defined on cells</pre>
</div>
<div>
<pre>+ numDof(1*(dim+1)+dim+1) = dim</pre>
</div>
<div>
<pre>+! Let v be defined on faces</pre>
</div>
<div>
<pre>+ numDof(2*(dim+1)+dim) = dim-1 (similarly, should not be number of faces time (dim-1))</pre>
</div><br><br><br><div class="gmail_quote">On Tue, Mar 5, 2013 at 9:06 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div>On Tue, Mar 5, 2013 at 2:18 AM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br></div><div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hello,<div><br> 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.<br>
</div></blockquote><div><br></div><div>I have now pushed your example, slightly changed, to the repository:</div><div><br></div><div> src/dm/impls/plex/examples/tutorials/ex1.c/ex1f90.F</div><div><br></div>
<div>and you can run with -dim 2 or -dim 3.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<span style="color:rgb(51,102,255)">petscDMTest_v2.o: In function `MAIN__':<br>petscDMTest_v2.F90:(.text+0x9b): undefined reference to `dmplexcreateboxmesh_'<br>make: [testDMMeshv2] Error 1 (ignored)</span><br>
<br>Also, If include finclude/petsc.h90 instead of finclude/petsch.h i get compile error :<br><br><span style="color:rgb(51,51,255)"><span>petscDMTest_v2.F90(73): error #6691: A pointer dummy argument may only be argument a<br>
ssociated with a pointer. [NUMCOMP]<br> call DMPlexCreateSection(dmMesh, topologyDim, numField, numComp, numDof, &<br>----------------------------------------------------------^<br>petscDMTest_v2.F90(73): error #6691: A pointer dummy argument may only be argument a<br>
ssociated with a pointer. [NUMDOF]<br> call DMPlexCreateSection(dmMesh, topologyDim, numField, numComp, numDof, &<br>-------------------------------------------------------------------^<br>petscDMTest_v2.F90(74): error #6691: A pointer dummy argument may only be argument a<br>
ssociated with a pointer. [BCFIELD]<br> numBC, bcField, bcPointIS,section,ierr)<br>----------------------------------^<br>petscDMTest_v2.F90(74): error #6691: A pointer dummy argument may only be argument a<br>
ssociated with a pointer. [BCPOINTIS]<br> numBC, bcField, bcPointIS,section,ierr)</span></span><br>-------------------------------------------^<br><br>Please have a look at the attached test case and Makefile<div>
<div><br>
<br><div class="gmail_quote">On Mon, Mar 4, 2013 at 7:39 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div>On Mon, Mar 4, 2013 at 7:50 PM, Dharmendar Reddy <span dir="ltr"><<a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a>></span> wrote:<br></div><div class="gmail_extra">
<div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hello,<br> 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. <br>
</blockquote><div><br></div></div><div>There is a fully worked out Stokes example (SNES ex62) and a Finite Volume example (TS ex11),</div><div>and there are a few tests. You should not need much of that stuff for defining a problem. I am</div>
<div>writing up a paper about ex11 right now. There is a short manual section on unstructured grids as well.</div><div><br></div><div>I think the key thing to understand is how to define a data layout over the mesh using a PetscSection.</div>
<div>Once that is done, all the DM functions work as normal, and the last hard part is coding your residual</div><div>loop. I have support for FEM schemes, but its undocumented and slightly complex in order to allow</div>
<div>GPU assembly, so you may be more comfortable with your own element loop to start.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Thanks<span><font color="#888888"><br>Reddy <br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</font></span></div></div>
</blockquote></div><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</div></div></blockquote></div></div></div><div><div><br><br clear="all"><span><font color="#888888"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</font></span></div></div></div></div><span><font color="#888888">
</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</font></span></blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</div></div></blockquote></div></div></div><div class="HOEnZb"><div class="h5"><br><br clear="all"><br>-- <br>-----------------------------------------------------<br>Dharmendar Reddy Palle<br>Graduate Student<br>Microelectronics Research center,<br>
University of Texas at Austin,<br>
10100 Burnet Road, Bldg. 160<br>MER 2.608F, TX 78758-4445<br>e-mail: <a href="mailto:dharmareddy84@gmail.com" target="_blank">dharmareddy84@gmail.com</a><br>Phone: <a href="tel:%2B1-512-350-9082" value="+15123509082" target="_blank">+1-512-350-9082</a><br>
United States of America.<br>Homepage: <a href="https://webspace.utexas.edu/~dpr342" target="_blank">https://webspace.utexas.edu/~dpr342</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>