[petsc-users] implementation of multi-level grid in petsc
Hi, I am working on multi-level grid for Poisson equation. I need to refine some sub-region in the computational domain. To this, I plan to build some boxes (patches) based on the coarsest level. I am using DM to manage the data. I found there is a new function DMPatachCreate() in the version 3.4. Is this function the right one I should use for the refined region? If it is not, which ones I should use? My proposed approach is to start with code dm/impls/patch/examples/tests/ex1.c. And then follow the code /dm/examples/tutorials/ex65dm.c. Is this approach the right way to my goal? In addition, I need to use not only the nodes but also the cells including nodes. Should I use DMMesh to create the cells? I noticed DMMesh is mainly for unstructured grid, but I didn't find other class that implements structured cells. Can anybody give me some suggestions on multi-level grid or let me know which examples I should start with? Thanks.
Re: [petsc-users] implementation of multi-level grid in petsc
On Thu, Aug 8, 2013 at 1:29 PM, Roc Wang pengxw...@hotmail.com wrote: Hi, I am working on multi-level grid for Poisson equation. I need to refine some sub-region in the computational domain. To this, I plan to build some boxes (patches) based on the coarsest level. I am using DM to manage the data. I found there is a new function DMPatachCreate() in the version 3.4. Is this function the right one I should use for the refined region? If it is not, which ones I should use? That is an experiment and does not work. My proposed approach is to start with code dm/impls/patch/examples/tests/ex1.c. And then follow the code /dm/examples/tutorials/ex65dm.c. Is this approach the right way to my goal? In addition, I need to use not only the nodes but also the cells including nodes. Should I use DMMesh to create the cells? I noticed DMMesh is mainly for unstructured grid, but I didn't find other class that implements structured cells. Can anybody give me some suggestions on multi-level grid or let me know which examples I should start with? Thanks. No, that is not appropriate. It sounds like you want structured AMR. PETSc does not do this, and there are packages that do it.: a) Chombo b) SAMRAI which are both patch-based AMR. If you want octree-style AMR you could use p4est, but it would mean a lot of coding along the lines of http://arxiv.org/abs/1308.1472, or Deal.II which is a complete package. I think Deal is the closest to using PETSc solvers. Thanks, Matt -- 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
Re: [petsc-users] implementation of multi-level grid in petsc
Thanks Mat, I tried Chombo for implementing AMR but not tried SAMRAI yet. Chombo can do AMR, but it seems the data structure is quite complicated for customizing usage. What I want to do with petsc is to compose a simple home-made like blocked multi-level grid, though it is not automatically adaptive. However, I don't have too much experiences on petsc. As of now, I suppose to use DM to manage the data for the big domain and all small sub-domains. I am not sure whether it is a good idea. So, any suggestions are appreciated very much. Thanks again. Best, Date: Thu, 8 Aug 2013 14:03:53 -0500 Subject: Re: [petsc-users] implementation of multi-level grid in petsc From: knep...@gmail.com To: pengxw...@hotmail.com CC: petsc-users@mcs.anl.gov On Thu, Aug 8, 2013 at 1:29 PM, Roc Wang pengxw...@hotmail.com wrote: Hi, I am working on multi-level grid for Poisson equation. I need to refine some sub-region in the computational domain. To this, I plan to build some boxes (patches) based on the coarsest level. I am using DM to manage the data. I found there is a new function DMPatachCreate() in the version 3.4. Is this function the right one I should use for the refined region? If it is not, which ones I should use? That is an experiment and does not work. My proposed approach is to start with code dm/impls/patch/examples/tests/ex1.c. And then follow the code /dm/examples/tutorials/ex65dm.c. Is this approach the right way to my goal? In addition, I need to use not only the nodes but also the cells including nodes. Should I use DMMesh to create the cells? I noticed DMMesh is mainly for unstructured grid, but I didn't find other class that implements structured cells. Can anybody give me some suggestions on multi-level grid or let me know which examples I should start with? Thanks. No, that is not appropriate. It sounds like you want structured AMR. PETSc does not do this, and there are packages that do it.: a) Chombo b) SAMRAI which are both patch-based AMR. If you want octree-style AMR you could use p4est, but it would mean a lot of coding along the lines of http://arxiv.org/abs/1308.1472, or Deal.II which is a complete package.I think Deal is the closest to using PETSc solvers. Thanks, Matt -- 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
Re: [petsc-users] implementation of multi-level grid in petsc
On Aug 8, 2013, at 3:32 PM, Roc Wang pengxw...@hotmail.com wrote: Thanks Mat, I tried Chombo for implementing AMR but not tried SAMRAI yet. Chombo can do AMR, but it seems the data structure is quite complicated for customizing usage. What I want to do with petsc is to compose a simple home-made like blocked multi-level grid, though it is not automatically adaptive. However, I don't have too much experiences on petsc. As of now, I suppose to use DM to manage the data for the big domain and all small sub-domains. I am not sure whether it is a good idea. So, any suggestions are appreciated very much. Thanks again. As Matt said, this is not what you want to do, most likely. Building AMR on DM/DA is a lot of work unless you have a simple application and have a clear idea of how to do it. Chombo is flexible but it is complex and takes time to get started. I'm not familiar wit SAMARI but I would guess it is like Chombo. Deall.II might be worth looking into. I'm not familiar. Best, Date: Thu, 8 Aug 2013 14:03:53 -0500 Subject: Re: [petsc-users] implementation of multi-level grid in petsc From: knep...@gmail.com To: pengxw...@hotmail.com CC: petsc-users@mcs.anl.gov On Thu, Aug 8, 2013 at 1:29 PM, Roc Wang pengxw...@hotmail.com wrote: Hi, I am working on multi-level grid for Poisson equation. I need to refine some sub-region in the computational domain. To this, I plan to build some boxes (patches) based on the coarsest level. I am using DM to manage the data. I found there is a new function DMPatachCreate() in the version 3.4. Is this function the right one I should use for the refined region? If it is not, which ones I should use? That is an experiment and does not work. My proposed approach is to start with code dm/impls/patch/examples/tests/ex1.c. And then follow the code /dm/examples/tutorials/ex65dm.c. Is this approach the right way to my goal? In addition, I need to use not only the nodes but also the cells including nodes. Should I use DMMesh to create the cells? I noticed DMMesh is mainly for unstructured grid, but I didn't find other class that implements structured cells. Can anybody give me some suggestions on multi-level grid or let me know which examples I should start with? Thanks. No, that is not appropriate. It sounds like you want structured AMR. PETSc does not do this, and there are packages that do it.: a) Chombo b) SAMRAI which are both patch-based AMR. If you want octree-style AMR you could use p4est, but it would mean a lot of coding along the lines of http://arxiv.org/abs/1308.1472, or Deal.II which is a complete package. I think Deal is the closest to using PETSc solvers. Thanks, Matt -- 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
Re: [petsc-users] implementation of multi-level grid in petsc
How big of an application are you looking into? If you are thinking in the range of couple of 10M grid points on couple of hundred processors, then I'd say the simplest approach is to create grid in serial and then use PETSc's interface to ParMetis to handle partitioning. I did this with my quadtree code and could easily scale quadtrees on the order of 16.5M grid points upto 75% on 256 processors for a Poisson equation test. If you are thinking way larger problem (think couple of 100M grids and order several thousands processors), I could recommend p4est if you want to do tree-based grids. In that case using deal.II interface will be really beneficial as p4est alone is really a bare bone package. I do not have enough experience with block-structured AMR so I cannot comment on that. On Thu, Aug 8, 2013 at 1:28 PM, Mark F. Adams mfad...@lbl.gov wrote: On Aug 8, 2013, at 3:32 PM, Roc Wang pengxw...@hotmail.com wrote: Thanks Mat, I tried Chombo for implementing AMR but not tried SAMRAI yet. Chombo can do AMR, but it seems the data structure is quite complicated for customizing usage. What I want to do with petsc is to compose a simple home-made like blocked multi-level grid, though it is not automatically adaptive. However, I don't have too much experiences on petsc. As of now, I suppose to use DM to manage the data for the big domain and all small sub-domains. I am not sure whether it is a good idea. So, any suggestions are appreciated very much. Thanks again. As Matt said, this is not what you want to do, most likely. Building AMR on DM/DA is a lot of work unless you have a simple application and have a clear idea of how to do it. Chombo is flexible but it is complex and takes time to get started. I'm not familiar wit SAMARI but I would guess it is like Chombo. Deall.II might be worth looking into. I'm not familiar. Best, Date: Thu, 8 Aug 2013 14:03:53 -0500 Subject: Re: [petsc-users] implementation of multi-level grid in petsc From: knep...@gmail.com To: pengxw...@hotmail.com CC: petsc-users@mcs.anl.gov On Thu, Aug 8, 2013 at 1:29 PM, Roc Wang pengxw...@hotmail.com wrote: Hi, I am working on multi-level grid for Poisson equation. I need to refine some sub-region in the computational domain. To this, I plan to build some boxes (patches) based on the coarsest level. I am using DM to manage the data. I found there is a new function DMPatachCreate() in the version 3.4. Is this function the right one I should use for the refined region? If it is not, which ones I should use? That is an experiment and does not work. My proposed approach is to start with code dm/impls/patch/examples/tests/ex1.c. And then follow the code /dm/examples/tutorials/ex65dm.c. Is this approach the right way to my goal? In addition, I need to use not only the nodes but also the cells including nodes. Should I use DMMesh to create the cells? I noticed DMMesh is mainly for unstructured grid, but I didn't find other class that implements structured cells. Can anybody give me some suggestions on multi-level grid or let me know which examples I should start with? Thanks. No, that is not appropriate. It sounds like you want structured AMR. PETSc does not do this, and there are packages that do it.: a) Chombo b) SAMRAI which are both patch-based AMR. If you want octree-style AMR you could use p4est, but it would mean a lot of coding along the lines of http://arxiv.org/abs/1308.1472, or Deal.II which is a complete package. I think Deal is the closest to using PETSc solvers. Thanks, Matt -- 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
