I forget to mention that, the stencil of the mesh has face connectivity. For each tetrahedron* *mesh point, it has a self-connectivity, and 4 other connectivities( tet has 4 faces). For Hexahedron, it has a self-connectivity, and 6 other connectivities( hex has 6 faces).
the dof 25 results from [u, v, w, p, a]^5, here 5 means 5 physical phase, for instance, bubble1, liquid1, bubble2, liquid2,solid1. u, v, w, p, a from conservation of the physics. Thanks, Yan On Sun, Sep 20, 2009 at 11:20 AM, Ryan Yan <vyan2000 at gmail.com> wrote: > Hi All, > I have a large size application. Mesh size is 30000 nodes, with dof 25 on > each vertex. And it's 3d unstructured, Tet, and Hex mesh. In the following > I will denote blksize=25 > > I am testing how to build up a PETSc matrix object quick and fast. > > The data I have is Block Compressed Sparse Row(BCSR) files. And my > objective is to read BCSR files and generate PETSc Binaries > > Firstly, I choose the MATMPIAIJ, I opened the BCSR data files on each > processor, and set up the preallocation use > MatMPIAIJSetPreallocation(A,blksize,PETSC_NULL,blksize,PETSC_NULL); The > reason why I choose 25 as the number for d_nz and o_nz is that I do not have > access to the ordering of the vertices. So it's the worst case set up, and > it takes about 7 minutes on 30 MIPS node(180 processors) to write the output > into PETSc binaries. > > Secondly, I choose the MatMPIBAIJ, and same procedure as above, but also > set up > MatMPIBAIJSetPreallocation(A,blksize,blksize,PETSC_NULL,blksize,PETSC_NULL), > here blksize = 25 and it's also the worst case; This experiments takes > forever and could not generate the PETSc binaries. > > I guess the reason why it takes so long in the MATMPIBAIJ case is that I > did not set up the preallocation accurately. Alougth I think the > preallocation is also not accurate in the MATMPIAIJ case, but it seems like > the preallocation effect is not as serious as for the MPIBAIJ. Correct me > please, if there are other reasons. > > Can I anyone please give a hint on how to set up the preallocation right > for a unstructured mesh without knowing the mesh ordering? > > Thank you very much in advance, > > Yan > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090920/85b08e21/attachment.htm>
