Hi Barry, Thank you very much for the suggestion, I will try it.
Yan On Sun, Sep 20, 2009 at 11:36 AM, Barry Smith <bsmith at mcs.anl.gov> wrote: > > Yan, > > Simply read through the ASCII file(s) twice. The first time count the > number of blocks per row, then preallocate then read through the ASCII file > again reading and setting the values. This will be very fast. > > Barry > > > On Sep 20, 2009, at 10:20 AM, Ryan Yan 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/d524ef01/attachment.htm>
