On Wed, Jun 10, 2015 at 9:04 AM, venkatesh g <[email protected]> wrote:
> Hi, > > Yes I will try Elemental but there is lots of complex routines and > functions with long codes in Matlab which goes in the creation of the A and > B matrices, so re-writing in C will take a long time. > > Even if Matlab takes 128 GB out of 256 GB, and the matrix A to be written > is around 25 GB, then PetscBinaryWrite.m is using more than 100 GB just to > run.. This is the problem. > > so is there any other way ? > Don't write it as a sparse matrix. Write it as a dense matrix. This is just a 4 integer header MAT_FILE_CLASSID, M, N, nz and then the data. https://bitbucket.org/petsc/petsc/src/7fe65498eb3a5a672e8885998851e0d5742e4c1e/src/mat/impls/dense/mpi/mpidense.c?at=master#cl-1571 Matt > cheers, > Venkatesh > > On Wed, Jun 10, 2015 at 7:07 PM, Matthew Knepley <[email protected]> > wrote: > >> On Wed, Jun 10, 2015 at 8:32 AM, venkatesh g <[email protected]> >> wrote: >> >>> The size of the matrix is 84500 x 84500 >>> >>> the no. of non-zero elements is 2.7338e+09 >>> >> >> This matrix is not sparse, it has 40% fill. You should treat it as dense. >> For dense matrices of this size, >> you should consider using Elemental. We have an interface to Elemental in >> PETSc. >> >> I recommend writing the code to create these entries on the fly since it >> will probably be faster than loading >> them from disk. >> >> Thanks, >> >> Matt >> >> >>> cheers, >>> Venkatesh >>> >>> On Wed, Jun 10, 2015 at 6:35 PM, Satish Balay <[email protected]> wrote: >>> >>>> Whats the size of the matrix? How many non-zeros? >>>> >>>> Satish >>>> >>>> On Wed, 10 Jun 2015, venkatesh g wrote: >>>> >>>> > Hi >>>> > >>>> > I am trying to write very large sparse matrices A and B for solving >>>> > generalized Eigenvalue problem >>>> > >>>> > so that I can use SLEPC ex7.c code. >>>> > >>>> > I want to read matrices from file according to that code. And I >>>> generate >>>> > these matrices from Matlab using PetscBinaryWrite.m >>>> > >>>> > However, it exceeds my 256 GB RAM in one of the machines. So I am >>>> unable to >>>> > generate these binary matrices. >>>> > >>>> > Kindly let me know how to write them efficiently. >>>> > >>>> > cheers, >>>> > >>>> > Venkatesh >>>> > >>>> >>>> >>> >> >> >> -- >> 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 >> > > -- 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
