[petsc-users] Storage space for symmetric (SBAIJ) matrix

[Daniel Langr]

Our preliminary idea is to construct a matrix with some legacy code, 
store matrix into a file (as we would do anyway for checkpointing 
purposes) and then load it into a solver. We are free to choose matrix 
storage scheme for a file, so we could prepare data to be in the format 
of arrays to be loaded into PETSc. For binary I/O we are experimenting 
with parallel HDF5 capabilities using MPI-I/O underneath. (PETSc has a 
HDF5 viewer, but if I am not wrong, it does not use parallel I/O). For 
really big problems parallel I/O is a must for us.

We are solving a nuclear structure problem, particularly a 
symmetry-adapted no-core shell model computations of a nuclei. (I do not 
understand much that kind of physics, my part is the eigensolver :).

Daniel




Dne 21.9.2010 16:24, Jed Brown napsal(a):
> On Tue, Sep 21, 2010 at 16:20, Daniel Langr<daniel.langr at gmail.com>  wrote:
>> thanks much for your comprehensive answer, it will certainly help. I will
>> look at the example codes. As for matrix assembly process, I would prefer
>> constructing a matrix from arrays (to avoid dynamic assembly and additional
>> memory costs) but there is nothing like MatCreateMPISBAIJWithArrays() or
>> better MatCreateMPISBAIJWithSplitArrays() for symmetric matrices as for
>> unsymmetric ones in PETSc.
>
> This would be easy to add, but how would you go about building the
> arrays yourself?  What sort of problems are you solving?
>
> Jed