[petsc-users] free unused allocated nonzeros after overestimating preallocation

[Sander Land]

Hi,

I am preallocating a matrix using
  MatMPIAIJSetPreallocation(HalfM,27,PETSC_NULL,26,PETSC_NULL);
Since I have no easy way to know whether the entries will end up in
petsc's 'diagonal' or 'nondiagonal'. After assembling the matrix this
results in:

Matrix Object:
 type=mpiaij, rows=9801, cols=9801
 total: nonzeros=231601, allocated nonzeros=519453
   [0] Local rows 9801 nz 231601 nz alloced 519453 mem 6551364, not
using I-node routines
   [0] on-diagonal part: nz 231601
   [0] off-diagonal part: nz 0

On 1 processor, and some numbers split between on/off on more, as
expected. So far no problem since I can temporarily spare the memory
for 1 such matrix.
Next, I would like to compress the storage somehow, to free the memory
not used, since I know this nonzero pattern will not change, but I
can't find a way to do this in petsc.
Worse, when I use MatConvert/MatDuplicate to initialize my other
matrices, they all seem to inherit this property of using about twice
as much memory as needed. This is a problem when taking the number of
rows to 1 million +.

What is the easiest way to free the unused memory?

Thanks,
Sander Land