Matt,

Thanks for replying back to me. Actually, we are only seeing this problem on debug, non-fortran compilations of PETSc. When we turn on fortran and turn off debugging in the configuration, the behavior is normal, the timing is fast (as to be expected), and the storage space is more in lines with our calculations. Maybe this is expected behavior for all debug/non-fortran builds? Or maybe this is a test case for finding an edge-case?

No. KSP is most used part of PETSc, and has been there for > 15 years. We run nightly valgrind tests to check for leaks.

I am confident that this is misconfiguration. Send a sample code to petsc-maint@mcs.anl.gov if -malloc_dump does

not find the problem.

Matt

Anyways, thanks for your help!

-Brenna

From: petsc-users-bounces@mcs.anl.gov [mailto:petsc-users-bounces@mcs.anl.gov] On Behalf Of Matthew Knepley
Sent: Thursday, May 17, 2012 10:59 AM
To: PETSc users list
Subject: [EXTERNAL] Re: [petsc-users] Problem creating an array of KSP objects

On Thu, May 17, 2012 at 12:37 PM, Hautzenroeder, Brenna M <bmhautz@sandia.gov> wrote:

I’m running into time and memory problems creating an array to store multiple KSP objects.

We are using a Fourier method for the temporal portion of our operator; currently, this is anywhere between 1024-2048 time samples equating to 1024-2048 frequencies to advance our solution. Each frequency has its own matrix, meaning there are 1024-2048 linear equations of the form Ax = b. So, while the matrices are different for each frequency, when we propagate the solution one step, the 1024-2048 matrices don’t change since the frequencies haven’t changed between steps.

We would like to store each KSP solution (all 1024-2048 of them) in an array so that we can reuse them for the next step since this saves us time factoring the matrix. The problem I am seeing is that storing these KSP objects in any kind of array increases the runtime and storage space exponentially – I am seeing times on the order of 30 mins to an hour and memory consumed hover around 20-30GB! Is there something inherent

I don't think you really mean "exponential", but just big. Did you calculate how much space you expect? Storing a factor can take

N^3 space, and then you have 1000 of them, so it will take 1000x the space of 1 KSP. Did you compare the storage for both cases?

There is really not enough information in your question, however

Yes, storing KSPs is the right thing here

No, they do not take more space than necessary

Matt

about the KSP object that I am missing and/or a better way to store these objects? I don’t have any problems if I use one KSP object and set the operators each time to the different matrices, except that it takes longer than it normally would after the first step since it has to recalculate the preconditioner matrix.

Note: We are using distributed matrices and vectors for our linear system.

I have included some pseudocode to illustrate our linear system, which works:

KSP k;

for steps = 1 to 100 do:

for time = 1 to 1024 do:

                create distributed matrix A and fill with local values (A[step=1,time=1] = A[step=2,time=1], etc)

                create distributed vector b and fill with local values for given time

                create distributed vector x for result

                create KSP k and set matrices

                KSPSolve(k, b, x) => takes a little extra time each step

However, the following creates time/storage problems:

KSP* kArray;

create kArray => takes inordinate amout of time and storage

for steps = 1 to 100 do:

        for time=1 to 1024 do:

                create distributed matrix A and fill with local values (A[step=1,time=1] = A[step=2,time=1], etc)

                create distributed vector b and fill with local values for given time

                create distributed vector x for result

                if time == 1 do:

set matrices on kArray[time] => also takes an inordinate amount of time and storage

                KSPSolve(kArray[time], b, x)

Any insight would be greatly appreciated!

Brenna

--
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