> On Nov 21, 2016, at 12:20 PM, Massoud Rezavand <[email protected]>
> wrote:
>
> Thank you very much.
>
> Yes I am developing the new 3D version in Parallel with the PPM (the new
> generation OpenFPM, not released yet) library which generates the particles
> and decomposes the domain.
>
> I don't have the parallel matrix generation yet. In the old version I had CSR
> format and a vector of knowns (b).
> So, should I use MatSetValuesStencil() ?
MatSetValuesStencil is for finite differences on a structured grid. I don't
think it makes sense for your application.
You need to use MatMPIAIJSetPreallocation() and then MatSetValues() to put
the entries in.
> What do you recommend for creating the vector of knowns (b)?
Just use VecCreateMPI()
>
> On the other hand, due to the convergence issues for millions of particles in
> ISPH, I have to use a preconditioner. In a paper I saw they have used
> BoomerAMG from HYPRE. Do you have any recommendation?
We have many to try, it is not clear that any would be particularly good for
SPH. Certainly try BoomerAMG
>
> I saw an example ( ex19.c) using BoomerAMG. Should I follow that?
>
>
> PS: regarding the unbalance sparsity in SPH, yes in contrast to the
> mesh-based methods, the A matrix in ISPH is changing over the time but the
> number of non-zeros is defined by the number of neighboring particles which
> in most cases is constant.
>
> Cheers,
>
> Massoud
>
>
>
> On 11/21/2016 06:18 PM, Barry Smith wrote:
>>> On Nov 21, 2016, at 10:33 AM, Massoud Rezavand <[email protected]>
>>> wrote:
>>>
>>> Dear all,
>>>
>>> I am going to use PETSc in an Incompressible SPH code to solve the pressure
>>> Poisson equation as a linear system of equations.
>>>
>>> In my old sequential code I used the PCG method or the BiCGSTAB with jacobi
>>> preconditioner.
>>> I used to store the coefficient matrix (A) in CSR (AIJ) format and solve it.
>>>
>>> My question is that how should I import the CSR metrix and the known vector
>>> (b) into the library to be solved? Is there an example to show how to
>>> import and external system of eqs. into PETSc?
>>>
>> For sequential code it is straightforward.
>>
>> If you already have the matrix in CSR format you can call
>> MatCreateSeqAIJWithArrays() to create the PETSc matrix without copying the
>> data. You can use VecCreateSeqWithArray() to provide the vector. Or you can
>> use VecPlaceArray() to use the array of vector values you provide.
>>
>>
>>> In my case, the computational domain is decomposed by another library, so
>>> does it effect the performance of PETSc?
>>>
>> I read this to mean you want the new code to be parallel (but the old one
>> is sequential)?
>>
>> If you don't currently have matrix generation in parallel I urge you
>> strongly to directly use MatSetValues() to generate your matrix, do not
>> first put the matrix entries into some kind of parallel CSR format. If you
>> already have the matrix in "parallel" CSR format you can use
>> MatCreateMPIAIJWithArrays() to copy the matrix over to CSR format.
>>
>> It is my understanding that SPH can produce matrices with very unbalance
>> sparsity. It is important to take this into account if you wish to run in
>> parallel since if you end up with some processes having many more nonzeros
>> than other processes you will get very poor performance.
>>
>>
>> Barry
>>
>>
>>
>>> With the best regards,
>>> Massoud
>>>
>>>
>
