[petsc-users] Cuda libraries and DMDA

Mon Apr 9 18:27:53 CDT 2018

On Mon, Apr 9, 2018 at 4:09 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Apr 9, 2018 at 6:12 PM, Manuel Valera <mvalera-w at sdsu.edu> wrote:
>
>> Hello guys,
>>
>> I've made advances in my CUDA acceleration project, as you remember i
>> have a CFD model in need of better execution times.
>>
>> So far i have been able to solve the pressure system in the GPU and the
>> rest in serial, using PETSc only for this pressure solve, the library i got
>> to work was ViennaCL. First question, do i still have to switch
>> installations to use either CUDA library? this was a suggestion before, so
>> in order to use CUSP instead of ViennaCL, for example, i currently have to
>> change installations, is this still the case?
>>
>
> I am not sure what that means exactly. However, you can build a PETSc with
> CUDA and ViennaCL support. The type of Vec/Mat is selected at runtime.
>

Karl Rupp wrote in a previous email:

* * Right now only one of {native CUDA, CUSP, ViennaCL} can be activated at
configure time. This will be fixed later this month.*

I was asking if this was already solved in 3.9,

>
>
>> Now, i started working in a fully parallelized version of the model,
>> which uses the DMs and DMDAs to distribute the arrays, if i try the same
>> flags as before i get an error saying "Currently only handles ViennaCL
>> matrices" when trying to solve for pressure, i get this is a feature still
>> not implemented? what options do i have to solve pressure, or assign a DMDA
>> array update to be done specifically in a GPU device?
>>
>
> If we can't see the error, we are just guessing. Please send the entire
> error message.
>

Got it, I will paste the error at the end of this email

>
> Note, we only do linear algebra on the GPU, so none of the
> FormFunction/FormJacobian stuff for DMDA would be on the GPU.
>

Yes, we only use it for linear algebra, e.g. solving a linear system and
updating an array with a problematic algorithm.

>
>
>> I was thinking of using the VecScatterCreateToZero for a regular vector,
>>
>
> Why do you want a serial vector?
>

Because it looks live ViennaCL doesn't handle arrays created with DMDAVec,
it was just an idea

> but then i would have to create a vector and copy the DMDAVec into it,
>>
>
> I do not understand what it means to copy the DM into the Vec.
>

I meant copying a DMDAVec into a Vec object, the first is created with a
DMDA object for it's mapping across processors,

>
>   Thanks,
>
>      Matt
>
>
>> is this accomplished with DMDAVecGetArrayReadF90 and then just copy? do
>> you think this will generate too much overhead?
>>
>> Thanks so much for your input,
>>
>> Manuel
>>
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
>

The error happens when trying to use KSPSolve() for a vector made with
DMDAVec routines, the matrix is created without any DMDA routines

Error:

[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Currently only handles ViennaCL matrices
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.8.4-2418-gd9c423b  GIT
Date: 2018-04-02 11:59:41 +0200
[0]PETSC ERROR: ./gcmBEAM on a cuda named node50 by valera Mon Apr  9
16:24:26 2018
[0]PETSC ERROR: Configure options PETSC_ARCH=cuda --download-mpich
--download-fblaslapack COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2
--with-shared-libraries=1 --download-hypre --with-debugging=no
--with-cuda=1 --CUDAFLAGS=-arch=sm_60 --download-hypre --download-viennacl
--download-cusp
[0]PETSC ERROR: #1 PCSetUp_SAVIENNACL() line 47 in
/home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
[0]PETSC ERROR: #2 PCSetUp() line 924 in
/home/valera/petsc/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #3 KSPSetUp() line 381 in
/home/valera/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Currently only handles ViennaCL matrices
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.8.4-2418-gd9c423b  GIT
Date: 2018-04-02 11:59:41 +0200
[0]PETSC ERROR: ./gcmBEAM on a cuda named node50 by valera Mon Apr  9
16:24:26 2018
[0]PETSC ERROR: Configure options PETSC_ARCH=cuda --download-mpich
--download-fblaslapack COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2
--with-shared-libraries=1 --download-hypre --with-debugging=no
--with-cuda=1 --CUDAFLAGS=-arch=sm_60 --download-hypre --download-viennacl
--download-cusp
[0]PETSC ERROR: #4 PCSetUp_SAVIENNACL() line 47 in
/home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
[0]PETSC ERROR: #5 PCSetUp() line 924 in
/home/valera/petsc/src/ksp/pc/interface/precon.c
 Finished setting up matrix objects
 Exiting PrepareNetCDF
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.8.4-2418-gd9c423b  GIT
Date: 2018-04-02 11:59:41 +0200
[0]PETSC ERROR: ./gcmBEAM on a cuda named node50 by valera Mon Apr  9
16:24:26 2018
[0]PETSC ERROR: Configure options PETSC_ARCH=cuda --download-mpich
--download-fblaslapack COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2
--with-shared-libraries=1 --download-hypre --with-debugging=no
--with-cuda=1 --CUDAFLAGS=-arch=sm_60 --download-hypre --download-viennacl
--download-cusp
[0]PETSC ERROR: #6 User provided function() line 0 in  unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
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