Matt,
1) great!
2) ??? that's precisely why I paste the output of "cat mattry.F90" in the
emails, so you have a small example that produces the errors I mention. Now I'm
also attaching it to this email.
Thanks,
Chris
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
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________________________________
From: Matthew Knepley <[email protected]>
Sent: Monday, August 01, 2016 4:15 PM
To: Klaij, Christiaan
Cc: [email protected]
Subject: Re: [petsc-users] block matrix without MatCreateNest
On Mon, Aug 1, 2016 at 8:59 AM, Klaij, Christiaan
<[email protected]<mailto:[email protected]>> wrote:
Matt,
Thanks for your suggestions. Here's the outcome:
1) without the "if type=nest" protection, I get a "Cannot
locate function MatNestSetSubMats_C" error when using
type mpiaij, see below.
That is a bug. It should be using PetscTryMethod() there, not PetscUseMethod().
We will fix it. That way
it can be called for any matrix type, which is the intention.
2) with the isg in a proper array, I get the same "Invalid
Pointer to Object" error, see below.
Can you send a small example that we can run? It obviously should work this way.
Thanks,
Matt
Chris
$ cat mattry.F90
program mattry
use petscksp
implicit none
#include <petsc/finclude/petsckspdef.h>
PetscInt :: n=4 ! setting 4 cells per process
PetscErrorCode :: ierr
PetscInt :: size,rank,i
Mat :: A,A02
MatType :: type
IS :: isg(3)
IS :: isl(3)
ISLocalToGlobalMapping :: map
integer, allocatable, dimension(:) :: idx
call PetscInitialize(PETSC_NULL_CHARACTER,ierr); CHKERRQ(ierr)
call MPI_Comm_size(PETSC_COMM_WORLD,size,ierr); CHKERRQ(ierr)
call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr);CHKERRQ(ierr)
! local index sets for 3 fields
allocate(idx(n))
idx=(/ (i-1, i=1,n) /)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isl(1),ierr);CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isl(2),ierr);CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isl(3),ierr);CHKERRQ(ierr)
! call ISView(isl3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
deallocate(idx)
! global index sets for 3 fields
allocate(idx(n))
idx=(/ (i-1+rank*3*n, i=1,n) /)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isg(1),ierr);CHKERRQ(ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isg(2),ierr);
CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isg(3),ierr);
CHKERRQ(ierr)
! call ISView(isg3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
deallocate(idx)
! local-to-global mapping
allocate(idx(3*n))
idx=(/ (i-1+rank*3*n, i=1,3*n) /)
call
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD,1,3*n,idx,PETSC_COPY_VALUES,map,ierr);
CHKERRQ(ierr)
! call ISLocalToGlobalMappingView(map,PETSC_VIEWER_STDOUT_WORLD,ierr);
CHKERRQ(ierr)
deallocate(idx)
! create the 3-by-3 block matrix
call MatCreate(PETSC_COMM_WORLD,A,ierr); CHKERRQ(ierr)
call MatSetSizes(A,3*n,3*n,PETSC_DECIDE,PETSC_DECIDE,ierr); CHKERRQ(ierr)
call MatSetUp(A,ierr); CHKERRQ(ierr)
call MatSetOptionsPrefix(A,"A_",ierr); CHKERRQ(ierr)
call MatSetLocalToGlobalMapping(A,map,map,ierr); CHKERRQ(ierr)
call MatSetFromOptions(A,ierr); CHKERRQ(ierr)
! setup nest
call MatNestSetSubMats(A,3,isg,3,isg,PETSC_NULL_OBJECT,ierr); CHKERRQ(ierr)
! set diagonal of block A02 to 0.65
call MatGetLocalSubmatrix(A,isl(1),isl(3),A02,ierr); CHKERRQ(ierr)
do i=1,n
call MatSetValuesLocal(A02,1,i-1,1,i-1,0.65d0,INSERT_VALUES,ierr);
CHKERRQ(ierr)
end do
call MatRestoreLocalSubMatrix(A,isl(1),isl(3),A02,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
! verify
call MatGetSubmatrix(A,isg(1),isg(3),MAT_INITIAL_MATRIX,A02,ierr);
CHKERRQ(ierr)
call MatView(A02,PETSC_VIEWER_STDOUT_WORLD,ierr);CHKERRQ(ierr)
call PetscFinalize(ierr)
end program mattry
$ mpiexec -n 2 ./mattry -A_mat_type mpiaij
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Cannot locate function MatNestSetSubMats_C in object
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
[0]PETSC ERROR: ./mattry
on a linux_64bit_debug named
lin0322.marin.local by cklaij Mon Aug 1 15:42:10 2016
[0]PETSC ERROR: Configure options
--with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7
--with-clanguage=c++ --with-x=1 --with-debugging=1
--with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl
--with-shared-libraries=0
[0]PETSC ERROR: #1 MatNestSetSubMats() line 1105 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 56.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch
system) has told this process to end
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
find memory corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[1]PETSC ERROR: INSTEAD the line number of the start of the function
[1]PETSC ERROR: is given.
[1]PETSC ERROR: [1] PetscSleep line 35
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/sys/utils/psleep.c
[1]PETSC ERROR: [1] PetscTraceBackErrorHandler line 193
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/sys/error/errtrace.c
[1]PETSC ERROR: [1] PetscError line 364
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/sys/error/err.c
[1]PETSC ERROR: [1] MatNestSetSubMats line 1092
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Signal received
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
[1]PETSC ERROR: ./mattry
on a linux_64bit_debug named
lin0322.marin.local by cklaij Mon Aug 1 15:42:10 2016
[1]PETSC ERROR: Configure options
--with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7
--with-clanguage=c++ --with-x=1 --with-debugging=1
--with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl
--with-shared-libraries=0
[1]PETSC ERROR: #1 User provided function() line 0 in unknown file
[lin0322.marin.local:19455] 1 more process has sent help message
help-mpi-api.txt / mpi-abort
[lin0322.marin.local:19455] Set MCA parameter "orte_base_help_aggregate" to 0
to see all help / error messages
$ mpiexec -n 2 ./mattry -A_mat_type nest
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Corrupt argument:
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: Invalid Pointer to Object: Parameter # 1
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Corrupt argument:
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: Invalid Pointer to Object: Parameter # 1
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
[1]PETSC ERROR: ./mattry
on a linux_64bit_debug named
lin0322.marin.local by cklaij Mon Aug 1 15:42:25 2016
[1]PETSC ERROR: Configure options
--with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7
--with-clanguage=c++ --with-x=1 --with-debugging=1
--with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl
--with-shared-libraries=0
[1]PETSC ERROR: #1 PetscObjectReference() line 534 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/sys/objects/inherit.c
[1]PETSC ERROR: #2 MatNestSetSubMats_Nest() line 1042 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
[1]PETSC ERROR: #3 MatNestSetSubMats() line 1105 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
[0]PETSC ERROR: Petsc Release Version 3.7.3, Jul, 24, 2016
[0]PETSC ERROR: ./mattry
on a linux_64bit_debug named
lin0322.marin.local by cklaij Mon Aug 1 15:42:25 2016
[0]PETSC ERROR: Configure options
--with-mpi-dir=/home/cklaij/ReFRESCO/Dev/trunk/Libs/install/openmpi/1.8.7
--with-clanguage=c++ --with-x=1 --with-debugging=1
--with-blas-lapack-dir=/opt/intel/composer_xe_2015.1.133/mkl
--with-shared-libraries=0
[0]PETSC ERROR: #1 PetscObjectReference() line 534 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/sys/objects/inherit.c
[0]PETSC ERROR: #2 MatNestSetSubMats_Nest() line 1042 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
[0]PETSC ERROR: #3 MatNestSetSubMats() line 1105 in
/home/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc/3.7.3-dbg/src/mat/impls/nest/matnest.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 64.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[lin0322.marin.local:19465] 1 more process has sent help message
help-mpi-api.txt / mpi-abort
[lin0322.marin.local:19465] Set MCA parameter "orte_base_help_aggregate" to 0
to see all help / error messages
$
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
MARIN | T +31 317 49 33 44 | mailto:[email protected]<mailto:[email protected]> |
http://www.marin.nl
MARIN news:
http://www.marin.nl/web/News/News-items/Ship-design-in-EU-project-Holiship.htm
--
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
program mattry
use petscksp
implicit none
#include <petsc/finclude/petsckspdef.h>
PetscInt :: n=4 ! setting 4 cells per process
PetscErrorCode :: ierr
PetscInt :: size,rank,i
Mat :: A,A02
MatType :: type
IS :: isg(3)
IS :: isl(3)
ISLocalToGlobalMapping :: map
integer, allocatable, dimension(:) :: idx
call PetscInitialize(PETSC_NULL_CHARACTER,ierr); CHKERRQ(ierr)
call MPI_Comm_size(PETSC_COMM_WORLD,size,ierr); CHKERRQ(ierr)
call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr);CHKERRQ(ierr)
! local index sets for 3 fields
allocate(idx(n))
idx=(/ (i-1, i=1,n) /)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isl(1),ierr);CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isl(2),ierr);CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isl(3),ierr);CHKERRQ(ierr)
! call ISView(isl3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
deallocate(idx)
! global index sets for 3 fields
allocate(idx(n))
idx=(/ (i-1+rank*3*n, i=1,n) /)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx,PETSC_COPY_VALUES,isg(1),ierr);CHKERRQ(ierr)
call ISCreateGeneral(PETSC_COMM_WORLD,n,idx+n,PETSC_COPY_VALUES,isg(2),ierr);
CHKERRQ(ierr)
call
ISCreateGeneral(PETSC_COMM_WORLD,n,idx+2*n,PETSC_COPY_VALUES,isg(3),ierr);
CHKERRQ(ierr)
! call ISView(isg3,PETSC_VIEWER_STDOUT_WORLD,ierr); CHKERRQ(ierr)
deallocate(idx)
! local-to-global mapping
allocate(idx(3*n))
idx=(/ (i-1+rank*3*n, i=1,3*n) /)
call
ISLocalToGlobalMappingCreate(PETSC_COMM_WORLD,1,3*n,idx,PETSC_COPY_VALUES,map,ierr);
CHKERRQ(ierr)
! call ISLocalToGlobalMappingView(map,PETSC_VIEWER_STDOUT_WORLD,ierr);
CHKERRQ(ierr)
deallocate(idx)
! create the 3-by-3 block matrix
call MatCreate(PETSC_COMM_WORLD,A,ierr); CHKERRQ(ierr)
call MatSetSizes(A,3*n,3*n,PETSC_DECIDE,PETSC_DECIDE,ierr); CHKERRQ(ierr)
call MatSetUp(A,ierr); CHKERRQ(ierr)
call MatSetOptionsPrefix(A,"A_",ierr); CHKERRQ(ierr)
call MatSetLocalToGlobalMapping(A,map,map,ierr); CHKERRQ(ierr)
call MatSetFromOptions(A,ierr); CHKERRQ(ierr)
! setup nest
call MatNestSetSubMats(A,3,isg,3,isg,PETSC_NULL_OBJECT,ierr); CHKERRQ(ierr)
! set diagonal of block A02 to 0.65
call MatGetLocalSubmatrix(A,isl(1),isl(3),A02,ierr); CHKERRQ(ierr)
do i=1,n
call MatSetValuesLocal(A02,1,i-1,1,i-1,0.65d0,INSERT_VALUES,ierr);
CHKERRQ(ierr)
end do
call MatRestoreLocalSubMatrix(A,isl(1),isl(3),A02,ierr); CHKERRQ(ierr)
call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
! verify
call MatGetSubmatrix(A,isg(1),isg(3),MAT_INITIAL_MATRIX,A02,ierr);
CHKERRQ(ierr)
call MatView(A02,PETSC_VIEWER_STDOUT_WORLD,ierr);CHKERRQ(ierr)
call PetscFinalize(ierr)
end program mattry
