[petsc-dev] Matlab interface
Barry Smith
bsmith at mcs.anl.gov
Fri Apr 5 19:25:42 CDT 2013
I have fixed the bug, it was introduced by me when changing MPIUni to have different MPI_COMM_SELF and WORLD. The fix is in next and in barry/fix-matlab
Note I did not update the MATLAB scripts that are out of date.
This fix needs to get into Master before the release.
Thanks for reporting the problem,
Barry
On Apr 5, 2013, at 10:52 AM, Jose E. Roman <jroman at dsic.upv.es> wrote:
> Has anyone tried the Matlab interface with petsc-dev?
>
> If I run exKSP.m three consecutive times, the first time it runs ok, the second time I see a memory leak (see below) and after that I get an error (with exKSP or any other one). This was not happening in 3.3.
>
> Also, some scripts are out-of-date. It is necessary to add mat.SetUp() and other minor fixes.
>
> Jose
>
>>> exKSP
> Vector Object: 1 MPI processes
> type: seq
> 12.5
> 14.5
> 3
> 4
> 5
> 6
> 7
> 8
> 9
> 10
> Matrix Object: 1 MPI processes
> type: seqaij
> row 0: (0, 10)
> row 1: (1, 10)
> row 2: (2, 10)
> row 3: (3, 10)
> row 4: (4, 10)
> row 5: (5, 10)
> row 6: (6, 10)
> row 7: (7, 10)
> row 8: (8, 10)
> row 9: (9, 10)
> 0 KSP Residual norm 2.732215218463e+00
> 1 KSP Residual norm 1.516684121884e-16
> Vector Object: 1 MPI processes
> type: seq
> 1.25
> 1.45
> 0.3
> 0.4
> 0.5
> 0.6
> 0.7
> 0.8
> 0.9
> 1
> KSP Object: 1 MPI processes
> type: gmres
> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
> GMRES: happy breakdown tolerance 1e-30
> maximum iterations=10000, initial guess is zero
> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object: 1 MPI processes
> type: ilu
> ILU: out-of-place factorization
> 0 levels of fill
> tolerance for zero pivot 2.22045e-14
> using diagonal shift on blocks to prevent zero pivot
> matrix ordering: natural
> factor fill ratio given 1, needed 1
> Factored matrix follows:
> Matrix Object: 1 MPI processes
> type: seqaij
> rows=10, cols=10
> package used to perform factorization: petsc
> total: nonzeros=10, allocated nonzeros=10
> total number of mallocs used during MatSetValues calls =0
> not using I-node routines
> linear system matrix = precond matrix:
> Matrix Object: 1 MPI processes
> type: seqaij
> rows=10, cols=10
> total: nonzeros=10, allocated nonzeros=50
> total number of mallocs used during MatSetValues calls =0
> not using I-node routines
> [0]Total space allocated 4880 bytes
> [ 0]16 bytes PetscThreadCommReductionCreate() line 448 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommReductionCreate() line 448 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]512 bytes PetscThreadCommReductionCreate() line 440 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommReductionCreate() line 440 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]128 bytes PetscThreadCommReductionCreate() line 436 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommReductionCreate() line 436 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]1280 bytes PetscThreadCommReductionCreate() line 435 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommReductionCreate() line 435 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]32 bytes PetscThreadCommReductionCreate() line 432 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommReductionCreate() line 432 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcommred.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]64 bytes PetscThreadCommWorldInitialize() line 1265 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1265 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]2432 bytes PetscThreadCommWorldInitialize() line 1264 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1264 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]16 bytes PetscThreadCommWorldInitialize() line 1256 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1256 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]16 bytes PetscThreadCommSetAffinities() line 423 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommSetAffinities() line 423 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]48 bytes PetscThreadCommCreate() line 150 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommCreate() line 150 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]320 bytes PetscThreadCommCreate() line 146 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommCreate() line 146 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscThreadCommWorldInitialize() line 1251 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscGetThreadCommWorld() line 80 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommGetThreadComm() line 114 in /Users/jroman/soft/petsc/src/sys/threadcomm/interface/threadcomm.c
> [0] PetscCommDuplicate() line 139 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
> [ 0]16 bytes PetscCommDuplicate() line 151 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscCommDuplicate() line 151 in /Users/jroman/soft/petsc/src/sys/objects/tagm.c
> [0] PetscHeaderCreate_Private() line 31 in /Users/jroman/soft/petsc/src/sys/objects/inherit.c
> [0] VecCreate() line 32 in /Users/jroman/soft/petsc/src/vec/vec/interface/veccreate.c
>>> exKSP
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Invalid argument!
> [0]PETSC ERROR: Wrong type of object: Parameter # 2!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development GIT revision: 854e096b3f56ee49eddbdee02830d60adb46893b GIT Date: 2013-04-03 20:53:18 -0500
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: matlab on a arch-darwin-c-debug-matlab named pptp243-73.vpns.upv.es by jroman Fri Apr 5 17:49:20 2013
> [0]PETSC ERROR: Libraries linked from /Users/jroman/soft/petsc/arch-darwin-c-debug-matlab/lib
> [0]PETSC ERROR: Configure run at Fri Apr 5 17:31:03 2013
> [0]PETSC ERROR: Configure options --with-matlab --with-matlab-engine --with-mpi=0
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: VecView() line 682 in /Users/jroman/soft/petsc/src/vec/vec/interface/vector.c
> ??? Error using ==> PetscCHKERRQ at 3
> Errors generated on calling Petsc library function
>
> Error in ==> PetscVec>PetscVec.View at 106
> err = calllib('libpetsc', 'VecView', obj.pobj,0);PetscCHKERRQ(err);
>
> Error in ==> PetscVec>PetscVec.subsref at 123
> [varargout{1:nargout}] = builtin('subsref', obj, S);
>
> Error in ==> exKSP at 18
> b.View;
>
>
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