[petsc-dev] Matlab interface
Barry Smith
bsmith at mcs.anl.gov
Fri Apr 5 16:16:27 CDT 2013
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?
I ran classes/examples/tests/ex2.c and had similar behavior as you report. I suspect something gotten broken with regard to PetscInitialize()/Finalize() being reentrant (that is callable multiple times) because of the thread kernel code. I'll try to debug through it. Don't know when I'll have any luck.
Barry
>
> 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 Also, some scripts are out-of-date.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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