[petsc-dev] Matlab interface
Jose E. Roman
jroman at dsic.upv.es
Fri Apr 5 10:52:24 CDT 2013
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Also, some scripts are out-of-date.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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