April 2011 - petsc-dev - mailman3.cels.anl.gov

MatSetFromOptions() after DMGetMatrix()
by Jed Brown 30 Apr '11

30 Apr '11

I was tired of writing MatSetOption(Ap,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE) into my code to find preallocation issues, so I added -mat_new_nonzero_allocation_err to MatSetFromOptions(). Now I actually call that function. In particular, I do things like PetscOptionsList("-Ap_mat_type","Matrix type for velocity operator","",MatList,mattype_Ap,mattype_Ap,sizeof(mattype_Ap),NULL); ... DMGetMatrix(fsu,mattype_Ap,&Ap); MatSetOptionsPrefix(Ap,"Ap_"); MatSetOption(Ap,MAT_SYMMETRIC,PETSC_TRUE); MatSetFromOptions(Ap); // Check type and set MAT_IGNORE_LOWER_TRIANGULAR if necessary Three problems: 1. This is too damn much work. 2. Checking the type is an ugly hack. Should MAT_IGNORE_LOWER_TRIANGULAR be default, or should nonsymmetric matrices ignore it, or should there be a new option with those semantics? 3. It's wrong to use "-Ap_mat_type sbaij" because the actual type becomes seqsbaij, and then preallocation is thrown away [*] when MatSetFromOptions finds "sbaij", calls MatSetType which compares it to "seqsbaij", and resets the type. This means that I have to use a different prefix to choose which type to pass to DMGetMatrix() than the prefix I subsequently set on the matrix. Any ideas how to make this work in a sane way? [*] I was getting a seg-fault, but I set mat->preallocated to false in MatSetType. It doesn't crash any more, but preallocation is still thrown away.

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Re: [petsc-dev] failing test
by Barry Smith 29 Apr '11

29 Apr '11

I also cannot reproduce the problem using shared libraries and mpich2-1.3.1 Suggest trying to reproduce the problem with another MPI implementation. Barry Also runs valgrind clean On Apr 29, 2011, at 9:34 AM, Lisandro Dalcin wrote: > On 29 April 2011 00:36, Hong Zhang <hzhang(a)mcs.anl.gov> wrote: >> Lisandro : >> Has this been fixed? I cannot reproduce it on petsc machine or my Mac. >> Hong >> > > Still failing here (shared lib build, using mpich2 1.2.1p1 from Fedora 13) > >>> Can any one take a look here? It is unlikely that is is caused by my >>> commit "dbddbea75f68". It smells as an issue with Viewers created on >>> subcommunicators. >>> >>> [dalcinl@trantor tutorials]$ cd $PETSC_DIR/src/ksp/ksp/examples/tutorials >>> [dalcinl@trantor tutorials]$ make runex2_bjacobi_2 >>> 42a43,56 >>>> [0]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >>>> [0]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >>>> [0]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >>>> [0]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>>> [0]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>>> [0]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >>>> [1]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >>>> [1]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >>>> [1]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >>>> [1]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>>> [1]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>>> [1]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >>>> rank 0 in job 7851 trantor_56062 caused collective abort of all ranks >>>> exit status of rank 0: return code 0 >>> Possible problem with ex2_bjacobi_2, diffs above >>> >>> >>> -- >>> Lisandro Dalcin >>> --------------- >>> CIMEC (INTEC/CONICET-UNL) >>> Predio CONICET-Santa Fe >>> Colectora RN 168 Km 472, Paraje El Pozo >>> 3000 Santa Fe, Argentina >>> Tel: +54-342-4511594 (ext 1011) >>> Tel/Fax: +54-342-4511169 >>> >> > > > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169

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Re: [petsc-dev] What should MatGetRowIJ(..., symmetric=TRUE, ...) do with empty diagonal?
by Jed Brown 29 Apr '11

29 Apr '11

On Fri, Apr 29, 2011 at 21:50, Barry Smith <bsmith(a)mcs.anl.gov> wrote: > > Jed, > > Could you perhaps save the matrix as a binary file and send it to > petsc-maint(a)mcs.anl.gov so I can track down why it crashes here and fix > it. > A test case is attached.

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Re: [petsc-dev] What should MatGetRowIJ(..., symmetric=TRUE, ...) do with empty diagonal?
by Barry Smith 29 Apr '11

29 Apr '11

Jed, Could you perhaps save the matrix as a binary file and send it to petsc-maint(a)mcs.anl.gov so I can track down why it crashes here and fix it. Please append this email so I know the bug I am tracking. Thanks Barry On Apr 23, 2011, at 12:02 PM, Jed Brown wrote: > MatGetOrdering is failing with the following matrix. Should it fail (i.e. diagonal is required) or not? It seems to work for many larger sizes even without setting a diagonal. > > Matrix Object: 1 MPI processes > type: seqaij > row 0: (2, 1) > row 1: (2, 1) > row 2: (0, 1) (1, 1) > > #0 0x00007ffff5a70ffc in MatGetRowIJ_SeqAIJ_Inode_Symmetric (A=0x1ee9a00, iia=0x7fffffffbe68, jja=0x7fffffffbe60, ishift=0, oshift=1) at /home/jed/petsc/src/mat/impls/aij/seq/inode.c:108 > #1 0x00007ffff5a72808 in MatGetRowIJ_SeqAIJ_Inode (A=0x1ee9a00, oshift=1, symmetric=PETSC_TRUE, blockcompressed=PETSC_TRUE, n=0x7fffffffbe74, ia=0x7fffffffbe68, ja=0x7fffffffbe60, done=0x7fffffffbe54) at /home/jed/petsc/src/mat/impls/aij/seq/inode.c:244 > #2 0x00007ffff5705629 in MatGetRowIJ (mat=0x1ee9a00, shift=1, symmetric=PETSC_TRUE, inodecompressed=PETSC_TRUE, n=0x7fffffffbe74, ia=0x7fffffffbe68, ja=0x7fffffffbe60, done=0x7fffffffbe54) at /home/jed/petsc/src/mat/interface/matrix.c:6650 > #3 0x00007ffff5b2318d in MatGetOrdering_RCM (mat=0x1ee9a00, type=0xa875b0 "rcm", row=0x7fffffffc1d0, col=0x7fffffffc1c8) at /home/jed/petsc/src/mat/order/sprcm.c:18 > #4 0x00007ffff5b260fb in MatGetOrdering (mat=0x1ee9a00, type=0xa875b0 "rcm", rperm=0x7fffffffc1d0, cperm=0x7fffffffc1c8) at /home/jed/petsc/src/mat/order/sorder.c:229 > #5 0x00007ffff7b8312d in dMeshPopulateOrderedSet_Private (mesh=0xa01920, orderedSet=0xb000000000000018, explicitSet=0xb000000000000019, dirichletSet=0xb00000000000001a, ghostSet=0xb00000000000001b, orderingtype=0xa875b0 "rcm") at /home/jed/dohp/src/fs/impls/cont/cont.c:159 > #6 0x00007ffff7b84f60 in dFSBuildSpace_Cont (fs=0xa864e0) at /home/jed/dohp/src/fs/impls/cont/cont.c:288 > #7 0x00007ffff7b533f9 in dFSBuildSpace (fs=0xa864e0) at /home/jed/dohp/src/fs/interface/fs.c:351 > #8 0x00007ffff7b61d00 in dFSSetFromOptions (fs=0xa864e0) at /home/jed/dohp/src/fs/interface/fsreg.c:127 > #9 0x0000000000409572 in EllipSetFromOptions (elp=0x9fdc80) at /home/jed/dohp/src/fs/tests/ellip.c:256 > #10 0x000000000040e95f in main (argc=15, argv=0x7fffffffd658) at /home/jed/dohp/src/fs/tests/ellip.c:644

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Re: [petsc-dev] failing test
by Lisandro Dalcin 29 Apr '11

29 Apr '11

On 29 April 2011 00:36, Hong Zhang <hzhang(a)mcs.anl.gov> wrote: > Lisandro : > Has this been fixed? I cannot reproduce it on petsc machine or my Mac. > Hong > Still failing here (shared lib build, using mpich2 1.2.1p1 from Fedora 13) >> Can any one take a look here? It is unlikely that is is caused by my >> commit "dbddbea75f68". It smells as an issue with Viewers created on >> subcommunicators. >> >> [dalcinl@trantor tutorials]$ cd $PETSC_DIR/src/ksp/ksp/examples/tutorials >> [dalcinl@trantor tutorials]$ make runex2_bjacobi_2 >> 42a43,56 >>> [0]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >>> [0]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >>> [0]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >>> [0]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>> [0]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>> [0]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >>> [1]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >>> [1]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >>> [1]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >>> [1]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>> [1]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >>> [1]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >>> rank 0 in job 7851 trantor_56062 caused collective abort of all ranks >>> exit status of rank 0: return code 0 >> Possible problem with ex2_bjacobi_2, diffs above >> >> >> -- >> Lisandro Dalcin >> --------------- >> CIMEC (INTEC/CONICET-UNL) >> Predio CONICET-Santa Fe >> Colectora RN 168 Km 472, Paraje El Pozo >> 3000 Santa Fe, Argentina >> Tel: +54-342-4511594 (ext 1011) >> Tel/Fax: +54-342-4511169 >> > -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] failing test
by Hong Zhang 28 Apr '11

28 Apr '11

Lisandro : Has this been fixed? I cannot reproduce it on petsc machine or my Mac. Hong > Can any one take a look here? It is unlikely that is is caused by my > commit "dbddbea75f68". It smells as an issue with Viewers created on > subcommunicators. > > [dalcinl@trantor tutorials]$ cd $PETSC_DIR/src/ksp/ksp/examples/tutorials > [dalcinl@trantor tutorials]$ make runex2_bjacobi_2 > 42a43,56 >> [0]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >> [0]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >> [0]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >> [0]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [0]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [0]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >> [1]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >> [1]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >> [1]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >> [1]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [1]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [1]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >> rank 0 in job 7851 trantor_56062 caused collective abort of all ranks >> exit status of rank 0: return code 0 > Possible problem with ex2_bjacobi_2, diffs above > > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169 >

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Re: [petsc-dev] failing test
by Hong Zhang 28 Apr '11

28 Apr '11

I'll check this. Hong On Thu, Apr 28, 2011 at 4:38 PM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > Can any one take a look here? It is unlikely that is is caused by my > commit "dbddbea75f68". It smells as an issue with Viewers created on > subcommunicators. > > [dalcinl@trantor tutorials]$ cd $PETSC_DIR/src/ksp/ksp/examples/tutorials > [dalcinl@trantor tutorials]$ make runex2_bjacobi_2 > 42a43,56 >> [0]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >> [0]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >> [0]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >> [0]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [0]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [0]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >> [1]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c >> [1]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c >> [1]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c >> [1]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [1]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c >> [1]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c >> rank 0 in job 7851 trantor_56062 caused collective abort of all ranks >> exit status of rank 0: return code 0 > Possible problem with ex2_bjacobi_2, diffs above > > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169 >

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Re: [petsc-dev] link error with parmetis
by Satish Balay 28 Apr '11

28 Apr '11

perhaps you are missing -lparmetis in your link command? Satish On Thu, 28 Apr 2011, Mark F. Adams wrote: > I'm getting this link error with petsc-dev, any ideas? > Thanks, > Mark > > /global/homes/m/madams/petsc-dev/cray-xe6_O/lib/libpetsc.a(pmetis.o): In function `MatPartitioningApply_Parmetis(_p_MatPartitioning*, _p_IS**)': > pmetis.c:(.text+0x53f): undefined reference to `ParMETIS_V3_PartKway' > /global/homes/m/madams/petsc-dev/cray-xe6_O/lib/libpetsc.a(pmetis.o): In function `MatMeshToCellGraph(_p_Mat*, int, _p_Mat**)': > pmetis.c:(.text+0x117d): undefined reference to `ParMETIS_V3_Mesh2Dual' > collect2: ld returned 1 exit status > >

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link error with parmetis
by Mark F. Adams 28 Apr '11

28 Apr '11

I'm getting this link error with petsc-dev, any ideas? Thanks, Mark /global/homes/m/madams/petsc-dev/cray-xe6_O/lib/libpetsc.a(pmetis.o): In function `MatPartitioningApply_Parmetis(_p_MatPartitioning*, _p_IS**)': pmetis.c:(.text+0x53f): undefined reference to `ParMETIS_V3_PartKway' /global/homes/m/madams/petsc-dev/cray-xe6_O/lib/libpetsc.a(pmetis.o): In function `MatMeshToCellGraph(_p_Mat*, int, _p_Mat**)': pmetis.c:(.text+0x117d): undefined reference to `ParMETIS_V3_Mesh2Dual' collect2: ld returned 1 exit status

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failing test
by Lisandro Dalcin 28 Apr '11

28 Apr '11

Can any one take a look here? It is unlikely that is is caused by my commit "dbddbea75f68". It smells as an issue with Viewers created on subcommunicators. [dalcinl@trantor tutorials]$ cd $PETSC_DIR/src/ksp/ksp/examples/tutorials [dalcinl@trantor tutorials]$ make runex2_bjacobi_2 42a43,56 > [0]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c > [0]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c > [0]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c > [0]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c > [0]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c > [0]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c > [1]PETSC ERROR: PetscCommDestroy() line 243 in /home/devel/petsc/dev/src/sys/objects/tagm.c > [1]PETSC ERROR: PetscHeaderDestroy_Private() line 107 in /home/devel/petsc/dev/src/sys/objects/inherit.c > [1]PETSC ERROR: PetscViewerDestroy() line 109 in /home/devel/petsc/dev/src/sys/viewer/interface/view.c > [1]PETSC ERROR: PetscObjectDestroy() line 73 in /home/devel/petsc/dev/src/sys/objects/destroy.c > [1]PETSC ERROR: PetscObjectRegisterDestroyAll() line 215 in /home/devel/petsc/dev/src/sys/objects/destroy.c > [1]PETSC ERROR: PetscFinalize() line 1032 in /home/devel/petsc/dev/src/sys/objects/pinit.c > rank 0 in job 7851 trantor_56062 caused collective abort of all ranks > exit status of rank 0: return code 0 Possible problem with ex2_bjacobi_2, diffs above -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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