[petsc-dev] [petsc-maint #89809] 3D DMDAs in petsc-3.2
Ethan Coon
ecoon at lanl.gov
Tue Oct 11 11:22:02 CDT 2011
My fault, will get on it.
Ethan
On Sun, 2011-10-09 at 22:54 -0500, Barry Smith wrote:
> Jed,
>
> It appears your some of your many
>
> if (s_t >= x*y*z) {s_t = bases[n26] + (i-1)*x_t;} /* 2d case */
>
> things are breaking the communication with a stencil width of 2
>
> In src/dm/examples/tests/ex38.c in petsc-3.2
>
> barry-smiths-macbook-pro:tests barrysmith$ petscmpiexec -n 2 ./ex38
> Vector Object: 1 MPI processes
> type: seq
> 0
> 1
> 2
> 3
> 4
> 5
> 6
> 7
> 8
> 9
> 10
> 11
> 112
> 113
> 114
> 115
> 116
> 117
> 112
> 113
> 114
> 115
> 116
> 117
>
> the second layer of ghost points uses the first layer instead of getting the second layer.
>
> Since I don't understand your /* 2d case */ business I leave it to you to fix
>
> So either I still have a bug in my test code (always possible) or you've introduced your first bug into PETSc (seems unlikely),
>
>
> Barry
>
>
>
> On Oct 9, 2011, at 8:09 PM, Jed Brown wrote:
>
> > Ex48 uses periodic in y and z and it works.
> >
> > On Oct 9, 2011 8:08 PM, "Barry Smith" <bsmith at mcs.anl.gov> wrote:
> >
> > Ok 3.1-p8 also fails with the same problems. Likely periodic boundary conditions have never worked in 3d? Yikes this looks bad
> >
> > Barry
> >
> > On Oct 9, 2011, at 3:28 PM, Barry Smith wrote:
> >
> > >
> > > I have created a new test example in petsc-3.2 for 3D global to local with periodic boundary conditions and it fails rather completely so whomever introduced all the IXs, IXe stuff into DMSetUp_DA_3d() likely introduced some bugs, or the bugs have always been there and no one has tested it properly.
> > >
> > > For example (with periodicity indicated only in the x direction) one gets:
> > >
> > >
> > > barry-smiths-macbook-pro:tests barrysmith$ petscmpiexec -n 2 ./ex38 -da_view -stencil_width 1 | more
> > > Processor [0] M 2 N 3 P 4 m 1 n 1 p 2 w 1 s 1
> > > X range of indices: 0 2, Y range of indices: 0 3, Z range of indices: 0 2
> > > Processor [1] M 2 N 3 P 4 m 1 n 1 p 2 w 1 s 1
> > > X range of indices: 0 2, Y range of indices: 0 3, Z range of indices: 2 4
> > > Vector Object: 1 MPI processes
> > > type: seq
> > > 1
> > > 0
> > > 1
> > > 0
> > > 3
> > > 2
> > > 3
> > > 2
> > > 5
> > > 4
> > > 5
> > > 4
> > > 7
> > > 6
> > > 7
> > > 6
> > > 9
> > > 8
> > > 9
> > > 8
> > > 11
> > > 10
> > > 11
> > > 10
> > > -1
> > > 112
> > > 113
> > > -1
> > > -1
> > > 114
> > > 115
> > > -1
> > > -1
> > > 116
> > > 117
> > > -1
> > >
> > > so it is not properly handling the periodicity on the "ghost plane" brought over from the rank 1 process to the rank 0.
> > >
> > > Note this happens also with a stencil width of 1, so it is not just a question of not handling the stencil width correctly.
> > >
> > > Barry
> > >
> > >
> > > On Oct 9, 2011, at 1:32 PM, Richard Katz wrote:
> > >
> > >>
> > >> Here's how I set up the problem:
> > >>
> > >> ierr = DMDACreate3d(user->comm,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_NONE,
> > >> DMDA_STENCIL_BOX,p->Ni,p->Nj,p->Nk,1,1,PETSC_DECIDE,
> > >> (PetscInt)(sizeof(SolVel3D)/sizeof(PetscReal)),2,
> > >> PETSC_NULL,PETSC_NULL,PETSC_NULL,&user->dav);CHKERRQ(ierr);
> > >> ierr = DMCreateGlobalVector(user->dav,&user->v);CHKERRQ(ierr);
> > >> ierr = DMCreateGlobalVector(user->daa,&user->an);CHKERRQ(ierr);
> > >> ierr = VecDuplicate(user->v,&user->vo);CHKERRQ(ierr);
> > >> ierr = VecDuplicate(user->v,&user->vm);CHKERRQ(ierr);
> > >> ierr = VecDuplicate(user->v,&user->rv);CHKERRQ(ierr);
> > >> ierr = VecDuplicate(user->an,&user->ano);CHKERRQ(ierr);
> > >> ierr = SNESCreate(user->comm,&user->snes);CHKERRQ(ierr);
> > >> if (D2(p)) { ierr = SNESSetFunction(user->snes,user->rv,FormResidual_v2d,user);CHKERRQ(ierr); }
> > >> else { ierr = SNESSetFunction(user->snes,user->rv,FormResidual_v3d,user);CHKERRQ(ierr); }
> > >> ierr = DMGetColoring(user->dav,IS_COLORING_GLOBAL,MATAIJ,&iscoloring);
> > >> ierr = DMGetMatrix(user->dav,MATAIJ,&user->Jv);CHKERRQ(ierr);
> > >> ierr = MatFDColoringCreate(user->Jv,iscoloring,&user->mfdcv);
> > >> ierr = MatFDColoringSetFromOptions(user->mfdcv);CHKERRQ(ierr);
> > >> if (D2(p)) { ierr = MatFDColoringSetFunction(user->mfdcv,(PetscErrorCode(*)(void))FormResidual_v2d,user); }
> > >> else { ierr = MatFDColoringSetFunction(user->mfdcv,(PetscErrorCode(*)(void))FormResidual_v3d,user); }
> > >> ierr = SNESSetJacobian(user->snes,user->Jv,user->Jv,SNESDefaultComputeJacobianColor,user->mfdcv);
> > >> ierr = ISColoringDestroy(&iscoloring);
> > >> ierr = SNESSetOptionsPrefix(user->snes,"PV_");CHKERRQ(ierr);
> > >> ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);
> > >>
> > >>
> > >> D2(p) is a macro that returns 1 if the problem is 2D, and 0 if 3D.
> > >>
> > >> Rich
> > >>
> > >>
> > >> On 9 Oct 2011, at 19:30, Barry Smith wrote:
> > >>
> > >>>
> > >>> box stencil or star stencil?
> > >>>
> > >>>
> > >>> On Oct 9, 2011, at 1:26 PM, Richard Katz wrote:
> > >>>
> > >>>>
> > >>>> On 9 Oct 2011, at 19:24, Barry Smith wrote:
> > >>>>
> > >>>>>
> > >>>>> To clarify: With this build valgrind generates no messages at all?
> > >>>>
> > >>>> That's correct.
> > >>>>
> > >>>>
> > >>>> [magmox:test]$ $PETSC_DIR/bin/petscmpiexec -valgrind -n 2 ../porbandsim -nd 3 -alpha 2 -theta 45 -output_file test2
> > >>>> --94613-- run: /usr/bin/dsymutil "../porbandsim"
> > >>>> --94612-- run: /usr/bin/dsymutil "../porbandsim"
> > >>>> --------------porbandsim: Sun Oct 9 17:24:24 2011---------------
> > >>>> Processes: 2, DOFs/Process: 2800
> > >>>> #PETSc Option Table entries:
> > >>>> -PV_snes_converged_reason
> > >>>> -PV_snes_monitor
> > >>>> -alpha 2
> > >>>> -ksp_gmres_restart 150
> > >>>> -nd 3
> > >>>> -output_file test2
> > >>>> -snes_converged_reason
> > >>>> -snes_monitor
> > >>>> -theta 45
> > >>>> #End of PETSc Option Table entries
> > >>>> -----------------------------------------------------------------
> > >>>> PetscBag Object: ParameterBag params for porosity band simulation
> > >>>> takei = TRUE; Use Takei & Holztman (2009) viscosity (T/F)
> > >>>> hperm = FALSE; Use harmonic mean for computing permeability (T/F)
> > >>>> lambda = 27; Porosity-weakening exponent in shear viscosity, dim'less
> > >>>> R = 0.57735; Ratio compaction length to domain height, dim'less
> > >>>> sigma_sat = 1; Saturation stress-difference for anisotropy, dim'less
> > >>>> n = 3; Exponent in porosity--permeability relationship, dim'less
> > >>>> phi0 = 0.1; Initial porosity, dim'less
> > >>>> phi1 = 0.01; Amplitude of porosity perturbation, dim'less
> > >>>> theta = 45; Fixed anisotropy angle, degrees (-1234567 indicates dynamic)
> > >>>> alpha = 2; Fixed anisotropy magnitude, 0<=alpha<=2 (-1234567 indicates dynamic)
> > >>>> viscratio = 1.66667; Ratio of bulk to shear viscosity at phi=phi0, dim'less
> > >>>> nsig = 1; Exponent in stress--strain rate relationship, dim'less
> > >>>> init_harmonic = FALSE; Use harmonic perturbation as IC (T/F)
> > >>>> input_file = null; Name base for input porosity file
> > >>>> test = FALSE; Just load parameters and then exit
> > >>>> output_file = test2; Name base for output files
> > >>>> output_all = FALSE; Make output after each time-step (T/F)
> > >>>> output_err = TRUE; Make output after failed time-step (T/F)
> > >>>> output_aux = TRUE; Output auxilliary fields (T/F)
> > >>>> converged = TRUE; Indicates whether a time-step converged (NO SET)
> > >>>> nb = 2; Number of buffer rows at top and bottom of domain
> > >>>> ns = 1000000; Maximum number of time-steps
> > >>>> nits = 1; Number of Picard iterations
> > >>>> nplot = 0; Output counter
> > >>>> advect = 1; Advection scheme: 0=FV, 1=Fromm, 2=TVD
> > >>>> time = 0; Time at current step, dim'less
> > >>>> cfl = 0.5; Courant-Friedrichs-Lewy number, dim'less
> > >>>> tmax = 20; Maximimum simulated time, dim'less
> > >>>> tout = 0.05; Output interval, dim'less
> > >>>> nd = 3; Number of spatial dimensions, 2 or 3
> > >>>> ni = 20; Grid points in x-direction (shear-direction, periodic)
> > >>>> nj = 5; Grid points in y-direction (cross-direction, periodic)
> > >>>> nk = 14; Grid points in z-direction, incl buffer points
> > >>>> -------------------------END PARAM REPORT------------------------
> > >>>> Continuation in lambda for initial condition
> > >>>> 0 SNES Function norm 2.512586736188e+01
> > >>>> 1 SNES Function norm 2.149396609776e-03
> > >>>> 2 SNES Function norm 1.863405745330e-08
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 1.0 in 205.35 seconds
> > >>>> 0 SNES Function norm 1.874271649438e+00
> > >>>> 1 SNES Function norm 8.642606950729e-06
> > >>>> 2 SNES Function norm 7.636114324949e-11
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 2.0 in 206.47 seconds
> > >>>> 0 SNES Function norm 3.748572573117e+00
> > >>>> 1 SNES Function norm 1.823985563954e-05
> > >>>> 2 SNES Function norm 1.446658479082e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 4.0 in 207.02 seconds
> > >>>> 0 SNES Function norm 7.498313656718e+00
> > >>>> 1 SNES Function norm 3.949293531885e-05
> > >>>> 2 SNES Function norm 3.092503935042e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 8.0 in 207.44 seconds
> > >>>> 0 SNES Function norm 1.500973207738e+01
> > >>>> 1 SNES Function norm 8.256012403101e-05
> > >>>> 2 SNES Function norm 6.728525270322e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 16.0 in 207.38 seconds
> > >>>> 0 SNES Function norm 2.066862203903e+01
> > >>>> 1 SNES Function norm 6.201694512543e-05
> > >>>> 2 SNES Function norm 5.537777484572e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Solved with lambda = 27.0 in 207.32 seconds
> > >>>> Generating output file: "test2_0000"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.914413986104e+01
> > >>>> 1 SNES Function norm 7.835942994856e-05
> > >>>> 2 SNES Function norm 2.520454050827e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 2.038885321297e+01
> > >>>> 1 SNES Function norm 1.727646593582e-04
> > >>>> 2 SNES Function norm 1.325429214752e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.050 in 213.4 seconds
> > >>>> Generating output file: "test2_0001"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.592319862889e+01
> > >>>> 1 SNES Function norm 5.602653646480e-05
> > >>>> 2 SNES Function norm 2.453571869974e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 1.321599310609e+01
> > >>>> 1 SNES Function norm 1.261023473773e-04
> > >>>> 2 SNES Function norm 1.163959209038e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.100 in 212.6 seconds
> > >>>> Generating output file: "test2_0002"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.422948512067e+01
> > >>>> 1 SNES Function norm 4.242156538283e-05
> > >>>> 2 SNES Function norm 1.625303993154e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 9.675556760630e+00
> > >>>> 1 SNES Function norm 1.362209365650e-04
> > >>>> 2 SNES Function norm 1.223382062021e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.150 in 212.9 seconds
> > >>>> Generating output file: "test2_0003"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.307890574732e+01
> > >>>> 1 SNES Function norm 3.214708350215e-05
> > >>>> 2 SNES Function norm 1.093103013350e-10
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 7.636762082099e+00
> > >>>> 1 SNES Function norm 1.308928801753e-04
> > >>>> 2 SNES Function norm 1.143217709967e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.200 in 212.8 seconds
> > >>>> Generating output file: "test2_0004"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.216229064046e+01
> > >>>> 1 SNES Function norm 2.441284335468e-05
> > >>>> 2 SNES Function norm 7.517551623210e-11
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 6.371107649815e+00
> > >>>> 1 SNES Function norm 1.185031269819e-04
> > >>>> 2 SNES Function norm 1.095566218658e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.250 in 213.0 seconds
> > >>>> Generating output file: "test2_0005"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.136564194223e+01
> > >>>> 1 SNES Function norm 1.865453423897e-05
> > >>>> 2 SNES Function norm 5.239501925142e-11
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 5.520895480607e+00
> > >>>> 1 SNES Function norm 1.025932275448e-04
> > >>>> 2 SNES Function norm 1.071648118984e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.300 in 213.0 seconds
> > >>>> Generating output file: "test2_0006"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 1.064481900239e+01
> > >>>> 1 SNES Function norm 1.438574893573e-05
> > >>>> 2 SNES Function norm 3.643963189108e-11
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 4.905069034291e+00
> > >>>> 1 SNES Function norm 8.961489700096e-05
> > >>>> 2 SNES Function norm 1.008198626576e-09
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> Stepped to time t = 0.350 in 212.7 seconds
> > >>>> Generating output file: "test2_0007"
> > >>>> -----------------------------------------------------------------
> > >>>> 0 SNES Function norm 9.981300326125e+00
> > >>>> 1 SNES Function norm 1.120717450009e-05
> > >>>> 2 SNES Function norm 2.503394538611e-11
> > >>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>> 0 SNES Function norm 4.428377952757e+00
> > >>>> ^CCtrl-C caught... cleaning up processes
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>>
> > >>>>> Barry
> > >>>>>
> > >>>>> On Oct 9, 2011, at 12:19 PM, Richard Katz wrote:
> > >>>>>
> > >>>>>> Hi Barry,
> > >>>>>>
> > >>>>>> I have now run the code with
> > >>>>>>
> > >>>>>> configure_options = [
> > >>>>>> '--download-mpich=1',
> > >>>>>> '--with-cxx=0',
> > >>>>>> '--with-fortran=0',
> > >>>>>> 'PETSC_ARCH=debug_mpich',
> > >>>>>> ]
> > >>>>>>
> > >>>>>> and
> > >>>>>>
> > >>>>>> $PETSC_DIR/bin/petscmpiexec -valgrind -n 2 ../porbandsim -nd 3 -alpha 2 -theta 45 -output_file test2
> > >>>>>>
> > >>>>>> The memory error goes away.
> > >>>>>>
> > >>>>>> The error in the calculated solution does not go away.
> > >>>>>>
> > >>>>>> Thanks,
> > >>>>>> Rich
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On 9 Oct 2011, at 17:01, Barry Smith wrote:
> > >>>>>>
> > >>>>>>>
> > >>>>>>> Rich,
> > >>>>>>>
> > >>>>>>> Could you do an identical run (to the valgrind run you made below) but using another PETSC_ARCH that uses --download-mpich
> > >>>>>>>
> > >>>>>>> I am suspecting openmpi because it is a bad read of something INSIDE OpenMPI that was just outside the range of memory allocated BY OpenMPI, it is hard to see how PETSc could induce this particular memory problem.
> > >>>>>>>
> > >>>>>>> Of course, it is also possible there are two bugs, one in OpenMPI and another in PETSc related to the DMDA.
> > >>>>>>>
> > >>>>>>> Barry
> > >>>>>>>
> > >>>>>>> On Oct 9, 2011, at 10:46 AM, Richard Katz wrote:
> > >>>>>>>
> > >>>>>>>> Hi all,
> > >>>>>>>>
> > >>>>>>>> I'm beginning to wonder if there is a bug in the filling of ghost-points for 3-dimensional DMDAs under petsc-3.2. I am working on a finite-volume code that uses a DMDACreate3d() to create several DMDAs, all with a stencil width of two.
> > >>>>>>>>
> > >>>>>>>> * The 2-dimensional mode for the same code runs without problems in parallel.
> > >>>>>>>>
> > >>>>>>>> * The initial SNES solve converges well, with no seg-faults, but when there are processor bounds in the k-direction, the solution is clearly incorrect at/near the boundaries.
> > >>>>>>>>
> > >>>>>>>> * When I run the same code in serial, or in parallel but with no processor boundaries in the k-direction, it works without problems.
> > >>>>>>>>
> > >>>>>>>> * When I run the code with processor boundaries in the k-direction, but zeroing-out the bits of the stencil that are at stencil-radius of 2, the processor-boundary errors don't appear.
> > >>>>>>>>
> > >>>>>>>> * Extending the stencil width to 3 has no effect on the problem.
> > >>>>>>>>
> > >>>>>>>> * There does seem to be a memory-corruption problem, but I'm not sure where it comes from, because it appears very high in the stack. The following is valgrind output for a run with 2 processors. The processor boundary is in the k-direction. This memory error ONLY appears on the first SNES solve, but not on any of the following ones. Also, the memory error seems to be associated with OpenMPI; it doesn't occur when running with MPICH2
> > >>>>>>>>
> > >>>>>>>> [magmox:test]$ $PETSC_DIR/bin/petscmpiexec -valgrind -n 2 ../porbandsim -malloc off -nd 3 -alpha 2 -theta 45 -output_file test2
> > >>>>>>>>
> > >>>>>>>> [...]
> > >>>>>>>>
> > >>>>>>>> Continuation in lambda for initial condition
> > >>>>>>>> 0 SNES Function norm 2.512586736188e+01
> > >>>>>>>> 1 SNES Function norm 2.149396609776e-03
> > >>>>>>>> ==4576== Invalid read of size 8
> > >>>>>>>> ==4576== at 0x7FFFFFE00BAC: ???
> > >>>>>>>> ==4576== by 0x101A34213: ompi_convertor_pack (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4576== by 0x10858909E: mca_pml_ob1_send_request_start_copy (in /usr/lib/openmpi/mca_pml_ob1.so)
> > >>>>>>>> ==4576== by 0x1085840D2: mca_pml_ob1_isend (in /usr/lib/openmpi/mca_pml_ob1.so)
> > >>>>>>>> ==4576== by 0x1085D11C3: ompi_coll_tuned_allreduce_intra_recursivedoubling (in /usr/lib/openmpi/mca_coll_tuned.so)
> > >>>>>>>> ==4576== by 0x101A4419B: MPI_Allreduce (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4576== by 0x1001D3F3E: VecMDot_MPI (pvec2.c:20)
> > >>>>>>>> ==4576== by 0x100204669: VecMDot (rvector.c:1144)
> > >>>>>>>> ==4576== by 0x10097E28B: KSPGMRESClassicalGramSchmidtOrthogonalization (borthog2.c:66)
> > >>>>>>>> ==4576== by 0x100975B33: GMREScycle (gmres.c:159)
> > >>>>>>>> ==4576== by 0x10097656E: KSPSolve_GMRES (gmres.c:231)
> > >>>>>>>> ==4576== by 0x1009A8606: KSPSolve (itfunc.c:423)
> > >>>>>>>> ==4576== by 0x100A0271A: SNES_KSPSolve (snes.c:3396)
> > >>>>>>>> ==4576== by 0x100A17F79: SNESSolve_LS (ls.c:190)
> > >>>>>>>> ==4576== by 0x1009FB635: SNESSolve (snes.c:2676)
> > >>>>>>>> ==4576== by 0x100008104: InitSolveElliptic (initialize.c:216)
> > >>>>>>>> ==4576== by 0x10000538A: FormInitialCondition (initialize.c:31)
> > >>>>>>>> ==4576== by 0x100001410: main (porbandsim.c:28)
> > >>>>>>>> ==4576== Address 0x10289f778 is 0 bytes after a block of size 136 alloc'd
> > >>>>>>>> ==4576== at 0x1010B05BF: malloc (vg_replace_malloc.c:266)
> > >>>>>>>> ==4576== by 0x1085D0F98: ompi_coll_tuned_allreduce_intra_recursivedoubling (in /usr/lib/openmpi/mca_coll_tuned.so)
> > >>>>>>>> ==4576== by 0x101A4419B: MPI_Allreduce (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4576== by 0x1001D3F3E: VecMDot_MPI (pvec2.c:20)
> > >>>>>>>> ==4576== by 0x100204669: VecMDot (rvector.c:1144)
> > >>>>>>>> ==4576== by 0x10097E28B: KSPGMRESClassicalGramSchmidtOrthogonalization (borthog2.c:66)
> > >>>>>>>> ==4576== by 0x100975B33: GMREScycle (gmres.c:159)
> > >>>>>>>> ==4576== by 0x10097656E: KSPSolve_GMRES (gmres.c:231)
> > >>>>>>>> ==4576== by 0x1009A8606: KSPSolve (itfunc.c:423)
> > >>>>>>>> ==4576== by 0x100A0271A: SNES_KSPSolve (snes.c:3396)
> > >>>>>>>> ==4576== by 0x100A17F79: SNESSolve_LS (ls.c:190)
> > >>>>>>>> ==4576== by 0x1009FB635: SNESSolve (snes.c:2676)
> > >>>>>>>> ==4576== by 0x100008104: InitSolveElliptic (initialize.c:216)
> > >>>>>>>> ==4576== by 0x10000538A: FormInitialCondition (initialize.c:31)
> > >>>>>>>> ==4576== by 0x100001410: main (porbandsim.c:28)
> > >>>>>>>> ==4576==
> > >>>>>>>> ==4577== Invalid read of size 8
> > >>>>>>>> ==4577== at 0x7FFFFFE00BAC: ???
> > >>>>>>>> ==4577== by 0x101A34213: ompi_convertor_pack (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4577== by 0x10858909E: mca_pml_ob1_send_request_start_copy (in /usr/lib/openmpi/mca_pml_ob1.so)
> > >>>>>>>> ==4577== by 0x1085840D2: mca_pml_ob1_isend (in /usr/lib/openmpi/mca_pml_ob1.so)
> > >>>>>>>> ==4577== by 0x1085D11C3: ompi_coll_tuned_allreduce_intra_recursivedoubling (in /usr/lib/openmpi/mca_coll_tuned.so)
> > >>>>>>>> ==4577== by 0x101A4419B: MPI_Allreduce (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4577== by 0x1001D3F3E: VecMDot_MPI (pvec2.c:20)
> > >>>>>>>> ==4577== by 0x100204669: VecMDot (rvector.c:1144)
> > >>>>>>>> ==4577== by 0x10097E28B: KSPGMRESClassicalGramSchmidtOrthogonalization (borthog2.c:66)
> > >>>>>>>> ==4577== by 0x100975B33: GMREScycle (gmres.c:159)
> > >>>>>>>> ==4577== by 0x10097656E: KSPSolve_GMRES (gmres.c:231)
> > >>>>>>>> ==4577== by 0x1009A8606: KSPSolve (itfunc.c:423)
> > >>>>>>>> ==4577== by 0x100A0271A: SNES_KSPSolve (snes.c:3396)
> > >>>>>>>> ==4577== by 0x100A17F79: SNESSolve_LS (ls.c:190)
> > >>>>>>>> ==4577== by 0x1009FB635: SNESSolve (snes.c:2676)
> > >>>>>>>> ==4577== by 0x100008104: InitSolveElliptic (initialize.c:216)
> > >>>>>>>> ==4577== by 0x10000538A: FormInitialCondition (initialize.c:31)
> > >>>>>>>> ==4577== by 0x100001410: main (porbandsim.c:28)
> > >>>>>>>> ==4577== Address 0x10289f778 is 0 bytes after a block of size 136 alloc'd
> > >>>>>>>> ==4577== at 0x1010B05BF: malloc (vg_replace_malloc.c:266)
> > >>>>>>>> ==4577== by 0x1085D0F98: ompi_coll_tuned_allreduce_intra_recursivedoubling (in /usr/lib/openmpi/mca_coll_tuned.so)
> > >>>>>>>> ==4577== by 0x101A4419B: MPI_Allreduce (in /usr/lib/libmpi.0.dylib)
> > >>>>>>>> ==4577== by 0x1001D3F3E: VecMDot_MPI (pvec2.c:20)
> > >>>>>>>> ==4577== by 0x100204669: VecMDot (rvector.c:1144)
> > >>>>>>>> ==4577== by 0x10097E28B: KSPGMRESClassicalGramSchmidtOrthogonalization (borthog2.c:66)
> > >>>>>>>> ==4577== by 0x100975B33: GMREScycle (gmres.c:159)
> > >>>>>>>> ==4577== by 0x10097656E: KSPSolve_GMRES (gmres.c:231)
> > >>>>>>>> ==4577== by 0x1009A8606: KSPSolve (itfunc.c:423)
> > >>>>>>>> ==4577== by 0x100A0271A: SNES_KSPSolve (snes.c:3396)
> > >>>>>>>> ==4577== by 0x100A17F79: SNESSolve_LS (ls.c:190)
> > >>>>>>>> ==4577== by 0x1009FB635: SNESSolve (snes.c:2676)
> > >>>>>>>> ==4577== by 0x100008104: InitSolveElliptic (initialize.c:216)
> > >>>>>>>> ==4577== by 0x10000538A: FormInitialCondition (initialize.c:31)
> > >>>>>>>> ==4577== by 0x100001410: main (porbandsim.c:28)
> > >>>>>>>> ==4577==
> > >>>>>>>> 2 SNES Function norm 1.863405745330e-08
> > >>>>>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>>>>>> 0 SNES Function norm 1.874271649438e+00
> > >>>>>>>> 1 SNES Function norm 8.642606950729e-06
> > >>>>>>>> 2 SNES Function norm 7.636114324949e-11
> > >>>>>>>> Nonlinear solve converged due to CONVERGED_FNORM_ABS
> > >>>>>>>>
> > >>>>>>>> [...]
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> Any suggestions about how to debug this? How well-tested are the parallel, 3D DMDA routines? Should I do some testing on a PETSc example code?
> > >>>>>>>>
> > >>>>>>>> I am running petsc-3.2 with
> > >>>>>>>>
> > >>>>>>>> changeset: 20338:fbd00cf1070e
> > >>>>>>>> tag: tip
> > >>>>>>>> parent: 20337:589176156279
> > >>>>>>>> parent: 20336:7abcced43e69
> > >>>>>>>> user: Barry Smith <bsmith at mcs.anl.gov>
> > >>>>>>>> date: Tue Oct 04 16:45:00 2011 -0500
> > >>>>>>>> summary: commit after merge
> > >>>>>>>>
> > >>>>>>>> and
> > >>>>>>>>
> > >>>>>>>> configure_options = [
> > >>>>>>>> '--download-fftw=true',
> > >>>>>>>> '--with-cxx=0',
> > >>>>>>>> '--with-debugging=1',
> > >>>>>>>> '--with-fortran=0',
> > >>>>>>>> '--with-mpi-dir=/usr',
> > >>>>>>>> 'PETSC_ARCH=debug',
> > >>>>>>>> ]
> > >>>>>>>>
> > >>>>>>>> or
> > >>>>>>>>
> > >>>>>>>> configure_options = [
> > >>>>>>>> '--download-blacs',
> > >>>>>>>> '--download-fftw=true',
> > >>>>>>>> '--download-mpich=yes',
> > >>>>>>>> '--download-mumps=yes',
> > >>>>>>>> '--download-parmetis',
> > >>>>>>>> '--download-scalapack',
> > >>>>>>>> '--with-cxx=0',
> > >>>>>>>> '--with-debugging=0',
> > >>>>>>>> 'PETSC_ARCH=optimize_mumps',
> > >>>>>>>> ]
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> Thanks,
> > >>>>>>>> Rich
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> ________________________________
> > >>>>>> Richard Foa Katz
> > >>>>>> Dept Earth Sciences, Univ Oxford
> > >>>>>> http://foalab.earth.ox.ac.uk
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>> ________________________________
> > >>>> Richard Foa Katz
> > >>>> Dept Earth Sciences, Univ Oxford
> > >>>> http://foalab.earth.ox.ac.uk
> > >>>>
> > >>>
> > >>
> > >> ________________________________
> > >> Richard Foa Katz
> > >> Dept Earth Sciences, Univ Oxford
> > >> http://foalab.earth.ox.ac.uk
> > >>
> > >
> >
>
--
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
------------------------------------
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