[petsc-users] Jacobian free in SNES

Konstantinos Kontzialis ckontzialis at lycos.com
Sat Nov 5 12:07:55 CDT 2011


On 11/05/2011 05:45 PM, petsc-users-request at mcs.anl.gov wrote:
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> Today's Topics:
>
>     1. Re:  Superlu based ILUT report Zero pivot (Xiaoye S. Li)
>     2. Re:  Is it possible to add KLU to petsc as external solver
>        package? (Jed Brown)
>     3. Re:  Jacobian free in SNES (Jed Brown)
>     4.  fixed point interations (Dominik Szczerba)
>     5. Re:  valgrind error only with MUMPS (Dominik Szczerba)
>     6. Re:  fixed point interations (Matthew Knepley)
>     7. Re:  fixed point interations (Jed Brown)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 4 Nov 2011 11:27:29 -0700
> From: "Xiaoye S. Li"<xsli at lbl.gov>
> Subject: Re: [petsc-users] Superlu based ILUT report Zero pivot
> To: PETSc users list<petsc-users at mcs.anl.gov>, gdiso at ustc.edu
> Message-ID:
> 	<CAFvbobW_GC5RAAKt+1mq6T9Knb5h31i7bZMdngu_RXBgXdajrw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> The default settings in ILUTP of superlu is "conservative", probably
> with less dropping than people want.   The 2 most relevant parameters
> to control this are:
>      ILU_DropTol :  (default 1e-4),  you can try to set it a larger, e.g., 0.01
>      ILU_FillFactor : (default 10),  this allows about a factor of 10
> growth in the L&  U factors.
>                                 You can set it lower, e.g., 5 or smaller.
>
> I am a little surprised that you see Zero Pivot (e.g., at column 74).
> Since the code does partial pivoting, always tries to pick up the
> largest magnitude entry in the current column to pivot. "Zero pivot at
> column 74" means at this step column 74 becomes entirely empty.
> Perhaps from numerical cancellation, Or the matrix is numerically
> singular?
>
> The default setting also uses MC64 to permute large entry to the
> diagonal during preprocessing.  (Hong, can you please confirm
> LargeDiag is set, right?)
>
> If you can send me the matrix in coordinate format (i.e., triplet for
> each nonzero), I will be happy to try it.
>
> Sherry Li
>
>
> On Wed, Nov 2, 2011 at 9:02 AM, Hong Zhang<hzhang at mcs.anl.gov>  wrote:
>> Gong :
>>
>>> I tried ASM + Superlu ILUT for my semicondcutor simulation code.
>>> For most of the problems, the ILUT preconditioner is very strong.
>>> Fewer KSP iterations are needed to get linear solver convergence compared with default ILU(0) preconditioner.
>>> However, ILUT is a bit slow with its default parameters.
>>> And sometimes it fault with
>>> Fatal Error:Zero pivot in row 74 at line 186 in superlu.c
>> We do not have much experience with Superlu ILUT.
>> What you can do is try various options provided by superlu
>> ?-mat_superlu_ilu_droptol<0.0001>: ILU_DropTol (None)
>> ?-mat_superlu_ilu_filltol<0.01>: ILU_FillTol (None)
>> ?-mat_superlu_ilu_fillfactor<10>: ILU_FillFactor (None)
>> ?-mat_superlu_ilu_droprull<9>: ILU_DropRule (None)
>> ?-mat_superlu_ilu_norm<2>: ILU_Norm (None)
>> ?-mat_superlu_ilu_milu<0>: ILU_MILU (None)
>>
>>> Any suggestion to set some parameters to make it more rubost (and fast)?
>> I would also test '-sub_pc_type lu' which might be more efficient than ilu
>> if memory is not an issue.
>> Mumps sequential LU often outperforms other sequential lu.
>> You can 1) install mumps (needs scalapack, blacs and F90 compiler), then
>> 2) run with '-sub_pc_type lu -pc_factor_mat_solver_package mumps'.
>>
>> Hong
>>> Gong Ding
>>>
>>>
>>>
>>>
>>>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 4 Nov 2011 22:39:34 -0600
> From: Jed Brown<jedbrown at mcs.anl.gov>
> Subject: Re: [petsc-users] Is it possible to add KLU to petsc as
> 	external solver package?
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> 	<CAM9tzS=jWQ9M=oa3U49srRXe9t-mzeX5=TOryZccFvtoeAezYg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 2011/11/4 Gong Ding<gdiso at ustc.edu>
>
>> KLU developed by Prof Tim Davis is suitable for solve circuit sparse
>> matrix.
>> And it shares some component with UMFPACK.
>>
> It's certainly possible, it just takes time. Do you know why it is a
> separate package from Umfpack? Doesn't it do the same thing on a matrix of
> the same format, just using a different algorithm?
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 4 Nov 2011 23:04:39 -0600
> From: Jed Brown<jedbrown at mcs.anl.gov>
> Subject: Re: [petsc-users] Jacobian free in SNES
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> 	<CAM9tzSkPV+SADixqT3NK_DM2_X=93v0BnXKAZUMmuWWaJRKJ-Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, Nov 4, 2011 at 03:27, Konstantinos Kontzialis<ckontzialis at lycos.com
>> wrote:
>> I solve the NS equations with the discontinuous galerkin method. The
>> system's residual before going to petsc is the following:
>>
>> M udot+R(u) = 0                         (1)
>>
>> R(u) is the part of the residual coming from the spatially discretized
>> terms. I need to say that the explicit version of my code runs very well.
>>
>> But, I want to implement an implicit method for time marching using first
>> the backward euler scheme. After linearization I get the following form:
>>
>> M/dt u^{n+1} + dR/du (u^{n+1}-u^{n}) = M/dt u^{n} -R(u^{n})  (2)
>>
> Why not just have your SNESFormFunction compute:
>
> G(u^{n+1}) = M (u^{n+1} - u^n) / dt + R(u^{n+1}) = 0
>
> and then J = dG/du^{n+1}?
>
> An alternative which I recommend is to use TSSetIFunction() and
> TSSetIJacobian(). Then you can run backward Euler with -ts_type beuler, but
> you can also run lots of other methods, e.g. -ts_type rosw to use
> Rosenbrock-W methods with adaptive error control (these also tolerate
> approximations to the Jacobian, such as dropping the non-stiff convective
> terms).
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>
> ------------------------------
>
> Message: 4
> Date: Sat, 5 Nov 2011 14:23:58 +0100
> From: Dominik Szczerba<dominik at itis.ethz.ch>
> Subject: [petsc-users] fixed point interations
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> 	<CALm7otpTDROmps+5Te8Km9OUXDLHupiPy6d2cz88vM6D9Y-RCQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am a newcomer to Petsc non-linear capabilities, so far implementing
> such things myself, only delegating linear solves to Petsc.
>
> I want to start small by porting a very simple code using fixed point
> iterations as follows: A(x)x = b(x) is approximated as A(x0)x = b(x0),
> then solved by KSP for x, then x0 is updated to x, then repeat until
> convergence.
>
> In the documentation chapter 5 I see all sorts of sophisticated Newton
> type methods, requiring computation of the Jacobian. Is the above
> defined simple method still accessible somehow in Petsc or such
> triviality can only be done by hand? Which one from the existing
> nonlinear solvers would be a closest match both in simplicity and
> robustness (even if slow performance)?
>
> Regards,
> Dominik
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 5 Nov 2011 14:52:23 +0100
> From: Dominik Szczerba<dominik at itis.ethz.ch>
> Subject: Re: [petsc-users] valgrind error only with MUMPS
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> 	<CALm7otrnCBqrPcT=kE+=F0B2xV0CC=DGx5U19LvTik_q+f+FHw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
>>> there are no errors reported. Problem with MUMPS?
>> ? Yes. Looks like they are being sloppy. Whether this is an actual error condition or irrelevant only they would know. Report it to them.
>>
>> ? Barry
> Reported. They responded that the valgrind error is harmless and will be fixed.
>
> Dominik
>
>>> ==19601== Syscall param writev(vector[...]) points to uninitialised byte(s)
>>> ==19601== ? ?at 0x6791F59: writev (writev.c:56)
>>> ==19601== ? ?by 0x552CD8: MPIDU_Sock_writev (sock_immed.i:610)
>>> ==19601== ? ?by 0x5550DB: MPIDI_CH3_iSendv (ch3_isendv.c:84)
>>> ==19601== ? ?by 0x53B83A: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:541)
>>> ==19601== ? ?by 0x53DA03: MPID_Isend (mpid_isend.c:130)
>>> ==19601== ? ?by 0x1440C71: PMPI_Isend (isend.c:124)
>>> ==19601== ? ?by 0x1453DED: MPI_ISEND (isendf.c:190)
>>> ==19601== ? ?by 0x124069F: __dmumps_comm_buffer_MOD_dmumps_62
>>> (dmumps_comm_buffer.F:567)
>>> ==19601== ? ?by 0x12C1B4C: dmumps_242_ (dmumps_part2.F:739)
>>> ==19601== ? ?by 0x120C987: dmumps_249_ (dmumps_part8.F:6541)
>>> ==19601== ? ?by 0x120599F: dmumps_245_ (dmumps_part8.F:3885)
>>> ==19601== ? ?by 0x1229BCF: dmumps_301_ (dmumps_part8.F:2120)
>>> ==19601== ? ?by 0x128D272: dmumps_ (dmumps_part1.F:665)
>>> ==19601== ? ?by 0x1178753: dmumps_f77_ (dmumps_part3.F:6651)
>>> ==19601== ? ?by 0x1151A79: dmumps_c (mumps_c.c:422)
>>> ==19601== ? ?by 0x791075: MatSolve_MUMPS (mumps.c:547)
>>> ==19601== ? ?by 0x73ABA0: MatSolve (matrix.c:3108)
>>> ==19601== ? ?by 0x7FC5B9: PCApply_LU (lu.c:204)
>>> ==19601== ? ?by 0xD95AAB: PCApply (precon.c:383)
>>> ==19601== ? ?by 0xD98A70: PCApplyBAorAB (precon.c:609)
>>> ==19601== ?Address 0x86df168 is 8 bytes inside a block of size 144 alloc'd
>>> ==19601== ? ?at 0x4C28F9F: malloc (vg_replace_malloc.c:236)
>>> ==19601== ? ?by 0x124235E: __dmumps_comm_buffer_MOD_dmumps_2
>>> (dmumps_comm_buffer.F:175)
>>> ==19601== ? ?by 0x12426E7: __dmumps_comm_buffer_MOD_dmumps_55
>>> (dmumps_comm_buffer.F:123)
>>> ==19601== ? ?by 0x121F28B: dmumps_301_ (dmumps_part8.F:989)
>>> ==19601== ? ?by 0x128D272: dmumps_ (dmumps_part1.F:665)
>>> ==19601== ? ?by 0x1178753: dmumps_f77_ (dmumps_part3.F:6651)
>>> ==19601== ? ?by 0x1151A79: dmumps_c (mumps_c.c:422)
>>> ==19601== ? ?by 0x791075: MatSolve_MUMPS (mumps.c:547)
>>> ==19601== ? ?by 0x73ABA0: MatSolve (matrix.c:3108)
>>> ==19601== ? ?by 0x7FC5B9: PCApply_LU (lu.c:204)
>>> ==19601== ? ?by 0xD95AAB: PCApply (precon.c:383)
>>> ==19601== ? ?by 0xD98A70: PCApplyBAorAB (precon.c:609)
>>> ==19601== ? ?by 0x8D817F: KSPSolve_BCGS (bcgs.c:79)
>>> ==19601== ? ?by 0x86B189: KSPSolve (itfunc.c:423)
>>> ==19601== ? ?by 0x56013D: PetscLinearSystem::Solve() (PetscLinearSystem.cxx:221)
>>> ==19601== ? ?by 0x4E34F6: SolidSolver::Solve() (SolidSolver.cxx:1153)
>>> ==19601== ? ?by 0x4EFF56: main (SolidSolverMain.cxx:684)
>
> ------------------------------
>
> Message: 6
> Date: Sat, 5 Nov 2011 14:06:02 +0000
> From: Matthew Knepley<knepley at gmail.com>
> Subject: Re: [petsc-users] fixed point interations
> To: PETSc users list<petsc-users at mcs.anl.gov>
> Message-ID:
> 	<CAMYG4Gnpci4wM0OiFJPqTc9RLA_KxohG6sbO8iYzOrF8x=AajA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Sat, Nov 5, 2011 at 1:23 PM, Dominik Szczerba<dominik at itis.ethz.ch>wrote:
>
>> I am a newcomer to Petsc non-linear capabilities, so far implementing
>> such things myself, only delegating linear solves to Petsc.
>>
>> I want to start small by porting a very simple code using fixed point
>> iterations as follows: A(x)x = b(x) is approximated as A(x0)x = b(x0),
>> then solved by KSP for x, then x0 is updated to x, then repeat until
>> convergence.
>>
>> In the documentation chapter 5 I see all sorts of sophisticated Newton
>> type methods, requiring computation of the Jacobian. Is the above
>> defined simple method still accessible somehow in Petsc or such
>> triviality can only be done by hand? Which one from the existing
>> nonlinear solvers would be a closest match both in simplicity and
>> robustness (even if slow performance)?
>>
> You want -snes_type nrichardson. All you need is to define the residual.
>
>     Matt
>
>
>> Regards,
>> Dominik
>>
>
>
Dear all,

Following the answer I got,I coded the following:

ierr = TSCreate(sys.comm,&sys.ts);
		CHKERRQ(ierr);

		ierr = TSSetProblemType(sys.ts, TS_NONLINEAR);
		CHKERRQ(ierr);

		ierr = TSSetIFunction(sys.ts, base_residual_implicit,&sys);
		CHKERRQ(ierr);

		ISColoring iscoloring;
		MatFDColoring fdcoloring;

		ierr = jacobian_diff_numerical(sys,&sys.P);
		CHKERRQ(ierr);

		ierr = MatGetColoring(sys.P, MATCOLORING_SL,&iscoloring);
		CHKERRQ(ierr);

		ierr = MatFDColoringCreate(sys.P, iscoloring,&fdcoloring);
		CHKERRQ(ierr);

		ierr = MatFDColoringSetFunction(fdcoloring, base_residual_implicit,
				&sys);
		CHKERRQ(ierr);

		ierr = TSSetIJacobian(sys.ts, sys.P, sys.P, TS, fdcoloring);
		CHKERRQ(ierr);

		ierr = TSSetInitialTimeStep(sys.ts, sys.con->tm, sys.con->dt);
		CHKERRQ(ierr);

		ierr = TSSetSolution(sys.ts, sys.gsv);
		CHKERRQ(ierr);

		ierr = TSSetDuration(sys.ts, 100e+6, sys.con->etime);
		CHKERRQ(ierr);

		ierr = TSSetFromOptions(sys.ts);
		CHKERRQ(ierr);

		ierr = TSSetUp(sys.ts);
		CHKERRQ(ierr);

		ierr = TSGetSNES(sys.ts,&sys.snes);
		CHKERRQ(ierr);

		ierr = MatCreateSNESMF(sys.snes,&sys.J);
		CHKERRQ(ierr);

		ierr = MatMFFDSetFromOptions(sys.J);
		CHKERRQ(ierr);

		ierr = SNESSetJacobian(sys.snes, sys.J, sys.P,
				SNESDefaultComputeJacobianColor, fdcoloring);
		CHKERRQ(ierr);

		ierr = TSView(sys.ts, PETSC_VIEWER_STDOUT_WORLD);
		CHKERRQ(ierr);

		i = 10000;
		ierr = TSStep(sys.ts,&i,&sys.con->etime);
		CHKERRQ(ierr);


I run with :

mpiexec -n 8 valgrind ./hoac cylinder -llf_flux -n_out 5 -end_time 10000.0 -ts_type beuler -pc_type asm -ksp_right_pc -sub_pc_type ilu -sub_pc_factor_mat_ordering_type rcm 1.0e-8 -gl -sub_pc_factor_levels 2 -dt 2.0e-1 -snes_monitor -snes_stol 1.0e-50 -snes_ksp_ew -snes_ls_maxstep 10.0 -snes_stol 1.0e-50 -snes_max_linear_solve_fail 50 -snes_max_fail 50 -ksp_monitor_true_residual


but I get the following:


**********************************************************************
   METIS 4.0.3 Copyright 1998, Regents of the University of Minnesota

Graph Information ---------------------------------------------------
   Name: mesh.graph, #Vertices: 400, #Edges: 780, #Parts: 8

Recursive Partitioning... -------------------------------------------
   8-way Edge-Cut:     102, Balance:  1.00

Timing Information --------------------------------------------------
   I/O:                     0.000
   Partitioning:            0.000   (PMETIS time)
   Total:                   0.000
**********************************************************************


Approximation order = 2
# DOF = 13680
# nodes in mesh = 400
# elements in mesh = 380
Euler solution
Using LLF flux


   0 KSP preconditioned resid norm 2.209663952405e+02 true resid norm 
2.209663952405e+02 ||Ae||/||Ax|| 1.000000000000e+00
   1 KSP preconditioned resid norm 6.104452938496e-14 true resid norm 
7.083522209975e-14 ||Ae||/||Ax|| 3.205701121324e-16
TS Object:
   type: beuler
   maximum steps=100000000
   maximum time=10000
   total number of nonlinear solver iterations=0
   total number of linear solver iterations=0
   SNES Object:
     type: ls
       line search variant: SNESLineSearchCubic
       alpha=0.0001, maxstep=10, minlambda=1e-12
     maximum iterations=50, maximum function evaluations=10000
     tolerances: relative=1e-08, absolute=1e-50, solution=1e-50
     total number of linear solver iterations=0
     total number of function evaluations=0
     Eisenstat-Walker computation of KSP relative tolerance (version 2)
       rtol_0=0.3, rtol_max=0.9, threshold=0.1
       gamma=1, alpha=1.61803, alpha2=1.61803
     KSP Object:
       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
       right preconditioning
       using PRECONDITIONED norm type for convergence test
     PC Object:
       type: asm
         Additive Schwarz: total subdomain blocks not yet set, amount of 
overlap = 1
         Additive Schwarz: restriction/interpolation type - RESTRICT
       linear system matrix = precond matrix:
       Matrix Object:
         type=mpibaij, rows=13680, cols=13680
         total: nonzeros=602640, allocated nonzeros=246960
             block size is 9
[0]PETSC ERROR: --------------------- Error Message 
------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer!
[0]PETSC ERROR: Null Object: Parameter # 1!
[0]PETSC ERROR: 
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 
13:37:48 CDT 2011
[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: ./hoac on a linux-gnu named PlusSodaL by kontzialis Sat 
Nov  5 19:02:12 2011
[0]PETSC ERROR: Libraries linked from 
/home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
[0]PETSC ERROR: Configure run at Tue Sep 27 13:09:04 2011
[0]PETSC ERROR: Configure options --with-debugging=1 --with-shared=1 
--with-shared-libraries --with-large-file-io=1 --with-precision=double 
--with-blacs=1 --download-blacs=yes --download-f-blas-lapack=yes 
--with-plapack=1 --download-plapack=yes --with-scalapack=1 
--download-scalapack=yes --with-superlu=1 --download-superlu=yes 
--with-superlu_dist=1 --download-superlu_dist=yes --with-ml=1 
--download-ml=yes --with-umfpack=1 --download-umfpack=yes 
--with-sundials=1 --download-sundials=1 --with-parmetis=1 
--download-parmetis=1 --with-hypre=1 --download-hypre=1 
--with-mpi-dir=/usr/lib/mpich2/bin
[0]PETSC ERROR: 
------------------------------------------------------------------------
[0]PETSC ERROR: MatMult() line 1878 in src/mat/interface/matrix.c
[3]PETSC ERROR: [5]PETSC ERROR: [4]PETSC ERROR: [1]PETSC ERROR: [2]PETSC 
ERROR: [7]PETSC ERROR: [6]PETSC ERROR: [0]PETSC ERROR: 
TSComputeRHSFunction() line 309 in src/ts/interface/ts.c
[0]PETSC ERROR: TSBEulerFunction() line 222 in 
src/ts/impls/implicit/beuler/beuler.c
--------------------- Error Message ------------------------------------
--------------------- Error Message ------------------------------------
[0]PETSC ERROR: --------------------- Error Message 
------------------------------------
--------------------- Error Message ------------------------------------
SNESComputeFunction() line 1109 in src/snes/interface/snes.c
--------------------- Error Message ------------------------------------
--------------------- Error Message ------------------------------------
[0]PETSC ERROR: SNESSolve_LS() line 159 in src/snes/impls/ls/ls.c
[0]PETSC ERROR: SNESSolve() line 2255 in src/snes/interface/snes.c
[3]PETSC ERROR: Null argument, when expecting valid pointer!
[1]PETSC ERROR: [4]PETSC ERROR: [5]PETSC ERROR: Null argument, when 
expecting valid pointer!
Null argument, when expecting valid pointer!
Null argument, when expecting valid pointer!
[0]PETSC ERROR: [3]PETSC ERROR: Null Object: Parameter # 1!
[1]PETSC ERROR: TSStep_BEuler_Nonlinear() line 176 in 
src/ts/impls/implicit/beuler/beuler.c
Null Object: Parameter # 1!
[4]PETSC ERROR: [2]PETSC ERROR: [5]PETSC ERROR: [7]PETSC ERROR: Null 
Object: Parameter # 1!
Null Object: Parameter # 1!
Null argument, when expecting valid pointer!
Null argument, when expecting valid pointer!
[3]PETSC ERROR: [1]PETSC ERROR: 
------------------------------------------------------------------------
------------------------------------------------------------------------
[4]PETSC ERROR: 
------------------------------------------------------------------------
[5]PETSC ERROR: 
------------------------------------------------------------------------
[7]PETSC ERROR: [3]PETSC ERROR: [1]PETSC ERROR: Null Object: Parameter # 1!
[2]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 
13:37:48 CDT 2011
Null Object: Parameter # 1!
Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
[5]PETSC ERROR: [4]PETSC ERROR: [7]PETSC ERROR: Petsc Release Version 
3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
[1]PETSC ERROR: [2]PETSC ERROR: [3]PETSC ERROR: Petsc Release Version 
3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
------------------------------------------------------------------------
See docs/changes/index.html for recent updates.
------------------------------------------------------------------------
See docs/changes/index.html for recent updates.
[5]PETSC ERROR: [4]PETSC ERROR: [3]PETSC ERROR: See 
docs/changes/index.html for recent updates.
[7]PETSC ERROR: [2]PETSC ERROR: See docs/faq.html for hints about 
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 
13:37:48 CDT 2011
See docs/changes/index.html for recent updates.
See docs/faq.html for hints about trouble shooting.
Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011
[5]PETSC ERROR: [3]PETSC ERROR: See docs/faq.html for hints about 
trouble shooting.
[7]PETSC ERROR: [4]PETSC ERROR: See docs/index.html for manual pages.
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
See docs/changes/index.html for recent updates.
See docs/index.html for manual pages.
[2]PETSC ERROR: [5]PETSC ERROR: See docs/changes/index.html for recent 
updates.
See docs/index.html for manual pages.
[4]PETSC ERROR: [1]PETSC ERROR: [3]PETSC ERROR: [7]PETSC ERROR: 
------------------------------------------------------------------------
------------------------------------------------------------------------
See docs/index.html for manual pages.
See docs/faq.html for hints about trouble shooting.
[2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[5]PETSC ERROR: 
------------------------------------------------------------------------
[4]PETSC ERROR: [7]PETSC ERROR: 
------------------------------------------------------------------------
[2]PETSC ERROR: [1]PETSC ERROR: [3]PETSC ERROR: See docs/index.html for 
manual pages.
See docs/index.html for manual pages.
./hoac on a linux-gnu named PlusSodaL by kontzialis Sat Nov  5 19:02:12 2011
./hoac on a linux-gnu named PlusSodaL by kontzialis Sat Nov  5 19:02:12 2011
[2]PETSC ERROR: [5]PETSC ERROR: [7]PETSC ERROR: 
------------------------------------------------------------------------
------------------------------------------------------------------------
./hoac on a linux-gnu named PlusSodaL by kontzialis Sat Nov  5 19:02:12 2011
[3]PETSC ERROR: [1]PETSC ERROR: [4]PETSC ERROR: Libraries linked from 
/home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
Libraries linked from /home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
[0]PETSC ERROR: ./hoac on a linux-gnu named PlusSodaL by kontzialis Sat 
Nov  5 19:02:12 2011
[5]PETSC ERROR: [1]PETSC ERROR: [7]PETSC ERROR: [2]PETSC ERROR: 
Libraries linked from /home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
[3]PETSC ERROR: Configure run at Tue Sep 27 13:09:04 2011
./hoac on a linux-gnu named PlusSodaL by kontzialis Sat Nov  5 19:02:12 2011
./hoac on a linux-gnu named PlusSodaL by kontzialis Sat Nov  5 19:02:12 2011
Configure run at Tue Sep 27 13:09:04 2011
[4]PETSC ERROR: [5]PETSC ERROR: Configure run at Tue Sep 27 13:09:04 2011
[1]PETSC ERROR: Libraries linked from 
/home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
[3]PETSC ERROR: [2]PETSC ERROR: TSStep() line 1693 in src/ts/interface/ts.c
Configure options --with-debugging=1 --with-shared=1 
--with-shared-libraries --with-large-file-io=1 --with-precision=double 
--with-blacs=1 --download-blacs=yes --download-f-blas-lapack=yes 
--with-plapack=1 --download-plapack=yes --with-scalapack=1 
--download-scalapack=yes --with-superlu=1 --download-superlu=yes 
--with-superlu_dist=1 --download-superlu_dist=yes --with-ml=1 
--download-ml=yes --with-umfpack=1 --download-umfpack=yes 
--with-sundials=1 --download-sundials=1 --with-parmetis=1 
--download-parmetis=1 --with-hypre=1 --download-hypre=1 
--with-mpi-dir=/usr/lib/mpich2/bin
Configure options --with-debugging=1 --with-shared=1 
--with-shared-libraries --with-large-file-io=1 --with-precision=double 
--with-blacs=1 --download-blacs=yes --download-f-blas-lapack=yes 
--with-plapack=1 --download-plapack=yes --with-scalapack=1 
--download-scalapack=yes --with-superlu=1 --download-superlu=yes 
--with-superlu_dist=1 --download-superlu_dist=yes --with-ml=1 
--download-ml=yes --with-umfpack=1 --download-umfpack=yes 
--with-sundials=1 --download-sundials=1 --with-parmetis=1 
--download-parmetis=1 --with-hypre=1 --download-hypre=1 
--with-mpi-dir=/usr/lib/mpich2/bin
[7]PETSC ERROR: Libraries linked from 
/home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
Libraries linked from /home/kontzialis/petsc-3.1-p8/linux-gnu-c-debug/lib
[5]PETSC ERROR: [4]PETSC ERROR: [1]PETSC ERROR: [3]PETSC ERROR: 
Configure options --with-debugging=1 --with-shared=1 
--with-shared-libraries --with-large-file-io=1 --with-precision=double 
--with-blacs=1 --download-blacs=yes --download-f-blas-lapack=yes 
--with-plapack=1 --download-plapack=yes --with-scalapack=1 
--download-scalapack=yes --with-superlu=1 --download-superlu=yes 
--with-superlu_dist=1 --download-superlu_dist=yes --with-ml=1 
--download-ml=yes --with-umfpack=1 --download-umfpack=yes 
--with-sundials=1 --download-sundials=1 --with-parmetis=1 
--download-parmetis=1 --with-hypre=1 --download-hypre=1 
--with-mpi-dir=/usr/lib/mpich2/bin


What should I do?

Kostas


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